From: <nik...@us...> - 2015-04-30 15:40:39
|
Revision: 2266 http://sourceforge.net/p/jsbml/code/2266 Author: niko-rodrigue Date: 2015-04-30 15:40:25 +0000 (Thu, 30 Apr 2015) Log Message: ----------- added the svn:keywords property to everything Modified Paths: -------------- branches/astnode2-merging-alternate/NEWS.txt branches/astnode2-merging-alternate/README.txt branches/astnode2-merging-alternate/build.xml branches/astnode2-merging-alternate/core/README branches/astnode2-merging-alternate/core/build.xml branches/astnode2-merging-alternate/core/doc/publications/Bioinformatics2011ApplicationNote/crop.sty branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/celldesigner/SimpleCellDesignerPlugin.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/celldesigner/SimpleCellDesignerPluginAction.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/celldesigner/cdplugin_example.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/demo/JSBMLexample.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/demo/package-info.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/gui/JSBMLvisualizer.java branches/astnode2-merging-alternate/core/doc/user_guide/src/org/sbml/jsbml/xml/libsbml/libSBMLio_example.java branches/astnode2-merging-alternate/core/licenses/lib-licenses/README.txt branches/astnode2-merging-alternate/core/pom.xml branches/astnode2-merging-alternate/core/resources/log4j.properties branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/ASTNodeTokens.xml branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/Alias2SBO.cfg branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/HTML_CharEncodingTable.txt branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/SBMLCoreElements.xml branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/SBMLElementsLevel1Version1.xml branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/cfg/annotationParsers.xml branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBaseWithUnit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractTreeNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AlgebraicRule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AnnotationElement.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Assignment.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AssignmentRule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CallableSBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Compartment.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CompartmentType.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Creator.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Delay.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/EventAssignment.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ExplicitRule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/FunctionDefinition.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/IdentifierException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/InitialAssignment.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/JSBML.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/LevelVersionError.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ListOf.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/LocalParameter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/MathContainer.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ModifierSpeciesReference.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/NamedSBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/NamedSBaseWithDerivedUnit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Parameter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Priority.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/PropertyException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/PropertyNotAvailableException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/PropertyUndefinedError.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Quantity.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/QuantityWithUnit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/RateRule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Rule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLErrorLog.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLInputConverter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLOutputConverter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLReader.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLTypeUndefinedException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBO.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBaseWithDerivedUnit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBaseWithUnit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SimpleSpeciesReference.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Species.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesType.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/StoichiometryMath.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Symbol.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Trigger.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UniqueNamedSBase.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Unit.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Variable.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ext/AbstractSBasePlugin.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ext/SBasePlugin.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ext/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTArithmeticOperatorNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTBinaryFunctionNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTBoolean.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCSymbolAvogadroNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCSymbolBaseNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCSymbolDelayNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCSymbolNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCSymbolTimeNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCiFunctionNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCiNumberNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnExponentialNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnIntegerNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnNumberNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnRationalNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTCnRealNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTConstantNumber.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTDivideNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTFactory.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTFunction.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTHyperbolicNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTLambdaFunctionNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTLogarithmNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTLogicalOperatorNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTMinusNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNode2.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTNumber.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTPiecewiseFunctionNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTPlusNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTPowerNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTQualifierNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTRelationalOperatorNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTRootNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTTimesNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTTrigonometricNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTUnaryFunctionNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/ASTUnknown.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/AbstractASTNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/ASTNode2Compiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/ASTNode2Value.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/FindUnitsCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/FormulaCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/HTMLFormula.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/LaTeXCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/LibSBMLFormulaCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/MathMLXMLStreamCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParser.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserASTNode2.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserASTNode2.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserASTNode2Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserASTNode2TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserConstants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3ASTNode2.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3ASTNode2.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3ASTNode2Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3ASTNode2TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserLL3TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/FormulaParserTokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/IFormulaParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/ParseException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/SimpleCharStream.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/Token.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/TokenMgrError.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/parser/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ontology/Term.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ontology/Triple.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/resources/Resource.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/resources/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserASTNode2.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserASTNode2.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserASTNode2Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserASTNode2TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserConstants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3ASTNode2.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3ASTNode2.jj branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3ASTNode2Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3ASTNode2TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3Constants.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3TokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/IFormulaParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/ParseException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/SimpleCharStream.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/Token.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/TokenMgrError.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/Detail.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/DocumentFactory.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/IdManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/JAXPFacade.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/ListOfWithName.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/Maths.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/Message.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/ModelBuilder.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/NodeWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/NotImplementedException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/Option.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/Pair.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/ProgressListener.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/ResourceManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/SAX2Parser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/SBMLtools.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/StringTools.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/SubModel.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeChangeEvent.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeRemovedEvent.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeWithChangeSupport.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/ValuePair.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/XMLResourceBundleControl.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/ASTNodeCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/ASTNodeValue.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/FindUnitsCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/FormulaCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/FormulaCompilerLibSBML.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/FormulaCompilerNoPiecewise.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/HTMLFormula.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/LaTeXCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/LibSBMLFormulaCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/UnitException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/UnitsCompiler.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/AndFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/AssignmentVariableFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/BoundaryConditionFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/CVTermFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/Filter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/IdenticalUnitDefinitionFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/NameFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/OrFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/SBOFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/SpeciesReferenceFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/XMLNodeFilter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/filters/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/validator/ModelOverdeterminedException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/validator/OverdeterminationValidator.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/validator/SBMLValidator.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/validator/SyntaxChecker.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/validator/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLException.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLNamespaces.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLNode.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLToken.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLTriple.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/AnnotationReader.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/AnnotationWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/PackageParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/PackageUtil.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ReadingParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLLevel1Rule.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/WritingParser.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/XMLNodeReader.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/XMLNodeWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/DateProcessor.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLObjectForXML.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/XMLLogger.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/package-info.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/xstream/converter/MessageConverter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/xstream/converter/SBMLErrorConverter.java branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/xstream/converter/package-info.java branches/astnode2-merging-alternate/core/src/overview.html branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTArithmeticOperatorNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTBinaryFunctionNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTBooleanTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCSymbolAvogadroNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCSymbolDelayNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCSymbolTimeNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCiNumberNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCnExponentialNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCnIntegerNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCnRationalNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTCnRealNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTConstantNumberTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTDivideNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTFactoryTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTFunctionTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTHyperbolicNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTLambdaFunctionTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTLogarithmNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTLogicalOperatorNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTMinusNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeFormulaToStringTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTPiecewiseFunctionNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTPlusNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTPowerNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTQualifierNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTRelationalOperatorNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTRootNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTTimesNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTTrigonometricNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTUnaryFunctionNodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/TestInfixOperatorPrecedence.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/package-info.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/HashCodeTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/IdRegistrationTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/PerformanceTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/PerformanceTestPureStax.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/RemoveFromModelTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/RemoveFromParentTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/TreeSearchTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/package-info.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestASTNode.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestCVTerms.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestCompartment.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestEvent.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestIncompatibilities.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestL3Parameter.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestModel.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestParameter.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestReaction.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestReadFromFile1.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestReadFromFile5.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestSBase.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestSpecies.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/test/sbml/TestUnitSimplification.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/ASTNode2Tests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/CVTermTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/CheckConsistencyTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/CreatorTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/GetNotesStringTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/LibsbmlCompatibilityTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/SBML_L1VxTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/SBML_L2V1Test.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/TestAbstractNamedSBaseWithUnits.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/Tests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/UnregisterTests.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/XMLTokenTest.java branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/data/libsbml-test-data/sbml-l1v1.xsd branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/xml/test/data/libsbml-test-data/sbml-l1v2.xsd branches/astnode2-merging-alternate/dev/README.txt branches/astnode2-merging-alternate/dev/eclipse/codetemplates.xml branches/astnode2-merging-alternate/dev/java.java branches/astnode2-merging-alternate/examples/resources/org/sbml/jsbml/gui/UserMessages.xml branches/astnode2-merging-alternate/examples/sbmlbargraph/build.xml branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/AboutPane.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/Config.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/Dialog.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/Log.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/LogFormatter.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/Main.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/MainWindow.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/OSXAdapter.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/SBMLStats.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/VerifiableFile.java branches/astnode2-merging-alternate/examples/sbmlbargraph/src/org/sbml/bargraph/Version.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/ext/spatial/test/SpatialTestModelWriter.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/gui/JSBMLvisualizer.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/gui/JTreeOfSBML.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/gui/SBMLFileFilter.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/gui/package-info.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/AddNamespace.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/CharsetTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/EventTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/FilterTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/FormulaTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/ListTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/ListenerTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/MathMLSpecialTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/MathMLTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/PriorityTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/SBMLWriterTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/SBOtest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/SpeciesAnnotationTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/SubModelTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/T1.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestAnnotation.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestClone.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestFunctionDefinition.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestFunctionDefinition2.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestLocalParameterIdentification.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/TestNotes.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/ToyModelTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/UnitDefinitionTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/test/ValidateSBML.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/xml/test/FormulaParserLL3Test.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/xml/test/FormulaParserTest.java branches/astnode2-merging-alternate/examples/test/src/org/sbml/jsbml/xml/test/MathMLTest.java branches/astnode2-merging-alternate/extensions/arrays/build.xml branches/astnode2-merging-alternate/extensions/arrays/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/arrays/pom.xml branches/astnode2-merging-alternate/extensions/arrays/resources/org/sbml/jsbml/ext/arrays/validator/constraints/Messages.xml branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysConstants.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Dimension.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Index.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/ArraysCompiler.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/StaticallyComputableCompiler.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/flattening/ArraysFlattening.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/flattening/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/util/ArraysMath.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/util/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/ArraysMathValidator.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/ArraysValidator.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/DimensionValidator.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/ExtendedSBaseValidator.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/IndexValidator.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/ArraysConstraint.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/ArraysMathCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/DimensionArrayDimCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/DimensionIDCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/DimensionSizeCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/IndexArrayDimCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/IndexAttributesCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/SBaseWithDimensionCheck.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/constraints/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/ext/arrays/validator/package-info.java branches/astnode2-merging-alternate/extensions/arrays/src/org/sbml/jsbml/xml/parsers/ArraysParser.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArrayExtensionTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysJUnitTests.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysValidationTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysWriteTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/CompilerTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/MathTest.java branches/astnode2-merging-alternate/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/package-info.java branches/astnode2-merging-alternate/extensions/comp/build.xml branches/astnode2-merging-alternate/extensions/comp/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/comp/pom.xml branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompConstants.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/ExternalModelDefinition.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/package-info.java branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/xml/parsers/CompParser.java branches/astnode2-merging-alternate/extensions/distrib/build.xml branches/astnode2-merging-alternate/extensions/distrib/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/distrib/pom.xml branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribConstants.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribInput.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/util/DistribModelBuilder.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/xml/parsers/DistribParser.java branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/xml/parsers/UncertMLXMLNodeReader.java branches/astnode2-merging-alternate/extensions/distrib/test/org/sbml/jsbml/ext/distrib/test/CreateUncertMLXMLNode.java branches/astnode2-merging-alternate/extensions/dyn/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/CBO.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynConstants.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynElement.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynSBasePlugin.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialComponent.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialKind.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/package-info.java branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/xml/parsers/DynParser.java branches/astnode2-merging-alternate/extensions/dyn/test/org/sbml/jsbml/ext/dyn/test/TestL3Dyn.java branches/astnode2-merging-alternate/extensions/fbc/build.xml branches/astnode2-merging-alternate/extensions/fbc/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/fbc/pom.xml branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/AbstractFBCSBasePlugin.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/And.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Association.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCList.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxBound.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Or.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/package-info.java branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java branches/astnode2-merging-alternate/extensions/fbc/test/org/sbml/jsbml/ext/fbc/test/FBCVersion2Test.java branches/astnode2-merging-alternate/extensions/fbc/test/org/sbml/jsbml/ext/fbc/test/FBCWritingTest.java branches/astnode2-merging-alternate/extensions/fbc/test/org/sbml/jsbml/ext/fbc/test/package-info.java branches/astnode2-merging-alternate/extensions/groups/build.xml branches/astnode2-merging-alternate/extensions/groups/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/groups/pom.xml branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupKind.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsConstants.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/package-info.java branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java branches/astnode2-merging-alternate/extensions/groups/test/org/sbml/jsbml/ext/groups/test/TestL3groups.java branches/astnode2-merging-alternate/extensions/layout/build.xml branches/astnode2-merging-alternate/extensions/layout/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/layout/pom.xml branches/astnode2-merging-alternate/extensions/layout/resources/org/sbml/jsbml/resources/cfg/SBMLLayoutElements.xml branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/AbstractReferenceGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutConstants.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/NamedSBaseReferenceFilter.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceRole.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/package-info.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/xml/parsers/L3LayoutParser.java branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/xml/parsers/LayoutParser.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutJUnitTests.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutTest.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/SpeciesReferenceGlyphTest.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/TestL3Layout.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/TestSpeciesReferenceGlyphCurve.java branches/astnode2-merging-alternate/extensions/layout/test/org/sbml/jsbml/ext/layout/test/TextGlyphTest.java branches/astnode2-merging-alternate/extensions/multi/build.xml branches/astnode2-merging-alternate/extensions/multi/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiConstants.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/package-info.java branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java branches/astnode2-merging-alternate/extensions/pom.xml branches/astnode2-merging-alternate/extensions/qual/build.xml branches/astnode2-merging-alternate/extensions/qual/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/qual/pom.xml branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/FunctionTerm.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Input.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/InputTransitionEffect.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Output.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/OutputTransitionEffect.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualConstants.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualList.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeModel.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Sign.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/package-info.java branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/xml/parsers/QualParser.java branches/astnode2-merging-alternate/extensions/qual/test/org/sbml/jsbml/ext/qual/test/BuildToyModelTest.java branches/astnode2-merging-alternate/extensions/qual/test/org/sbml/jsbml/ext/qual/test/QualExample.java branches/astnode2-merging-alternate/extensions/render/build.xml branches/astnode2-merging-alternate/extensions/render/doc/img/type_hierarchy.dot branches/astnode2-merging-alternate/extensions/render/pom.xml branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/AbstractRenderPlugin.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/ColorDefinition.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Ellipse.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/FontFamily.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/FontRenderStyle.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GraphicalPrimitive1D.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GraphicalPrimitive2D.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java ... [truncated message content] |