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From: <luc...@us...> - 2019-12-04 21:22:38
|
Revision: 26197
http://sourceforge.net/p/sbml/code/26197
Author: luciansmith
Date: 2019-12-04 21:21:47 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Merge changes from libsbml-experimental. Hopefully without clobbering the changes for extendedMath.
Modified Paths:
--------------
branches/libsbml-experimental-lucian/COPYING.html
branches/libsbml-experimental-lucian/LICENSE.html
branches/libsbml-experimental-lucian/VERSION_PACKAGES.ac
branches/libsbml-experimental-lucian/arrays-package.cmake
branches/libsbml-experimental-lucian/cmake_uninstall.cmake.in
branches/libsbml-experimental-lucian/configure.ac
branches/libsbml-experimental-lucian/distrib-package.cmake
branches/libsbml-experimental-lucian/dyn-package.cmake
branches/libsbml-experimental-lucian/examples/c++/CMakeLists.txt
branches/libsbml-experimental-lucian/examples/c++/distrib/createTestSuiteModels.cpp
branches/libsbml-experimental-lucian/examples/c++/distrib/distrib_example1.cpp
branches/libsbml-experimental-lucian/fbc-package.cmake
branches/libsbml-experimental-lucian/groups-package.cmake
branches/libsbml-experimental-lucian/l3v2extendedmath-package.cmake
branches/libsbml-experimental-lucian/layout-package.cmake
branches/libsbml-experimental-lucian/libtoolize.sh
branches/libsbml-experimental-lucian/multi-package.cmake
branches/libsbml-experimental-lucian/qual-package.cmake
branches/libsbml-experimental-lucian/render-package.cmake
branches/libsbml-experimental-lucian/req-package.cmake
branches/libsbml-experimental-lucian/spatial-package.cmake
branches/libsbml-experimental-lucian/src/bindings/csharp/Compiler.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/compile-native-files.cmake
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-astplugins-arrays.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-astplugins-distrib.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-astplugins-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-astplugins-multi.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-astplugins.i.in
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-converters-comp.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-converters-fbc.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-converters-layout.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-converters-qual.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-converters.i.in
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-arrays.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-distrib.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-dyn.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-groups.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-multi.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-extension-render.i
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branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-arrays.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-distrib.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-dyn.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-groups.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-multi.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-render.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-req.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-downcast-namespaces-spatial.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-arrays.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-distrib.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-dyn.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-groups.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-multi.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-render.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-req.i
branches/libsbml-experimental-lucian/src/bindings/csharp/local-packages-spatial.i
branches/libsbml-experimental-lucian/src/bindings/csharp/swig-binding.cmake.in
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestAncestor.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestCopyAndClone.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestEvent_newSetters.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestL3Event.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestModel.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestReaction_newSetters.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestRequiredElements.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestSBMLDocument.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestSBase.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
branches/libsbml-experimental-lucian/src/bindings/csharp/test/sbml/TestSpeciesReference_newSetters.cs
branches/libsbml-experimental-lucian/src/bindings/java/AutoTestRunner.java
branches/libsbml-experimental-lucian/src/bindings/java/TestPrintVersion.java
branches/libsbml-experimental-lucian/src/bindings/java/compile-native-files.cmake
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-astplugins-arrays.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-astplugins-distrib.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-astplugins-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-astplugins-multi.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-astplugins.i.in
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-converters-comp.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-converters-fbc.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-converters-layout.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-converters-qual.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-converters.i.in
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-arrays.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-distrib.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-dyn.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-groups.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-multi.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-render.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-req.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-extension-spatial.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-arrays.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-distrib.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-dyn.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-groups.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-multi.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-render.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-req.i
branches/libsbml-experimental-lucian/src/bindings/java/local-downcast-namespaces-spatial.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-arrays.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-distrib.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-dyn.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-groups.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-l3v2extendedmath.i
branches/libsbml-experimental-lucian/src/bindings/java/local-packages-multi.i
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branches/libsbml-experimental-lucian/src/bindings/java/local-packages-req.i
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branches/libsbml-experimental-lucian/src/bindings/java/swig-binding.cmake.in
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestCVTerms.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestCVTerms_newSetters.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestCopyAndClone.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestDate_newSetters.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestL3ModelHistory.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestModelCreator_newSetters.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestModelHistory.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestModelHistory_newSetters.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotation.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotation2.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotationC.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestValidation.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestASTNode.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile1.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadFromFile2.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestReadMathML.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestValidASTNode.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/math/TestWriteMathML.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestAlgebraicRule.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestAncestor.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestAssignmentRule.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartment.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartmentType.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartmentType_newSetters.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartmentVolumeRule.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestConstraint.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCopyAndClone.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestDelay.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestEventAssignment.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestGetMultipleObjects.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInitialAssignment.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestKineticLaw.java
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branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Event.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3KineticLaw.java
branches/libsbml-experimental-lucian/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3LocalParameter.java
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[truncated message content] |
|
From: <luc...@us...> - 2019-12-04 20:15:02
|
Revision: 26196
http://sourceforge.net/p/sbml/code/26196
Author: luciansmith
Date: 2019-12-04 20:14:55 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Pull in all changes in sbml/ directory from trunk through revision 26194.
Revision Links:
--------------
http://sourceforge.net/p/sbml/code/26194
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/AlgebraicRule.cpp
branches/libsbml-experimental/src/sbml/AlgebraicRule.h
branches/libsbml-experimental/src/sbml/AssignmentRule.cpp
branches/libsbml-experimental/src/sbml/AssignmentRule.h
branches/libsbml-experimental/src/sbml/Compartment.cpp
branches/libsbml-experimental/src/sbml/Compartment.h
branches/libsbml-experimental/src/sbml/CompartmentType.cpp
branches/libsbml-experimental/src/sbml/CompartmentType.h
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branches/libsbml-experimental/src/sbml/Delay.cpp
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branches/libsbml-experimental/src/sbml/SpeciesReference.cpp
branches/libsbml-experimental/src/sbml/SpeciesReference.h
branches/libsbml-experimental/src/sbml/SpeciesType.cpp
branches/libsbml-experimental/src/sbml/SpeciesType.h
branches/libsbml-experimental/src/sbml/Trigger.cpp
branches/libsbml-experimental/src/sbml/Trigger.h
branches/libsbml-experimental/src/sbml/Unit.cpp
branches/libsbml-experimental/src/sbml/Unit.h
branches/libsbml-experimental/src/sbml/UnitDefinition.cpp
branches/libsbml-experimental/src/sbml/UnitDefinition.h
branches/libsbml-experimental/src/sbml/annotation/RDFAnnotationParser.h
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationL3.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationL3_2.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationL3_3.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationNested-l2v5.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationNested-l3v1.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationNested-l3v2.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationVcard4-l3v1.xml
branches/libsbml-experimental/src/sbml/annotation/test/test-data/annotationVcard4.xml
branches/libsbml-experimental/src/sbml/common/common-documentation.h
branches/libsbml-experimental/src/sbml/common/libsbml-version.h
branches/libsbml-experimental/src/sbml/conversion/SBMLConverterRegistry.cpp
branches/libsbml-experimental/src/sbml/conversion/SBMLFunctionDefinitionConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/SBMLLevelVersionConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/SBMLRuleConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/test/TestLevelVersionConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/test/test-data/00856-sbml-l3v1.xml
branches/libsbml-experimental/src/sbml/extension/ASTBasePlugin.h
branches/libsbml-experimental/src/sbml/extension/ISBMLExtensionNamespaces.cpp
branches/libsbml-experimental/src/sbml/extension/SBaseExtensionPoint.cpp
branches/libsbml-experimental/src/sbml/math/ASTNode.cpp
branches/libsbml-experimental/src/sbml/math/ASTNode.h
branches/libsbml-experimental/src/sbml/math/ASTNodeType.h
branches/libsbml-experimental/src/sbml/math/DefinitionURLRegistry.cpp
branches/libsbml-experimental/src/sbml/math/DefinitionURLRegistry.h
branches/libsbml-experimental/src/sbml/math/FormulaFormatter.cpp
branches/libsbml-experimental/src/sbml/math/FormulaFormatter.h
branches/libsbml-experimental/src/sbml/math/FormulaParser.cpp
branches/libsbml-experimental/src/sbml/math/FormulaParser.h
branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.cpp
branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.h
branches/libsbml-experimental/src/sbml/math/L3FormulaFormatter.cpp
branches/libsbml-experimental/src/sbml/math/L3FormulaFormatter.h
branches/libsbml-experimental/src/sbml/math/L3ParserSettings.cpp
branches/libsbml-experimental/src/sbml/math/L3ParserSettings.h
branches/libsbml-experimental/src/sbml/math/MathML.h
branches/libsbml-experimental/src/sbml/packages/comp/extension/CompSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/comp/sbml/CompBase.cpp
branches/libsbml-experimental/src/sbml/packages/comp/sbml/ListOfModelDefinitions.cpp
branches/libsbml-experimental/src/sbml/packages/comp/sbml/ListOfReplacedElements.cpp
branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestAttributeNamespaces.cpp
branches/libsbml-experimental/src/sbml/packages/comp/util/SBMLResolverRegistry.cpp
branches/libsbml-experimental/src/sbml/packages/comp/validator/CompConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/comp/validator/CompConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/comp/validator/CompUnitConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/comp/validator/CompUnitConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/comp/validator/constraints/CompConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcReactionPlugin.h
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcSpeciesPlugin.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/Association.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/Association.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAnd.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAnd.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAssociation.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAssociation.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcOr.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcOr.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FluxBound.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FluxBound.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FluxObjective.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FluxObjective.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProduct.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProduct.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductAssociation.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductAssociation.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductRef.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductRef.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/Objective.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/Objective.h
branches/libsbml-experimental/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsModelPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Group.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Group.h
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Member.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Member.h
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathMathMLConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathUnitConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathMathMLConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathUnitConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/layout/sbml/CompartmentGlyph.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/GeneralGlyph.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/Point.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/ReactionGlyph.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/ReferenceGlyph.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/SpeciesGlyph.h
branches/libsbml-experimental/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.h
branches/libsbml-experimental/src/sbml/packages/multi/extension/MultiASTPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/multi/extension/MultiASTPlugin.h
branches/libsbml-experimental/src/sbml/packages/multi/extension/MultiListOfReactionsPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/multi/sbml/SubListOfSpeciesFeatures.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/MultiMathMLConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueCRefIdsWithinCompartment.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueCRefIdsWithinCompartment.h
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueISTBIdsWithinMultiSpeciesType.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueISTBIdsWithinMultiSpeciesType.h
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSFTIdsWithinMultiSpeciesType.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSFTIdsWithinMultiSpeciesType.h
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSLOSFIdsWithinSpecies.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSLOSFIdsWithinSpecies.h
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSTCIdsWithinMultiSpeciesType.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSTCIdsWithinMultiSpeciesType.h
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSTIIdsWithinMultiSpeciesType.cpp
branches/libsbml-experimental/src/sbml/packages/multi/validator/constraints/UniqueSTIIdsWithinMultiSpeciesType.h
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualModelPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/DefaultTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/DefaultTerm.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/FunctionTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/FunctionTerm.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Input.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Input.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Output.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Output.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/QualitativeSpecies.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/QualitativeSpecies.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Transition.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Transition.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualMathConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/ColorDefinition.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/ColorDefinition.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/DefaultValues.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/DefaultValues.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientBase.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientBase.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientStop.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientStop.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/LineEnding.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/LineEnding.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCurve.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCurve.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderGroup.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderGroup.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderInformationBase.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderInformationBase.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Style.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Style.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation2D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation2D.h
branches/libsbml-experimental/src/sbml/packages/render/util/RenderLayoutConverter.cpp
branches/libsbml-experimental/src/sbml/util/IdFilter.cpp
branches/libsbml-experimental/src/sbml/util/MetaIdFilter.cpp
branches/libsbml-experimental/src/sbml/util/util.h
branches/libsbml-experimental/src/sbml/validator/VConstraint.cpp
branches/libsbml-experimental/src/sbml/validator/constraints/AssignmentCycles.cpp
branches/libsbml-experimental/src/sbml/validator/constraints/CompatibilityConstraints.cxx
branches/libsbml-experimental/src/sbml/validator/constraints/RateOfCycles.cpp
branches/libsbml-experimental/src/sbml/xml/XMLError.cpp
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/conversion/test/test-data/01800-fail-sbml-l3v1.xml
branches/libsbml-experimental/src/sbml/conversion/test/test-data/01800-sbml-l3v1.xml
branches/libsbml-experimental/src/sbml/conversion/test/test-data/01800-sbml-l3v2.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-22.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-23.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-07.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-08.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-09.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-10.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-11.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-12.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-07.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-08.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-10.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-20.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-21.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-22.xml
Property Changed:
----------------
branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationNestedCVTerms.cpp
branches/libsbml-experimental/src/sbml/annotation/test/TestRDFAnnotationVCard4.cpp
branches/libsbml-experimental/src/sbml/conversion/SBMLLevel1Version1Converter.cpp
branches/libsbml-experimental/src/sbml/conversion/SBMLRateOfConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/test/TestLevelVersionConverter.cpp
branches/libsbml-experimental/src/sbml/conversion/test/TestRateOfConverter.cpp
branches/libsbml-experimental/src/sbml/math/ASTNodeType.h
branches/libsbml-experimental/src/sbml/math/DefinitionURLRegistry.cpp
branches/libsbml-experimental/src/sbml/math/DefinitionURLRegistry.h
branches/libsbml-experimental/src/sbml/math/FormulaFormatter.cpp
branches/libsbml-experimental/src/sbml/math/FormulaParser.cpp
branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.cpp
branches/libsbml-experimental/src/sbml/math/L3FormulaFormatter.cpp
branches/libsbml-experimental/src/sbml/math/test/TestGetValue.cpp
branches/libsbml-experimental/src/sbml/math/test/TestReadFromFileL3V2.cpp
branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestAttributeNamespaces.cpp
branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompFlatteningConverterStripPackage.cpp
branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestCompLevelVersionConverter.cpp
branches/libsbml-experimental/src/sbml/packages/comp-register.cxx
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcReactionPlugin.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAnd.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAnd.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAssociation.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcAssociation.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcOr.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/FbcOr.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProduct.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProduct.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductAssociation.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductAssociation.h
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductRef.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/sbml/GeneProductRef.h
branches/libsbml-experimental/src/sbml/packages/fbc/util/FbcV1ToV2Converter.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/util/FbcV1ToV2Converter.h
branches/libsbml-experimental/src/sbml/packages/fbc/util/FbcV2ToV1Converter.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/util/FbcV2ToV1Converter.h
branches/libsbml-experimental/src/sbml/packages/fbc/validator/constraints/UniqueGeneProductLabels.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/validator/constraints/UniqueGeneProductLabels.h
branches/libsbml-experimental/src/sbml/packages/fbc-register.cxx
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathASTPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/extension/L3v2extendedmathSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathMathMLConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/L3v2extendedmathUnitConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathMathMLConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathUnitConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/layout-register.cxx
branches/libsbml-experimental/src/sbml/packages/multi/extension/MultiListOfReactionsPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/qual-register.cxx
branches/libsbml-experimental/src/sbml/packages/render/sbml/DefaultValues.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/DefaultValues.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/ListOfGlobalRenderInformation.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/ListOfLocalRenderInformation.cpp
branches/libsbml-experimental/src/sbml/packages/render-register.cxx
branches/libsbml-experimental/src/sbml/test/test-data/sbml-l1v1.xsd
branches/libsbml-experimental/src/sbml/test/test-data/sbml-l1v2.xsd
branches/libsbml-experimental/src/sbml/test/test-data/sbml-l2v1.xsd
branches/libsbml-experimental/src/sbml/validator/constraints/CiElementNot0DComp.h
branches/libsbml-experimental/src/sbml/validator/constraints/CompatibilityConstraints.cxx
branches/libsbml-experimental/src/sbml/validator/constraints/FunctionDefinitionRecursion.h
branches/libsbml-experimental/src/sbml/validator/constraints/RateOfCycles.cpp
Modified: branches/libsbml-experimental/src/sbml/AlgebraicRule.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/AlgebraicRule.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/AlgebraicRule.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -144,7 +144,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
int
AlgebraicRule::getAttribute(const std::string& attributeName,
@@ -162,7 +162,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
int
AlgebraicRule::getAttribute(const std::string& attributeName,
@@ -180,7 +180,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
int
AlgebraicRule::getAttribute(const std::string& attributeName,
@@ -198,7 +198,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
int
AlgebraicRule::getAttribute(const std::string& attributeName,
@@ -216,7 +216,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
int
AlgebraicRule::getAttribute(const std::string& attributeName,
@@ -234,7 +234,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*/
//int
//AlgebraicRule::getAttribute(const std::string& attributeName,
Modified: branches/libsbml-experimental/src/sbml/AlgebraicRule.h
===================================================================
--- branches/libsbml-experimental/src/sbml/AlgebraicRule.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/AlgebraicRule.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -222,7 +222,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -242,7 +242,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -261,7 +261,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -281,7 +281,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -301,7 +301,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -321,7 +321,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ * Returns the value of the "attributeName" attribute of this AlgebraicRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -599,7 +599,7 @@
/**
- * Gets the mathematical expression of this AlgebraicRule_t structure as an
+ * Returns the mathematical expression of this AlgebraicRule_t structure as an
* ASTNode_t structure.
*
* @param ar the AlgebraicRule_t structure.
Modified: branches/libsbml-experimental/src/sbml/AssignmentRule.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/AssignmentRule.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/AssignmentRule.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -136,7 +136,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
@@ -154,7 +154,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
@@ -172,7 +172,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
@@ -190,7 +190,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
@@ -208,7 +208,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
@@ -252,7 +252,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*/
//int
//AssignmentRule::getAttribute(const std::string& attributeName,
Modified: branches/libsbml-experimental/src/sbml/AssignmentRule.h
===================================================================
--- branches/libsbml-experimental/src/sbml/AssignmentRule.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/AssignmentRule.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -284,7 +284,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -304,7 +304,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -323,7 +323,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -343,7 +343,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -363,7 +363,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -383,7 +383,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ * Returns the value of the "attributeName" attribute of this AssignmentRule.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -673,7 +673,7 @@
/**
- * Gets the mathematical expression of this AssignmentRule_t structure as an
+ * Returns the mathematical expression of this AssignmentRule_t structure as an
* ASTNode_t structure.
*
* @param ar the AssignmentRule_t structure.
Modified: branches/libsbml-experimental/src/sbml/Compartment.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Compartment.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Compartment.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -1018,7 +1018,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
int
Compartment::getAttribute(const std::string& attributeName, bool& value) const
@@ -1046,7 +1046,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
int
Compartment::getAttribute(const std::string& attributeName, int& value) const
@@ -1063,7 +1063,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
int
Compartment::getAttribute(const std::string& attributeName,
@@ -1102,7 +1102,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
int
Compartment::getAttribute(const std::string& attributeName,
@@ -1131,7 +1131,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
int
Compartment::getAttribute(const std::string& attributeName,
@@ -1170,7 +1170,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*/
//int
//Compartment::getAttribute(const std::string& attributeName,
@@ -1450,8 +1450,21 @@
/** @endcond */
+/** @cond doxygenLibsbmlInternal */
+bool Compartment::isExplicitlySetSpatialDimensions() const
+{
+ return mExplicitlySetSpatialDimensions;
+}
+/** @endcond */
+/** @cond doxygenLibsbmlInternal */
+bool Compartment::isExplicitlySetConstant() const
+{
+ return mExplicitlySetConstant;
+}
+/** @endcond */
+
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
@@ -1770,6 +1783,7 @@
//
mIsSetConstant = attributes.readInto("constant", mConstant,
getErrorLog(), false, getLine(), getColumn());
+ mExplicitlySetConstant = mIsSetConstant;
if (!mIsSetConstant)
{
logError(AllowedAttributesOnCompartment, level, version,
Modified: branches/libsbml-experimental/src/sbml/Compartment.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Compartment.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Compartment.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -1328,7 +1328,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1348,7 +1348,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1367,7 +1367,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1387,7 +1387,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1407,7 +1407,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1427,7 +1427,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Compartment.
+ * Returns the value of the "attributeName" attribute of this Compartment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1594,8 +1594,14 @@
/** @endcond */
+ /** @cond doxygenLibsbmlInternal */
+ bool isExplicitlySetSpatialDimensions() const;
+ bool isExplicitlySetConstant() const;
+ /** @endcond */
+
+
#endif /* !SWIG */
@@ -1633,12 +1639,7 @@
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
- bool isExplicitlySetSpatialDimensions() const {
- return mExplicitlySetSpatialDimensions; };
- bool isExplicitlySetConstant() const { return mExplicitlySetConstant; } ;
-
-
//std::string mId;
//std::string mName;
std::string mCompartmentType;
Modified: branches/libsbml-experimental/src/sbml/CompartmentType.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/CompartmentType.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/CompartmentType.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -312,7 +312,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
int
CompartmentType::getAttribute(const std::string& attributeName,
@@ -330,7 +330,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
int
CompartmentType::getAttribute(const std::string& attributeName,
@@ -348,7 +348,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
int
CompartmentType::getAttribute(const std::string& attributeName,
@@ -366,7 +366,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
int
CompartmentType::getAttribute(const std::string& attributeName,
@@ -384,7 +384,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
int
CompartmentType::getAttribute(const std::string& attributeName,
@@ -402,7 +402,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*/
//int
//CompartmentType::getAttribute(const std::string& attributeName,
Modified: branches/libsbml-experimental/src/sbml/CompartmentType.h
===================================================================
--- branches/libsbml-experimental/src/sbml/CompartmentType.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/CompartmentType.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -321,7 +321,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -341,7 +341,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -360,7 +360,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -380,7 +380,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -400,7 +400,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -420,7 +420,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this CompartmentType.
+ * Returns the value of the "attributeName" attribute of this CompartmentType.
*
* @param attributeName, the name of the attribute to retrieve.
*
Modified: branches/libsbml-experimental/src/sbml/Constraint.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Constraint.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Constraint.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -482,7 +482,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
int
Constraint::getAttribute(const std::string& attributeName, bool& value) const
@@ -499,7 +499,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
int
Constraint::getAttribute(const std::string& attributeName, int& value) const
@@ -516,7 +516,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
int
Constraint::getAttribute(const std::string& attributeName,
@@ -534,7 +534,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
int
Constraint::getAttribute(const std::string& attributeName,
@@ -552,7 +552,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
int
Constraint::getAttribute(const std::string& attributeName,
@@ -570,7 +570,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*/
//int
//Constraint::getAttribute(const std::string& attributeName,
Modified: branches/libsbml-experimental/src/sbml/Constraint.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Constraint.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Constraint.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -410,7 +410,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -430,7 +430,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -449,7 +449,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -469,7 +469,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -489,7 +489,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -509,7 +509,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Constraint.
+ * Returns the value of the "attributeName" attribute of this Constraint.
*
* @param attributeName, the name of the attribute to retrieve.
*
Modified: branches/libsbml-experimental/src/sbml/Delay.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Delay.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Delay.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -447,7 +447,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
int
Delay::getAttribute(const std::string& attributeName, bool& value) const
@@ -464,7 +464,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
int
Delay::getAttribute(const std::string& attributeName, int& value) const
@@ -481,7 +481,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
int
Delay::getAttribute(const std::string& attributeName, double& value) const
@@ -498,7 +498,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
int
Delay::getAttribute(const std::string& attributeName,
@@ -516,7 +516,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
int
Delay::getAttribute(const std::string& attributeName,
@@ -534,7 +534,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*/
//int
//Delay::getAttribute(const std::string& attributeName, const char* value) const
Modified: branches/libsbml-experimental/src/sbml/Delay.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Delay.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Delay.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -533,7 +533,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -553,7 +553,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -572,7 +572,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -592,7 +592,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -612,7 +612,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -632,7 +632,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Delay.
+ * Returns the value of the "attributeName" attribute of this Delay.
*
* @param attributeName, the name of the attribute to retrieve.
*
Modified: branches/libsbml-experimental/src/sbml/Event.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Event.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Event.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -1370,7 +1370,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
int
Event::getAttribute(const std::string& attributeName, bool& value) const
@@ -1398,7 +1398,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
int
Event::getAttribute(const std::string& attributeName, int& value) const
@@ -1415,7 +1415,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
int
Event::getAttribute(const std::string& attributeName, double& value) const
@@ -1432,7 +1432,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
int
Event::getAttribute(const std::string& attributeName,
@@ -1450,7 +1450,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
int
Event::getAttribute(const std::string& attributeName,
@@ -1479,7 +1479,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*/
//int
//Event::getAttribute(const std::string& attributeName, const char* value) const
@@ -1853,6 +1853,12 @@
/** @endcond */
+/** @cond doxygenLibsbmlInternal */
+bool Event::isExplicitlySetUVFTT() const
+{
+ return mExplicitlySetUVFTT;
+}
+/** @endcond */
/** @cond doxygenLibsbmlInternal */
@@ -2039,6 +2045,7 @@
mIsSetUseValuesFromTriggerTime = attributes.readInto(
"useValuesFromTriggerTime", mUseValuesFromTriggerTime,
getErrorLog(),false, getLine(), getColumn());
+ mExplicitlySetUVFTT = mIsSetUseValuesFromTriggerTime;
if (!mIsSetUseValuesFromTriggerTime)
{
Modified: branches/libsbml-experimental/src/sbml/Event.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Event.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/Event.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -1121,7 +1121,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1141,7 +1141,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1160,7 +1160,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1180,7 +1180,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1200,7 +1200,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1220,7 +1220,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event.
+ * Returns the value of the "attributeName" attribute of this Event.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -1466,9 +1466,13 @@
/** @endcond */
+ /** @cond doxygenLibsbmlInternal */
+ bool isExplicitlySetUVFTT() const;
+ /** @endcond */
+
#endif /* !SWIG */
@@ -1514,9 +1518,7 @@
*/
virtual void writeAttributes (XMLOutputStream& stream) const;
- bool isExplicitlySetUVFTT() const { return mExplicitlySetUVFTT; } ;
-
//std::string mId;
//std::string mName;
Trigger* mTrigger;
Modified: branches/libsbml-experimental/src/sbml/EventAssignment.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/EventAssignment.cpp 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/EventAssignment.cpp 2019-12-04 20:14:55 UTC (rev 26196)
@@ -485,7 +485,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
int
EventAssignment::getAttribute(const std::string& attributeName,
@@ -503,7 +503,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
int
EventAssignment::getAttribute(const std::string& attributeName,
@@ -521,7 +521,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
int
EventAssignment::getAttribute(const std::string& attributeName,
@@ -539,7 +539,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
int
EventAssignment::getAttribute(const std::string& attributeName,
@@ -557,7 +557,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
int
EventAssignment::getAttribute(const std::string& attributeName,
@@ -586,7 +586,7 @@
/** @cond doxygenLibsbmlInternal */
/*
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*/
//int
//EventAssignment::getAttribute(const std::string& attributeName,
Modified: branches/libsbml-experimental/src/sbml/EventAssignment.h
===================================================================
--- branches/libsbml-experimental/src/sbml/EventAssignment.h 2019-12-04 20:14:03 UTC (rev 26195)
+++ branches/libsbml-experimental/src/sbml/EventAssignment.h 2019-12-04 20:14:55 UTC (rev 26196)
@@ -663,7 +663,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -683,7 +683,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -702,7 +702,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this EventAssignment.
+ * Returns the value of the "attributeName" attribute of this EventAssignment.
*
* @param attributeName, the name of the attribute to retrieve.
*
@@ -722,7 +722,7 @@
/** @cond doxygenLibsbmlInternal */
/**
- * Gets the value of the "attributeName" attribute of this Event...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-04 19:49:11
|
Revision: 26194
http://sourceforge.net/p/sbml/code/26194
Author: luciansmith
Date: 2019-12-04 19:49:08 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Native line endings for .cmake files.
Modified Paths:
--------------
branches/libsbml-experimental/src/arrays-package.cmake
branches/libsbml-experimental/src/distrib-package.cmake
branches/libsbml-experimental/src/dyn-package.cmake
branches/libsbml-experimental/src/l3v2extendedmath-package.cmake
branches/libsbml-experimental/src/multi-package.cmake
branches/libsbml-experimental/src/render-package.cmake
branches/libsbml-experimental/src/req-package.cmake
branches/libsbml-experimental/src/spatial-package.cmake
Property Changed:
----------------
branches/libsbml-experimental/src/arrays-package.cmake
branches/libsbml-experimental/src/distrib-package.cmake
branches/libsbml-experimental/src/dyn-package.cmake
branches/libsbml-experimental/src/fbc-package.cmake
branches/libsbml-experimental/src/groups-package.cmake
branches/libsbml-experimental/src/l3v2extendedmath-package.cmake
branches/libsbml-experimental/src/layout-package.cmake
branches/libsbml-experimental/src/multi-package.cmake
branches/libsbml-experimental/src/qual-package.cmake
branches/libsbml-experimental/src/render-package.cmake
branches/libsbml-experimental/src/req-package.cmake
branches/libsbml-experimental/src/spatial-package.cmake
Modified: branches/libsbml-experimental/src/arrays-package.cmake
===================================================================
--- branches/libsbml-experimental/src/arrays-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/arrays-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,89 +1,89 @@
-###############################################################################
-#
-# Description : CMake include file for SBML Level 3 Arrays package
-# Original author(s): Frank Bergmann <fbe...@ca...>
-# Organization : California Institute of Technology
-#
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2009-2011 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-#
-###############################################################################
-
-if(ENABLE_ARRAYS)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/arrays-package.cmake)
-
-#build up sources
-set(ARRAYS_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml util validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.h)
-
- # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
- # they are #included directly, instead.
- if ("${dir}" STREQUAL "validator/constraints")
- foreach(tempFile ${current})
- if ("${tempFile}" MATCHES ".*Constraints.cpp")
- set_source_files_properties(
- ${tempFile}
- PROPERTIES HEADER_FILE_ONLY true
- )
- endif()
- endforeach()
- endif()
-
- # add sources
- set(ARRAYS_SOURCES ${ARRAYS_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB arrays_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.h)
-
- install(FILES ${arrays_headers}
- DESTINATION include/sbml/packages/arrays/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(arrays_package FILES ${ARRAYS_SOURCES})
-
-# add arrays sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${ARRAYS_SOURCES})
-
-####################################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/arrays/extension/test)
- add_subdirectory(sbml/packages/arrays/util/test)
-
-endif()
-
-endif()
+###############################################################################
+#
+# Description : CMake include file for SBML Level 3 Arrays package
+# Original author(s): Frank Bergmann <fbe...@ca...>
+# Organization : California Institute of Technology
+#
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2009-2011 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+#
+###############################################################################
+
+if(ENABLE_ARRAYS)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/arrays-package.cmake)
+
+#build up sources
+set(ARRAYS_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml util validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.h)
+
+ # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
+ # they are #included directly, instead.
+ if ("${dir}" STREQUAL "validator/constraints")
+ foreach(tempFile ${current})
+ if ("${tempFile}" MATCHES ".*Constraints.cpp")
+ set_source_files_properties(
+ ${tempFile}
+ PROPERTIES HEADER_FILE_ONLY true
+ )
+ endif()
+ endforeach()
+ endif()
+
+ # add sources
+ set(ARRAYS_SOURCES ${ARRAYS_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB arrays_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/arrays/${dir}/*.h)
+
+ install(FILES ${arrays_headers}
+ DESTINATION include/sbml/packages/arrays/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(arrays_package FILES ${ARRAYS_SOURCES})
+
+# add arrays sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${ARRAYS_SOURCES})
+
+####################################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/arrays/extension/test)
+ add_subdirectory(sbml/packages/arrays/util/test)
+
+endif()
+
+endif()
Property changes on: branches/libsbml-experimental/src/arrays-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/distrib-package.cmake
===================================================================
--- branches/libsbml-experimental/src/distrib-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/distrib-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,87 +1,87 @@
-#################################################
- # @file distrib-package.cmake
- # @brief Src CMake file for distrib package
- # @author SBMLTeam
- #
- # <!--------------------------------------------------------------------------
- # This file is part of libSBML. Please visit http://sbml.org for more
- # information about SBML, and the latest version of libSBML.
- #
- # Copyright (C) 2019 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2013-2018 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
- # ------------------------------------------------------------------------ -->
- #
-
-if (ENABLE_DISTRIB)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/distrib-package.cmake)
-
- # build up sources
-set(DISTRIB_SOURCES)
-
- # go through all directories
-foreach(dir common extension sbml util validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.h)
-
- # add sources
- set(DISTRIB_SOURCES ${DISTRIB_SOURCES} ${current})
-
- # mark headers for installation
- file(GLOB distrib_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.h)
-
- install(FILES ${distrib_headers} DESTINATION include/sbml/packages/distrib/${dir} )
-
-endforeach()
-
- # create source group for IDEs
-source_group(distrib_package FILES ${DISTRIB_SOURCES})
-
- # add distrib sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${DISTRIB_SOURCES})
-
-#################################################
- #
- # add test scripts
- #
-if (WITH_CHECK)
-
- add_subdirectory(sbml/packages/distrib/extension/test)
- add_subdirectory(sbml/packages/distrib/sbml/test)
- add_subdirectory(sbml/packages/distrib/util/test)
- add_subdirectory(sbml/packages/distrib/validator/test)
-
-
-endif()
-
-endif()
-
+#################################################
+ # @file distrib-package.cmake
+ # @brief Src CMake file for distrib package
+ # @author SBMLTeam
+ #
+ # <!--------------------------------------------------------------------------
+ # This file is part of libSBML. Please visit http://sbml.org for more
+ # information about SBML, and the latest version of libSBML.
+ #
+ # Copyright (C) 2019 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2013-2018 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+ # ------------------------------------------------------------------------ -->
+ #
+
+if (ENABLE_DISTRIB)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/distrib-package.cmake)
+
+ # build up sources
+set(DISTRIB_SOURCES)
+
+ # go through all directories
+foreach(dir common extension sbml util validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.h)
+
+ # add sources
+ set(DISTRIB_SOURCES ${DISTRIB_SOURCES} ${current})
+
+ # mark headers for installation
+ file(GLOB distrib_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/distrib/${dir}/*.h)
+
+ install(FILES ${distrib_headers} DESTINATION include/sbml/packages/distrib/${dir} )
+
+endforeach()
+
+ # create source group for IDEs
+source_group(distrib_package FILES ${DISTRIB_SOURCES})
+
+ # add distrib sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${DISTRIB_SOURCES})
+
+#################################################
+ #
+ # add test scripts
+ #
+if (WITH_CHECK)
+
+ add_subdirectory(sbml/packages/distrib/extension/test)
+ add_subdirectory(sbml/packages/distrib/sbml/test)
+ add_subdirectory(sbml/packages/distrib/util/test)
+ add_subdirectory(sbml/packages/distrib/validator/test)
+
+
+endif()
+
+endif()
+
Property changes on: branches/libsbml-experimental/src/distrib-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/dyn-package.cmake
===================================================================
--- branches/libsbml-experimental/src/dyn-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/dyn-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,82 +1,82 @@
-#################################################################################
-#
-# @file: dyn-package.cmake
-# @brief: CMake configuration for L3 Dyn package
-# @author: Generated by autocreate code
-#
-# <!--------------------------------------------------------------------------
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2018 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-# 3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# ------------------------------------------------------------------------ -->
-#
-
-if (ENABLE_DYN )
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/dyn-package.cmake)
-
-#build up sources
-set(DYN_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.h)
-
- # add sources
- set(DYN_SOURCES ${DYN_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB dyn_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.h)
-
- install(FILES ${dyn_headers}
- DESTINATION include/sbml/packages/dyn/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(dyn_package FILES ${DYN_SOURCES})
-
-# add dyn sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${DYN_SOURCES})
-
-######################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/dyn/extension/test)
-
-endif()
-
-endif()
-
+#################################################################################
+#
+# @file: dyn-package.cmake
+# @brief: CMake configuration for L3 Dyn package
+# @author: Generated by autocreate code
+#
+# <!--------------------------------------------------------------------------
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2013-2018 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+# 3. University of Heidelberg, Heidelberg, Germany
+#
+# Copyright (C) 2009-2013 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# ------------------------------------------------------------------------ -->
+#
+
+if (ENABLE_DYN )
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/dyn-package.cmake)
+
+#build up sources
+set(DYN_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.h)
+
+ # add sources
+ set(DYN_SOURCES ${DYN_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB dyn_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/dyn/${dir}/*.h)
+
+ install(FILES ${dyn_headers}
+ DESTINATION include/sbml/packages/dyn/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(dyn_package FILES ${DYN_SOURCES})
+
+# add dyn sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${DYN_SOURCES})
+
+######################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/dyn/extension/test)
+
+endif()
+
+endif()
+
Property changes on: branches/libsbml-experimental/src/dyn-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: branches/libsbml-experimental/src/fbc-package.cmake
===================================================================
--- branches/libsbml-experimental/src/fbc-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/fbc-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
Property changes on: branches/libsbml-experimental/src/fbc-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: branches/libsbml-experimental/src/groups-package.cmake
===================================================================
--- branches/libsbml-experimental/src/groups-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/groups-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
Property changes on: branches/libsbml-experimental/src/groups-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/l3v2extendedmath-package.cmake
===================================================================
--- branches/libsbml-experimental/src/l3v2extendedmath-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/l3v2extendedmath-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,80 +1,80 @@
-#################################################
- # @file l3v2extendedmath-package.cmake
- # @brief Src CMake file for l3v2extendedmath package
- # @author SBMLTeam
- #
- # <!--------------------------------------------------------------------------
- # This file is part of libSBML. Please visit http://sbml.org for more
- # information about SBML, and the latest version of libSBML.
- #
- # Copyright (C) 2013-2018 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
- # ------------------------------------------------------------------------ -->
- #
-
-if (ENABLE_L3V2EXTENDEDMATH)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/l3v2extendedmath-package.cmake)
-
- # build up sources
-set(L3V2EXTENDEDMATH_SOURCES)
-
- # go through all directories
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
-
- # add sources
- set(L3V2EXTENDEDMATH_SOURCES ${L3V2EXTENDEDMATH_SOURCES} ${current})
-
- # mark headers for installation
- file(GLOB l3v2extendedmath_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
-
- install(FILES ${l3v2extendedmath_headers} DESTINATION include/sbml/packages/l3v2extendedmath/${dir} )
-
-endforeach()
-
- # create source group for IDEs
-source_group(l3v2extendedmath_package FILES ${L3V2EXTENDEDMATH_SOURCES})
-
- # add l3v2extendedmath sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${L3V2EXTENDEDMATH_SOURCES})
-
-#################################################
- #
- # add test scripts
- #
-if (WITH_CHECK)
-
- add_subdirectory(sbml/packages/l3v2extendedmath/validator/test)
- add_subdirectory(sbml/packages/l3v2extendedmath/extension/test)
-
-endif()
-
-endif()
-
+#################################################
+ # @file l3v2extendedmath-package.cmake
+ # @brief Src CMake file for l3v2extendedmath package
+ # @author SBMLTeam
+ #
+ # <!--------------------------------------------------------------------------
+ # This file is part of libSBML. Please visit http://sbml.org for more
+ # information about SBML, and the latest version of libSBML.
+ #
+ # Copyright (C) 2013-2018 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+ # ------------------------------------------------------------------------ -->
+ #
+
+if (ENABLE_L3V2EXTENDEDMATH)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/l3v2extendedmath-package.cmake)
+
+ # build up sources
+set(L3V2EXTENDEDMATH_SOURCES)
+
+ # go through all directories
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
+
+ # add sources
+ set(L3V2EXTENDEDMATH_SOURCES ${L3V2EXTENDEDMATH_SOURCES} ${current})
+
+ # mark headers for installation
+ file(GLOB l3v2extendedmath_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
+
+ install(FILES ${l3v2extendedmath_headers} DESTINATION include/sbml/packages/l3v2extendedmath/${dir} )
+
+endforeach()
+
+ # create source group for IDEs
+source_group(l3v2extendedmath_package FILES ${L3V2EXTENDEDMATH_SOURCES})
+
+ # add l3v2extendedmath sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${L3V2EXTENDEDMATH_SOURCES})
+
+#################################################
+ #
+ # add test scripts
+ #
+if (WITH_CHECK)
+
+ add_subdirectory(sbml/packages/l3v2extendedmath/validator/test)
+ add_subdirectory(sbml/packages/l3v2extendedmath/extension/test)
+
+endif()
+
+endif()
+
Property changes on: branches/libsbml-experimental/src/l3v2extendedmath-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: branches/libsbml-experimental/src/layout-package.cmake
===================================================================
--- branches/libsbml-experimental/src/layout-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/layout-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
Property changes on: branches/libsbml-experimental/src/layout-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/multi-package.cmake
===================================================================
--- branches/libsbml-experimental/src/multi-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/multi-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,84 +1,84 @@
-#################################################################################
-#
-# @file: multi-package.cmake
-# @brief: CMake configuration for L3 Multi package
-# @author: Generated by autocreate code
-#
-# <!--------------------------------------------------------------------------
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2018 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-# 3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# ------------------------------------------------------------------------ -->
-#
-
-if (ENABLE_MULTI )
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/multi-package.cmake)
-
-#build up sources
-set(MULTI_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
-
- # add sources
- set(MULTI_SOURCES ${MULTI_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB multi_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
-
- install(FILES ${multi_headers}
- DESTINATION include/sbml/packages/multi/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(multi_package FILES ${MULTI_SOURCES})
-
-# add multi sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${MULTI_SOURCES})
-
-######################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
- add_subdirectory(sbml/packages/multi/extension/test)
- #add_subdirectory(sbml/packages/multi/sbml/test)
- #add_subdirectory(sbml/packages/multi/util/test)
- add_subdirectory(sbml/packages/multi/validator/test)
-
-endif()
-
-endif()
-
+#################################################################################
+#
+# @file: multi-package.cmake
+# @brief: CMake configuration for L3 Multi package
+# @author: Generated by autocreate code
+#
+# <!--------------------------------------------------------------------------
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2013-2018 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+# 3. University of Heidelberg, Heidelberg, Germany
+#
+# Copyright (C) 2009-2013 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# ------------------------------------------------------------------------ -->
+#
+
+if (ENABLE_MULTI )
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/multi-package.cmake)
+
+#build up sources
+set(MULTI_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
+
+ # add sources
+ set(MULTI_SOURCES ${MULTI_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB multi_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
+
+ install(FILES ${multi_headers}
+ DESTINATION include/sbml/packages/multi/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(multi_package FILES ${MULTI_SOURCES})
+
+# add multi sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${MULTI_SOURCES})
+
+######################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+ add_subdirectory(sbml/packages/multi/extension/test)
+ #add_subdirectory(sbml/packages/multi/sbml/test)
+ #add_subdirectory(sbml/packages/multi/util/test)
+ add_subdirectory(sbml/packages/multi/validator/test)
+
+endif()
+
+endif()
+
Property changes on: branches/libsbml-experimental/src/multi-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: branches/libsbml-experimental/src/qual-package.cmake
===================================================================
--- branches/libsbml-experimental/src/qual-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/qual-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
Property changes on: branches/libsbml-experimental/src/qual-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/render-package.cmake
===================================================================
--- branches/libsbml-experimental/src/render-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/render-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,91 +1,91 @@
-#################################################
- # @file render-package.cmake
- # @brief Src CMake file for render package
- # @author SBMLTeam
- #
- # <!--------------------------------------------------------------------------
- # This file is part of libSBML. Please visit http://sbml.org for more
- # information about SBML, and the latest version of libSBML.
- #
- # Copyright (C) 2013-2017 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
- # ------------------------------------------------------------------------ -->
- #
-
-if(ENABLE_RENDER)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/render-package.cmake)
-
-#build up sources
-set(RENDER_SOURCES)
-
- # go through all directories
-foreach(dir common extension sbml util validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
-
- # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
- # they are #included directly, instead.
- if ("${dir}" STREQUAL "validator/constraints")
- foreach(tempFile ${current})
- if ("${tempFile}" MATCHES ".*Constraints.cpp")
- set_source_files_properties(
- ${tempFile}
- PROPERTIES HEADER_FILE_ONLY true
- )
- endif()
- endforeach()
- endif()
-
- # add sources
- set(RENDER_SOURCES ${RENDER_SOURCES} ${current})
-
- # mark headers for installation
- file(GLOB render_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
-
- install(FILES ${render_headers} DESTINATION include/sbml/packages/render/${dir})
-
-endforeach()
-
-# create source group for IDEs
-source_group(render_package FILES ${RENDER_SOURCES})
-
- # add render sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${RENDER_SOURCES})
-
-####################################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/render/sbml/test)
- add_subdirectory(sbml/packages/render/validator/test)
-
-endif()
-
-endif()
+#################################################
+ # @file render-package.cmake
+ # @brief Src CMake file for render package
+ # @author SBMLTeam
+ #
+ # <!--------------------------------------------------------------------------
+ # This file is part of libSBML. Please visit http://sbml.org for more
+ # information about SBML, and the latest version of libSBML.
+ #
+ # Copyright (C) 2013-2017 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+ # ------------------------------------------------------------------------ -->
+ #
+
+if(ENABLE_RENDER)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/render-package.cmake)
+
+#build up sources
+set(RENDER_SOURCES)
+
+ # go through all directories
+foreach(dir common extension sbml util validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
+
+ # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
+ # they are #included directly, instead.
+ if ("${dir}" STREQUAL "validator/constraints")
+ foreach(tempFile ${current})
+ if ("${tempFile}" MATCHES ".*Constraints.cpp")
+ set_source_files_properties(
+ ${tempFile}
+ PROPERTIES HEADER_FILE_ONLY true
+ )
+ endif()
+ endforeach()
+ endif()
+
+ # add sources
+ set(RENDER_SOURCES ${RENDER_SOURCES} ${current})
+
+ # mark headers for installation
+ file(GLOB render_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
+
+ install(FILES ${render_headers} DESTINATION include/sbml/packages/render/${dir})
+
+endforeach()
+
+# create source group for IDEs
+source_group(render_package FILES ${RENDER_SOURCES})
+
+ # add render sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${RENDER_SOURCES})
+
+####################################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/render/sbml/test)
+ add_subdirectory(sbml/packages/render/validator/test)
+
+endif()
+
+endif()
Property changes on: branches/libsbml-experimental/src/render-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/req-package.cmake
===================================================================
--- branches/libsbml-experimental/src/req-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/req-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,97 +1,97 @@
-#################################################################################
-#
-# @file: req-package.cmake
-# @brief: CMake configuration for L3 Req package
-# @author: Generated by autocreate code
-#
-# <!--------------------------------------------------------------------------
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2018 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-# 3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# ------------------------------------------------------------------------ -->
-#
-
-if(ENABLE_REQUIREDELEMENTS)
-
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/req-package.cmake)
-
-#build up sources
-set(REQ_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.h)
-
- # set the *Constraints.cpp files to be 'header' files so they won't be compiled--
- # they are #included directly, instead.
- if ("${dir}" STREQUAL "validator/constraints")
- foreach(tempFile ${current})
- if ("${tempFile}" MATCHES ".*Constraints.cpp")
- set_source_files_properties(
- ${tempFile}
- PROPERTIES HEADER_FILE_ONLY true
- )
- endif()
- endforeach()
- endif()
-
- # add sources
- set(REQ_SOURCES ${REQ_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB req_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.h)
-
- install(FILES ${req_headers}
- DESTINATION include/sbml/packages/req/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(req_package FILES ${REQ_SOURCES})
-
-# add req sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${REQ_SOURCES})
-
-######################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/req/extension/test)
-
-
-endif()
-
-endif()
-
+#################################################################################
+#
+# @file: req-package.cmake
+# @brief: CMake configuration for L3 Req package
+# @author: Generated by autocreate code
+#
+# <!--------------------------------------------------------------------------
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2013-2018 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+# 3. University of Heidelberg, Heidelberg, Germany
+#
+# Copyright (C) 2009-2013 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# ------------------------------------------------------------------------ -->
+#
+
+if(ENABLE_REQUIREDELEMENTS)
+
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/req-package.cmake)
+
+#build up sources
+set(REQ_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.h)
+
+ # set the *Constraints.cpp files to be 'header' files so they won't be compiled--
+ # they are #included directly, instead.
+ if ("${dir}" STREQUAL "validator/constraints")
+ foreach(tempFile ${current})
+ if ("${tempFile}" MATCHES ".*Constraints.cpp")
+ set_source_files_properties(
+ ${tempFile}
+ PROPERTIES HEADER_FILE_ONLY true
+ )
+ endif()
+ endforeach()
+ endif()
+
+ # add sources
+ set(REQ_SOURCES ${REQ_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB req_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/req/${dir}/*.h)
+
+ install(FILES ${req_headers}
+ DESTINATION include/sbml/packages/req/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(req_package FILES ${REQ_SOURCES})
+
+# add req sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${REQ_SOURCES})
+
+######################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/req/extension/test)
+
+
+endif()
+
+endif()
+
Property changes on: branches/libsbml-experimental/src/req-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: branches/libsbml-experimental/src/spatial-package.cmake
===================================================================
--- branches/libsbml-experimental/src/spatial-package.cmake 2019-12-04 19:31:17 UTC (rev 26193)
+++ branches/libsbml-experimental/src/spatial-package.cmake 2019-12-04 19:49:08 UTC (rev 26194)
@@ -1,100 +1,100 @@
-#################################################################################
- # @file spatial-package.cmake
- # @brief Src CMake file for spatial package
- # @author SBMLTeam
- #
-# <!--------------------------------------------------------------------------
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
- # Copyright (C) 2019 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2013-2018 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
-# ------------------------------------------------------------------------ -->
-#
-
-if (ENABLE_SPATIAL )
-
-include(${CMAKE_SOURCE_DIR}/spatial-package.cmake)
-
-#build up sources
-set(SPATIAL_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.h)
-
- # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
- # they are #included directly, instead.
- if ("${dir}" STREQUAL "validator/constraints")
- foreach(tempFile ${current})
- if ("${tempFile}" MATCHES ".*Constraints.cpp")
- set_source_files_properties(
- ${tempFile}
- PROPERTIES HEADER_FILE_ONLY true
- )
- endif()
- endforeach()
- endif()
-
- # add sources
- set(SPATIAL_SOURCES ${SPATIAL_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB spatial_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.h)
-
- install(FILES ${spatial_headers}
- DESTINATION include/sbml/packages/spatial/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(spatial_package FILES ${SPATIAL_SOURCES})
-
-# add spatial sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${SPATIAL_SOURCES})
-
-######################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/spatial/extension/test)
- add_subdirectory(sbml/packages/spatial/sbml/test)
- add_subdirectory(sbml/packages/spatial/validator/test)
-
-endif()
-
-endif()
-
+#################################################################################
+ # @file spatial-package.cmake
+ # @brief Src CMake file for spatial package
+ # @author SBMLTeam
+ #
+# <!--------------------------------------------------------------------------
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+ # Copyright (C) 2019 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2013-2018 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+# ------------------------------------------------------------------------ -->
+#
+
+if (ENABLE_SPATIAL )
+
+include(${CMAKE_SOURCE_DIR}/spatial-package.cmake)
+
+#build up sources
+set(SPATIAL_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.h)
+
+ # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
+ # they are #included directly, instead.
+ if ("${dir}" STREQUAL "validator/constraints")
+ foreach(tempFile ${current})
+ if ("${tempFile}" MATCHES ".*Constraints.cpp")
+ set_source_files_properties(
+ ${tempFile}
+ PROPERTIES HEADER_FILE_ONLY true
+ )
+ endif()
+ endforeach()
+ endif()
+
+ # add sources
+ set(SPATIAL_SOURCES ${SPATIAL_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB spatial_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/spatial/${dir}/*.h)
+
+ install(FILES ${spatial_headers}
+ DESTINATION include/sbml/packages/spatial/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(spatial_package FILES ${SPATIAL_SOURCES})
+
+# add spatial sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${SPATIAL_SOURCES})
+
+######################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/spatial/extension/test)
+ add_subdirectory(sbml/packages/spatial/sbml/test)
+ add_subdirectory(sbml/packages/spatial/validator/test)
+
+endif()
+
+endif()
+
Property changes on: bran...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-04 19:05:27
|
Revision: 26192
http://sourceforge.net/p/sbml/code/26192
Author: luciansmith
Date: 2019-12-04 19:05:23 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Set eol-style on various files.
Modified Paths:
--------------
trunk/libsbml/src/l3v2extendedmath-package.cmake
trunk/libsbml/src/multi-package.cmake
trunk/libsbml/src/render-package.cmake
trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake
trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake
trunk/libsbml/src/sbml/common/libsbml-package.h.cmake
trunk/libsbml/src/sbml/common/libsbml-version.h.cmake
trunk/libsbml/src/sbml/compress/ioapi_mem.c
trunk/libsbml/src/sbml/math/DefinitionURLRegistry.cpp
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-import-external_v1v2.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-import-external_v2v1.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-simple-aggregate_v2.xml
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/general-constraints/1021006-fail-01-02.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/general-constraints/ext_models/rbc_parasite_model_reduced.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/1010501-fail-01-12.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/1010501-pass-00-10.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/ext_models/rbc_parasite_model_reduced.xml
trunk/libsbml/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/fbc/validator/constraints/FbcIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/TestReadWriteInfix.cpp
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/TestRunner.c
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathMathMLConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/layout/validator/constraints/LayoutConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/layout/validator/constraints/LayoutIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualMathConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/sbml/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/render/validator/constraints/RenderConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/validator/constraints/RenderIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/validator/test/CMakeLists.txt
trunk/libsbml/src/sbml/util/CallbackRegistry.cpp
trunk/libsbml/src/sbml/validator/constraints/CompatibilityConstraints.cxx
trunk/libsbml/src/sbml/validator/constraints/ConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/IdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/InternalConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v2CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v3CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v4CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L3v1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L3v2CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/MathMLConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/ModelingPracticeConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/OverdeterminedConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/SBOConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/StrictUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/UnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-01.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-02.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-03.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-04.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-pass-00-01.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-pass-00-02.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99505-pass-00-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-22.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-23.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-07.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-09.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-11.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-12.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21121-pass-00-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21121-pass-00-11.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10201-fail-01-19.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10201-fail-01-20.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10202-fail-01-13.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10203-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10204-fail-01-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10206-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10208-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10209-fail-01-21-10217.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-07.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-20.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-21.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-22.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10218-fail-01-15.xml
Property Changed:
----------------
trunk/libsbml/src/fbc-package.cmake
trunk/libsbml/src/groups-package.cmake
trunk/libsbml/src/l3v2extendedmath-package.cmake
trunk/libsbml/src/layout-package.cmake
trunk/libsbml/src/multi-package.cmake
trunk/libsbml/src/qual-package.cmake
trunk/libsbml/src/render-package.cmake
trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake
trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake
trunk/libsbml/src/sbml/common/libsbml-package.h.cmake
trunk/libsbml/src/sbml/common/libsbml-version.h.cmake
trunk/libsbml/src/sbml/compress/ioapi_mem.c
trunk/libsbml/src/sbml/conversion/test/test-data/01224-sbml-l3v1.xml
trunk/libsbml/src/sbml/conversion/test/test-data/01800-fail-sbml-l3v1.xml
trunk/libsbml/src/sbml/conversion/test/test-data/01800-sbml-l3v1.xml
trunk/libsbml/src/sbml/conversion/test/test-data/01800-sbml-l3v2.xml
trunk/libsbml/src/sbml/math/DefinitionURLRegistry.cpp
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-import-external_v1v2.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-import-external_v2v1.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/eg-simple-aggregate_v2.xml
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/general-constraints/1021006-fail-01-02.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/general-constraints/ext_models/rbc_parasite_model_reduced.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/1010501-fail-01-12.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/1010501-pass-00-10.xml
trunk/libsbml/src/sbml/packages/comp/validator/test/test-data/units-constraints/ext_models/rbc_parasite_model_reduced.xml
trunk/libsbml/src/sbml/packages/fbc/validator/constraints/FbcConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/fbc/validator/constraints/FbcIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/TestReadWriteInfix.cpp
trunk/libsbml/src/sbml/packages/l3v2extendedmath/extension/test/TestRunner.c
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathMathMLConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/constraints/L3v2extendedmathUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/l3v2extendedmath/validator/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/layout/validator/constraints/LayoutConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/layout/validator/constraints/LayoutIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/qual/validator/constraints/QualMathConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/sbml/test/CMakeLists.txt
trunk/libsbml/src/sbml/packages/render/validator/constraints/RenderConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/validator/constraints/RenderIdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/packages/render/validator/test/CMakeLists.txt
trunk/libsbml/src/sbml/util/CallbackRegistry.cpp
trunk/libsbml/src/sbml/validator/constraints/CompatibilityConstraints.cxx
trunk/libsbml/src/sbml/validator/constraints/ConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/IdentifierConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/InternalConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v2CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v3CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L2v4CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L3v1CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/L3v2CompatibilityConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/MathMLConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/ModelingPracticeConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/OverdeterminedConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/SBOConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/StrictUnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/constraints/UnitConsistencyConstraintsDeclared.cxx
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-01.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-02.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-03.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-fail-01-04.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-pass-00-01.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99304-pass-00-02.xml
trunk/libsbml/src/sbml/validator/test/test-data/libsbml-constraints/99505-pass-00-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-22.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20906-pass-00-23.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-07.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-09.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-11.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20912-pass-00-12.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21121-pass-00-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21121-pass-00-11.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10201-fail-01-19.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10201-fail-01-20.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10202-fail-01-13.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10203-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10204-fail-01-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10206-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10208-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10209-fail-01-21-10217.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-07.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-08.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-10.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-20.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-21.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-22.xml
trunk/libsbml/src/sbml/validator/test/test-data/sbml-mathml-constraints/10218-fail-01-15.xml
Index: trunk/libsbml/src/fbc-package.cmake
===================================================================
--- trunk/libsbml/src/fbc-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/fbc-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
Property changes on: trunk/libsbml/src/fbc-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: trunk/libsbml/src/groups-package.cmake
===================================================================
--- trunk/libsbml/src/groups-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/groups-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
Property changes on: trunk/libsbml/src/groups-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/l3v2extendedmath-package.cmake
===================================================================
--- trunk/libsbml/src/l3v2extendedmath-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/l3v2extendedmath-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,80 +1,80 @@
-#################################################
- # @file l3v2extendedmath-package.cmake
- # @brief Src CMake file for l3v2extendedmath package
- # @author SBMLTeam
- #
- # <!--------------------------------------------------------------------------
- # This file is part of libSBML. Please visit http://sbml.org for more
- # information about SBML, and the latest version of libSBML.
- #
- # Copyright (C) 2013-2018 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
- # ------------------------------------------------------------------------ -->
- #
-
-if (ENABLE_L3V2EXTENDEDMATH)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/l3v2extendedmath-package.cmake)
-
- # build up sources
-set(L3V2EXTENDEDMATH_SOURCES)
-
- # go through all directories
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
-
- # add sources
- set(L3V2EXTENDEDMATH_SOURCES ${L3V2EXTENDEDMATH_SOURCES} ${current})
-
- # mark headers for installation
- file(GLOB l3v2extendedmath_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
-
- install(FILES ${l3v2extendedmath_headers} DESTINATION include/sbml/packages/l3v2extendedmath/${dir} )
-
-endforeach()
-
- # create source group for IDEs
-source_group(l3v2extendedmath_package FILES ${L3V2EXTENDEDMATH_SOURCES})
-
- # add l3v2extendedmath sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${L3V2EXTENDEDMATH_SOURCES})
-
-#################################################
- #
- # add test scripts
- #
-if (WITH_CHECK)
-
- add_subdirectory(sbml/packages/l3v2extendedmath/validator/test)
- add_subdirectory(sbml/packages/l3v2extendedmath/extension/test)
-
-endif()
-
-endif()
-
+#################################################
+ # @file l3v2extendedmath-package.cmake
+ # @brief Src CMake file for l3v2extendedmath package
+ # @author SBMLTeam
+ #
+ # <!--------------------------------------------------------------------------
+ # This file is part of libSBML. Please visit http://sbml.org for more
+ # information about SBML, and the latest version of libSBML.
+ #
+ # Copyright (C) 2013-2018 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+ # ------------------------------------------------------------------------ -->
+ #
+
+if (ENABLE_L3V2EXTENDEDMATH)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/l3v2extendedmath-package.cmake)
+
+ # build up sources
+set(L3V2EXTENDEDMATH_SOURCES)
+
+ # go through all directories
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
+
+ # add sources
+ set(L3V2EXTENDEDMATH_SOURCES ${L3V2EXTENDEDMATH_SOURCES} ${current})
+
+ # mark headers for installation
+ file(GLOB l3v2extendedmath_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/l3v2extendedmath/${dir}/*.h)
+
+ install(FILES ${l3v2extendedmath_headers} DESTINATION include/sbml/packages/l3v2extendedmath/${dir} )
+
+endforeach()
+
+ # create source group for IDEs
+source_group(l3v2extendedmath_package FILES ${L3V2EXTENDEDMATH_SOURCES})
+
+ # add l3v2extendedmath sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${L3V2EXTENDEDMATH_SOURCES})
+
+#################################################
+ #
+ # add test scripts
+ #
+if (WITH_CHECK)
+
+ add_subdirectory(sbml/packages/l3v2extendedmath/validator/test)
+ add_subdirectory(sbml/packages/l3v2extendedmath/extension/test)
+
+endif()
+
+endif()
+
Property changes on: trunk/libsbml/src/l3v2extendedmath-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: trunk/libsbml/src/layout-package.cmake
===================================================================
--- trunk/libsbml/src/layout-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/layout-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
Property changes on: trunk/libsbml/src/layout-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/multi-package.cmake
===================================================================
--- trunk/libsbml/src/multi-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/multi-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,84 +1,84 @@
-#################################################################################
-#
-# @file: multi-package.cmake
-# @brief: CMake configuration for L3 Multi package
-# @author: Generated by autocreate code
-#
-# <!--------------------------------------------------------------------------
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2018 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-# 3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-# ------------------------------------------------------------------------ -->
-#
-
-if (ENABLE_MULTI )
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/multi-package.cmake)
-
-#build up sources
-set(MULTI_SOURCES)
-
-# go through all directories: common, extension and sbml
-foreach(dir common extension sbml validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.c
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
-
- # add sources
- set(MULTI_SOURCES ${MULTI_SOURCES} ${current})
-
- # mark header files for installation
- file(GLOB multi_headers
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
-
- install(FILES ${multi_headers}
- DESTINATION include/sbml/packages/multi/${dir} )
-
-endforeach()
-
-# create source group for IDEs
-source_group(multi_package FILES ${MULTI_SOURCES})
-
-# add multi sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${MULTI_SOURCES})
-
-######################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
- add_subdirectory(sbml/packages/multi/extension/test)
- #add_subdirectory(sbml/packages/multi/sbml/test)
- #add_subdirectory(sbml/packages/multi/util/test)
- add_subdirectory(sbml/packages/multi/validator/test)
-
-endif()
-
-endif()
-
+#################################################################################
+#
+# @file: multi-package.cmake
+# @brief: CMake configuration for L3 Multi package
+# @author: Generated by autocreate code
+#
+# <!--------------------------------------------------------------------------
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2013-2018 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+# 3. University of Heidelberg, Heidelberg, Germany
+#
+# Copyright (C) 2009-2013 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+# ------------------------------------------------------------------------ -->
+#
+
+if (ENABLE_MULTI )
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/multi-package.cmake)
+
+#build up sources
+set(MULTI_SOURCES)
+
+# go through all directories: common, extension and sbml
+foreach(dir common extension sbml validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
+
+ # add sources
+ set(MULTI_SOURCES ${MULTI_SOURCES} ${current})
+
+ # mark header files for installation
+ file(GLOB multi_headers
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/multi/${dir}/*.h)
+
+ install(FILES ${multi_headers}
+ DESTINATION include/sbml/packages/multi/${dir} )
+
+endforeach()
+
+# create source group for IDEs
+source_group(multi_package FILES ${MULTI_SOURCES})
+
+# add multi sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${MULTI_SOURCES})
+
+######################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+ add_subdirectory(sbml/packages/multi/extension/test)
+ #add_subdirectory(sbml/packages/multi/sbml/test)
+ #add_subdirectory(sbml/packages/multi/util/test)
+ add_subdirectory(sbml/packages/multi/validator/test)
+
+endif()
+
+endif()
+
Property changes on: trunk/libsbml/src/multi-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Index: trunk/libsbml/src/qual-package.cmake
===================================================================
--- trunk/libsbml/src/qual-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/qual-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
Property changes on: trunk/libsbml/src/qual-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/render-package.cmake
===================================================================
--- trunk/libsbml/src/render-package.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/render-package.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,91 +1,91 @@
-#################################################
- # @file render-package.cmake
- # @brief Src CMake file for render package
- # @author SBMLTeam
- #
- # <!--------------------------------------------------------------------------
- # This file is part of libSBML. Please visit http://sbml.org for more
- # information about SBML, and the latest version of libSBML.
- #
- # Copyright (C) 2013-2017 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- # 3. University of Heidelberg, Heidelberg, Germany
- #
- # Copyright (C) 2009-2013 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- #
- # Copyright (C) 2006-2008 by the California Institute of Technology,
- # Pasadena, CA, USA
- #
- # Copyright (C) 2002-2005 jointly by the following organizations:
- # 1. California Institute of Technology, Pasadena, CA, USA
- # 2. Japan Science and Technology Agency, Japan
- #
- # This library is free software; you can redistribute it and/or modify it
- # under the terms of the GNU Lesser General Public License as published by the
- # Free Software Foundation. A copy of the license agreement is provided in the
- # file named "LICENSE.txt" included with this software distribution and also
- # available online as http://sbml.org/software/libsbml/license.html
- # ------------------------------------------------------------------------ -->
- #
-
-if(ENABLE_RENDER)
-
-include(${LIBSBML_ROOT_SOURCE_DIR}/render-package.cmake)
-
-#build up sources
-set(RENDER_SOURCES)
-
- # go through all directories
-foreach(dir common extension sbml util validator validator/constraints)
-
- # add to include directory
- include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir})
-
- # file sources
- file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
-
- # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
- # they are #included directly, instead.
- if ("${dir}" STREQUAL "validator/constraints")
- foreach(tempFile ${current})
- if ("${tempFile}" MATCHES ".*Constraints.cpp")
- set_source_files_properties(
- ${tempFile}
- PROPERTIES HEADER_FILE_ONLY true
- )
- endif()
- endforeach()
- endif()
-
- # add sources
- set(RENDER_SOURCES ${RENDER_SOURCES} ${current})
-
- # mark headers for installation
- file(GLOB render_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
-
- install(FILES ${render_headers} DESTINATION include/sbml/packages/render/${dir})
-
-endforeach()
-
-# create source group for IDEs
-source_group(render_package FILES ${RENDER_SOURCES})
-
- # add render sources to SBML sources
-SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${RENDER_SOURCES})
-
-####################################################################
-#
-# add test scripts
-#
-if(WITH_CHECK)
-
- add_subdirectory(sbml/packages/render/sbml/test)
- add_subdirectory(sbml/packages/render/validator/test)
-
-endif()
-
-endif()
+#################################################
+ # @file render-package.cmake
+ # @brief Src CMake file for render package
+ # @author SBMLTeam
+ #
+ # <!--------------------------------------------------------------------------
+ # This file is part of libSBML. Please visit http://sbml.org for more
+ # information about SBML, and the latest version of libSBML.
+ #
+ # Copyright (C) 2013-2017 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ # 3. University of Heidelberg, Heidelberg, Germany
+ #
+ # Copyright (C) 2009-2013 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ #
+ # Copyright (C) 2006-2008 by the California Institute of Technology,
+ # Pasadena, CA, USA
+ #
+ # Copyright (C) 2002-2005 jointly by the following organizations:
+ # 1. California Institute of Technology, Pasadena, CA, USA
+ # 2. Japan Science and Technology Agency, Japan
+ #
+ # This library is free software; you can redistribute it and/or modify it
+ # under the terms of the GNU Lesser General Public License as published by the
+ # Free Software Foundation. A copy of the license agreement is provided in the
+ # file named "LICENSE.txt" included with this software distribution and also
+ # available online as http://sbml.org/software/libsbml/license.html
+ # ------------------------------------------------------------------------ -->
+ #
+
+if(ENABLE_RENDER)
+
+include(${LIBSBML_ROOT_SOURCE_DIR}/render-package.cmake)
+
+#build up sources
+set(RENDER_SOURCES)
+
+ # go through all directories
+foreach(dir common extension sbml util validator validator/constraints)
+
+ # add to include directory
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir})
+
+ # file sources
+ file(GLOB current ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.cpp
+ ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
+
+ # Set the *Constraints.cpp files to be 'header' files so they won't be compiled--
+ # they are #included directly, instead.
+ if ("${dir}" STREQUAL "validator/constraints")
+ foreach(tempFile ${current})
+ if ("${tempFile}" MATCHES ".*Constraints.cpp")
+ set_source_files_properties(
+ ${tempFile}
+ PROPERTIES HEADER_FILE_ONLY true
+ )
+ endif()
+ endforeach()
+ endif()
+
+ # add sources
+ set(RENDER_SOURCES ${RENDER_SOURCES} ${current})
+
+ # mark headers for installation
+ file(GLOB render_headers ${CMAKE_CURRENT_SOURCE_DIR}/sbml/packages/render/${dir}/*.h)
+
+ install(FILES ${render_headers} DESTINATION include/sbml/packages/render/${dir})
+
+endforeach()
+
+# create source group for IDEs
+source_group(render_package FILES ${RENDER_SOURCES})
+
+ # add render sources to SBML sources
+SET(LIBSBML_SOURCES ${LIBSBML_SOURCES} ${RENDER_SOURCES})
+
+####################################################################
+#
+# add test scripts
+#
+if(WITH_CHECK)
+
+ add_subdirectory(sbml/packages/render/sbml/test)
+ add_subdirectory(sbml/packages/render/validator/test)
+
+endif()
+
+endif()
Property changes on: trunk/libsbml/src/render-package.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,115 +1,115 @@
-/**
- * @file libsbml-config-common.h
- * @brief Configuration variables
- * @author Ben Bornstein
- *
- * $Id$
- * $HeadURL$
- *
- *<!---------------------------------------------------------------------------
- * This file is part of libSBML. Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2019 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2013-2018 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- * 3. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2009-2013 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- *
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- * Pasadena, CA, USA
- *
- * Copyright (C) 2002-2005 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. Japan Science and Technology Agency, Japan
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution and
- * also available online as http://sbml.org/software/libsbml/license.html
- *------------------------------------------------------------------------- -->
- *
- * If this file is named <tt>libsbml-config-unix.h</tt>, then it was
- * generated from <tt>libsbml-config-unix.h.in</tt> by the @c configure
- * script at the top level of the libSBML source tree.
- *
- * @note This file is handled unusually. The file itself is generated by
- * @c configure, but unlike other files that are likewise automatically
- * generated, it is also checked into the source repository. The need for
- * this is due to the fact that under Windows, developers may not be
- * running @c configure at all (e.g., if they are using the MSVC
- * environment). The <tt>libsbml-config-win.h</tt> file therefore needs to
- * be provided directly in order for people to be able to compile the
- * sources under Windows. For consistency, the file
- * <tt>libsbml-config-unix.h</tt> is also similarly checked in. Developers
- * must remember to check in the .h version of this file in the source code
- * repository prior to major releases, so that an up-to-date .h file is
- * present in distributions. This is admittedly an undesirable and
- * error-prone situation, but it is currently the best alternative we have
- * been able to find.
- */
-
-
-/* Define to 1 if you have the <check.h> header file. */
-#cmakedefine HAVE_CHECK_H 1
-
-/* Define to 1 if you have the <expat.h> header file. */
-#cmakedefine HAVE_EXPAT_H 1
-
-/* Define to 1 to use the Expat XML library */
-#cmakedefine USE_EXPAT
-
-
-/* Define to 1 if you have the <errno.h> header file. */
-#cmakedefine HAVE_ERRNO_H 1
-
-/* Define to 1 if you have the <ieeefp.h> header file. */
-#cmakedefine HAVE_IEEEFP_H 1
-
-/* Define to 1 if you have the ANSI C header files. */
-#cmakedefine STDC_HEADERS 1
-
-/* Define to 1 if you have the <math.h> header file. */
-#cmakedefine HAVE_MATH_H 1
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#cmakedefine HAVE_SYS_TYPES_H 1
-
-/* Define to 1 if you have the `m' library (-lm). */
-#cmakedefine HAVE_LIBM 1
-
-
-/* Define to 1 to enable primitive memory tracing. */
-#cmakedefine TRACE_MEMORY
-
-/* Define to 1 to build the SBML layout extension. */
-#cmakedefine USE_LAYOUT
-
-/* Define to 1 to build the SBML groups extension. */
-#cmakedefine USE_GROUPS
-
-/* Define to build the SBML FBC extension. */
-#cmakedefine USE_FBC 1
-
-/* Define to 1 if your processor stores words with the most significant byte
- first (like Motorola and SPARC, unlike Intel and VAX). */
-#cmakedefine WORDS_BIGENDIAN 1
-
-/* Define to allow the c-functions in util.c and memory.c exit the
- application in case of an allocation / file system error. */
-#cmakedefine EXIT_ON_ERROR 1
-
-/* Define to specify that the legacy math implementation ought to be used. */
-/* This is no longer an option but in case other programs compiling against
- libsbml have used the flag it is always on */
-#cmakedefine LIBSBML_USE_LEGACY_MATH 1
-
-#include <sbml/common/libsbml-config-packages.h>
+/**
+ * @file libsbml-config-common.h
+ * @brief Configuration variables
+ * @author Ben Bornstein
+ *
+ * $Id$
+ * $HeadURL$
+ *
+ *<!---------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ * 3. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution and
+ * also available online as http://sbml.org/software/libsbml/license.html
+ *------------------------------------------------------------------------- -->
+ *
+ * If this file is named <tt>libsbml-config-unix.h</tt>, then it was
+ * generated from <tt>libsbml-config-unix.h.in</tt> by the @c configure
+ * script at the top level of the libSBML source tree.
+ *
+ * @note This file is handled unusually. The file itself is generated by
+ * @c configure, but unlike other files that are likewise automatically
+ * generated, it is also checked into the source repository. The need for
+ * this is due to the fact that under Windows, developers may not be
+ * running @c configure at all (e.g., if they are using the MSVC
+ * environment). The <tt>libsbml-config-win.h</tt> file therefore needs to
+ * be provided directly in order for people to be able to compile the
+ * sources under Windows. For consistency, the file
+ * <tt>libsbml-config-unix.h</tt> is also similarly checked in. Developers
+ * must remember to check in the .h version of this file in the source code
+ * repository prior to major releases, so that an up-to-date .h file is
+ * present in distributions. This is admittedly an undesirable and
+ * error-prone situation, but it is currently the best alternative we have
+ * been able to find.
+ */
+
+
+/* Define to 1 if you have the <check.h> header file. */
+#cmakedefine HAVE_CHECK_H 1
+
+/* Define to 1 if you have the <expat.h> header file. */
+#cmakedefine HAVE_EXPAT_H 1
+
+/* Define to 1 to use the Expat XML library */
+#cmakedefine USE_EXPAT
+
+
+/* Define to 1 if you have the <errno.h> header file. */
+#cmakedefine HAVE_ERRNO_H 1
+
+/* Define to 1 if you have the <ieeefp.h> header file. */
+#cmakedefine HAVE_IEEEFP_H 1
+
+/* Define to 1 if you have the ANSI C header files. */
+#cmakedefine STDC_HEADERS 1
+
+/* Define to 1 if you have the <math.h> header file. */
+#cmakedefine HAVE_MATH_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#cmakedefine HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the `m' library (-lm). */
+#cmakedefine HAVE_LIBM 1
+
+
+/* Define to 1 to enable primitive memory tracing. */
+#cmakedefine TRACE_MEMORY
+
+/* Define to 1 to build the SBML layout extension. */
+#cmakedefine USE_LAYOUT
+
+/* Define to 1 to build the SBML groups extension. */
+#cmakedefine USE_GROUPS
+
+/* Define to build the SBML FBC extension. */
+#cmakedefine USE_FBC 1
+
+/* Define to 1 if your processor stores words with the most significant byte
+ first (like Motorola and SPARC, unlike Intel and VAX). */
+#cmakedefine WORDS_BIGENDIAN 1
+
+/* Define to allow the c-functions in util.c and memory.c exit the
+ application in case of an allocation / file system error. */
+#cmakedefine EXIT_ON_ERROR 1
+
+/* Define to specify that the legacy math implementation ought to be used. */
+/* This is no longer an option but in case other programs compiling against
+ libsbml have used the flag it is always on */
+#cmakedefine LIBSBML_USE_LEGACY_MATH 1
+
+#include <sbml/common/libsbml-config-packages.h>
Property changes on: trunk/libsbml/src/sbml/common/libsbml-config-common.h.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,72 +1,72 @@
-/**
- * @file libsbml-namespace.h
- * @brief Defines C++ namespace of libSBML
- * @author Akiya Jouraku
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML. Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2019 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2013-2018 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- * 3. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2009-2013 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- *
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- * Pasadena, CA, USA
- *
- * Copyright (C) 2002-2005 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. Japan Science and Technology Agency, Japan
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution and
- * also available online as http://sbml.org/software/libsbml/license.html
- *------------------------------------------------------------------------- -->
- *
- */
-
-#ifndef LIBSBML_NAMESPACE_H
-#define LIBSBML_NAMESPACE_H 1
-
-/*
- *
- * The idea of the following marcors are borrowed from
- * Xerces-C++ XML Parser (http://xerces.apache.org/xerces-c/).
- *
- */
-
-/* Define to enable libSBML C++ namespace */
-#cmakedefine LIBSBML_USE_CPP_NAMESPACE 1
-
-
-#if defined(__cplusplus) && defined(LIBSBML_USE_CPP_NAMESPACE) && !defined(SWIG)
- /* C++ namespace of libSBML */
- #define LIBSBML_CPP_NAMESPACE libsbml
- #define LIBSBML_CPP_NAMESPACE_BEGIN namespace LIBSBML_CPP_NAMESPACE {
- #define LIBSBML_CPP_NAMESPACE_END }
- #define LIBSBML_CPP_NAMESPACE_USE using namespace LIBSBML_CPP_NAMESPACE;
- #define LIBSBML_CPP_NAMESPACE_QUALIFIER LIBSBML_CPP_NAMESPACE::
-
- namespace LIBSBML_CPP_NAMESPACE {}
-#else
- #define LIBSBML_CPP_NAMESPACE
- #define LIBSBML_CPP_NAMESPACE_BEGIN
- #define LIBSBML_CPP_NAMESPACE_END
- #define LIBSBML_CPP_NAMESPACE_USE
- #define LIBSBML_CPP_NAMESPACE_QUALIFIER
-#endif
-
-
-#endif /* LIBSBML_NAMESPACE_H */
-
+/**
+ * @file libsbml-namespace.h
+ * @brief Defines C++ namespace of libSBML
+ * @author Akiya Jouraku
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ * 3. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution and
+ * also available online as http://sbml.org/software/libsbml/license.html
+ *------------------------------------------------------------------------- -->
+ *
+ */
+
+#ifndef LIBSBML_NAMESPACE_H
+#define LIBSBML_NAMESPACE_H 1
+
+/*
+ *
+ * The idea of the following marcors are borrowed from
+ * Xerces-C++ XML Parser (http://xerces.apache.org/xerces-c/).
+ *
+ */
+
+/* Define to enable libSBML C++ namespace */
+#cmakedefine LIBSBML_USE_CPP_NAMESPACE 1
+
+
+#if defined(__cplusplus) && defined(LIBSBML_USE_CPP_NAMESPACE) && !defined(SWIG)
+ /* C++ namespace of libSBML */
+ #define LIBSBML_CPP_NAMESPACE libsbml
+ #define LIBSBML_CPP_NAMESPACE_BEGIN namespace LIBSBML_CPP_NAMESPACE {
+ #define LIBSBML_CPP_NAMESPACE_END }
+ #define LIBSBML_CPP_NAMESPACE_USE using namespace LIBSBML_CPP_NAMESPACE;
+ #define LIBSBML_CPP_NAMESPACE_QUALIFIER LIBSBML_CPP_NAMESPACE::
+
+ namespace LIBSBML_CPP_NAMESPACE {}
+#else
+ #define LIBSBML_CPP_NAMESPACE
+ #define LIBSBML_CPP_NAMESPACE_BEGIN
+ #define LIBSBML_CPP_NAMESPACE_END
+ #define LIBSBML_CPP_NAMESPACE_USE
+ #define LIBSBML_CPP_NAMESPACE_QUALIFIER
+#endif
+
+
+#endif /* LIBSBML_NAMESPACE_H */
+
Property changes on: trunk/libsbml/src/sbml/common/libsbml-namespace.h.cmake
___________________________________________________________________
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/libsbml/src/sbml/common/libsbml-package.h.cmake
===================================================================
--- trunk/libsbml/src/sbml/common/libsbml-package.h.cmake 2019-12-04 17:30:23 UTC (rev 26191)
+++ trunk/libsbml/src/sbml/common/libsbml-package.h.cmake 2019-12-04 19:05:23 UTC (rev 26192)
@@ -1,58 +1,58 @@
-/**
- * @file libsbml-package.h
- * @brief Definitions of the PACKAGE_ variables.
- * @author Ben Bornstein
- *
- * <!--------------------------------------------------------------------------
- * This file is part of libSBML. Please visit http://sbml.org for more
- * information about SBML, and the latest version of libSBML.
- *
- * Copyright (C) 2019 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2013-2018 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- * 3. University of Heidelberg, Heidelberg, Germany
- *
- * Copyright (C) 2009-2013 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- *
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- * Pasadena, CA, USA
- *
- * Copyright (C) 2002-2005 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. Japan Science and Technology Agency, Japan
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution and
- * also available online as http://sbml.org/software/libsbml/license.html
- *------------------------------------------------------------------------- -->
- *
- * The file <tt>libsbml-package.h</tt> is generated from the file
- * <tt>libsbml-package.h.cmake</tt> by the @c cmake script at the top
- * level of the libSBML source tree.
- *
- */
-
-
-/* Define to the address where bug reports for this package should be sent. */
-#define PACKAGE_BUGREPORT "lib...@go..."
-
-/* Define to the full name of this package. */
-#define PACKAGE_NAME "@PACKAGE_NAME@"
-
-/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "@PACKAGE_NAME@ @PACKAGE_VERSION@"
-
-/* Define to the one symbol short name of this package. */
-#define PACKAGE_TARNAME "libsbml"
-
-/* Define to the version of this package. */
-#define PACKAGE_VERSION "@PACKAGE_VERSION@"
-
+/**
+ * @file libsbml-package.h
+ * @brief Definitions of the PACKAGE_ variables.
+ * @author Ben Bornstein
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2019 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ * 3. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution and
+ * also available online as http://sbml.org/software/libsbml/license.html
+ *------------------------------------------------------------------------- -->
+ *
+ * The file <tt>libsbml-package.h</tt> is generated from the file
+ * <tt>libsbml-package.h.cmake</tt> by the @c cmake script at the top
+ * level of the libSBML...
[truncated message content] |
|
From: <luc...@us...> - 2019-12-04 17:30:24
|
Revision: 26191
http://sourceforge.net/p/sbml/code/26191
Author: luciansmith
Date: 2019-12-04 17:30:23 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Update creation of test suite models and spec examples.
Modified Paths:
--------------
branches/libsbml-experimental/examples/c++/distrib/createTestSuiteModels.cpp
branches/libsbml-experimental/examples/c++/distrib/distrib_example1.cpp
Modified: branches/libsbml-experimental/examples/c++/distrib/createTestSuiteModels.cpp
===================================================================
--- branches/libsbml-experimental/examples/c++/distrib/createTestSuiteModels.cpp 2019-12-04 17:21:17 UTC (rev 26190)
+++ branches/libsbml-experimental/examples/c++/distrib/createTestSuiteModels.cpp 2019-12-04 17:30:23 UTC (rev 26191)
@@ -468,7 +468,7 @@
testid.str("");
testnum++;
testid << "000" << testnum << "/000" << testnum << "-sbml-l3v1.xml";
- args.push_back("lognormal");
+ args.push_back("logNormal");
args.push_back("logScale");
args.push_back("shape");
setupDistrib(document->getModel(), "logNormalDistribution", args, "1, 2");
Modified: branches/libsbml-experimental/examples/c++/distrib/distrib_example1.cpp
===================================================================
--- branches/libsbml-experimental/examples/c++/distrib/distrib_example1.cpp 2019-12-04 17:21:17 UTC (rev 26190)
+++ branches/libsbml-experimental/examples/c++/distrib/distrib_example1.cpp 2019-12-04 17:30:23 UTC (rev 26191)
@@ -78,48 +78,6 @@
return ia;
}
-//void setupArguments(DistribDrawFromDistribution* dfd, InitialAssignment* ia, Model* model, vector<string> arguments)
-//{
-// string infix = "distribution(";
-// for (size_t i = 0; i < arguments.size(); i++) {
-// string arg = arguments[i];
-// Parameter* param = model->createParameter();
-// param->setConstant(true);
-// param->setId(arg);
-// DistribInput* di = dfd->createDistribInput();
-// di->setId(arg);
-// di->setIndex(i);
-// if (i > 0) {
-// infix += ", ";
-// }
-// infix += arg;
-// }
-// infix += ")";
-// ASTNode* math = SBML_parseL3Formula(infix.c_str());
-// ia->setMath(math);
-// delete math;
-//}
-
-//void addNormal(DistribDrawFromDistribution* dfd)
-//{
-// DistribNormalDistribution normal(3, coreVersion, 1);
-// DistribUncertValue* mean = normal.createMean();
-// mean->setVar("mean");
-// DistribUncertValue* stddev = normal.createStddev();
-// stddev->setVar("stddev");
-// dfd->setDistribution(&normal);
-//}
-
-//void addNormalWithValues(DistribDrawFromDistribution* dfd)
-//{
-// DistribNormalDistribution normal(3, coreVersion, 1);
-// DistribUncertValue* mean = normal.createMean();
-// mean->setValue(5.2);
-// DistribUncertValue* stddev = normal.createStddev();
-// stddev->setValue(1.3);
-// dfd->setDistribution(&normal);
-//}
-
void createExample1()
{
SBMLDocument* doc = setupBasicModel();
@@ -495,62 +453,43 @@
// delete document;
//}
-//void createUserDefined()
-//{
-// DistribDrawFromDistribution* dfd = setupBasicModel();
-// SBMLDocument* doc = dfd->getSBMLDocument();
-// Model* model = doc->getModel();
-// InitialAssignment* ia = addParamAndIA(model);
-// addNormal(dfd);
-//
-// vector<string> arguments;
-// arguments.push_back("mean");
-// arguments.push_back("stddev");
-// setupArguments(dfd, ia, model, arguments);
-// Parameter* param = model->createParameter();
-// param->setConstant(true);
-// param->setId("V_pop");
-// param->setValue(100);
-// param = model->createParameter();
-// param->setConstant(true);
-// param->setId("V_omega");
-// param->setValue(0.25);
-// ASTNode* astn = SBML_parseL3Formula("normal(V_pop, V_omega)");
-// ia->setMath(astn);
-// param = model->getParameter("P1");
-// param->setId("V");
-// ia->setSymbol("V");
-// delete astn;
-// DistribSBasePlugin* dsbp = static_cast<DistribSBasePlugin*>(ia->getPlugin("distrib"));
-// DistribUncertainty* uncert = dsbp->createDistribUncertainty();
-// DistribUncertStatistics* stats = uncert->createUncertStatistics();
-// DistribUncertValue uv(3, coreVersion, 1);
-// uv.setVar("V_pop");
-// stats->setMean(&uv);
-// uv.setVar("V_omega");
-// stats->setStandardDeviation(&uv);
-//
-// dsbp = static_cast<DistribSBasePlugin*>(param->getPlugin("distrib"));
-// dsbp->setDistribUncertainty(uncert);
-//
-// model->removeParameter("mean");
-// model->removeParameter("stddev");
-// FunctionDefinition* fd = model->getFunctionDefinition(0);
-// fd->setId("normal");
-// if (coreVersion == 1)
-// {
-// ASTNode* math = SBML_parseL3Formula("lambda(x, y, notanumber)");
-// fd->setMath(math);
-// delete math;
-// }
-// else
-// {
-// fd->setMath(NULL);
-// }
-// writeSBMLToFile(doc, "user-defined.xml");
-// delete doc;
-//}
+void createUserDefined()
+{
+ SBMLDocument* doc = setupBasicModel();
+ Model* model = doc->getModel();
+ InitialAssignment* ia = addParamAndIA(model);
+ ASTNode* astn = SBML_parseL3Formula("normal(V_pop, V_omega)");
+ ia->setMath(astn);
+ delete astn;
+
+ Parameter* param = model->createParameter();
+ param->setId("V_pop");
+ param->setValue(100);
+ param->setConstant(true);
+
+ param = model->createParameter();
+ param->setId("V_omega");
+ param->setValue(0.25);
+ param->setConstant(true);
+
+ param = model->getParameter("P1");
+ DistribSBasePlugin* dsbp = static_cast<DistribSBasePlugin*>(param->getPlugin("distrib"));
+ Uncertainty* uncert = dsbp->createUncertainty();
+ UncertParameter* uparam = uncert->createUncertParameter();
+ uparam->setType(DISTRIB_UNCERTTYPE_MEAN);
+ uparam->setVar("V_pop");
+ uparam = uncert->createUncertParameter();
+ uparam->setType(DISTRIB_UNCERTTYPE_STANDARDDEVIATION);
+ uparam->setVar("V_omega");
+
+ dsbp = static_cast<DistribSBasePlugin*>(ia->getPlugin("distrib"));
+ dsbp->addUncertainty(uncert);
+
+ writeSBMLToFile(doc, "user-defined.xml");
+ delete doc;
+}
+
void createConfidenceIntervalEx()
{
SBMLNamespaces sbmlns(3, coreVersion, "distrib", 1);
@@ -560,14 +499,47 @@
= static_cast<DistribSBMLDocumentPlugin*>(document->getPlugin("distrib"));
distdoc->setRequired(true);
Model* model = document->createModel();
+
+ Species species(&sbmlns);
+ species.setConstant(false);
+ species.setBoundaryCondition(false);
+ species.setHasOnlySubstanceUnits(false);
+ species.setCompartment("C");
+ DistribSBasePlugin* dsbp = static_cast<DistribSBasePlugin*>(species.getPlugin("distrib"));
+ Uncertainty* uncert = dsbp->createUncertainty();
+ UncertParameter* uparam = uncert->createUncertParameter();
+ uparam->setType(DISTRIB_UNCERTTYPE_STANDARDDEVIATION);
+ species.setId("S1");
+ species.setInitialAmount(5.2);
+ uparam->setValue(0.3);
+ model->addSpecies(&species);
+
+ species.setId("S2");
+ species.setInitialAmount(8.7);
+ uparam->setValue(0.01);
+ model->addSpecies(&species);
+
+ species.setId("S3");
+ species.setInitialAmount(1102);
+ uparam->setValue(53);
+ model->addSpecies(&species);
+
+ species.setId("S4");
+ species.setInitialAmount(0.026);
+ uparam->setValue(0.004);
+ model->addSpecies(&species);
+
+
+
+
Parameter param(&sbmlns);
param.setConstant(true);
- DistribSBasePlugin* dsbp = static_cast<DistribSBasePlugin*>(param.getPlugin("distrib"));
- Uncertainty* uncert = dsbp->createUncertainty();
+ dsbp = static_cast<DistribSBasePlugin*>(param.getPlugin("distrib"));
+ uncert = dsbp->createUncertainty();
UncertSpan* span = uncert->createUncertSpan();
+ span->setType(DISTRIB_UNCERTTYPE_CONFIDENCEINTERVAL);
param.setId("P1");
param.setValue(5.13);
- span->setType("confidenceInterval");
span->setValueLower(5.0);
span->setValueUpper(5.32);
model->addParameter(¶m);
@@ -574,7 +546,6 @@
param.setId("P2");
param.setValue(15.0);
- span->setType("confidenceInterval");
span->setValueLower(10.22);
span->setValueUpper(15.02);
model->addParameter(¶m);
@@ -581,7 +552,6 @@
param.setId("P3");
param.setValue(0.003);
- span->setType("confidenceInterval");
span->setValueLower(-0.001);
span->setValueUpper(0.0041);
model->addParameter(¶m);
@@ -588,7 +558,6 @@
param.setId("P4");
param.setValue(.34);
- span->setType("confidenceInterval");
span->setValueLower(0.22);
span->setValueUpper(0.51);
model->addParameter(¶m);
@@ -595,7 +564,6 @@
param.setId("P5");
param.setValue(92);
- span->setType("confidenceInterval");
span->setValueLower(90);
span->setValueUpper(99);
model->addParameter(¶m);
@@ -627,6 +595,6 @@
//createUncertainGender();
createPkPd();
//createExternalExponential();
- //createUserDefined();
+ createUserDefined();
createConfidenceIntervalEx();
}
|
|
From: <luc...@us...> - 2019-12-04 17:21:19
|
Revision: 26190
http://sourceforge.net/p/sbml/code/26190
Author: luciansmith
Date: 2019-12-04 17:21:17 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Add method to sort a list by ID (for help in xml text comparison tests).
Modified Paths:
--------------
branches/libsbml-experimental-lucian/src/sbml/ListOf.cpp
branches/libsbml-experimental-lucian/src/sbml/ListOf.h
Modified: branches/libsbml-experimental-lucian/src/sbml/ListOf.cpp
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/ListOf.cpp 2019-12-04 17:06:12 UTC (rev 26189)
+++ branches/libsbml-experimental-lucian/src/sbml/ListOf.cpp 2019-12-04 17:21:17 UTC (rev 26190)
@@ -471,7 +471,17 @@
/** @endcond */
-/**
+bool SBaseCompare(const SBase* sb1, const SBase* sb2)
+{
+ return sb1->getId() < sb2->getId();
+}
+
+void ListOf::sort()
+{
+ std::sort(mItems.begin(), mItems.end(), SBaseCompare);
+}
+
+ /**
* Used by ListOf::setSBMLDocument().
*/
struct SetSBMLDocument : public unary_function<SBase*, void>
Modified: branches/libsbml-experimental-lucian/src/sbml/ListOf.h
===================================================================
--- branches/libsbml-experimental-lucian/src/sbml/ListOf.h 2019-12-04 17:06:12 UTC (rev 26189)
+++ branches/libsbml-experimental-lucian/src/sbml/ListOf.h 2019-12-04 17:21:17 UTC (rev 26190)
@@ -575,6 +575,8 @@
virtual void enablePackageInternal(const std::string& pkgURI, const std::string& pkgPrefix, bool flag);
/** @endcond */
+ virtual void sort();
+
/** @cond doxygenLibsbmlInternal */
virtual void updateSBMLNamespace(const std::string& package,
|
|
From: <luc...@us...> - 2019-12-04 17:06:13
|
Revision: 26189
http://sourceforge.net/p/sbml/code/26189
Author: luciansmith
Date: 2019-12-04 17:06:12 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Rename this branch so it's clear that this is where I'm adding everything that I find useful for my own projects, but which have not yet been vetted by the libsbml team in general.
Added Paths:
-----------
branches/libsbml-experimental-lucian/
Removed Paths:
-------------
branches/libsbml-experimental-extendedmath/
|
|
From: <luc...@us...> - 2019-12-04 17:04:09
|
Revision: 26188
http://sourceforge.net/p/sbml/code/26188
Author: luciansmith
Date: 2019-12-04 17:04:08 +0000 (Wed, 04 Dec 2019)
Log Message:
-----------
Add in remaining MathML to the ASTNodeType enum, so future packages can use them without altering core files.
Modified Paths:
--------------
trunk/libsbml/src/sbml/math/ASTNodeType.h
Modified: trunk/libsbml/src/sbml/math/ASTNodeType.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNodeType.h 2019-11-23 08:33:12 UTC (rev 26187)
+++ trunk/libsbml/src/sbml/math/ASTNodeType.h 2019-12-04 17:04:08 UTC (rev 26188)
@@ -47,9 +47,10 @@
typedef enum
{
- EM_L3V2 /*!< Extended math added in l3v2 */
- , EM_DISTRIB /*!< Extended math added by the 'distrib' package */
- , EM_ARRAYS /*!< Extended math added by the 'arrays' package */
+ EM_L3V2 /*!< Extended math added in l3v2 */
+ , EM_DISTRIB /*!< Extended math added by the 'distrib' package */
+ , EM_ARRAYS /*!< Extended math added by the 'arrays' package */
+ , EM_REMAINING /*!< Extended math not added by any other package */
, EM_UNKNOWN /*!< Unknown node: will not produce any MathML */
} ExtendedMathType_t;
@@ -56,10 +57,10 @@
typedef enum
{
- ALLOWED_CHILDREN_ANY /*!< Extended math added in l3v2 */
- , ALLOWED_CHILDREN_ATLEAST /*!< Extended math added by the 'distrib' package */
+ ALLOWED_CHILDREN_ANY /*!< Any number of children (0+) are allowed */
+ , ALLOWED_CHILDREN_ATLEAST /*!< Any number of children above some minimum are allowed */
- , ALLOWED_CHILDREN_EXACTLY /*!< Unknown node: will not produce any MathML */
+ , ALLOWED_CHILDREN_EXACTLY /*!< Only specific number(s) of children are allowed */
, ALLOWED_CHILDREN_UNKNOWN
} AllowedChildrenType_t;
@@ -173,10 +174,10 @@
, AST_DISTRIB_FUNCTION_RAYLEIGH
/* Arrays */
- , AST_LINEAR_ALGEBRA_VECTOR
+ , AST_LINEAR_ALGEBRA_VECTOR = 600
, AST_LINEAR_ALGEBRA_SELECTOR
- /* Other arrays-associated things that are not (yet?) in the 'arrays' package */
+ /* Other linear algebra elements that are not (yet?) in the 'arrays' package */
, AST_LINEAR_ALGEBRA_MATRIX
, AST_LINEAR_ALGEBRA_MATRIXROW
, AST_LINEAR_ALGEBRA_DETERMINANT
@@ -184,18 +185,89 @@
, AST_LINEAR_ALGEBRA_VECTOR_PRODUCT
, AST_LINEAR_ALGEBRA_SCALAR_PRODUCT
, AST_LINEAR_ALGEBRA_OUTER_PRODUCT
- , AST_LOGICAL_EXISTS
+
+ /* Arithmetic logic */
+ , AST_LOGICAL_EXISTS = 700
, AST_LOGICAL_FORALL
- , AST_STATISTICS_MEAN
+
+ /* Statistics*/
+ , AST_STATISTICS_MEAN = 800
, AST_STATISTICS_MEDIAN
, AST_STATISTICS_MODE
, AST_STATISTICS_MOMENT
- , AST_SERIES_PRODUCT
, AST_STATISTICS_SDEV
- , AST_SERIES_SUM
, AST_STATISTICS_VARIANCE
+ , AST_STATISTICS_MOMENTABOUT
- , AST_UNKNOWN /*!< Unknown node: will not produce any MathML */
+ /* Sequences and Series*/
+ , AST_SERIES_PRODUCT = 900
+ , AST_SERIES_SUM
+ , AST_SERIES_LIMIT
+ , AST_SERIES_TENDSTO
+
+ /* Arithmetic algebra */
+ , AST_ALGEBRA_GCD = 1000
+ , AST_ALGEBRA_CONJUGATE
+ , AST_ALGEBRA_ARG
+ , AST_ALGEBRA_REAL
+ , AST_ALGEBRA_IMAGINARY
+ , AST_ALGEBRA_LCM
+
+ /* Relations */
+ , AST_RELATIONS_EQUIVALENT = 1100
+ , AST_RELATIONS_APPROX
+ , AST_RELATIONS_FACTOROF
+
+ /* Calculus and vector calculus*/
+ , AST_CALCULUS_INT = 1200
+ , AST_CALCULUS_DIFF
+ , AST_CALCULUS_PARTIALDIFF
+ , AST_CALCULUS_LOWLIMIT
+ , AST_CALCULUS_UPLIMIT
+ , AST_CALCULUS_DIVERGENCE
+ , AST_CALCULUS_GRAD
+ , AST_CALCULUS_CURL
+ , AST_CALCULUS_LAPLACIAN
+
+ /* Set Theory */
+ , AST_SET_THEORY_SET = 1300
+ , AST_SET_THEORY_LIST
+ , AST_SET_THEORY_UNION
+ , AST_SET_THEORY_INTERSECT
+ , AST_SET_THEORY_IN
+ , AST_SET_THEORY_NOTIN
+ , AST_SET_THEORY_SUBSET
+ , AST_SET_THEORY_PRSUBSET
+ , AST_SET_THEORY_NOTSUBSET
+ , AST_SET_THEORY_NOTPRSUBSET
+ , AST_SET_THEORY_SETDIFF
+ , AST_SET_THEORY_CARD
+ , AST_SET_THEORY_CARTESIANPRODUCT
+
+ /* Constants and symbol elements*/
+ , AST_CONSTANT_IMAGINARYI = 1400
+ , AST_CONSTANTS_INTEGERS
+ , AST_CONSTANTS_REALS
+ , AST_CONSTANTS_RATIONALS
+ , AST_CONSTANTS_NATURALNUMBERS
+ , AST_CONSTANTS_COMPLEXES
+ , AST_CONSTANTS_PRIMES
+ , AST_CONSTANTS_EMPTYSET
+ , AST_CONSTANTS_EULERGAMMA
+
+ /* Basic MathML Content elements*/
+ , AST_BASIC_CONTENT_INTERVAL = 1500
+ , AST_BASIC_CONTENT_INVERSE
+ , AST_BASIC_CONTENT_CONDITION
+ , AST_BASIC_CONTENT_DECLARE
+ , AST_BASIC_CONTENT_COMPOSE
+ , AST_BASIC_CONTENT_IDENT
+ , AST_BASIC_CONTENT_DOMAIN
+ , AST_BASIC_CONTENT_CODOMAIN
+ , AST_BASIC_CONTENT_IMAGE
+ , AST_BASIC_CONTENT_DOMAINOFAPPLICATION
+
+ , AST_UNKNOWN = 9999/*!< Unknown node: will not produce any MathML */
} ASTNodeType_t;
END_C_DECLS
|
|
From: <fbe...@us...> - 2019-11-23 08:33:14
|
Revision: 26187
http://sourceforge.net/p/sbml/code/26187
Author: fbergmann
Date: 2019-11-23 08:33:12 +0000 (Sat, 23 Nov 2019)
Log Message:
-----------
- issue #169923908: rename duplicated symbol
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfAnalyticVolumes.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfCSGObjects.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfDomains.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfParametricObjects.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfSampledVolumes.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfAnalyticVolumes.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfAnalyticVolumes.cpp 2019-11-23 05:28:25 UTC (rev 26186)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfAnalyticVolumes.cpp 2019-11-23 08:33:12 UTC (rev 26187)
@@ -277,11 +277,11 @@
* Used by ListOfAnalyticVolumes::get() to lookup an AnalyticVolume based on
* its DomainType.
*/
-struct IdEqDT : public std::unary_function<SBase*, bool>
+struct IdEqDT1 : public std::unary_function<SBase*, bool>
{
const string& id;
- IdEqDT (const string& id) : id(id) { }
+ IdEqDT1 (const string& id) : id(id) { }
bool operator() (SBase* sb)
{
return (static_cast<AnalyticVolume*>(sb)->getDomainType() == id);
@@ -297,7 +297,7 @@
ListOfAnalyticVolumes::getByDomainType(const std::string& sid) const
{
vector<SBase*>::const_iterator result;
- result = find_if(mItems.begin(), mItems.end(), IdEqDT(sid));
+ result = find_if(mItems.begin(), mItems.end(), IdEqDT1(sid));
return (result == mItems.end()) ? 0 : static_cast <const AnalyticVolume*>
(*result);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfCSGObjects.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfCSGObjects.cpp 2019-11-23 05:28:25 UTC (rev 26186)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfCSGObjects.cpp 2019-11-23 08:33:12 UTC (rev 26187)
@@ -273,11 +273,11 @@
* Used by ListOfCSGObjects::get() to lookup a CSGObject based on its
* DomainType.
*/
-struct IdEqDT : public std::unary_function<SBase*, bool>
+struct IdEqDT2 : public std::unary_function<SBase*, bool>
{
const string& id;
- IdEqDT (const string& id) : id(id) { }
+ IdEqDT2 (const string& id) : id(id) { }
bool operator() (SBase* sb)
{
return (static_cast<CSGObject*>(sb)->getDomainType() == id);
@@ -293,7 +293,7 @@
ListOfCSGObjects::getByDomainType(const std::string& sid) const
{
vector<SBase*>::const_iterator result;
- result = find_if(mItems.begin(), mItems.end(), IdEqDT(sid));
+ result = find_if(mItems.begin(), mItems.end(), IdEqDT2(sid));
return (result == mItems.end()) ? 0 : static_cast <const CSGObject*>
(*result);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfDomains.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfDomains.cpp 2019-11-23 05:28:25 UTC (rev 26186)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfDomains.cpp 2019-11-23 08:33:12 UTC (rev 26187)
@@ -270,11 +270,11 @@
/*
* Used by ListOfDomains::get() to lookup a Domain based on its DomainType.
*/
-struct IdEqDT : public std::unary_function<SBase*, bool>
+struct IdEqDT3 : public std::unary_function<SBase*, bool>
{
const string& id;
- IdEqDT (const string& id) : id(id) { }
+ IdEqDT3 (const string& id) : id(id) { }
bool operator() (SBase* sb)
{
return (static_cast<Domain*>(sb)->getDomainType() == id);
@@ -290,7 +290,7 @@
ListOfDomains::getByDomainType(const std::string& sid) const
{
vector<SBase*>::const_iterator result;
- result = find_if(mItems.begin(), mItems.end(), IdEqDT(sid));
+ result = find_if(mItems.begin(), mItems.end(), IdEqDT3(sid));
return (result == mItems.end()) ? 0 : static_cast <const Domain*> (*result);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfParametricObjects.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfParametricObjects.cpp 2019-11-23 05:28:25 UTC (rev 26186)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfParametricObjects.cpp 2019-11-23 08:33:12 UTC (rev 26187)
@@ -275,11 +275,11 @@
* Used by ListOfParametricObjects::get() to lookup a ParametricObject based on
* its DomainType.
*/
-struct IdEqDT : public std::unary_function<SBase*, bool>
+struct IdEqDT4 : public std::unary_function<SBase*, bool>
{
const string& id;
- IdEqDT (const string& id) : id(id) { }
+ IdEqDT4 (const string& id) : id(id) { }
bool operator() (SBase* sb)
{
return (static_cast<ParametricObject*>(sb)->getDomainType() == id);
@@ -295,7 +295,7 @@
ListOfParametricObjects::getByDomainType(const std::string& sid) const
{
vector<SBase*>::const_iterator result;
- result = find_if(mItems.begin(), mItems.end(), IdEqDT(sid));
+ result = find_if(mItems.begin(), mItems.end(), IdEqDT4(sid));
return (result == mItems.end()) ? 0 : static_cast <const ParametricObject*>
(*result);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfSampledVolumes.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfSampledVolumes.cpp 2019-11-23 05:28:25 UTC (rev 26186)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ListOfSampledVolumes.cpp 2019-11-23 08:33:12 UTC (rev 26187)
@@ -270,11 +270,11 @@
* Used by ListOfSampledVolumes::get() to lookup a SampledVolume based on its
* DomainType.
*/
-struct IdEqDT : public std::unary_function<SBase*, bool>
+struct IdEqDT5 : public std::unary_function<SBase*, bool>
{
const string& id;
- IdEqDT (const string& id) : id(id) { }
+ IdEqDT5 (const string& id) : id(id) { }
bool operator() (SBase* sb)
{
return (static_cast<SampledVolume*>(sb)->getDomainType() == id);
@@ -290,7 +290,7 @@
ListOfSampledVolumes::getByDomainType(const std::string& sid) const
{
vector<SBase*>::const_iterator result;
- result = find_if(mItems.begin(), mItems.end(), IdEqDT(sid));
+ result = find_if(mItems.begin(), mItems.end(), IdEqDT5(sid));
return (result == mItems.end()) ? 0 : static_cast <const SampledVolume*>
(*result);
}
|
|
From: <luc...@us...> - 2019-11-23 05:28:28
|
Revision: 26186
http://sourceforge.net/p/sbml/code/26186
Author: luciansmith
Date: 2019-11-23 05:28:25 +0000 (Sat, 23 Nov 2019)
Log Message:
-----------
Move the validation rules from the abstract class CSGTransformation to its child classes.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTransformation.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTransformation.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTransformation.cpp 2019-11-23 00:25:09 UTC (rev 26185)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTransformation.cpp 2019-11-23 05:28:25 UTC (rev 26186)
@@ -1100,7 +1100,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGPrimitiveAllowedCoreElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1114,7 +1114,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGTranslationAllowedElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1128,7 +1128,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGRotationAllowedElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1142,7 +1142,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGScaleAllowedElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1156,7 +1156,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGHomogeneousTransformationAllowedElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1170,7 +1170,7 @@
if (isSetCSGNode())
{
getErrorLog()->logPackageError("spatial",
- SpatialCSGTransformationAllowedElements, getPackageVersion(), getLevel(),
+ SpatialCSGSetOperatorAllowedElements, getPackageVersion(), getLevel(),
getVersion(), "", getLine(), getColumn());
}
@@ -1227,6 +1227,21 @@
if (log)
{
numErrs = log->getNumErrors();
+ SpatialSBMLErrorCode_t errcode = SpatialCSGTranslationAllowedAttributes;
+ switch (getTypeCode()) {
+ case SBML_SPATIAL_CSGTRANSLATION:
+ errcode = SpatialCSGTranslationAllowedCoreAttributes;
+ break;
+ case SBML_SPATIAL_CSGHOMOGENEOUSTRANSFORMATION:
+ errcode = SpatialCSGHomogeneousTransformationAllowedCoreAttributes;
+ break;
+ case SBML_SPATIAL_CSGSCALE:
+ errcode = SpatialCSGScaleAllowedCoreAttributes;
+ break;
+ case SBML_SPATIAL_CSGROTATION:
+ errcode = SpatialCSGRotationAllowedCoreAttributes;
+ break;
+ }
for (int n = numErrs-1; n >= 0; n--)
{
@@ -1242,7 +1257,7 @@
const std::string details = log->getError(n)->getMessage();
log->remove(UnknownCoreAttribute);
log->logPackageError("spatial",
- SpatialCSGTransformationAllowedCoreAttributes, pkgVersion, level,
+ errcode, pkgVersion, level,
version, details, getLine(), getColumn());
}
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-23 00:25:09 UTC (rev 26185)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-23 05:28:25 UTC (rev 26186)
@@ -224,9 +224,6 @@
, SpatialCSGNodeAllowedCoreElements = 1222402
, SpatialCSGNodeAllowedAttributes = 1222403
, SpatialCSGNodeNameMustBeString = 1222404
-, SpatialCSGTransformationAllowedCoreAttributes = 1222501
-, SpatialCSGTransformationAllowedCoreElements = 1222502
-, SpatialCSGTransformationAllowedElements = 1222503
, SpatialCSGTranslationAllowedCoreAttributes = 1222601
, SpatialCSGTranslationAllowedCoreElements = 1222602
, SpatialCSGTranslationAllowedAttributes = 1222603
@@ -233,6 +230,7 @@
, SpatialCSGTranslationTranslateXMustBeDouble = 1222604
, SpatialCSGTranslationTranslateYMustBeDouble = 1222605
, SpatialCSGTranslationTranslateZMustBeDouble = 1222606
+, SpatialCSGTranslationAllowedElements = 1222650
, SpatialCSGRotationAllowedCoreAttributes = 1222701
, SpatialCSGRotationAllowedCoreElements = 1222702
, SpatialCSGRotationAllowedAttributes = 1222703
@@ -240,6 +238,7 @@
, SpatialCSGRotationRotateAngleInRadiansMustBeDouble = 1222705
, SpatialCSGRotationRotateYMustBeDouble = 1222706
, SpatialCSGRotationRotateZMustBeDouble = 1222707
+, SpatialCSGRotationAllowedElements = 1222750
, SpatialCSGScaleAllowedCoreAttributes = 1222801
, SpatialCSGScaleAllowedCoreElements = 1222802
, SpatialCSGScaleAllowedAttributes = 1222803
@@ -246,6 +245,7 @@
, SpatialCSGScaleScaleXMustBeDouble = 1222804
, SpatialCSGScaleScaleYMustBeDouble = 1222805
, SpatialCSGScaleScaleZMustBeDouble = 1222806
+, SpatialCSGScaleAllowedElements = 1222850
, SpatialCSGHomogeneousTransformationAllowedCoreAttributes = 1222901
, SpatialCSGHomogeneousTransformationAllowedCoreElements = 1222902
, SpatialCSGHomogeneousTransformationAllowedElements = 1222903
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-23 00:25:09 UTC (rev 26185)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-23 05:28:25 UTC (rev 26186)
@@ -1952,42 +1952,6 @@
}
},
- // 1222501
- { SpatialCSGTransformationAllowedCoreAttributes,
- "Core attributes allowed on <csgTransformation>.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <csgTransformation> object may have the optional SBML Level 3 Core "
- "attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level "
- "3 Core namespaces are permitted on a <csgTransformation>.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
- // 1222502
- { SpatialCSGTransformationAllowedCoreElements,
- "Core elements allowed on <csgTransformation>.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <csgTransformation> object may have the optional SBML Level 3 Core "
- "subobjects for notes and annotations. No other elements from the SBML "
- "Level 3 Core namespaces are permitted on a <csgTransformation>.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
- // 1222503
- { SpatialCSGTransformationAllowedElements,
- "Elements allowed on <csgTransformation>.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "A <csgTransformation> object may contain one and only one instance of the "
- "CSGNode element. No other elements from the SBML Level 3 Spatial Processes "
- "namespaces are permitted on a <csgTransformation> object. ",
- { "L3V1 Spatial V1 Section"
- }
- },
-
// 1222601
{ SpatialCSGTranslationAllowedCoreAttributes,
"Core attributes allowed on <csgTranslation>.",
@@ -2059,6 +2023,18 @@
}
},
+ // 1222650
+ { SpatialCSGTranslationAllowedElements,
+ "Elements allowed on <csgTranslation>.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <csgTranslation> object may contain one and only one child "
+ "CSGNode element. No other elements from the SBML Level 3 Spatial Processes "
+ "namespaces are permitted on a <csgTransformation> object. ",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1222701
{ SpatialCSGRotationAllowedCoreAttributes,
"Core attributes allowed on <csgRotation>.",
@@ -2141,6 +2117,18 @@
}
},
+ // 1222750
+ { SpatialCSGRotationAllowedElements,
+ "Elements allowed on <csgRotation>.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <csgRotation> object may contain one and only one child "
+ "CSGNode element. No other elements from the SBML Level 3 Spatial Processes "
+ "namespaces are permitted on a <csgRotation> object. ",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1222801
{ SpatialCSGScaleAllowedCoreAttributes,
"Core attributes allowed on <csgScale>.",
@@ -2211,6 +2199,18 @@
}
},
+ // 1222850
+ { SpatialCSGScaleAllowedElements,
+ "Elements allowed on <csgScale>.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A <csgScale> object may contain one and only one child "
+ "CSGNode element. No other elements from the SBML Level 3 Spatial Processes "
+ "namespaces are permitted on a <csgScale> object. ",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1222901
{ SpatialCSGHomogeneousTransformationAllowedCoreAttributes,
"Core attributes allowed on <csgHomogeneousTransformation>.",
@@ -2243,7 +2243,7 @@
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
"A <csgHomogeneousTransformation> object must contain one and only one "
- "instance of the TransformationComponent element. No other elements from "
+ "child <forwardTransformation> element of type 'TransformationComponent', and may additionally contain one and only one child CSGNode element. No other elements from "
"the SBML Level 3 Spatial Processes namespaces are permitted on a "
"<csgHomogeneousTransformation> object. ",
{ "L3V1 Spatial V1 Section"
|
|
From: <luc...@us...> - 2019-11-23 00:25:11
|
Revision: 26185
http://sourceforge.net/p/sbml/code/26185
Author: luciansmith
Date: 2019-11-23 00:25:09 +0000 (Sat, 23 Nov 2019)
Log Message:
-----------
Add support for spatial rules 23254.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-04.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 23:41:40 UTC (rev 26184)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-23 00:25:09 UTC (rev 26185)
@@ -273,6 +273,7 @@
, SpatialCSGSetOperatorNoComplementsUnionIntersection = 1223251
, SpatialCSGSetOperatorDifferenceMustHaveTwoChildren = 1223252
, SpatialCSGSetOperatorComplementsMustReferenceChildren = 1223253
+, SpatialCSGSetOperatorShouldHaveTwoPlusChildren = 1223254
, SpatialSpatialSymbolReferenceAllowedCoreAttributes = 1223301
, SpatialSpatialSymbolReferenceAllowedCoreElements = 1223302
, SpatialSpatialSymbolReferenceAllowedAttributes = 1223303
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:41:40 UTC (rev 26184)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-23 00:25:09 UTC (rev 26185)
@@ -2532,6 +2532,16 @@
}
},
+ // 1223254
+ { SpatialCSGSetOperatorShouldHaveTwoPlusChildren,
+ "The <csgSetOperator> should have two or more children.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_INFO,
+ "A <csgSetOperator> should usually have at least two children, as operations involving zero or one child can be accomplished more efficiently in other ways.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
{ SpatialSpatialSymbolReferenceAllowedCoreAttributes,
"Core attributes allowed on <spatialSymbolReference>.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:41:40 UTC (rev 26184)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-23 00:25:09 UTC (rev 26185)
@@ -1528,6 +1528,33 @@
END_CONSTRAINT
+// 1223254
+START_CONSTRAINT(SpatialCSGSetOperatorShouldHaveTwoPlusChildren, CSGSetOperator, setop)
+{
+ SetOperation_t type = setop.getOperationType();
+ pre(type == SPATIAL_SETOPERATION_INTERSECTION || type == SPATIAL_SETOPERATION_UNION);
+ unsigned long nchildren = setop.getNumCSGNodes();
+ pre(nchildren < 2);
+ stringstream ss_msg;
+ ss_msg << "A <csgSetOperator>";
+ if (setop.isSetId())
+ {
+ ss_msg << " with id '" << setop.getId() << "'";
+ }
+ ss_msg << " has an 'operationType' of '";
+ ss_msg << setop.getOperationTypeAsString() + "', but has ";
+ if (nchildren == 0) {
+ ss_msg << "no children. This is equivalent to not including the <csgSetOperator> at all.";
+ }
+ else if (nchildren == 1) {
+ ss_msg << "one child. This is equivalent to replacing the <csgSetOperator> with its single child.";
+ }
+ msg = ss_msg.str();
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:41:40 UTC (rev 26184)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-23 00:25:09 UTC (rev 26185)
@@ -89,6 +89,7 @@
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorNoComplementsUnionIntersection(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorDifferenceMustHaveTwoChildren(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorComplementsMustReferenceChildren(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorShouldHaveTwoPlusChildren(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-01.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-02.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-03.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-fail-01-04.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-01.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-02.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-03.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223254-pass-00-04.xml 2019-11-23 00:25:09 UTC (rev 26185)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-22 23:41:42
|
Revision: 26184
http://sourceforge.net/p/sbml/code/26184
Author: luciansmith
Date: 2019-11-22 23:41:40 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Add support for spatial rules 23251. Also fix some wording in similar rules.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-02.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 23:25:13 UTC (rev 26183)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 23:41:40 UTC (rev 26184)
@@ -269,8 +269,8 @@
, SpatialCSGSetOperatorComplementBMustBeCSGNode = 1223207
, SpatialCSGSetOperatorLOCSGNodesAllowedCoreElements = 1223208
, SpatialCSGSetOperatorLOCSGNodesAllowedCoreAttributes = 1223209
-, SpatialCSGSetOperatorTwoComponentsForDifference = 1223250
-, SpatialCSGSetOperatorNoComponentsUnionIntersection = 1223251
+, SpatialCSGSetOperatorTwoComplementsForDifference = 1223250
+, SpatialCSGSetOperatorNoComplementsUnionIntersection = 1223251
, SpatialCSGSetOperatorDifferenceMustHaveTwoChildren = 1223252
, SpatialCSGSetOperatorComplementsMustReferenceChildren = 1223253
, SpatialSpatialSymbolReferenceAllowedCoreAttributes = 1223301
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:25:13 UTC (rev 26183)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:41:40 UTC (rev 26184)
@@ -2493,7 +2493,7 @@
},
// 1223250
- { SpatialCSGSetOperatorTwoComponentsForDifference,
+ { SpatialCSGSetOperatorTwoComplementsForDifference,
"Need two components for 'difference' type.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
@@ -2503,7 +2503,7 @@
},
// 1223251
- { SpatialCSGSetOperatorNoComponentsUnionIntersection,
+ { SpatialCSGSetOperatorNoComplementsUnionIntersection,
"No components for 'union' or 'intersection' types.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:25:13 UTC (rev 26183)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:41:40 UTC (rev 26184)
@@ -1422,15 +1422,15 @@
// 1223250
-START_CONSTRAINT(SpatialCSGSetOperatorTwoComponentsForDifference, CSGSetOperator, setop)
+START_CONSTRAINT(SpatialCSGSetOperatorTwoComplementsForDifference, CSGSetOperator, setop)
{
bool fail = false;
pre(setop.getOperationType() == SPATIAL_SETOPERATION_DIFFERENCE);
- unsigned int nchildren = setop.getNumCSGNodes();
msg = "A <csgSetOperator>";
if (setop.isSetId()) {
- msg += " with the id '" + setop.getId() + "' has an 'operationType' of 'difference', but";
+ msg += " with the id '" + setop.getId() + "'";
}
+ msg += " has an 'operationType' of 'difference', but";
if (setop.isSetComplementA() == false) {
fail = true;
msg += " does not have a value for its 'complementA' attribute";
@@ -1448,6 +1448,37 @@
END_CONSTRAINT
+// 1223251
+START_CONSTRAINT(SpatialCSGSetOperatorNoComplementsUnionIntersection, CSGSetOperator, setop)
+{
+ bool fail = false;
+ SetOperation_t type = setop.getOperationType();
+ pre(type == SPATIAL_SETOPERATION_INTERSECTION || type == SPATIAL_SETOPERATION_UNION);
+ msg = "A <csgSetOperator>";
+ if (setop.isSetId()) {
+ msg += " with the id '" + setop.getId() + "'";
+ }
+ msg += " has an 'operationType' of '";
+ msg += setop.getOperationTypeAsString() + "', but";
+ if (setop.isSetComplementA()) {
+ fail = true;
+ msg += " has a value of '";
+ msg += setop.getComplementA() + "' for its 'complementA' attribute";
+ }
+ if (setop.isSetComplementB()) {
+ if (fail) {
+ msg += ", and also";
+ }
+ fail = true;
+ msg += " has a value of '";
+ msg += setop.getComplementB() + "' for its 'complementB' attribute";
+ }
+ msg += ".";
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 1223252
START_CONSTRAINT(SpatialCSGSetOperatorDifferenceMustHaveTwoChildren, CSGSetOperator, setop)
{
@@ -1461,7 +1492,7 @@
{
ss_msg << " with id '" << setop.getId() << "'";
}
- ss_msg << " has a 'spatial:operationType' attribute of 'difference', but has ";
+ ss_msg << " has an 'operationType' value of 'difference', but has ";
ss_msg << nchildren << " children.";
msg = ss_msg.str();
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:25:13 UTC (rev 26183)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:41:40 UTC (rev 26184)
@@ -85,7 +85,8 @@
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive3DShapes(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive2DShapes(*this));
-addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorTwoComponentsForDifference(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorTwoComplementsForDifference(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorNoComplementsUnionIntersection(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorDifferenceMustHaveTwoChildren(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorComplementsMustReferenceChildren(*this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-01.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-02.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-03.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union" spatial:complementA="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-04.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-05.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-fail-01-06.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection" spatial:complementA="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-01.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="union">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223251-pass-00-02.xml 2019-11-22 23:41:40 UTC (rev 26184)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="intersection">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-22 23:25:14
|
Revision: 26183
http://sourceforge.net/p/sbml/code/26183
Author: luciansmith
Date: 2019-11-22 23:25:13 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Add support for spatial rules 23250.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:16:12 UTC (rev 26182)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:25:13 UTC (rev 26183)
@@ -2497,7 +2497,7 @@
"Need two components for 'difference' type.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "If the attribute 'spatial:operationType' of a <csgSetOperator> has the value 'difference', it must also define values for the attributes 'spatial:componentA' and 'spatial:componentB'.",
+ "If the attribute 'spatial:operationType' of a <csgSetOperator> has the value 'difference', it must also define values for the attributes 'spatial:complementA' and 'spatial:complementB'.",
{ "L3V1 Spatial V1 Section"
}
},
@@ -2507,7 +2507,7 @@
"No components for 'union' or 'intersection' types.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "If the attribute 'spatial:operationType' of a <csgSetOperator> has the value 'union' or 'intersection', it must not define values for the attributes 'spatial:componentA' nor 'spatial:componentB'.",
+ "If the attribute 'spatial:operationType' of a <csgSetOperator> has the value 'union' or 'intersection', it must not define values for the attributes 'spatial:complementA' nor 'spatial:complementB'.",
{ "L3V1 Spatial V1 Section"
}
},
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:16:12 UTC (rev 26182)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:25:13 UTC (rev 26183)
@@ -1421,6 +1421,33 @@
END_CONSTRAINT
+// 1223250
+START_CONSTRAINT(SpatialCSGSetOperatorTwoComponentsForDifference, CSGSetOperator, setop)
+{
+ bool fail = false;
+ pre(setop.getOperationType() == SPATIAL_SETOPERATION_DIFFERENCE);
+ unsigned int nchildren = setop.getNumCSGNodes();
+ msg = "A <csgSetOperator>";
+ if (setop.isSetId()) {
+ msg += " with the id '" + setop.getId() + "' has an 'operationType' of 'difference', but";
+ }
+ if (setop.isSetComplementA() == false) {
+ fail = true;
+ msg += " does not have a value for its 'complementA' attribute";
+ }
+ if (setop.isSetComplementB() == false) {
+ if (fail) {
+ msg += ", and also";
+ }
+ fail = true;
+ msg += " does not have a value for its 'complementB' attribute";
+ }
+ msg += ".";
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 1223252
START_CONSTRAINT(SpatialCSGSetOperatorDifferenceMustHaveTwoChildren, CSGSetOperator, setop)
{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:16:12 UTC (rev 26182)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:25:13 UTC (rev 26183)
@@ -85,6 +85,7 @@
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive3DShapes(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive2DShapes(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorTwoComponentsForDifference(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorDifferenceMustHaveTwoChildren(*this));
addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorComplementsMustReferenceChildren(*this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-01.xml 2019-11-22 23:25:13 UTC (rev 26183)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-02.xml 2019-11-22 23:25:13 UTC (rev 26183)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementB="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-fail-01-03.xml 2019-11-22 23:25:13 UTC (rev 26183)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223250-pass-00-01.xml 2019-11-22 23:25:13 UTC (rev 26183)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-22 23:16:14
|
Revision: 26182
http://sourceforge.net/p/sbml/code/26182
Author: luciansmith
Date: 2019-11-22 23:16:12 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Got the names of the attributes wrong.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex
Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex 2019-11-22 23:11:53 UTC (rev 26181)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex 2019-11-22 23:16:12 UTC (rev 26182)
@@ -1435,10 +1435,10 @@
a \ListOfCSGNodes object. (Reference: SBML Level~3 Specification for
Spatial Processes, Version~1, \sec{listofcsgnodes-class}.)}
-\validRule{spatial-23250}{\changed{If the \token{spa\-tial:\-operationType} attribute of a \CSGSetOperator has the value \val{difference}, it must also define values for the attributes \token{spa\-tial:\-componentA} and \token{spa\-tial:\-componentB}.
+\validRule{spatial-23250}{\changed{If the \token{spa\-tial:\-operationType} attribute of a \CSGSetOperator has the value \val{difference}, it must also define values for the attributes \token{spa\-tial:\-complementA} and \token{spa\-tial:\-complementB}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
-\validRule{spatial-23251}{\changed{If the attribute \token{spa\-tial:\-operationType} of a \CSGSetOperator has the value \val{union} or \val{in\-ter\-sec\-tion}, it must not define values for the attributes \token{spa\-tial:\-componentA} nor \token{spa\-tial:\-componentB}.
+\validRule{spatial-23251}{\changed{If the attribute \token{spa\-tial:\-operationType} of a \CSGSetOperator has the value \val{union} or \val{in\-ter\-sec\-tion}, it must not define values for the attributes \token{spa\-tial:\-complementA} nor \token{spa\-tial:\-complementB}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
\validRule{spatial-23251}{\changed{If the attribute \token{spatial:operationType} of a \CSGSetOperator is \val{difference}, it must have exactly two \CSGNode children.
|
|
From: <luc...@us...> - 2019-11-22 23:11:55
|
Revision: 26181
http://sourceforge.net/p/sbml/code/26181
Author: luciansmith
Date: 2019-11-22 23:11:53 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Add support for spatial rules 23252 and 23253.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-01.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 21:34:06 UTC (rev 26180)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 23:11:53 UTC (rev 26181)
@@ -271,6 +271,8 @@
, SpatialCSGSetOperatorLOCSGNodesAllowedCoreAttributes = 1223209
, SpatialCSGSetOperatorTwoComponentsForDifference = 1223250
, SpatialCSGSetOperatorNoComponentsUnionIntersection = 1223251
+, SpatialCSGSetOperatorDifferenceMustHaveTwoChildren = 1223252
+, SpatialCSGSetOperatorComplementsMustReferenceChildren = 1223253
, SpatialSpatialSymbolReferenceAllowedCoreAttributes = 1223301
, SpatialSpatialSymbolReferenceAllowedCoreElements = 1223302
, SpatialSpatialSymbolReferenceAllowedAttributes = 1223303
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 21:34:06 UTC (rev 26180)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 23:11:53 UTC (rev 26181)
@@ -2512,7 +2512,26 @@
}
},
- // 1223301
+ // 1223252
+ { SpatialCSGSetOperatorDifferenceMustHaveTwoChildren,
+ "A <csgSetOperator> difference must have two children.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "If the 'operationType' of a <csgSetOperator> is 'difference', it must have exactly two <csgNode> children.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
+ // 1223253
+ { SpatialCSGSetOperatorComplementsMustReferenceChildren,
+ "The 'complement' attributes of a <csgSetOperator> must reference its children.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The attributes 'complementA' and 'complementB' of a <csgSetOperator> must reference its two <csgNode> children.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
{ SpatialSpatialSymbolReferenceAllowedCoreAttributes,
"Core attributes allowed on <spatialSymbolReference>.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 21:34:06 UTC (rev 26180)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 23:11:53 UTC (rev 26181)
@@ -1421,6 +1421,55 @@
END_CONSTRAINT
+// 1223252
+START_CONSTRAINT(SpatialCSGSetOperatorDifferenceMustHaveTwoChildren, CSGSetOperator, setop)
+{
+ bool fail = false;
+ pre(setop.getOperationType() == SPATIAL_SETOPERATION_DIFFERENCE);
+ unsigned int nchildren = setop.getNumCSGNodes();
+ if (nchildren != 2) {
+ stringstream ss_msg;
+ ss_msg << "A <csgSetOperator>";
+ if (setop.isSetId())
+ {
+ ss_msg << " with id '" << setop.getId() << "'";
+ }
+ ss_msg << " has a 'spatial:operationType' attribute of 'difference', but has ";
+ ss_msg << nchildren << " children.";
+ msg = ss_msg.str();
+
+ fail = true;
+ }
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
+// 1223253
+START_CONSTRAINT(SpatialCSGSetOperatorComplementsMustReferenceChildren, CSGSetOperator, setop)
+{
+ pre(setop.getOperationType() == SPATIAL_SETOPERATION_DIFFERENCE);
+ pre(setop.getNumCSGNodes()==2);
+ pre(setop.isSetComplementA());
+ pre(setop.isSetComplementB());
+ string child1 = setop.getCSGNode(0)->getId();
+ string child2 = setop.getCSGNode(1)->getId();
+ string compA = setop.getComplementA();
+ string compB = setop.getComplementB();
+ pre(!((child1 == compA && child2 == compB) || (child1 == compB && child2 == compA)));
+ msg = "A <csgSetOperator>";
+ if (setop.isSetId()) {
+ msg += " with the id '" + setop.getId() + "'";
+ }
+ msg += " has as 'complementA' value of '";
+ msg += compA + "', and a 'complementB' value of '" + compB;
+ msg += "', which are not the two IDs of its two children: '";
+ msg += child1 + "' and '" + child2 + "'.";
+ inv(false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 21:34:06 UTC (rev 26180)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 23:11:53 UTC (rev 26181)
@@ -85,6 +85,8 @@
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive3DShapes(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive2DShapes(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorDifferenceMustHaveTwoChildren(*this));
+addConstraint(new VConstraintCSGSetOperatorSpatialCSGSetOperatorComplementsMustReferenceChildren(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-01.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-02.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ <spatial:csgPrimitive spatial:id="cone2" spatial:primitiveType="cone"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-fail-01-03.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223252-pass-00-01.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-01.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="sphere1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-02.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="cube1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-fail-01-03.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="cube1" spatial:complementB="domainType_1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223253-pass-00-01.xml 2019-11-22 23:11:53 UTC (rev 26181)
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgSetOperator spatial:operationType="difference" spatial:complementA="sphere1" spatial:complementB="cube1">
+ <spatial:listOfCSGNodes>
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:listOfCSGNodes>
+ </spatial:csgSetOperator>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-22 21:34:09
|
Revision: 26180
http://sourceforge.net/p/sbml/code/26180
Author: luciansmith
Date: 2019-11-22 21:34:06 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
New draft of spatial spec with all the new validation rules.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex
trunk/specifications/sbml-level-3/version-1/spatial/specification/macros.tex
trunk/specifications/sbml-level-3/version-1/spatial/specification/main.tex
trunk/specifications/sbml-level-3/version-1/spatial/specification/syntax.tex
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf
Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex 2019-11-22 00:47:38 UTC (rev 26179)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/apdx-validation.tex 2019-11-22 21:34:06 UTC (rev 26180)
@@ -61,7 +61,7 @@
shorter than to write a full explanation everywhere we refer to an
attribute or element in the \SpatialProcessesPackage namespace.
-\changed{Attributes from this package are listed in these rules as having the \val{distrib:} prefix, but as is convention for SBML packages, this prefix is optional.}
+\changed{Attributes from this package are listed in these rules as having the \val{spatial:} prefix, but as is convention for SBML packages, this prefix is optional.}
\subsubsection*{General rules about this package}
@@ -140,7 +140,7 @@
SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{extended-species-class}.)}
-\validRule{spatial-20450}{\changed{The \Compartment of any \Species that has a value of 'true' for the 'spatial:isSpatial' attribute must have a child \CompartmentMapping.
+\validRule{spatial-20450}{\changed{The \Compartment of any \Species that has a value of \val{true} for the \token{spatial:isSpatial} attribute must have a child \CompartmentMapping.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{extended-species-class}.)}}
@@ -210,6 +210,9 @@
\validRule{spatial-20752}{\changed{If the \Geometry of the \Model has exactly one \CoordinateComponent child, the attribute \token{spa\-tial:\-spa\-tial\-Di\-men\-sions} of a \DomainType may only have a value of \val{0} or \val{1}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{domaintype-class}.)}}
+\validRule{spatial-20753}{\changed{If a \Parameter has a child \SpatialSymbolReference that points to a \DomainType, that \Parameter may not be the target of an \InitialAssignment, \EventAssignment, \RateRule, or \AssignmentRule, may not be determined by an \AlgebraicRule, and may not define the \token{value} attribute.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{domaintype-class}.)}}
+
\subsubsection*{Rules for \class{Domain} object}
\validRule{spatial-20801}{A \Domain object may have the optional SBML
@@ -259,7 +262,10 @@
SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{listofinteriorpoints-class}.)}
+\validRule{spatial-20850}{\changed{If a \Parameter has a child \SpatialSymbolReference that points to a \Domain, that \Parameter may not be the target of an \InitialAssignment, \EventAssignment, \RateRule, or \AssignmentRule, may not be determined by an \AlgebraicRule, and may not define the \token{value} attribute.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{domain-class}.)}}
+
\subsubsection*{Rules for \class{InteriorPoint} object}
\validRule{spatial-20901}{An \InteriorPoint object may have the optional
@@ -274,29 +280,41 @@
\InteriorPoint. (Reference: SBML Level~3 Version~1 Core, Section~3.2.)}
\validRule{spatial-20903}{An \InteriorPoint object must have the
-required attribute \token{spatial:\-coordOne}, and may have the optional
-attributes \token{spatial:\-coordTwo} and \token{spatial:\-coordThree}.
+required attribute \token{spatial:\-coord1}, and may have the optional
+attributes \token{spatial:\-coord2} and \token{spatial:\-coord3}.
No other attributes from the SBML Level~3 Spatial Processes namespaces
are permitted on an \InteriorPoint object. (Reference: SBML Level~3
Specification for Spatial Processes, Version~1,
\sec{interiorpoint-class}.)}
-\validRule{spatial-20904}{The attribute \token{spatial:\-coordOne} on an
+\validRule{spatial-20904}{The attribute \token{spatial:\-coord1} on an
\InteriorPoint must have a value of data type \token{double}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{interiorpoint-class}.)}
-\validRule{spatial-20905}{The attribute \token{spatial:\-coordTwo} on an
+\validRule{spatial-20905}{The attribute \token{spatial:\-coord2} on an
\InteriorPoint must have a value of data type \token{double}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{interiorpoint-class}.)}
-\validRule{spatial-20906}{The attribute \token{spatial:\-coordThree} on
+\validRule{spatial-20906}{The attribute \token{spatial:\-coord3} on
an \InteriorPoint must have a value of data type \token{double}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{interiorpoint-class}.)}
+\validRule{spatial-20950}{\changed{If the \Geometry of the \Model has exactly one \CoordinateComponent child, an \InteriorPoint object must define the attribute \token{coord1}, and must not define the attributes \token{coord2} and \token{coord3}.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{interiorpoint-class}.)}}
+\validRule{spatial-20951}{\changed{If the \Geometry of the \Model has exactly two \CoordinateComponent children, an \InteriorPoint object must define the attributes \token{coord1} and \token{coord2}, and must not define the attribute \token{coord3}.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{interiorpoint-class}.)}}
+
+\validRule{spatial-20952}{\changed{If the \Geometry of the \Model has exactly three \CoordinateComponent children, an \InteriorPoint object must define the attributes \token{coord1}, \token{coord2}, and \token{coord3}.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{interiorpoint-class}.)}}
+
+
\subsubsection*{Rules for \class{Boundary} object}
\validRule{spatial-21001}{A \Boundary object may have the optional SBML
@@ -330,7 +348,15 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{coordinatecomponent-class}.)}}
+\validRule{spatial-21051}{\changed{If a \Parameter has a child \SpatialSymbolReference that points to a \Boundary, the \token{constant} attribute of that \Parameter must have a value of \val{true}.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{coordinatecomponent-class}.)}}
+\consistencyRule{spatial-21051}{\changed{If a \Parameter has a child \SpatialSymbolReference that points to a \Boundary, the units of that \Parameter should be equal to the units of the \Boundary's parent \CoordinateComponent.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{coordinatecomponent-class}.)}}
+
+
\subsubsection*{Rules for \class{AdjacentDomains} object}
\validRule{spatial-21101}{An \AdjacentDomains object may have the
@@ -346,8 +372,8 @@
Section~3.2.)}
\validRule{spatial-21103}{An \AdjacentDomains object must have the
-required attributes \token{spatial:\-id}, \token{spatial:\-do\-main\-One}
-and \token{spatial:\-domainTwo}, and may have the optional attribute
+required attributes \token{spatial:\-id}, \token{spatial:\-do\-main\-1}
+and \token{spatial:\-domain2}, and may have the optional attribute
\token{spatial:\-name}. No other attributes from the SBML Level~3
Spatial Processes namespaces are permitted on an \AdjacentDomains
object. (Reference: SBML Level~3 Specification for Spatial Processes,
@@ -354,13 +380,13 @@
Version~1, \sec{adjacentdomains-class}.)}
\validRule{spatial-21104}{The value of the attribute
-\token{spatial:\-domainOne} of an \AdjacentDomains object must be the
+\token{spatial:\-domain1} of an \AdjacentDomains object must be the
identifier of an existing \Domain object defined in the enclosing \Model
object. (Reference: SBML Level~3 Specification for Spatial Processes,
Version~1, \sec{adjacentdomains-class}.)}
\validRule{spatial-21105}{The value of the attribute
-\token{spatial:\-domainTwo} of an \AdjacentDomains object must be the
+\token{spatial:\-domain2} of an \AdjacentDomains object must be the
identifier of an existing \Domain object defined in the enclosing \Model
object. (Reference: SBML Level~3 Specification for Spatial Processes,
Version~1, \sec{adjacentdomains-class}.)}
@@ -442,11 +468,11 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{compartmentmapping-class}.)}
-\validRule{spatial-21350}{\changed{The value of the attribute 'spatial:unitSize' on a \CompartmentMapping must have a value between 0 and 1.
+\validRule{spatial-21350}{\changed{The value of the attribute \token{spatial:unitSize} on a \CompartmentMapping must have a value between 0 and 1.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{compartmentmapping-class}.)}}
-\consistencyRule{spatial-21351}{\changed{The values of the 'spatial:unitSize' attributes of every \CompartmentMapping with the same 'spatial:domainType' should sum to 1.
+\consistencyRule{spatial-21351}{\changed{The values of the \token{spatial:unitSize} attributes of every \CompartmentMapping with the same \token{spatial:domainType} should sum to 1.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{compartmentmapping-class}.)}}
@@ -642,6 +668,21 @@
\validRule{spatial-21652}{\changed{If the \Geometry of the \Model has exactly three \CoordinateComponent children, a \SampledField object must define the attributes \token{spa\-tial:\-numSamples1}, \token{spa\-tial:\-numSamples2}, and \token{spa\-tial:\-numSamples3}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+\validRule{spatial-21653}{\changed{If the \token{spatial:compression} attribute of a \SampledField has the value \val{uncompressed}, the \token{spatial:samplesLength} attribute of that \SampledField must equal the number of entries in the \ArrayData child of the \SampledField.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+
+\validRule{spatial-21654}{\changed{If the \token{spatial:compression} attribute of a \SampledField has the value \val{deflated}, the \token{spa\-tial:\-samples\-Length} attribute of that \SampledField must equal the number of non-whitespace characters of the \ArrayData child of the \SampledField.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+
+\validRule{spatial-21655}{\changed{If the \token{spatial:dataType} attribute of a \SampledField has the value \val{float}, none of the uncompressed entries in the \ArrayData child of the \SampledField may have a value outside of the range of an IEEE 754-1985 single-precision floating point value (approximately +/-3.4028235e38, and +/-1.17549e-38).
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+
+\validRule{spatial-21656}{\changed{If the \token{spatial:dataType} attribute of a \SampledField has the value \val{uint}, none of the uncompressed entries in the \ArrayData child of the \SampledField may be negative.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+
+\validRule{spatial-21657}{\changed{If the \token{spatial:dataType} attribute of a \SampledField has the value \val{uint} or \val{int}, all of the uncompressed entries in the \ArrayData child of the \SampledField must be integers.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledfield-class}.)}}
+
\subsubsection*{Rules for \class{SampledVolume} object}
\validRule{spatial-21701}{A \SampledVolume object may have the optional
@@ -690,19 +731,19 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{sampledvolume-class}.)}
-\validRule{spatial-21750}{\changed{A \SampledVolume with a defined \token{spa\-tial:\-minValue} attribute must also define the \token{spa\-tial:\-maxValue} attribute.
+\validRule{spatial-21750}{\changed{A \SampledVolume either must define the attribute \token{spatial:sampledValue} or must define both the \token{spatial:minValue} and \token{spatial:maxValue} attributes, but may not define any other combination of those three attributes.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledvolume-class}.)}}
-\validRule{spatial-21751}{\changed{A \SampledVolume with a defined \token{spa\-tial:\-maxValue} attribute must also define the \token{spa\-tial:\-minValue} attribute.
+\validRule{spatial-21751}{\changed{The attribute \token{spatial:minValue} of a \SampledVolume must have a value less than or equal to the value of the \token{spatial:maxValue} attribute of that \SampledVolume.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledvolume-class}.)}}
-\validRule{spatial-21752}{\changed{A \SampledVolume with defined \token{spa\-tial:\-minValue} and \token{spa\-tial:\-maxValue} attributes must not define the \token{spa\-tial:\-sam\-pled\-Value} attribute.
+\validRule{spatial-21752}{\changed{The \token{spatial:sampledValue} of one \SampledVolume may not be the same as a \token{spa\-tial\-:sam\-pled\-Value} from a different \SampledVolume from the same \SampledFieldGeometry.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledvolume-class}.)}}
-\validRule{spatial-21753}{\changed{A \SampledVolume with a defined \token{spa\-tial:\-sampledValue} attribute may not define the \token{spa\-tial:\-minValue} nor the \token{spa\-tial:\-maxValue} attribute.
+\validRule{spatial-21753}{\changed{The \token{spatial:sampledValue} from one \SampledVolume may not be less than the value of the attribute \token{spatial:maxValue} and greater than or equal to the value of the attribute \token{spatial:minValue} of a different \SampledVolume from the same \SampledFieldGeometry.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledvolume-class}.)}}
-\validRule{spatial-21754}{\changed{A \SampledVolume must either define its \token{spa\-tial:\-sampledValue} attribute or must define both the \token{spa\-tial:\-minValue} and \token{spa\-tial:\-maxValue} attributes.
+\validRule{spatial-21754}{\changed{The \token{spatial:minValue} and \token{spatial:maxValue} attribute values from one \SampledVolume may not define a range that overlaps the \token{spatial:minValue} and \token{spatial:maxValue} attribute values of a different \SampledVolume from the same \SampledFieldGeometry, with the exception that the \token{spatial:maxValue} of one \SampledVolume may equal the \token{spatial:minValue} of another \SampledVolume from the same \SampledFieldGeometry.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{sampledvolume-class}.)}}
@@ -772,8 +813,8 @@
\validRule{spatial-21905}{The value of the attribute
\token{spatial:\-functionType} of an \AnalyticVolume object must conform
to the syntax of SBML data type \primtype{FunctionKind} and may only
-take on the allowed values of \primtype{FunctionKind} defined in SBML;
-that is, the value must be one of the following: \val{layered}.
+take on the allowed \changed{value} of \primtype{FunctionKind} defined in SBML;
+that is, the value \changed{must be \val{layered}}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{analyticvolume-class}.)}
@@ -811,7 +852,7 @@
Section~3.2.)}
\validRule{spatial-22003}{A \ParametricGeometry object may contain one
-and only one instance of each of the SpatialPoints and
+and only one instance of each of the \SpatialPoints and
\ListOfParametricObjects elements. No other elements from the SBML
Level~3 Spatial Processes namespaces are permitted on a
\ParametricGeometry object. (Reference: SBML Level~3 Specification for
@@ -830,7 +871,11 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{listofparametricobjects-class}.)}
+\validRule{spatial-22050}{\changed{A \Model may not have a \ParametricGeometry and a \Geometry with exactly one \CoordinateComponent child.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{listofparametricobjects-class}.)}}
+
\subsubsection*{Rules for \class{ParametricObject} object}
\validRule{spatial-22101}{A \ParametricObject object may have the
@@ -904,7 +949,43 @@
Specification for Spatial Processes, Version~1,
\sec{parametricobject-class}.)}
+\validRule{spatial-22150}{\changed{If the \token{spatial:compression} attribute of a \ParametricObject has the value \val{uncompressed}, the \token{spatial:pointIndexLength} attribute of that \ParametricObject must equal the number of entries in the \ArrayData child of the \ParametricObject.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+\validRule{spatial-22151}{\changed{If the \token{spatial:compression} attribute of a \ParametricObject has the value \val{deflated}, the \token{spatial:pointIndexLength} attribute of that \ParametricObject must equal the number of non-whitespace characters of the \ArrayData child of the \ParametricObject.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22152}{\changed{If the attribute \token{spatial:polygonType} of a \ParametricObject has the value \val{triangle}, the number of uncompressed entries in its \ArrayData child must be evenly divisible by three.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22153}{\changed{If the attribute \token{spatial:polygonType} of a \ParametricObject has the value \val{quadrilateral}, the number of uncompressed entries in its \ArrayData child must be evenly divisible by four.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22154}{\changed{Every element of an uncompressed \ArrayData child of a \ParametricObject must be a non-negative integer.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22155}{\changed{Every element of an uncompressed \ArrayData child of a \ParametricObject must be less than the number of points described by the \SpatialPoints object in the same \ParametricGeometry.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\consistencyRule{spatial-22156}{\changed{Every face defined in the \ArrayData child of a \ParametricObject should be consistently defined in a clockwise or counter-clockwise fashion across all faces in the same \ParametricObject.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22157}{\changed{No two faces defined in the \ArrayData child of a \ParametricObject may share more than two coordinates.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+\validRule{spatial-22158}{\changed{No three faces defined in the \ArrayData child of a \ParametricObject may share more than one coordinate.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{parametricobject-class}.)}}
+
+
\subsubsection*{Rules for \class{CSGeometry} object}
\validRule{spatial-22201}{A \CSGeometry object may have the optional
@@ -958,7 +1039,7 @@
\sec{csgobject-class}.)}
\validRule{spatial-22304}{A \CSGObject object must contain one and only
-one instance of the CSGNode element. No other elements from the SBML
+one instance of the \CSGNode element. No other elements from the SBML
Level~3 Spatial Processes namespaces are permitted on a \CSGObject
object. (Reference: SBML Level~3 Specification for Spatial Processes,
Version~1, \sec{csgobject-class}.)}
@@ -982,6 +1063,9 @@
\consistencyRule{spatial-22350}{\changed{No \CSGObject should have an \token{spa\-tial:\-ordinal} attribute with the same value as a different \CSGObject.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgobject-class}.)}}
+\validRule{spatial-22351}{\changed{Any \InteriorPoint of the \DomainType referenced by a \CSGObject must be inside the geometry the \CSGObject describes.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgobject-class}.)}}
+
\subsubsection*{Rules for \class{CSGNode} object}
\validRule{spatial-22401}{A \CSGNode object may have the optional SBML
@@ -1006,27 +1090,6 @@
\sec{csgnode-class}.)}
-\subsubsection*{Rules for \class{CSGTransformation} object}
-
-\validRule{spatial-22501}{A \CSGTransformation object may have the
-optional SBML Level~3 Core attributes \token{metaid} and
-\token{sboTerm}. No other attributes from the SBML Level~3 Core
-namespaces are permitted on a \CSGTransformation. (Reference: SBML
-Level~3 Version~1 Core, Section~3.2.)}
-
-\validRule{spatial-22502}{A \CSGTransformation object may have the
-optional SBML Level~3 Core subobjects for notes and annotations. No
-other elements from the SBML Level~3 Core namespaces are permitted on a
-\CSGTransformation. (Reference: SBML Level~3 Version~1 Core,
-Section~3.2.)}
-
-\validRule{spatial-22503}{A \CSGTransformation object may contain one
-and only one instance of the CSGNode element. No other elements from the
-SBML Level~3 Spatial Processes namespaces are permitted on a
-\CSGTransformation object. (Reference: SBML Level~3 Specification for
-Spatial Processes, Version~1, \sec{csgtransformation-class}.)}
-
-
\subsubsection*{Rules for \class{CSGTranslation} object}
\validRule{spatial-22601}{A \CSGTranslation object may have the optional
@@ -1063,7 +1126,29 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{csgtranslation-class}.)}
+\validRule{spatial-22650}{\changed{A \CSGTranslation object may contain one
+and only one child \CSGNode element. No other elements from the
+SBML Level~3 Spatial Processes namespaces are permitted on a
+\CSGTranslation object. (Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+\validRule{spatial-22651}{\changed{The attribute \token{spatial:translateY} on a \CSGTranslation is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+
+\validRule{spatial-22652}{\changed{The attribute \token{spatial:translateZ} on a \CSGTranslation is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+
+\validRule{spatial-22653}{\changed{The attribute \token{spatial:translateY} on a \CSGTranslation must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+
+\validRule{spatial-22654}{\changed{The attribute \token{spatial:translateZ} on a \CSGTranslation must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+
+
\subsubsection*{Rules for \class{CSGRotation} object}
\validRule{spatial-22701}{A \CSGRotation object may have the optional
@@ -1106,7 +1191,33 @@
SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{csgrotation-class}.)}
+\validRule{spatial-22750}{\changed{A \CSGRotation object may contain one
+and only one child \CSGNode element. No other elements from the
+SBML Level~3 Spatial Processes namespaces are permitted on a
+\CSGRotation object. (Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+\validRule{spatial-22751}{\changed{The attribute \token{spatial:rotateY} on a \CSGRotation is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgrotation-class}.)}}
+
+\validRule{spatial-22752}{\changed{The attribute \token{spatial:rotateZ} on a \CSGRotation is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgrotation-class}.)}}
+
+\validRule{spatial-22753}{\changed{The attribute \token{spatial:rotateY} on a \CSGRotation must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgrotation-class}.)}}
+
+\validRule{spatial-22754}{\changed{The attribute \token{spatial:rotateZ} on a \CSGRotation must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgrotation-class}.)}}
+
+\validRule{spatial-22755}{\changed{If the \Geometry of the \Model has exactly three \CoordinateComponent children, at least one of the attributes \token{spatial:rotateX}, \token{spatial:rotateY}, or \token{spatial:rotateZ} of a \CSGRotation must not be equal to zero.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgrotation-class}.)}}
+
+
\subsubsection*{Rules for \class{CSGScale} object}
\validRule{spatial-22801}{A \CSGScale object may have the optional SBML
@@ -1141,7 +1252,29 @@
SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{csgscale-class}.)}
+\validRule{spatial-22850}{\changed{A \CSGScale object may contain one
+and only one child \CSGNode element. No other elements from the
+SBML Level~3 Spatial Processes namespaces are permitted on a
+\CSGScale object. (Reference: SBML Level~3 Specification for
+Spatial Processes, Version~1, \sec{csgtransformation-class}.)}}
+\validRule{spatial-22851}{\changed{The attribute \token{spatial:scaleY} on a \CSGScale is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgscale-class}.)}}
+
+\validRule{spatial-22852}{\changed{The attribute \token{spatial:scaleZ} on a \CSGScale is required if the \Geometry of the \Model has a \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgscale-class}.)}}
+
+\validRule{spatial-22853}{\changed{The attribute \token{spatial:scaleY} on a \CSGScale must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianY}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgscale-class}.)}}
+
+\validRule{spatial-22854}{\changed{The attribute \token{spatial:scaleZ} on a \CSGScale must not be defined if the \Geometry of the \Model has no \CoordinateComponent child of type \val{cartesianZ}.
+(Reference: SBML Level~3 Specification for Spatial Processes,
+Version~1, \sec{csgscale-class}.)}}
+
+
\subsubsection*{Rules for \class{CSGHomogeneousTransformation} object}
\validRule{spatial-22901}{A \CSGHomogeneousTransformation object may
@@ -1157,8 +1290,7 @@
Version~1 Core, Section~3.2.)}
\validRule{spatial-22903}{A \CSGHomogeneousTransformation object must
-contain one and only one instance of the TransformationComponent
-element. No other elements from the SBML Level~3 Spatial Processes
+contain one and only one \changed{child \token{for\-ward\-Trans\-for\-ma\-tion} element of type \TransformationComponent, and may additionally contain one and only one child \CSGNode element.} No other elements from the SBML Level~3 Spatial Processes
namespaces are permitted on a \CSGHomogeneousTransformation object.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{csghomogeneoustransformation-class}.)}
@@ -1197,7 +1329,17 @@
Specification for Spatial Processes, Version~1,
\sec{transformationcomponent-class}.)}
+\validRule{spatial-23050}{\changed{The attribute \token{spatial:componentsLength} on a \TransformationComponent must have a value of \val{16}.
+(Reference: SBML Level~3
+Specification for Spatial Processes, Version~1,
+\sec{transformationcomponent-class}.)}}
+\validRule{spatial-23051}{\changed{The length of the array of the attribute \token{spatial:components} on a \TransformationComponent must be 16.
+(Reference: SBML Level~3
+Specification for Spatial Processes, Version~1,
+\sec{transformationcomponent-class}.)}}
+
+
\subsubsection*{Rules for \class{CSGPrimitive} object}
\validRule{spatial-23101}{A \CSGPrimitive object may have the optional
@@ -1225,7 +1367,14 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{csgprimitive-class}.)}
+\validRule{spatial-23150}{\changed{The \token{spatial:primitiveType} attribute of a \CSGPrimitive may have the values \val{sphere}, \val{cube}, \val{cylinder}, or \val{cone} only if the \Geometry of the \Model has exactly three \CoordinateComponent children.
+(Reference: SBML Level~3 Specification for Spatial
+Processes, Version~1, \sec{csgprimitive-class}.)}}
+\validRule{spatial-23151}{\changed{The \token{spatial:primitiveType} attribute of a \CSGPrimitive may have the values \val{circle} or \val{square} only if the \Geometry of the \Model has exactly two or three \CoordinateComponent children.
+(Reference: SBML Level~3 Specification for Spatial
+Processes, Version~1, \sec{csgprimitive-class}.)}}
+
\subsubsection*{Rules for \class{CSGSetOperator} object}
\validRule{spatial-23201}{A \CSGSetOperator object may have the optional
@@ -1292,6 +1441,15 @@
\validRule{spatial-23251}{\changed{If the attribute \token{spa\-tial:\-operationType} of a \CSGSetOperator has the value \val{union} or \val{in\-ter\-sec\-tion}, it must not define values for the attributes \token{spa\-tial:\-componentA} nor \token{spa\-tial:\-componentB}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
+\validRule{spatial-23251}{\changed{If the attribute \token{spatial:operationType} of a \CSGSetOperator is \val{difference}, it must have exactly two \CSGNode children.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
+
+\validRule{spatial-23252}{\changed{The attributes \token{spatial:complementA} and \token{spatial:complementB} of a \CSGSetOperator must reference its two \CSGNode children.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
+
+\modelingRule{spatial-23252}{\changed{A \CSGSetOperator should usually have at least two children, as operations involving zero or one child can be accomplished more efficiently in other ways.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{csgsetoperator-class}.)}}
+
\subsubsection*{Rules for \class{SpatialSymbolReference} object}
\validRule{spatial-23301}{A \SpatialSymbolReference object may have the
@@ -1392,16 +1550,16 @@
\consistencyRule{spatial-23453}{\changed{The units of a \Parameter with a \DiffusionCoefficient child should be $length^2/time$.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{diffusioncoefficient-class}.)}}
-\validRule{spatial-23454}{\changed{The \DiffusionCoefficient attribute 'spatial:coordinateReference2', if defined, must have a value different from that of the attribute 'spatial:coordinateReference1'.
+\validRule{spatial-23454}{\changed{The \DiffusionCoefficient attribute \token{spatial:coordinateReference2}, if defined, must have a value different from that of the attribute \token{spatial:coordinateReference1}.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{diffusioncoefficient-class}.)}}
-\validRule{spatial-23455}{\changed{The \DiffusionCoefficient attributes 'spatial:coordinateReference1' and 'spatial:coordinateReference2' may not have a value of 'cartesianY' if the Geometry has exactly one CoordinateComponent child.
+\validRule{spatial-23455}{\changed{The \DiffusionCoefficient attributes \token{spatial:coordinateReference1} and \token{spa\-tial\-:co\-or\-di\-nate\-Re\-fer\-ence2} may not have a value of \val{cartesianY} if the Geometry has exactly one CoordinateComponent child.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{diffusioncoefficient-class}.)}}
-\validRule{spatial-23456}{\changed{The \DiffusionCoefficient attributes 'spatial:coordinateReference1' and 'spatial:coordinateReference2' may not have a value of 'cartesianZ' if the Geometry has exactly one or two CoordinateComponent children.
+\validRule{spatial-23456}{\changed{The \DiffusionCoefficient attributes \token{spatial:coordinateReference1} and \token{spa\-tial\-:co\-or\-di\-nate\-Re\-fer\-ence2} may not have a value of \val{cartesianZ} if the Geometry has exactly one or two CoordinateComponent children.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{diffusioncoefficient-class}.)}}
-\validRule{spatial-23457}{\changed{Any Species may only have a single DiffusionCoefficient that applies to any given axis. A DiffusionCoefficient of type 'isotropic' is considered to apply to all the axes in the Geometry, and other types to all axes they reference.
+\validRule{spatial-23457}{\changed{Any \Species may only have a single \DiffusionCoefficient that applies to any given axis or plane. A \DiffusionCoefficient of type \val{anisotropic} applies to the axis it references, and any plane in the Geometry that contains that axis. A \DiffusionCoefficient of type \val{tensor} applies to the plane defined by the two axes it references. A \DiffusionCoefficient of type \val{isotropic} is considered to apply to all axes and planes in the \Geometry.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{diffusioncoefficient-class}.)}}
\subsubsection*{Rules for \class{AdvectionCoefficient} object}
@@ -1497,7 +1655,7 @@
enclosing \Model object. (Reference: SBML Level~3 Specification for
Spatial Processes, Version~1, \sec{boundarycondition-class}.)}
-\validRule{spatial-23650}{\changed{A \BoundaryCondition must define a value for either the attribute \token{spa\-tial:\-coordinateBoundary} or \token{spa\-tial:\-boun\-da\-ry\-Do\-main\-Type}, but not both.
+\validRule{spatial-23650}{\changed{A \BoundaryCondition must define a value for either the attribute \token{spa\-tial:\-co\-or\-di\-nate\-Boun\-da\-ry} or \token{spa\-tial:\-boun\-da\-ry\-Do\-main\-Type}, but not both.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{boundarycondition-class}.)}}
\validRule{spatial-23651}{\changed{For every combination of species and boundary, there must be at most exactly one \BoundaryCondition of type \val{Neumann}, or exactly one \BoundaryCondition of type \val{Dirichlet}, or exactly three \BoundaryCondition elements, one of each of the three \val{Robin\_} types.
@@ -1512,7 +1670,7 @@
\consistencyRule{spatial-23654}{\changed{The units of a \Parameter with a \BoundaryCondition child of type \val{Robin\_valueCoefficient} should scale with the other \val{Robin\_} boundary conditions for the same species and boundary, with suggested base units of dimensionless.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{boundarycondition-class}.)}}
-\consistencyRule{spatial-23655}{\changed{The units of a \Parameter with a \BoundaryCondition child of type \val{Robin\_inwardNormalGradientCoefficient} should scale with the other \val{Robin\_} boundary conditions for the same species and boundary, with suggested base units of $1/length$.
+\consistencyRule{spatial-23655}{\changed{The units of a \Parameter with a \BoundaryCondition child of type \val{Robin\_inwardNormal\-Gra\-di\-ent\-Co\-ef\-fi\-cient} should scale with the other \val{Robin\_} boundary conditions for the same species and boundary, with suggested base units of $1/length$.
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1, \sec{boundarycondition-class}.)}}
\consistencyRule{spatial-23656}{\changed{The units of a \Parameter with a \BoundaryCondition child of type \val{Robin\_sum} should scale with the other \val{Robin\_} boundary conditions for the same species and boundary, with suggested base units of the concentration of the referenced \Species.
@@ -1717,7 +1875,7 @@
\validRule{spatial-23904}{The value of the attribute
\token{spatial:\-geometryDefinition} of an \OrdinalMapping object must
be the identifier of an existing \GeometryDefinition object defined in
-the enclosing \Model object. (Reference: SBML Level~3 Specification for
+the \changed{parent \MixedGeometry object}. (Reference: SBML Level~3 Specification for
Spatial Processes, Version~1, \sec{ordinalmapping-class}.)}
\validRule{spatial-23905}{The attribute \token{spatial:\-ordinal} on an
@@ -1725,7 +1883,11 @@
(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
\sec{ordinalmapping-class}.)}
+\consistencyRule{spatial-23950}{\changed{No OrdinalMapping should have a \token{spatial:ordinal} attribute with the same value as a different OrdinalMapping child of the same MixedGeometry.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{ordinalmapping-class}.)}}
+
\subsubsection*{Rules for \class{SpatialPoints} object}
\validRule{spatial-24001}{A \SpatialPoints object may have the optional
@@ -1781,4 +1943,29 @@
Specification for Spatial Processes, Version~1,
\sec{spatialpoints-class}.)}
+\validRule{spatial-24050}{\changed{If the \token{spatial:compression} attribute of a \SpatialPoints has the value \val{uncompressed}, the \token{spatial:arrayDataLength} attribute of that \SpatialPoints must equal the number of entries in the \ArrayData child of the \SpatialPoints.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+\validRule{spatial-24051}{\changed{If the \token{spatial:compression} attribute of a \SpatialPoints has the value \val{deflated}, the \token{spa\-tial\-:ar\-ray\-Da\-ta\-Length} attribute of that \SpatialPoints must equal the number of non-white\-space characters of the \ArrayData child of the \SpatialPoints.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+
+\validRule{spatial-24052}{\changed{When uncompressed, the number of entries in the \ArrayData child of a \SpatialPoints must be evenly divisible by the number of \CoordinateComponent children of the \Geometry of the \Model (two or three).
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+
+\validRule{spatial-24053}{\changed{If the \token{spatial:dataType} attribute of a \SpatialPoints has the value \val{float}, none of the uncompressed entries in the \ArrayData child of the \SpatialPoints may have a value outside of the range of an IEEE 754-1985 single-precision floating point value (approximately +/-3.4028235e38, and +/-1.17549e-38).
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+
+\validRule{spatial-24054}{\changed{If the \token{spatial:dataType} attribute of a \SpatialPoints has the value \val{uint}, none of the uncompressed entries in the \ArrayData child of the \SpatialPoints may be negative.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+
+\validRule{spatial-24055}{\changed{If the \token{spatial:dataType} attribute of a \SpatialPoints has the value \val{uint} or \val{int}, all of the uncompressed entries in the \ArrayData child of the \SpatialPoints must be integers.
+(Reference: SBML Level~3 Specification for Spatial Processes, Version~1,
+\sec{spatialpoints-class}.)}}
+
+
+
Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/macros.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/macros.tex 2019-11-22 00:47:38 UTC (rev 26179)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/macros.tex 2019-11-22 21:34:06 UTC (rev 26180)
@@ -10,45 +10,46 @@
\newcommand{\AdjacentDomains}{\defRef{AdjacentDomains}{adjacentdomains-class}}
\newcommand{\AdvectionCoefficient}{\defRef{AdvectionCoefficient}{advectioncoefficient-class}}
\newcommand{\AnalyticGeometry}{\defRef{AnalyticGeometry}{analyticgeometry-class}}
+\newcommand{\AnalyticVolumes}{\defRef{AnalyticVolumes}{analyticvolume-class}}
\newcommand{\AnalyticVolume}{\defRef{AnalyticVolume}{analyticvolume-class}}
-\newcommand{\AnalyticVolumes}{\defRef{AnalyticVolumes}{analyticvolume-class}}
+\newcommand{\ArrayData}{\defRef{ArrayData}{arraydata-class}}
\newcommand{\BoundaryCondition}{\defRef{BoundaryCondition}{boundarycondition-class}}
\newcommand{\Boundary}{\defRef{Boundary}{boundary-class}}
\newcommand{\CSGHomogeneousTransformation}{\defRef{CSGHomogeneousTransformation}{csghomogeneoustransformation-class}}
+\newcommand{\CSGNodes}{\absDefRef{CSGNodes}{csgnode-class}}
\newcommand{\CSGNode}{\absDefRef{CSGNode}{csgnode-class}}
-\newcommand{\CSGNodes}{\absDefRef{CSGNodes}{csgnode-class}}
+\newcommand{\CSGObjects}{\defRef{CSGObjects}{csgobject-class}}
\newcommand{\CSGObject}{\defRef{CSGObject}{csgobject-class}}
-\newcommand{\CSGObjects}{\defRef{CSGObjects}{csgobject-class}}
+\newcommand{\CSGPrimitives}{\defRef{CSGPrimitives}{csgprimitive-class}}
\newcommand{\CSGPrimitive}{\defRef{CSGPrimitive}{csgprimitive-class}}
-\newcommand{\CSGPrimitives}{\defRef{CSGPrimitives}{csgprimitive-class}}
%\newcommand{\CSGPseudoPrimitive}{\defRef{CSGPseudoPrimitive}{csgpseudoprimitive-class}}
\newcommand{\CSGRotation}{\defRef{CSGRotation}{csgrotation-class}}
\newcommand{\CSGScale}{\defRef{CSGScale}{csgscale-class}}
+\newcommand{\CSGSetOperators}{\defRef{CSGSetOperators}{csgsetoperator-class}}
\newcommand{\CSGSetOperator}{\defRef{CSGSetOperator}{csgsetoperator-class}}
-\newcommand{\CSGSetOperators}{\defRef{CSGSetOperators}{csgsetoperator-class}}
+\newcommand{\CSGTransformations}{\absDefRef{CSGTransformations}{csgtransformation-class}}
\newcommand{\CSGTransformation}{\absDefRef{CSGTransformation}{csgtransformation-class}}
-\newcommand{\CSGTransformations}{\absDefRef{CSGTransformations}{csgtransformation-class}}
\newcommand{\CSGTranslation}{\defRef{CSGTranslation}{csgtranslation-class}}
\newcommand{\CSGeometry}{\defRef{CSGeometry}{csgeometry-class}}
+\newcommand{\CompartmentMappings}{\defRef{CompartmentMappings}{compartmentmapping-class}}
\newcommand{\CompartmentMapping}{\defRef{CompartmentMapping}{compartmentmapping-class}}
-\newcommand{\CompartmentMappings}{\defRef{CompartmentMappings}{compartmentmapping-class}}
+\newcommand{\CoordinateComponents}{\defRef{CoordinateComponents}{coordinatecomponent-class}}
\newcommand{\CoordinateComponent}{\defRef{CoordinateComponent}{coordinatecomponent-class}}
-\newcommand{\CoordinateComponents}{\defRef{CoordinateComponents}{coordinatecomponent-class}}
\newcommand{\CoordinateReference}{\defRef{CoordinateReference}{coordinatereference-class}}
\newcommand{\DiffusionCoefficient}{\defRef{DiffusionCoefficient}{diffusioncoefficient-class}}
+\newcommand{\DomainTypes}{\defRef{DomainTypes}{domaintype-class}}
\newcommand{\DomainType}{\defRef{DomainType}{domaintype-class}}
-\newcommand{\DomainTypes}{\defRef{DomainTypes}{domaintype-class}}
+\newcommand{\Domains}{\defRef{Domains}{domain-class}}
\newcommand{\Domain}{\defRef{Domain}{domain-class}}
-\newcommand{\Domains}{\defRef{Domains}{domain-class}}
+\newcommand{\GeometryDefinitions}{\absDefRef{GeometryDefinitions}{geometrydefinition-class}}
\newcommand{\GeometryDefinition}{\absDefRef{GeometryDefinition}{geometrydefinition-class}}
-\newcommand{\GeometryDefinitions}{\absDefRef{GeometryDefinitions}{geometrydefinition-class}}
\newcommand{\Geometry}{\defRef{Geometry}{geometry-class}}
+\newcommand{\InteriorPoints}{\defRef{InteriorPoints}{interiorpoint-class}}
\newcommand{\InteriorPoint}{\defRef{InteriorPoint}{interiorpoint-class}}
-\newcommand{\InteriorPoints}{\defRef{InteriorPoints}{interiorpoint-class}}
\newcommand{\ListOfAdjacentDomains}{\defRef{List\-Of\-AdjacentDomains}{listofadjacentdomains-class}}
\newcommand{\ListOfAnalyticVolumes}{\defRef{ListOfAnalyticVolumes}{listofanalyticvolumes-class}}
+\newcommand{\ListOfCSGNodes}{\defRef{ListOfCSGNodes}{listofcsgnodes-class}}
\newcommand{\ListOfCSGObjects}{\defRef{ListOfCSGObjects}{listofcsgobjects-class}}
-\newcommand{\ListOfCSGNodes}{\defRef{ListOfCSGNodes}{listofcsgnodes-class}}
\newcommand{\ListOfCoordinateComponents}{\defRef{ListOfCoordinateComponents}{listofcoordinatecomponents-class}}
\newcommand{\ListOfDomainTypes}{\defRef{ListOfDomainTypes}{listofdomaintypes-class}}
\newcommand{\ListOfDomains}{\defRef{ListOfDomains}{listofdomains-class}}
@@ -56,19 +57,19 @@
\newcommand{\ListOfInteriorPoints}{\defRef{ListOfInteriorPoints}{listofinteriorpoints-class}}
\newcommand{\ListOfOrdinalMappings}{\defRef{ListOfOrdinalMappings}{listofordinalmappings-class}}
\newcommand{\ListOfParametricObjects}{\defRef{ListOfParametricObjects}{listofparametricobjects-class}}
+\newcommand{\ListOfSampledFields}{\defRef{ListOfSampledFields}{listofsampledfields-class}}
\newcommand{\ListOfSampledVolumes}{\defRef{ListOfSampledVolumes}{listofsampledvolumes-class}}
-\newcommand{\ListOfSampledFields}{\defRef{ListOfSampledFields}{listofsampledfields-class}}
-\newcommand{\SpatialPoints}{\defRef{SpatialPoints}{spatialpoints-class}}
\newcommand{\MixedGeometry}{\defRef{MixedGeometry}{mixedgeometry-class}}
\newcommand{\OrdinalMapping}{\defRef{OrdinalMapping}{ordinalmapping-class}}
\newcommand{\ParametricGeometry}{\defRef{ParametricGeometry}{parametricgeometry-class}}
+\newcommand{\ParametricObjects}{\defRef{ParametricObjects}{parametricobject-class}}
\newcommand{\ParametricObject}{\defRef{ParametricObject}{parametricobject-class}}
-\newcommand{\ParametricObjects}{\defRef{ParametricObjects}{parametricobject-class}}
\newcommand{\PolygonObject}{\defRef{PolygonObject}{polygonobject-class}}
\newcommand{\SampledFieldGeometry}{\defRef{SampledFieldGeometry}{sampledfieldgeometry-class}}
\newcommand{\SampledField}{\defRef{SampledField}{sampledfield-class}}
+\newcommand{\SampledVolumes}{\defRef{SampledVolumes}{sampledvolume-class}}
\newcommand{\SampledVolume}{\defRef{SampledVolume}{sampledvolume-class}}
-\newcommand{\SampledVolumes}{\defRef{SampledVolumes}{sampledvolume-class}}
+\newcommand{\SpatialPoints}{\defRef{SpatialPoints}{spatialpoints-class}}
\newcommand{\SpatialSymbolReference}{\defRef{SpatialSymbolReference}{spatialsymbolreference-class}}
\newcommand{\TransformationComponent}{\defRef{TransformationComponent}{transformationcomponent-class}}
Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/main.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/main.tex 2019-11-22 00:47:38 UTC (rev 26179)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/main.tex 2019-11-22 21:34:06 UTC (rev 26180)
@@ -6,7 +6,7 @@
\packageTitle{Spatial Processes}
\packageVersion{Version 1, Release \changed{0.94} (Draft)}
-\packageVersionDate{\changed{August 2019}}
+\packageVersionDate{\changed{November 2019}}
\packageGeneralURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/spatial}
\packageThisVersionURL{TBD}
Added: trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf
===================================================================
(Binary files differ)
Index: trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf 2019-11-22 00:47:38 UTC (rev 26179)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf 2019-11-22 21:34:06 UTC (rev 26180)
Property changes on: trunk/specifications/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.94.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/specifications/sbml-level-3/version-1/spatial/specification/syntax.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/spatial/specification/syntax.tex 2019-11-22 00:47:38 UTC (rev 26179)
+++ trunk/specifications/sbml-level-3/version-1/spatial/specification/syntax.tex 2019-11-22 21:34:06 UTC (rev 26180)
@@ -267,7 +267,7 @@
\subsubsection{The \fixttspace\tokenNC{type} and \tokenNC{coordinateReference} attributes}
The required \token{type} attribute of \DiffusionCoefficient is of type \primtype{DiffusionKind} and indicates whether the diffusion coefficient is \val{isotropic} (i.e. applies equally in all dimensions/directions), \val{anisotropic} (i.e. applies only for a single coordinate), or \val{tensor} (i.e. applies only for a particular pair of coordinates). Coefficients of type \val{isotropic} may not have any \token{coordinateReference} attributes defined, since diffusion is defined for all axes. Coefficients of type \val{anisotropic} must define the \token{coordinateReference1} attribute and not the \token{coordinateReference2} attribute, and applies in the direction of that axis. Coefficients of type \val{tensor} must define both the attributes \token{coordinateReference1} and \token{coordinateReference2}, defining diffusion in relation to the direction due to a gradient in the diagonal term of the diffusion tensor for the two coordinates. In no case may \token{coordinateReference2} be defined but not \token{coordinateReference1}.
-\subsubsection{\DiffusionCoefficient uniqueness}
+\subsubsection{\class{DiffusionCoefficient} uniqueness}
Only one \DiffusionCoefficient may be defined per \Species per axis or pair of valid axes in the \Compartment in which it resides. Since isotropic diffusion is defined for all axes at once, this means that if an isotropic \DiffusionCoefficient is defined for a \Species, it may have no other diffusuion coefficients. \changed{Similarly, if a tensor \DiffusionCoefficient is defined for a \Species for a pair of axes, the model must not also define an anisotopic \DiffusionCoefficient for either of those axes. This means that the following types of diffusion coefficients are allowed in a three-dimensional \Geometry:}
\begin{blockChanged}
\begin{itemize}
@@ -656,7 +656,7 @@
-\subsection{\AnalyticGeometry example}
+\subsection{\class{AnalyticGeometry} example}
\label{analyticvolume-example}
The following is an example of an analytic geometry, with a single volume described by the formula \val{$8*(x-1)^2 + 8*(y-1)^2 + 8*(z-1)^2 < 1$} (the formula for a sphere).
@@ -716,7 +716,7 @@
Having the \token{minValue} be included and the \token{maxValue} be excluded allows modelers to define adjacent volumes without ambiguity at the boundaries. One \SampledVolume may be defined from 0 to 100, and a second volume defined from 100 to 200, and any location with a \SampledField value of exactly 100 is only assigned to the first \SampledVolume, and every location with a value close to 100 is included in exactly one \SampledVolume.
-\subsection{\SampledFieldGeometry example}
+\subsection{\class{SampledFieldGeometry} example}
\label{sampledfieldgeometry-example}
The following is an example of a sampled field geometry with three volumes. The referenced \SampledField (defined in \sec{sampledfield-class}) is also included (though truncated).
@@ -1020,6 +1020,7 @@
The \token{dataType} attribute is of type \primtype{DataKind} and is optional. It is used to specify the type of the data being stored\changed{, so that the uncompressed data can be stored in an appropriate storage type. The three main value types are \val{uint} for unsigned integers, \val{int} for signed integers, and \val{double} for double-precision floating point values. For backwards compatibility, and for cases where storage space might be an issue, other values may also be used:} \val{float} to indicate single-precision (32-bit) floating point values, and \val{uint8}, \val{uint16}, and \val{uint32} to indicate 8-bit, 16-bit, and 32-bit unsigned integer values, respectively.
\subsubsection{The \fixttspace\tokenNC{ArrayData} text child}
+\label{arraydata-class}
The \token{ArrayData} text child of the \SpatialPoints is in \token{arrayData} format, and represents an ordered list of sets of coordinates that will be used as the vertices of \ParametricObject elements in this \ParametricGeometry, with \val{0} representing the first such coordinate, \val{1} the second, etc. The list will define vertexes with as many values as there are \CoordinateComponent children of the parent \Geometry: three values for representing the X, Y, and Z coordinates (respectively) of 3-dimensional geometries, or two values for representing the X and Y coordinates (respectively) of 2-dimensional geometries. (\ParametricGeometry elements cannot be created in 1-dimensional geometries.) It is suggested, but not required, that if the data is uncompressed, that the grouped points be separated from each other with the use of a semicolon.
\begin{blockChanged}
|
|
From: <luc...@us...> - 2019-11-22 00:47:40
|
Revision: 26179
http://sourceforge.net/p/sbml/code/26179
Author: luciansmith
Date: 2019-11-22 00:47:38 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Fix more *TypeAsString functions.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialPoints.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.cpp 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.cpp 2019-11-22 00:47:38 UTC (rev 26179)
@@ -192,11 +192,10 @@
/*
* Returns the value of the "functionType" attribute of this AnalyticVolume.
*/
-const std::string&
+std::string
AnalyticVolume::getFunctionTypeAsString() const
{
- static const std::string code_str = FunctionKind_toString(mFunctionType);
- return code_str;
+ return FunctionKind_toString(mFunctionType);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.h 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.h 2019-11-22 00:47:38 UTC (rev 26179)
@@ -211,7 +211,7 @@
* @li @c "layered"
* @li @c "invalid FunctionKind value"
*/
- const std::string& getFunctionTypeAsString() const;
+ std::string getFunctionTypeAsString() const;
/**
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.cpp 2019-11-22 00:47:38 UTC (rev 26179)
@@ -161,8 +161,7 @@
std::string
CSGSetOperator::getOperationTypeAsString() const
{
- std::string code_str = SetOperation_toString(mOperationType);
- return code_str;
+ return SetOperation_toString(mOperationType);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.cpp 2019-11-22 00:47:38 UTC (rev 26179)
@@ -191,8 +191,7 @@
std::string
ParametricObject::getPolygonTypeAsString() const
{
- std::string code_str = PolygonKind_toString(mPolygonType);
- return code_str;
+ return PolygonKind_toString(mPolygonType);
}
@@ -269,8 +268,7 @@
std::string
ParametricObject::getDataTypeAsString() const
{
- std::string code_str = DataKind_toString(mDataType);
- return code_str;
+ return DataKind_toString(mDataType);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp 2019-11-22 00:47:38 UTC (rev 26179)
@@ -323,8 +323,7 @@
std::string
SampledField::getDataTypeAsString() const
{
- std::string code_str = DataKind_toString(mDataType);
- return code_str;
+ return DataKind_toString(mDataType);
}
@@ -374,8 +373,7 @@
std::string
SampledField::getInterpolationTypeAsString() const
{
- std::string code_str = InterpolationKind_toString(mInterpolationType);
- return code_str;
+ return InterpolationKind_toString(mInterpolationType);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialPoints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialPoints.cpp 2019-11-22 00:31:23 UTC (rev 26178)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialPoints.cpp 2019-11-22 00:47:38 UTC (rev 26179)
@@ -228,8 +228,7 @@
std::string
SpatialPoints::getDataTypeAsString() const
{
- std::string code_str = DataKind_toString(mDataType);
- return code_str;
+ return DataKind_toString(mDataType);
}
|
|
From: <luc...@us...> - 2019-11-22 00:31:25
|
Revision: 26178
http://sourceforge.net/p/sbml/code/26178
Author: luciansmith
Date: 2019-11-22 00:31:23 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Define, but don't implement support for, spatial rule 22351. (Support needs spatial understanding.)
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 00:23:13 UTC (rev 26177)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 00:31:23 UTC (rev 26178)
@@ -219,6 +219,7 @@
, SpatialCSGObjectNameMustBeString = 1222306
, SpatialCSGObjectOrdinalMustBeInteger = 1222307
, SpatialCSGObjectOrdinalShouldBeUnique = 1222350
+, SpatialCSGObjectMustEncompassInteriorPoints = 1222351
, SpatialCSGNodeAllowedCoreAttributes = 1222401
, SpatialCSGNodeAllowedCoreElements = 1222402
, SpatialCSGNodeAllowedAttributes = 1222403
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 00:23:13 UTC (rev 26177)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 00:31:23 UTC (rev 26178)
@@ -1895,6 +1895,16 @@
}
},
+ // 1222351
+ { SpatialCSGObjectMustEncompassInteriorPoints,
+ "CSGObjects must encompass their domainType's interior points.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_WARNING,
+ "Any <interiorPoint> of the <domainType> referenced by a <csgObject> must be inside the geometry the <csgObject> describes.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1222401
{ SpatialCSGNodeAllowedCoreAttributes,
"Core attributes allowed on <csgNode>.",
|
|
From: <luc...@us...> - 2019-11-22 00:23:15
|
Revision: 26177
http://sourceforge.net/p/sbml/code/26177
Author: luciansmith
Date: 2019-11-22 00:23:13 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Add support for spatial rule 23151.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-04.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 00:04:24 UTC (rev 26176)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 00:23:13 UTC (rev 26177)
@@ -258,6 +258,7 @@
, SpatialCSGPrimitiveAllowedAttributes = 1223103
, SpatialCSGPrimitivePrimitiveTypeMustBePrimitiveKindEnum = 1223104
, SpatialCSGPrimitive3DShapes = 1223150
+, SpatialCSGPrimitive2DShapes = 1223151
, SpatialCSGSetOperatorAllowedCoreAttributes = 1223201
, SpatialCSGSetOperatorAllowedCoreElements = 1223202
, SpatialCSGSetOperatorAllowedAttributes = 1223203
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 00:04:24 UTC (rev 26176)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 00:23:13 UTC (rev 26177)
@@ -2360,6 +2360,16 @@
}
},
+ // 1223150
+ { SpatialCSGPrimitive2DShapes,
+ "Any <csgPrimitive> with a 2D shape must be in 2D or 3D geometry.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The 'spatial:primitiveType' attribute of a <csgPrimitive> may have the values 'circle' or 'square' only if the <geometry> of the model has exactly two or three <coordinateComponent> children.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1223201
{ SpatialCSGSetOperatorAllowedCoreAttributes,
"Core attributes allowed on <csgSetOperator>.",
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 00:04:24 UTC (rev 26176)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 00:23:13 UTC (rev 26177)
@@ -1386,6 +1386,41 @@
END_CONSTRAINT
+// 1223150
+START_CONSTRAINT(SpatialCSGPrimitive2DShapes, CSGPrimitive, csgp)
+{
+ bool fail = false;
+
+ SpatialModelPlugin *mplug = (SpatialModelPlugin*)(m.getPlugin("spatial"));
+ pre(mplug != NULL);
+ Geometry* geom = mplug->getGeometry();
+ pre(geom != NULL);
+ pre(geom->getNumCoordinateComponents()==1);
+ switch(csgp.getPrimitiveType()){
+ case SPATIAL_PRIMITIVEKIND_SPHERE:
+ case SPATIAL_PRIMITIVEKIND_CUBE:
+ case SPATIAL_PRIMITIVEKIND_CYLINDER:
+ case SPATIAL_PRIMITIVEKIND_CONE:
+ case SPATIAL_PRIMITIVEKIND_INVALID:
+ break;
+ case SPATIAL_PRIMITIVEKIND_CIRCLE:
+ case SPATIAL_PRIMITIVEKIND_SQUARE:
+ msg = "A <csgPrimitive>";
+ if (csgp.isSetId()) {
+ msg += " with the id '" + csgp.getId() + "'";
+ }
+ msg += " has as 'primitiveType' of '";
+ msg += csgp.getPrimitiveTypeAsString();
+ msg += "', but the <geometry> only has one <coordinateComponent> child.";
+ fail = true;
+ break;
+ }
+
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 00:04:24 UTC (rev 26176)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 00:23:13 UTC (rev 26177)
@@ -84,6 +84,7 @@
addConstraint(new VConstraintAdjacentDomainsSpatialAdjacentDomainsMustBeAdjacent(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive3DShapes(*this));
+addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive2DShapes(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-01.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="circle1" spatial:primitiveType="circle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-fail-01-02.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="square1" spatial:primitiveType="square"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-01.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="circle1" spatial:primitiveType="circle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-02.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="square1" spatial:primitiveType="square"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-03.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="circle1" spatial:primitiveType="circle"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223151-pass-00-04.xml 2019-11-22 00:23:13 UTC (rev 26177)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="square1" spatial:primitiveType="square"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-22 00:04:26
|
Revision: 26176
http://sourceforge.net/p/sbml/code/26176
Author: luciansmith
Date: 2019-11-22 00:04:24 +0000 (Fri, 22 Nov 2019)
Log Message:
-----------
Add support for spatial rule 23150. Also fix broken 'getPrimitiveTypeAsString' function, and wording of a validation rule.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-07.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-08.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-04.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.cpp 2019-11-22 00:04:24 UTC (rev 26176)
@@ -134,11 +134,10 @@
/*
* Returns the value of the "primitiveType" attribute of this CSGPrimitive.
*/
-const std::string&
+std::string
CSGPrimitive::getPrimitiveTypeAsString() const
{
- static const std::string code_str = PrimitiveKind_toString(mPrimitiveType);
- return code_str;
+ return PrimitiveKind_toString(mPrimitiveType);
}
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.h 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.h 2019-11-22 00:04:24 UTC (rev 26176)
@@ -208,7 +208,7 @@
* @li @c "square"
* @li @c "invalid PrimitiveKind value"
*/
- const std::string& getPrimitiveTypeAsString() const;
+ std::string getPrimitiveTypeAsString() const;
/**
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-22 00:04:24 UTC (rev 26176)
@@ -257,6 +257,7 @@
, SpatialCSGPrimitiveAllowedCoreElements = 1223102
, SpatialCSGPrimitiveAllowedAttributes = 1223103
, SpatialCSGPrimitivePrimitiveTypeMustBePrimitiveKindEnum = 1223104
+, SpatialCSGPrimitive3DShapes = 1223150
, SpatialCSGSetOperatorAllowedCoreAttributes = 1223201
, SpatialCSGSetOperatorAllowedCoreElements = 1223202
, SpatialCSGSetOperatorAllowedAttributes = 1223203
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-22 00:04:24 UTC (rev 26176)
@@ -1383,7 +1383,7 @@
"No two <sampleVolume> ranges may overlap.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "The 'minValue' and 'maxValue' attribute values from one <sampledVolume> may not define a range that overlaps the 'minValue' and 'maxValue' attribute values of a different <sampledVolume> from the same <sampledFieldGeometry>, with the exception that the 'maxValue' of one <sampledVolume> may equal the 'minValue' of another <sampledVolume> from the same SampledFieldGeometry.",
+ "The 'minValue' and 'maxValue' attribute values from one <sampledVolume> may not define a range that overlaps the 'minValue' and 'maxValue' attribute values of a different <sampledVolume> from the same <sampledFieldGeometry>, with the exception that the 'maxValue' of one <sampledVolume> may equal the 'minValue' of another <sampledVolume> from the same <sampledFieldGeometry>.",
{ "L3V1 Spatial V1 Section"
}
},
@@ -2350,6 +2350,16 @@
}
},
+ // 1223150
+ { SpatialCSGPrimitive3DShapes,
+ "Any <csgPrimitive> with a 3D shape must be in 3D geometry.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The 'spatial:primitiveType' attribute of a <csgPrimitive> may have the values 'sphere', 'cube', 'cylinder', or 'cone' only if the <geometry> of the model has exactly three <coordinateComponent> children.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1223201
{ SpatialCSGSetOperatorAllowedCoreAttributes,
"Core attributes allowed on <csgSetOperator>.",
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-22 00:04:24 UTC (rev 26176)
@@ -1345,6 +1345,47 @@
END_CONSTRAINT
+// 1223150
+START_CONSTRAINT(SpatialCSGPrimitive3DShapes, CSGPrimitive, csgp)
+{
+ bool fail = false;
+
+ SpatialModelPlugin *mplug = (SpatialModelPlugin*)(m.getPlugin("spatial"));
+ pre(mplug != NULL);
+ Geometry* geom = mplug->getGeometry();
+ pre(geom != NULL);
+ unsigned int dim = geom->getNumCoordinateComponents();
+ pre(dim < 3);
+ switch(csgp.getPrimitiveType()){
+ case SPATIAL_PRIMITIVEKIND_SPHERE:
+ case SPATIAL_PRIMITIVEKIND_CUBE:
+ case SPATIAL_PRIMITIVEKIND_CYLINDER:
+ case SPATIAL_PRIMITIVEKIND_CONE:
+ msg = "A <csgPrimitive>";
+ if (csgp.isSetId()) {
+ msg += " with the id '" + csgp.getId() + "'";
+ }
+ msg += " has as 'primitiveType' of '";
+ msg += csgp.getPrimitiveTypeAsString() + "', but the <geometry> only has ";
+ if (dim == 1) {
+ msg += "one <coordinateComponent> child.";
+ }
+ else {
+ msg += "two <coordinateComponent> children.";
+ }
+ fail = true;
+ break;
+ case SPATIAL_PRIMITIVEKIND_CIRCLE:
+ case SPATIAL_PRIMITIVEKIND_SQUARE:
+ case SPATIAL_PRIMITIVEKIND_INVALID:
+ break;
+ }
+
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 21:56:13 UTC (rev 26175)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-22 00:04:24 UTC (rev 26176)
@@ -83,6 +83,7 @@
addConstraint(new VConstraintInteriorPointSpatialInteriorPointThreeCoordsIn3DGeometry(*this));
addConstraint(new VConstraintAdjacentDomainsSpatialAdjacentDomainsMustBeAdjacent(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
+addConstraint(new VConstraintCSGPrimitiveSpatialCSGPrimitive3DShapes(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-01.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-02.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-03.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cylinder1" spatial:primitiveType="cylinder"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-04.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-05.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-06.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-07.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-07.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-07.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cylinder1" spatial:primitiveType="cylinder"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-08.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-08.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-fail-01-08.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="2"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-01.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="sphere1" spatial:primitiveType="sphere"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-02.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cube1" spatial:primitiveType="cube"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-03.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cylinder1" spatial:primitiveType="cylinder"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1223150-pass-00-04.xml 2019-11-22 00:04:24 UTC (rev 26176)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_2" spatial:type="cartesianY" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_3" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_4" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_3" spatial:type="cartesianZ" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_5" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_6" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="3"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfDomains>
+ <spatial:domain spatial:domainType="domainType_1" spatial:id="domain_1">
+ <spatial:listOfInteriorPoints>
+ <spatial:interiorPoint spatial:coord1="0" spatial:coord2="0" spatial:coord3="0"/>
+ </spatial:listOfInteriorPoints>
+ </spatial:domain>
+ </spatial:listOfDomains>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:csGeometry spatial:id="csGeometryDefinition_1" spatial:isActive="true">
+ <spatial:listOfCSGObjects>
+ <spatial:csgObject spatial:domainType="domainType_1" spatial:id="csgObject_1" spatial:ordinal="0">
+ <spatial:csgPrimitive spatial:id="cone1" spatial:primitiveType="cone"/>
+ </spatial:csgObject>
+ </spatial:listOfCSGObjects>
+ </spatial:csGeometry>
+ </spatial:listOfGeometryDefinitions>
+ </spatial:geometry>
+ </model>
+</sbml>
+
|
|
From: <luc...@us...> - 2019-11-21 21:56:15
|
Revision: 26175
http://sourceforge.net/p/sbml/code/26175
Author: luciansmith
Date: 2019-11-21 21:56:13 +0000 (Thu, 21 Nov 2019)
Log Message:
-----------
Add support for spatial rule 21754.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-07.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-08.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-09.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-03.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 20:14:41 UTC (rev 26174)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 21:56:13 UTC (rev 26175)
@@ -176,6 +176,7 @@
, SpatialSampledVolumeMinLessThanMax = 1221751
, SpatialSampledVolumeValuesMustDiffer = 1221752
, SpatialSampledVolumeValuesNotInOtherRange = 1221753
+, SpatialSampledVolumeRangesCantOverlap = 1221754
, SpatialAnalyticGeometryAllowedCoreAttributes = 1221801
, SpatialAnalyticGeometryAllowedCoreElements = 1221802
, SpatialAnalyticGeometryAllowedElements = 1221803
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 20:14:41 UTC (rev 26174)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 21:56:13 UTC (rev 26175)
@@ -1378,6 +1378,16 @@
}
},
+ // 1221754
+ { SpatialSampledVolumeRangesCantOverlap,
+ "No two <sampleVolume> ranges may overlap.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "The 'minValue' and 'maxValue' attribute values from one <sampledVolume> may not define a range that overlaps the 'minValue' and 'maxValue' attribute values of a different <sampledVolume> from the same <sampledFieldGeometry>, with the exception that the 'maxValue' of one <sampledVolume> may equal the 'minValue' of another <sampledVolume> from the same SampledFieldGeometry.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1221801
{ SpatialAnalyticGeometryAllowedCoreAttributes,
"Core attributes allowed on <analyticGeometry>.",
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.cpp (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.cpp 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,146 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSampledVolumeRangeOverlapCheck.cpp
+* @brief Ensure that spatial compartment mappings' unit sizes sum to one.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2009-2013 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* Copyright (C) 2006-2008 by the California Institute of Technology,
+* Pasadena, CA, USA
+*
+* Copyright (C) 2002-2005 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. Japan Science and Technology Agency, Japan
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#include "SpatialSampledVolumeRangeOverlapCheck.h"
+#include <sbml/packages/spatial/extension/SpatialParameterPlugin.h>
+#include <sbml/packages/spatial/extension/SpatialModelPlugin.h>
+#include <sbml/packages/spatial/sbml/SampledFieldGeometry.h>
+#include <sbml/packages/spatial/sbml/MixedGeometry.h>
+
+#include <map>
+
+/** @cond doxygenIgnored */
+using namespace std;
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+#ifdef __cplusplus
+
+
+/*
+* Creates a new Constraint with the given constraint id.
+*/
+SpatialSampledVolumeRangeOverlapCheck::SpatialSampledVolumeRangeOverlapCheck(unsigned int id, SpatialValidator & v):
+ TConstraint<Model>(id, v)
+{
+}
+
+/*
+* Destroys this Constraint.
+*/
+SpatialSampledVolumeRangeOverlapCheck::~SpatialSampledVolumeRangeOverlapCheck ()
+{
+}
+
+
+/*
+* Checks that all ids on the following Model objects are unique:
+* event assignments and assignment rules.
+*/
+void
+SpatialSampledVolumeRangeOverlapCheck::check_(const Model& m, const Model&)
+{
+ if (m.getLevel() < 3) {
+ return;
+ }
+ const SpatialModelPlugin* mplug = static_cast<const SpatialModelPlugin*>(m.getPlugin("spatial"));
+ if (mplug == NULL) {
+ return;
+ }
+ const Geometry* geom = mplug->getGeometry();
+ if (geom == NULL) {
+ return;
+ }
+ for (unsigned long g = 0; g < geom->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(geom->getGeometryDefinition(g), m);
+ }
+}
+
+void SpatialSampledVolumeRangeOverlapCheck::checkGeometryDefinition(const GeometryDefinition * gd, const Model& m)
+{
+ if (gd->getTypeCode() == SBML_SPATIAL_SAMPLEDFIELDGEOMETRY) {
+ checkSampledFieldGeometry(static_cast<const SampledFieldGeometry*>(gd), m);
+ }
+ if (gd->getTypeCode() == SBML_SPATIAL_MIXEDGEOMETRY) {
+ const MixedGeometry* mg = static_cast<const MixedGeometry*>(gd);
+ for (unsigned long g = 0; g < mg->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(mg->getGeometryDefinition(g), m);
+ }
+ }
+}
+
+void SpatialSampledVolumeRangeOverlapCheck::checkSampledFieldGeometry(const SampledFieldGeometry * sfg, const Model& m)
+{
+ bool fail = false;
+ map<pair<double, double>, string> ranges;
+ for (unsigned long sv = 0; sv < sfg->getNumSampledVolumes(); sv++) {
+ const SampledVolume* svol = sfg->getSampledVolume(sv);
+ if (svol->isSetMinValue() && svol->isSetMaxValue() && !svol->isSetSampledValue()) {
+ double min2 = svol->getMinValue();
+ double max2 = svol->getMaxValue();
+ string id2 = svol->getId();
+ for (map<pair<double, double>, string>::iterator range = ranges.begin(); range != ranges.end(); range++) {
+ double min = range->first.first;
+ double max = range->first.second;
+ string id = range->second;
+ if ((min2 < max && min2 >= min) || (max2 <= max && max2 > min)
+ || (min < max2 && min >= min2) || (max <= max2 && max > min2)) {
+ stringstream ss_msg;
+ ss_msg << "The first <sampledVolume> ";
+ if (!id.empty())
+ {
+ ss_msg << " with id '" << id << "'";
+ }
+ ss_msg << " has a rage of " << min << " to " << max << ", while a second <sampledVolume>";
+ if (!id2.empty()) {
+ ss_msg << " with id '" << id2 << "'";
+ }
+ ss_msg << " has a range of " << min2 << " to " << max2 << ".";
+ msg = ss_msg.str();
+ logFailure(m);
+ }
+ }
+ ranges.insert(make_pair(make_pair(min2, max2), id2));
+ }
+ }
+}
+
+#endif /* __cplusplus */
+
+LIBSBML_CPP_NAMESPACE_END
+/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,76 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSampledVolumeRangeOverlapCheck.h
+* @brief Ensure that all samples volume values are unique.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright 2011-2012 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#ifndef SpatialSampledVolumeRangeOverlapCheck_h
+#define SpatialSampledVolumeRangeOverlapCheck_h
+
+
+#ifdef __cplusplus
+
+#include <sbml/validator/VConstraint.h>
+#include <sbml/packages/spatial/validator/SpatialValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class GeometryDefinition;
+class SampledFieldGeometry;
+
+class SpatialSampledVolumeRangeOverlapCheck: public TConstraint<Model>
+{
+public:
+
+ /**
+ * Creates a new Constraint with the given constraint id.
+ */
+ SpatialSampledVolumeRangeOverlapCheck (unsigned int id, SpatialValidator& v);
+
+ /**
+ * Destroys this Constraint.
+ */
+ virtual ~SpatialSampledVolumeRangeOverlapCheck ();
+
+
+protected:
+
+ virtual void check_ (const Model& m, const Model& object);
+
+private:
+ virtual void checkGeometryDefinition(const GeometryDefinition* gd, const Model& m);
+ virtual void checkSampledFieldGeometry(const SampledFieldGeometry* sfg, const Model& m);
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* SpatialSampledVolumeRangeOverlapCheck_h */
+/** @endcond */
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 20:14:41 UTC (rev 26174)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 21:56:13 UTC (rev 26175)
@@ -52,6 +52,7 @@
#include <sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h>
#include <sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h>
#include <sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h>
+#include <sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h>
#include <sbml/Species.h>
#endif /* AddingConstraintsToValidator */
@@ -67,6 +68,7 @@
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueBoundaryConditionsCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueSampledVolumeValueCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialSampledVolumeValueNotInRangeCheck);
+EXTERN_CONSTRAINT(ErrorEnumValue, SpatialSampledVolumeRangeOverlapCheck);
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 20:14:41 UTC (rev 26174)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 21:56:13 UTC (rev 26175)
@@ -45,6 +45,7 @@
#include "sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h"
#include "sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h"
#include "sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h"
+#include "sbml/packages/spatial/validator/SpatialSampledVolumeRangeOverlapCheck.h"
//Constraints declared in SpatialConsistencyConstraints.cpp
addConstraint(new VConstraintDomainSpatialDomainDomainTypeMustBeDomainType(*this));
@@ -91,6 +92,7 @@
addConstraint(new SpatialUniqueBoundaryConditionsCheck(SpatialBoundaryConditionsMustBeUnique, *this));
addConstraint(new SpatialUniqueSampledVolumeValueCheck(SpatialSampledVolumeValuesMustDiffer, *this));
addConstraint(new SpatialSampledVolumeValueNotInRangeCheck(SpatialSampledVolumeValuesNotInOtherRange, *this));
+addConstraint(new SpatialSampledVolumeRangeOverlapCheck(SpatialSampledVolumeRangesCantOverlap, *this));
/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-01.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.6"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0.5" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-02.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="0.6"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-03.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0.2" spatial:maxValue="0.3"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-04.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.2" spatial:maxValue="0.3"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-05.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-06.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-06.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-07.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-07.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-07.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-08.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-08.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-08.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-09.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-09.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-fail-01-09.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0.5" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-01.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.6" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-02.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0.5" spatial:maxValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221754-pass-00-03.xml 2019-11-21 21:56:13 UTC (rev 26175)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:minValue="0" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
|
|
From: <luc...@us...> - 2019-11-21 20:14:43
|
Revision: 26174
http://sourceforge.net/p/sbml/code/26174
Author: luciansmith
Date: 2019-11-21 20:14:41 +0000 (Thu, 21 Nov 2019)
Log Message:
-----------
Remove signed/unsigned warning.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp 2019-11-21 20:14:05 UTC (rev 26173)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.cpp 2019-11-21 20:14:41 UTC (rev 26174)
@@ -2083,7 +2083,7 @@
if (mCompression == SPATIAL_COMPRESSIONKIND_DEFLATED)
{
char* csamples = (char*)malloc(sizeof(char) * length);
- for (int i = 0; i < length; ++i)
+ for (unsigned int i = 0; i < length; ++i)
csamples[i] = (char)samples[i];
SampledField::uncompress_data(csamples, length, mUncompressedSamples, mUncompressedLength);
free(csamples);
@@ -2112,7 +2112,7 @@
return LIBSBML_OPERATION_SUCCESS;
char* csamples = (char*)malloc(sizeof(char) * length);
- for (int i = 0; i < length; ++i)
+ for (unsigned int i = 0; i < length; ++i)
csamples[i] = (char)samples[i];
mSamples = SampledField::uncompress_data(csamples, length);
|
|
From: <luc...@us...> - 2019-11-21 20:14:07
|
Revision: 26173
http://sourceforge.net/p/sbml/code/26173
Author: luciansmith
Date: 2019-11-21 20:14:05 +0000 (Thu, 21 Nov 2019)
Log Message:
-----------
Add support for spatial rule 21753.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-04.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 19:15:49 UTC (rev 26172)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 20:14:05 UTC (rev 26173)
@@ -175,6 +175,7 @@
, SpatialSampledVolumeSampledValueMinMax = 1221750
, SpatialSampledVolumeMinLessThanMax = 1221751
, SpatialSampledVolumeValuesMustDiffer = 1221752
+, SpatialSampledVolumeValuesNotInOtherRange = 1221753
, SpatialAnalyticGeometryAllowedCoreAttributes = 1221801
, SpatialAnalyticGeometryAllowedCoreElements = 1221802
, SpatialAnalyticGeometryAllowedElements = 1221803
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 19:15:49 UTC (rev 26172)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 20:14:05 UTC (rev 26173)
@@ -1368,6 +1368,16 @@
}
},
+ // 1221753
+ { SpatialSampledVolumeValuesNotInOtherRange,
+ "Every <sampleVolume> 'sampledValue' must not fall in another's range.",
+ LIBSBML_CAT_GENERAL_CONSISTENCY,
+ LIBSBML_SEV_ERROR,
+ "A 'sampledValue' from one <sampledVolume> may not be less than the value of the attribute 'maxValue' and greater than or equal to the value of the attribute 'minValue' of a different <sampledVolume> from the same <sampledFieldGeometry>.",
+ { "L3V1 Spatial V1 Section"
+ }
+ },
+
// 1221801
{ SpatialAnalyticGeometryAllowedCoreAttributes,
"Core attributes allowed on <analyticGeometry>.",
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.cpp (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.cpp 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,151 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSampledVolumeValueNotInRangeCheck.cpp
+* @brief Ensure that spatial compartment mappings' unit sizes sum to one.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2009-2013 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* Copyright (C) 2006-2008 by the California Institute of Technology,
+* Pasadena, CA, USA
+*
+* Copyright (C) 2002-2005 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. Japan Science and Technology Agency, Japan
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#include "SpatialSampledVolumeValueNotInRangeCheck.h"
+#include <sbml/packages/spatial/extension/SpatialParameterPlugin.h>
+#include <sbml/packages/spatial/extension/SpatialModelPlugin.h>
+#include <sbml/packages/spatial/sbml/SampledFieldGeometry.h>
+#include <sbml/packages/spatial/sbml/MixedGeometry.h>
+
+#include <map>
+
+/** @cond doxygenIgnored */
+using namespace std;
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+#ifdef __cplusplus
+
+
+/*
+* Creates a new Constraint with the given constraint id.
+*/
+SpatialSampledVolumeValueNotInRangeCheck::SpatialSampledVolumeValueNotInRangeCheck(unsigned int id, SpatialValidator & v):
+ TConstraint<Model>(id, v)
+{
+}
+
+/*
+* Destroys this Constraint.
+*/
+SpatialSampledVolumeValueNotInRangeCheck::~SpatialSampledVolumeValueNotInRangeCheck ()
+{
+}
+
+
+/*
+* Checks that all ids on the following Model objects are unique:
+* event assignments and assignment rules.
+*/
+void
+SpatialSampledVolumeValueNotInRangeCheck::check_(const Model& m, const Model&)
+{
+ if (m.getLevel() < 3) {
+ return;
+ }
+ const SpatialModelPlugin* mplug = static_cast<const SpatialModelPlugin*>(m.getPlugin("spatial"));
+ if (mplug == NULL) {
+ return;
+ }
+ const Geometry* geom = mplug->getGeometry();
+ if (geom == NULL) {
+ return;
+ }
+ for (unsigned long g = 0; g < geom->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(geom->getGeometryDefinition(g), m);
+ }
+}
+
+void SpatialSampledVolumeValueNotInRangeCheck::checkGeometryDefinition(const GeometryDefinition * gd, const Model& m)
+{
+ if (gd->getTypeCode() == SBML_SPATIAL_SAMPLEDFIELDGEOMETRY) {
+ checkSampledFieldGeometry(static_cast<const SampledFieldGeometry*>(gd), m);
+ }
+ if (gd->getTypeCode() == SBML_SPATIAL_MIXEDGEOMETRY) {
+ const MixedGeometry* mg = static_cast<const MixedGeometry*>(gd);
+ for (unsigned long g = 0; g < mg->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(mg->getGeometryDefinition(g), m);
+ }
+ }
+}
+
+void SpatialSampledVolumeValueNotInRangeCheck::checkSampledFieldGeometry(const SampledFieldGeometry * sfg, const Model& m)
+{
+ bool fail = false;
+ map<double, string> values;
+ for (unsigned long sv = 0; sv < sfg->getNumSampledVolumes(); sv++) {
+ const SampledVolume* svol = sfg->getSampledVolume(sv);
+ if (svol->isSetSampledValue()) {
+ values.insert(make_pair(svol->getSampledValue(), svol->getId()));
+ }
+ }
+ for (unsigned long sv = 0; sv < sfg->getNumSampledVolumes(); sv++) {
+ const SampledVolume* svol = sfg->getSampledVolume(sv);
+ if (svol->isSetMinValue() && svol->isSetMaxValue() && !svol->isSetSampledValue()) {
+ double min = svol->getMinValue();
+ double max = svol->getMaxValue();
+ for (map<double, string>::iterator valpair = values.begin(); valpair != values.end(); valpair++) {
+ double val = valpair->first;
+ string val_id = valpair->second;
+ if (val < max && val >= min) {
+ stringstream ss_msg;
+ ss_msg << "A <sampledVolume>";
+ if (!val_id.empty())
+ {
+ ss_msg << " with id '" << val_id << "'";
+ }
+ ss_msg << " has a 'spatial:sampledValue' attribute value of '";
+ ss_msg << val;
+ ss_msg << "', which is within the range (" << min << " to " << max << ") of a different <sampledVolume>";
+ if (svol->isSetId()) {
+ ss_msg << " with id '" << svol->getId() << "'";
+ }
+ ss_msg << ".";
+ msg = ss_msg.str();
+ logFailure(m);
+
+ }
+ }
+ }
+ }
+}
+
+#endif /* __cplusplus */
+
+LIBSBML_CPP_NAMESPACE_END
+/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,76 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialSampledVolumeValueNotInRangeCheck.h
+* @brief Ensure that all samples volume values are unique.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright 2011-2012 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#ifndef SpatialSampledVolumeValueNotInRangeCheck_h
+#define SpatialSampledVolumeValueNotInRangeCheck_h
+
+
+#ifdef __cplusplus
+
+#include <sbml/validator/VConstraint.h>
+#include <sbml/packages/spatial/validator/SpatialValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class GeometryDefinition;
+class SampledFieldGeometry;
+
+class SpatialSampledVolumeValueNotInRangeCheck: public TConstraint<Model>
+{
+public:
+
+ /**
+ * Creates a new Constraint with the given constraint id.
+ */
+ SpatialSampledVolumeValueNotInRangeCheck (unsigned int id, SpatialValidator& v);
+
+ /**
+ * Destroys this Constraint.
+ */
+ virtual ~SpatialSampledVolumeValueNotInRangeCheck ();
+
+
+protected:
+
+ virtual void check_ (const Model& m, const Model& object);
+
+private:
+ virtual void checkGeometryDefinition(const GeometryDefinition* gd, const Model& m);
+ virtual void checkSampledFieldGeometry(const SampledFieldGeometry* sfg, const Model& m);
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* SpatialSampledVolumeValueNotInRangeCheck_h */
+/** @endcond */
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 19:15:49 UTC (rev 26172)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 20:14:05 UTC (rev 26173)
@@ -51,6 +51,7 @@
#include <sbml/packages/spatial/validator/SpatialUniqueAdvectionCoefficientsCheck.h>
#include <sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h>
#include <sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h>
+#include <sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h>
#include <sbml/Species.h>
#endif /* AddingConstraintsToValidator */
@@ -65,6 +66,7 @@
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueAdvectionCoefficientsCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueBoundaryConditionsCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueSampledVolumeValueCheck);
+EXTERN_CONSTRAINT(ErrorEnumValue, SpatialSampledVolumeValueNotInRangeCheck);
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 19:15:49 UTC (rev 26172)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 20:14:05 UTC (rev 26173)
@@ -44,6 +44,7 @@
#include "sbml/packages/spatial/validator/SpatialUniqueAdvectionCoefficientsCheck.h"
#include "sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h"
#include "sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h"
+#include "sbml/packages/spatial/validator/SpatialSampledVolumeValueNotInRangeCheck.h"
//Constraints declared in SpatialConsistencyConstraints.cpp
addConstraint(new VConstraintDomainSpatialDomainDomainTypeMustBeDomainType(*this));
@@ -89,6 +90,7 @@
addConstraint(new SpatialUniqueAdvectionCoefficientsCheck(SpatialAdvectionCoefficientsMustBeUnique, *this));
addConstraint(new SpatialUniqueBoundaryConditionsCheck(SpatialBoundaryConditionsMustBeUnique, *this));
addConstraint(new SpatialUniqueSampledVolumeValueCheck(SpatialSampledVolumeValuesMustDiffer, *this));
+addConstraint(new SpatialSampledVolumeValueNotInRangeCheck(SpatialSampledVolumeValuesNotInOtherRange, *this));
/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0.25"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-02.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0.25"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="0.3"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-02-03.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0.25"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0.3"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:minValue="0" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_1" spatial:isActive="true" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:minValue="0" spatial:maxValue="0.5"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-03.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-04.xml 2019-11-21 20:14:05 UTC (rev 26173)
@@ -0,0 +1,31 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_1" spatial:isActive="true" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="0.25"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
|
|
From: <luc...@us...> - 2019-11-21 19:15:51
|
Revision: 26172
http://sourceforge.net/p/sbml/code/26172
Author: luciansmith
Date: 2019-11-21 19:15:49 +0000 (Thu, 21 Nov 2019)
Log Message:
-----------
Add support for spatial rule 21752.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.cpp (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.cpp 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,143 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialUniqueSampledVolumeValueCheck.cpp
+* @brief Ensure that spatial compartment mappings' unit sizes sum to one.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2009-2013 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* Copyright (C) 2006-2008 by the California Institute of Technology,
+* Pasadena, CA, USA
+*
+* Copyright (C) 2002-2005 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. Japan Science and Technology Agency, Japan
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#include "SpatialUniqueSampledVolumeValueCheck.h"
+#include <sbml/packages/spatial/extension/SpatialParameterPlugin.h>
+#include <sbml/packages/spatial/extension/SpatialModelPlugin.h>
+#include <sbml/packages/spatial/sbml/SampledFieldGeometry.h>
+#include <sbml/packages/spatial/sbml/MixedGeometry.h>
+
+#include <map>
+
+/** @cond doxygenIgnored */
+using namespace std;
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+#ifdef __cplusplus
+
+
+/*
+* Creates a new Constraint with the given constraint id.
+*/
+SpatialUniqueSampledVolumeValueCheck::SpatialUniqueSampledVolumeValueCheck(unsigned int id, SpatialValidator & v):
+ TConstraint<Model>(id, v)
+{
+}
+
+/*
+* Destroys this Constraint.
+*/
+SpatialUniqueSampledVolumeValueCheck::~SpatialUniqueSampledVolumeValueCheck ()
+{
+}
+
+
+/*
+* Checks that all ids on the following Model objects are unique:
+* event assignments and assignment rules.
+*/
+void
+SpatialUniqueSampledVolumeValueCheck::check_(const Model& m, const Model&)
+{
+ if (m.getLevel() < 3) {
+ return;
+ }
+ const SpatialModelPlugin* mplug = static_cast<const SpatialModelPlugin*>(m.getPlugin("spatial"));
+ if (mplug == NULL) {
+ return;
+ }
+ const Geometry* geom = mplug->getGeometry();
+ if (geom == NULL) {
+ return;
+ }
+ for (unsigned long g = 0; g < geom->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(geom->getGeometryDefinition(g), m);
+ }
+}
+
+void SpatialUniqueSampledVolumeValueCheck::checkGeometryDefinition(const GeometryDefinition * gd, const Model& m)
+{
+ if (gd->getTypeCode() == SBML_SPATIAL_SAMPLEDFIELDGEOMETRY) {
+ checkSampledFieldGeometry(static_cast<const SampledFieldGeometry*>(gd), m);
+ }
+ if (gd->getTypeCode() == SBML_SPATIAL_MIXEDGEOMETRY) {
+ const MixedGeometry* mg = static_cast<const MixedGeometry*>(gd);
+ for (unsigned long g = 0; g < mg->getNumGeometryDefinitions(); g++) {
+ checkGeometryDefinition(mg->getGeometryDefinition(g), m);
+ }
+ }
+}
+
+void SpatialUniqueSampledVolumeValueCheck::checkSampledFieldGeometry(const SampledFieldGeometry * sfg, const Model& m)
+{
+ bool fail = false;
+ map<double, string> values;
+ for (unsigned long sv = 0; sv < sfg->getNumSampledVolumes(); sv++) {
+ const SampledVolume* svol = sfg->getSampledVolume(sv);
+ if (svol->isSetSampledValue()) {
+ double val = svol->getSampledValue();
+ if (values.find(val) != values.end()) {
+ stringstream ss_msg;
+ ss_msg << "A <sampledVolume>";
+ if (svol->isSetId())
+ {
+ ss_msg << " with id '" << svol->getId() << "'";
+ }
+ ss_msg << " has a 'spatial:sampledValue' attribute value of '";
+ ss_msg << svol->getSampledValue();
+ ss_msg << "', which is the sampledValue of a different <sampledVolume>";
+ string svid = values[val];
+ if (!svid.empty()) {
+ ss_msg << " with id '" << svid << "'";
+ }
+ ss_msg << ".";
+ msg = ss_msg.str();
+ logFailure(m);
+ }
+ else {
+ values.insert(make_pair(val, svol->getId()));
+ }
+ }
+ }
+}
+
+#endif /* __cplusplus */
+
+LIBSBML_CPP_NAMESPACE_END
+/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,76 @@
+/**
+* @cond doxygenLibsbmlInternal
+*
+* @file SpatialUniqueSampledVolumeValueCheck.h
+* @brief Ensure that all samples volume values are unique.
+* @author Sarah Keating, Lucian Smith
+*
+* <!--------------------------------------------------------------------------
+* This file is part of libSBML. Please visit http://sbml.org for more
+* information about SBML, and the latest version of libSBML.
+*
+* Copyright (C) 2019 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright (C) 2013-2018 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+* 3. University of Heidelberg, Heidelberg, Germany
+*
+* Copyright 2011-2012 jointly by the following organizations:
+* 1. California Institute of Technology, Pasadena, CA, USA
+* 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+*
+* This library is free software; you can redistribute it and/or modify it
+* under the terms of the GNU Lesser General Public License as published by
+* the Free Software Foundation. A copy of the license agreement is provided
+* in the file named "LICENSE.txt" included with this software distribution
+* and also available online as http://sbml.org/software/libsbml/license.html
+* ---------------------------------------------------------------------- -->*/
+
+#ifndef SpatialUniqueSampledVolumeValueCheck_h
+#define SpatialUniqueSampledVolumeValueCheck_h
+
+
+#ifdef __cplusplus
+
+#include <sbml/validator/VConstraint.h>
+#include <sbml/packages/spatial/validator/SpatialValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+class GeometryDefinition;
+class SampledFieldGeometry;
+
+class SpatialUniqueSampledVolumeValueCheck: public TConstraint<Model>
+{
+public:
+
+ /**
+ * Creates a new Constraint with the given constraint id.
+ */
+ SpatialUniqueSampledVolumeValueCheck (unsigned int id, SpatialValidator& v);
+
+ /**
+ * Destroys this Constraint.
+ */
+ virtual ~SpatialUniqueSampledVolumeValueCheck ();
+
+
+protected:
+
+ virtual void check_ (const Model& m, const Model& object);
+
+private:
+ virtual void checkGeometryDefinition(const GeometryDefinition* gd, const Model& m);
+ virtual void checkSampledFieldGeometry(const SampledFieldGeometry* sfg, const Model& m);
+
+};
+
+LIBSBML_CPP_NAMESPACE_END
+
+#endif /* __cplusplus */
+#endif /* SpatialUniqueSampledVolumeValueCheck_h */
+/** @endcond */
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 17:41:01 UTC (rev 26171)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 19:15:49 UTC (rev 26172)
@@ -50,6 +50,7 @@
#include <sbml/packages/spatial/validator/SpatialUniqueDiffusionCoefficientsCheck.h>
#include <sbml/packages/spatial/validator/SpatialUniqueAdvectionCoefficientsCheck.h>
#include <sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h>
+#include <sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h>
#include <sbml/Species.h>
#endif /* AddingConstraintsToValidator */
@@ -63,6 +64,7 @@
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueDiffusionCoefficientsCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueAdvectionCoefficientsCheck);
EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueBoundaryConditionsCheck);
+EXTERN_CONSTRAINT(ErrorEnumValue, SpatialUniqueSampledVolumeValueCheck);
@@ -1339,46 +1341,6 @@
END_CONSTRAINT
-// 1221751
-START_CONSTRAINT(SpatialSampledVolumeValuesMustDiffer, SampledFieldGeometry, sfg)
-{
- bool fail = false;
- set<double> values;
- msg = "";
- for (unsigned long sv = 0; sv < sfg.getNumSampledVolumes(); sv++) {
- const SampledVolume* svol = sfg.getSampledVolume(sv);
- if (svol->isSetSampledValue()) {
- double val = svol->getSampledValue();
- if (values.find(val) != values.end()) {
- stringstream ss_msg;
- if (!msg.empty()) {
- ss_msg << endl << "Also: a";
- }
- else {
- ss_msg << "A";
- }
- ss_msg << " <sampledVolume>";
- if (svol->isSetId())
- {
- ss_msg << " with id '" << svol->getId() << "'";
- }
- ss_msg << " has a 'spatial:sampledValue' attribute of '";
- ss_msg << svol->getSampledValue();
- ss_msg << "', which another <sampledVolume> already has.";
- msg = ss_msg.str();
- fail = true;
-
- }
- values.insert(val);
- }
- }
-
-
- inv(fail == false);
-}
-END_CONSTRAINT
-
-
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 17:41:01 UTC (rev 26171)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 19:15:49 UTC (rev 26172)
@@ -43,6 +43,7 @@
#include "sbml/packages/spatial/validator/SpatialUniqueDiffusionCoefficientsCheck.h"
#include "sbml/packages/spatial/validator/SpatialUniqueAdvectionCoefficientsCheck.h"
#include "sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.h"
+#include "sbml/packages/spatial/validator/SpatialUniqueSampledVolumeValueCheck.h"
//Constraints declared in SpatialConsistencyConstraints.cpp
addConstraint(new VConstraintDomainSpatialDomainDomainTypeMustBeDomainType(*this));
@@ -80,7 +81,6 @@
addConstraint(new VConstraintInteriorPointSpatialInteriorPointThreeCoordsIn3DGeometry(*this));
addConstraint(new VConstraintAdjacentDomainsSpatialAdjacentDomainsMustBeAdjacent(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
-addConstraint(new VConstraintSampledFieldGeometrySpatialSampledVolumeValuesMustDiffer(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
@@ -88,6 +88,7 @@
addConstraint(new SpatialUniqueDiffusionCoefficientsCheck(SpatialNoDiffusionCoefficientOverlap, *this));
addConstraint(new SpatialUniqueAdvectionCoefficientsCheck(SpatialAdvectionCoefficientsMustBeUnique, *this));
addConstraint(new SpatialUniqueBoundaryConditionsCheck(SpatialBoundaryConditionsMustBeUnique, *this));
+addConstraint(new SpatialUniqueSampledVolumeValueCheck(SpatialSampledVolumeValuesMustDiffer, *this));
/** @endcond */
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-02.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-03.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-04.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_1" spatial:isActive="true" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="1"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-05.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-02-05.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_1" spatial:isActive="true" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Added: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml 2019-11-21 19:15:49 UTC (rev 26172)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_1" spatial:isActive="true" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_2" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_3" spatial:sampledValue="0"/>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_4" spatial:sampledValue="1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
|
|
From: <luc...@us...> - 2019-11-21 17:41:06
|
Revision: 26171
http://sourceforge.net/p/sbml/code/26171
Author: luciansmith
Date: 2019-11-21 17:41:01 +0000 (Thu, 21 Nov 2019)
Log Message:
-----------
Collapse spatial rules 21750-21752 into a single rule; add a new 21751.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
Added Paths:
-----------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-05.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-06.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-02.xml
Removed Paths:
-------------
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLError.h 2019-11-21 17:41:01 UTC (rev 26171)
@@ -172,10 +172,9 @@
, SpatialSampledVolumeSampledValueMustBeDouble = 1221706
, SpatialSampledVolumeMinValueMustBeDouble = 1221707
, SpatialSampledVolumeMaxValueMustBeDouble = 1221708
-, SpatialSampledVolumeNeedsMaxWithMin = 1221750
-, SpatialSampledVolumeNeedsMinWithMax = 1221751
-, SpatialSampledVolumeSampledValueMinMax = 1221752
-, SpatialSampledVolumeMinLessThanMax = 1221753
+, SpatialSampledVolumeSampledValueMinMax = 1221750
+, SpatialSampledVolumeMinLessThanMax = 1221751
+, SpatialSampledVolumeValuesMustDiffer = 1221752
, SpatialAnalyticGeometryAllowedCoreAttributes = 1221801
, SpatialAnalyticGeometryAllowedCoreElements = 1221802
, SpatialAnalyticGeometryAllowedElements = 1221803
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1339,45 +1339,35 @@
},
// 1221750
- { SpatialSampledVolumeNeedsMaxWithMin,
- "A 'minValue' attribute goes with the 'maxValue' attribute.",
+ { SpatialSampledVolumeSampledValueMinMax,
+ "Every <sampleVolume> must have a 'sampledValue' attribute or the 'min' and 'max' attributes.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <sampledVolume> with a defined 'spatial:minValue' attribute must also define the 'spatial:maxValue' attribute.",
+ "A <sampledVolume> must either define the attribute 'spatial:sampledValue' or must define both the 'spatial:minValue' and 'spatial:maxValue' attributes, but may not define any other combination of those three attributes.",
{ "L3V1 Spatial V1 Section"
}
},
// 1221751
- { SpatialSampledVolumeNeedsMinWithMax,
- "A 'maxValue' attribute goes with the 'minValue' attribute.",
+ { SpatialSampledVolumeMinLessThanMax,
+ "A <sampleVolume> 'minValue' must be less than or equal to the 'maxValue'.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <sampledVolume> with a defined 'spatial:maxValue' attribute must also define the 'spatial:minValue' attribute.",
+ "The attribute 'minValue' of a <sampledVolume> must have a value less than or equal to the value of the 'maxValue' attribute of that <sampledVolume>.",
{ "L3V1 Spatial V1 Section"
}
},
// 1221752
- { SpatialSampledVolumeSampledValueMinMax,
- "Every <sampleVolume> must have a 'sampledValue' attribute or the 'min' and 'max' attributes.",
+ { SpatialSampledVolumeValuesMustDiffer,
+ "Every <sampleVolume> 'sampledValue' must be unique.",
LIBSBML_CAT_GENERAL_CONSISTENCY,
LIBSBML_SEV_ERROR,
- "A <sampledVolume> must either define the attribute 'spatial:sampledValue' or must define both the 'spatial:minValue' and 'spatial:maxValue' attributes, but may not define any other combination of those three attributes.",
+ "A 'sampledValue' from one <sampledVolume> may not be the same as a different 'sampledValue' from another <sampledVolume> from the same <sampledFieldGeometry>.",
{ "L3V1 Spatial V1 Section"
}
},
- // 1221753
- { SpatialSampledVolumeMinLessThanMax,
- "A <sampleVolume> 'minValue' must be less than or equal to the 'maxValue'.",
- LIBSBML_CAT_GENERAL_CONSISTENCY,
- LIBSBML_SEV_ERROR,
- "The attribute 'minValue' of a <sampledVolume> must have a value less than or equal to the value of the 'maxValue' attribute of that <sampledVolume>.",
- { "L3V1 Spatial V1 Section"
- }
- },
-
// 1221801
{ SpatialAnalyticGeometryAllowedCoreAttributes,
"Core attributes allowed on <analyticGeometry>.",
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraints.cpp 2019-11-21 17:41:01 UTC (rev 26171)
@@ -38,6 +38,7 @@
* ------------------------------------------------------------------------ -->
*/
#ifndef AddingConstraintsToValidator
+#include <set>
#include <sbml/validator/VConstraint.h>
@@ -538,7 +539,7 @@
// 1221750
-START_CONSTRAINT(SpatialSampledVolumeNeedsMaxWithMin, SampledVolume, svol)
+START_CONSTRAINT(SpatialSampledVolumeSampledValueMinMax, SampledVolume, svol)
{
bool fail = false;
if (svol.isSetMinValue() && !svol.isSetMaxValue() && !svol.isSetSampledValue()) {
@@ -553,16 +554,7 @@
msg = ss_msg.str();
}
- inv(fail == false);
-}
-END_CONSTRAINT
-
-
-// 1221751
-START_CONSTRAINT(SpatialSampledVolumeNeedsMinWithMax, SampledVolume, svol)
-{
- bool fail = false;
- if (svol.isSetMaxValue() && !svol.isSetMinValue() && !svol.isSetSampledValue()) {
+ else if (svol.isSetMaxValue() && !svol.isSetMinValue() && !svol.isSetSampledValue()) {
fail = true;
stringstream ss_msg;
ss_msg << "A SampledVolume";
@@ -574,16 +566,7 @@
msg = ss_msg.str();
}
- inv(fail == false);
-}
-END_CONSTRAINT
-
-
-// 1221752
-START_CONSTRAINT(SpatialSampledVolumeSampledValueMinMax, SampledVolume, svol)
-{
- bool fail = false;
- if (svol.isSetMaxValue() && svol.isSetMinValue() && svol.isSetSampledValue()) {
+ else if (svol.isSetMaxValue() && svol.isSetMinValue() && svol.isSetSampledValue()) {
fail = true;
stringstream ss_msg;
ss_msg << "A SampledVolume";
@@ -1345,7 +1328,7 @@
ss_msg << svol.getMaxValue();
ss_msg << "', which is less than '";
ss_msg << svol.getMinValue();
- ss_msg << "', the value of the attribute 'spatial:minValue'";
+ ss_msg << "', the value of the attribute 'spatial:minValue'.";
msg = ss_msg.str();
fail = true;
@@ -1356,6 +1339,46 @@
END_CONSTRAINT
+// 1221751
+START_CONSTRAINT(SpatialSampledVolumeValuesMustDiffer, SampledFieldGeometry, sfg)
+{
+ bool fail = false;
+ set<double> values;
+ msg = "";
+ for (unsigned long sv = 0; sv < sfg.getNumSampledVolumes(); sv++) {
+ const SampledVolume* svol = sfg.getSampledVolume(sv);
+ if (svol->isSetSampledValue()) {
+ double val = svol->getSampledValue();
+ if (values.find(val) != values.end()) {
+ stringstream ss_msg;
+ if (!msg.empty()) {
+ ss_msg << endl << "Also: a";
+ }
+ else {
+ ss_msg << "A";
+ }
+ ss_msg << " <sampledVolume>";
+ if (svol->isSetId())
+ {
+ ss_msg << " with id '" << svol->getId() << "'";
+ }
+ ss_msg << " has a 'spatial:sampledValue' attribute of '";
+ ss_msg << svol->getSampledValue();
+ ss_msg << "', which another <sampledVolume> already has.";
+ msg = ss_msg.str();
+ fail = true;
+
+ }
+ values.insert(val);
+ }
+ }
+
+
+ inv(fail == false);
+}
+END_CONSTRAINT
+
+
// 122__
//START_CONSTRAINT(Spatial, Class, class)
//{
Modified: branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/constraints/SpatialConsistencyConstraintsDeclared.cxx 2019-11-21 17:41:01 UTC (rev 26171)
@@ -59,8 +59,6 @@
addConstraint(new VConstraintSampledFieldSpatialSampledFieldOneSampleIn1DGeometry(*this));
addConstraint(new VConstraintSampledFieldSpatialSampledFieldTwoSamplesIn2DGeometry(*this));
addConstraint(new VConstraintSampledFieldSpatialSampledFieldThreeSamplesIn3DGeometry(*this));
-addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNeedsMaxWithMin(*this));
-addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeNeedsMinWithMax(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeSampledValueMinMax(*this));
addConstraint(new VConstraintCompartmentMappingSpatialCompartmentMappingUnitSizeMustBeFraction(*this));
addConstraint(new VConstraintSpeciesSpatialCompartmentsMustHaveCompartmentMapping(*this));
@@ -82,6 +80,7 @@
addConstraint(new VConstraintInteriorPointSpatialInteriorPointThreeCoordsIn3DGeometry(*this));
addConstraint(new VConstraintAdjacentDomainsSpatialAdjacentDomainsMustBeAdjacent(*this));
addConstraint(new VConstraintSampledVolumeSpatialSampledVolumeMinLessThanMax(*this));
+addConstraint(new VConstraintSampledFieldGeometrySpatialSampledVolumeValuesMustDiffer(*this));
//Constraints defined in their own class ('global constraints')
addConstraint(new SpatialCompartmentMappingUnitSizesCheck(SpatialCompartmentMappingUnitSizesSum, *this));
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-02.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-02.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-03.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-03.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-03.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-04.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-04.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-04.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-05.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-05.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-05.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0.5" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-06.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-06.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-fail-01-06.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-02.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221750-pass-00-02.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0.5"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-fail-01-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="0"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Copied: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-02.xml (from rev 26170, branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-02.xml)
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-02.xml (rev 0)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221751-pass-00-02.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
+ <model>
+ <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
+ <spatial:listOfCoordinateComponents>
+ <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
+ <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
+ <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
+ </spatial:coordinateComponent>
+ </spatial:listOfCoordinateComponents>
+ <spatial:listOfDomainTypes>
+ <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
+ </spatial:listOfDomainTypes>
+ <spatial:listOfGeometryDefinitions>
+ <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
+ <spatial:listOfSampledVolumes>
+ <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="0.5"/>
+ </spatial:listOfSampledVolumes>
+ </spatial:sampledFieldGeometry>
+ </spatial:listOfGeometryDefinitions>
+ <spatial:listOfSampledFields>
+ <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
+ </spatial:listOfSampledFields>
+ </spatial:geometry>
+ </model>
+</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-02.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-03.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:maxValue="0.5" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-fail-01-04.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221752-pass-00-02.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:sampledValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-fail-01-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0.5" spatial:maxValue="0"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>
- </spatial:geometry>
- </model>
-</sbml>
Deleted: branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml 2019-11-21 00:51:29 UTC (rev 26170)
+++ branches/libsbml-experimental/src/sbml/packages/spatial/validator/test/test-data/general-constraints/1221753-pass-00-01.xml 2019-11-21 17:41:01 UTC (rev 26171)
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml level="3" spatial:required="true" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1">
- <model>
- <spatial:geometry spatial:coordinateSystem="cartesian" spatial:id="geometry_1">
- <spatial:listOfCoordinateComponents>
- <spatial:coordinateComponent spatial:id="coordinateComponent_1" spatial:type="cartesianX" spatial:unit="dimensionless">
- <spatial:boundaryMin spatial:id="boundary_1" spatial:value="0"/>
- <spatial:boundaryMax spatial:id="boundary_2" spatial:value="1"/>
- </spatial:coordinateComponent>
- </spatial:listOfCoordinateComponents>
- <spatial:listOfDomainTypes>
- <spatial:domainType spatial:id="domainType_1" spatial:spatialDimensions="1"/>
- </spatial:listOfDomainTypes>
- <spatial:listOfGeometryDefinitions>
- <spatial:sampledFieldGeometry spatial:id="geometryDefinition_2" spatial:isActive="false" spatial:sampledField="sampledField_1">
- <spatial:listOfSampledVolumes>
- <spatial:sampledVolume spatial:domainType="domainType_1" spatial:id="sampledVolume_1" spatial:minValue="0" spatial:maxValue="0.5"/>
- </spatial:listOfSampledVolumes>
- </spatial:sampledFieldGeometry>
- </spatial:listOfGeometryDefinitions>
- <spatial:listOfSampledFields>
- <spatial:sampledField spatial:compression="uncompressed" spatial:dataType="double" spatial:id="sampledField_1" spatial:interpolationType="nearestNeighbor" spatial:numSamples1="3" spatial:samplesLength="3">0 0 1</spatial:sampledField>
- </spatial:listOfSampledFields>...
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