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[Jsbml-svn] SF.net SVN: jsbml:[2432] trunk
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From: <nik...@us...> - 2015-12-03 17:04:08
|
Revision: 2432
http://sourceforge.net/p/jsbml/code/2432
Author: niko-rodrigue
Date: 2015-12-03 17:04:05 +0000 (Thu, 03 Dec 2015)
Log Message:
-----------
detected and corrected more package namespace error while checking the tests outputs + reduced the default output of the arrays flattening tests a lot which allow to see some of the errors
Modified Paths:
--------------
trunk/NEWS.txt
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ExternalModelDefinition.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/NEWS.txt 2015-12-03 17:04:05 UTC (rev 2432)
@@ -11,9 +11,9 @@
package definitions.
- Improved the Maven pom files, and changed the Maven group ids and
- artifact ids. They should be stable now. With these changes in place, we
- can update the Maven repository much more quickly and easily. Next steps
- are to make JSBML available in Maven Central.
+ artifact ids. They should be stable now. With these changes in place,
+ we can update the Maven repository much more quickly and easily. Next
+ steps are to make JSBML available in Maven Central.
- Added some utility classes to improve support for SBML files written by
the Cobra toolbox before the SBML Level 3 FBC package was created. The
@@ -32,9 +32,12 @@
- SBML L1 rules were not correctly written: the wrong XML element name
was used. Now it uses the correct L1 names and attributes.
- - The clone constructor for the Species class did not copy the speciesType
- attribute. Thanks to Olivier Martin who reported the problem.
+ - The clone constructor for the Species class did not copy the
+ speciesType attribute. Thanks to Olivier Martin who reported the
+ problem.
+ - The clone constructor for the FunctionDefinition class did not copy the
+ id attribute.
===========================================================================
Version 1.1-beta1 (12-10-2015)
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -793,7 +793,7 @@
* <i>real</i> check, rather than to indicate potential errors.
*/
protected boolean checkAndSetPackageNamespaceAndVersion(SBase sbase) {
- String expectedPackageNamespace = "";
+ String expectedPackageNamespace = null;
int expectedPackageVersion = -1;
String packageLabel = sbase.getPackageName();
@@ -2116,7 +2116,7 @@
* @param namespace the XML namespace to which this {@link SBase} belong.
*/
public void setNamespace(String namespace) {
- if ((elementNamespace != null) && (!elementNamespace.equals(namespace))) {
+ if ((elementNamespace != null) && (namespace != null) && (!elementNamespace.equals(namespace))) { // TODO - test if elementNamespace or namespace is empty before throwing the error !
// if we implement proper conversion some days, we need to unset the namespace before changing it.
logger.error(MessageFormat.format(
resourceBundle.getString("AbstractSBase.setNamespaceExc"),
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -2273,7 +2273,7 @@
throws SBMLException {
FunctionDefinition func = model.getFunctionDefinition(functionDefinitionName);
if (func == null) {
- throw new SBMLException();
+ throw new SBMLException("FunctionDefinition with id ' " + functionDefinitionName + "' cannot be found in the model.");
}
function(func, args);
return dummy;
Modified: trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -26,6 +26,7 @@
import javax.xml.stream.XMLStreamException;
+import org.apache.log4j.Logger;
import org.junit.Test;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.AssignmentRule;
@@ -60,6 +61,7 @@
*/
public class FlatteningTest {
+ private static Logger logger = Logger.getLogger(FlatteningTest.class);
@Test
public void sizeZeroTest() {
@@ -218,11 +220,23 @@
ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
rule.setMath(ruleMath);
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFlatteningRule, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFlatteningRule, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().getParameterCount() == 21);
assertTrue(flattened.getModel().getRuleCount() == 10);
} catch (SBMLException e) {
@@ -284,11 +298,23 @@
Dimension dim = reactPlugin.createDimension("i");
dim.setSize(n.getId());
dim.setArrayDimension(0);
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testReaction, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testReaction, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().getParameterCount() == 3);
assertTrue(flattened.getModel().getReactionCount() == 2);
} catch (SBMLException e) {
@@ -348,12 +374,22 @@
dim.setSize(n.getId());
dim.setArrayDimension(0);
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testEvent, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
+ SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
- SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testEvent, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().getEventCount() == 3);
assertTrue(flattened.getModel().getEvent(0).getEventAssignmentCount() == 3);
} catch (SBMLException e) {
@@ -413,11 +449,22 @@
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testEventAssignmentWithParentDimension, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testEventAssignmentWithParentDimension, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().getEventCount() == 3);
assertTrue(flattened.getModel().getEvent(0).getEventAssignmentCount() == 1);
} catch (SBMLException e) {
@@ -439,7 +486,11 @@
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/BIOMD0000000012.xml"));
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ String docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testBioModelFlattening, document after convert:\n" + docStr);
+ }
assertTrue(doc.getModel().getCompartmentCount() == flattened.getModel().getCompartmentCount());
assertTrue(doc.getModel().getSpeciesCount() == flattened.getModel().getSpeciesCount());
@@ -505,11 +556,23 @@
Dimension dim = reactPlugin.createDimension("i");
dim.setSize(n.getId());
dim.setArrayDimension(0);
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testSpeciesReference, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testSpeciesReference, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().getSpeciesCount() == 4);
assertTrue(flattened.getModel().findNamedSBase(flattened.getModel().getReaction(0).getReactant(0).getSpecies()) != null);
assertTrue(flattened.getModel().findNamedSBase(flattened.getModel().getReaction(0).getProduct(0).getSpecies()) != null);
@@ -596,12 +659,22 @@
impb.setArrayDimension(0);
impb.setMath(ASTNode.parseFormula("j"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testSpeciesReferenceImplicitDim, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testSpeciesReferenceImplicitDim, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().findNamedSBase(flattened.getModel().getReaction(0).getReactant(0).getSpecies()) != null);
assertTrue(flattened.getModel().findNamedSBase(flattened.getModel().getReaction(0).getReactant(1).getSpecies()) != null);
assertTrue(flattened.getModel().findNamedSBase(flattened.getModel().getReaction(0).getProduct(0).getSpecies()) != null);
@@ -694,12 +767,23 @@
ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
rule.setMath(ruleMath);
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testUniqueID, document before convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testUniqueID, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
assertTrue(flattened.getModel().findNamedSBase("X_0") != null);
assertTrue(flattened.getModel().findNamedSBase("X__0") != null);
assertTrue(flattened.getModel().findNamedSBase("X___0") != null);
@@ -723,17 +807,37 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/SubModel.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("SubModel, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- System.out.println("\n-------------------------------------------");
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- System.out.println("\n-------------------------------------------");
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("SubModel, document after convert:\n" + docStr);
+ System.out.println("\n-------------------------------------------");
+ }
+
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/SubSubModel.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("SubSubModel, document before convert:\n" + docStr);
+ }
+
flattened = ArraysFlattening.convert(doc);
- System.out.println("\n-------------------------------------------");
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("SubSubModel, document after convert:\n" + docStr);
+ }
+
} catch (XMLStreamException e) {
assertTrue(false);
}
@@ -748,11 +852,21 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml"));
- //SBMLWriter.write(doc, System.out, ' ', (short) 2);
- //SBMLDocument flattened = ArraysFlattening.convert(doc);
- //SBMLWriter.write(flattened, System.out, ' ', (short) 2);
- ArraysFlattening.convert(doc);
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFBC, document before convert:\n" + docStr);
+ }
+
+ SBMLDocument flattened = ArraysFlattening.convert(doc);
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFBC, document after convert:\n" + docStr);
+ }
+
} catch (XMLStreamException e) {
assertTrue(false);
}
@@ -767,11 +881,21 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/NEWFBC.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFBC, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
-
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
-
+
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testFBC, document after convert:\n" + docStr);
+ }
+
} catch (XMLStreamException e) {
assertTrue(false);
}
@@ -783,10 +907,20 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/layoutTest.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testLayout, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testLayout, document after convert:\n" + docStr);
+ }
} catch (XMLStreamException e) {
assertTrue(false);
@@ -815,10 +949,20 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/example04.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("getmodel, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("getmodel, document after convert:\n" + docStr);
+ }
} catch (XMLStreamException e) {
assertTrue(false);
@@ -850,10 +994,20 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/and.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testTime, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("testTime, document after convert:\n" + docStr);
+ }
} catch (XMLStreamException e) {
assertTrue(false);
@@ -866,10 +1020,20 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
+
+ String docStr = new SBMLWriter().writeSBMLToString(doc);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("toggleTime, document before convert:\n" + docStr);
+ }
+
SBMLDocument flattened = ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ docStr = new SBMLWriter().writeSBMLToString(flattened);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("toggleTime, document after convert:\n" + docStr);
+ }
} catch (XMLStreamException e) {
assertTrue(false);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -120,6 +120,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
/* (non-Javadoc)
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ExternalModelDefinition.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ExternalModelDefinition.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ExternalModelDefinition.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -139,7 +139,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI);
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -89,6 +89,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -109,6 +109,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -327,8 +327,12 @@
public ListOf<FluxObjective> getListOfFluxObjectives() {
if (!isSetListOfFluxObjectives()) {
listOfFluxObjectives = new ListOf<FluxObjective>(getLevel(), getVersion());
- listOfFluxObjectives.setNamespace(FBCConstants.namespaceURI);
+ listOfFluxObjectives.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'fbc'
+ listOfFluxObjectives.setPackageName(null);
+ listOfFluxObjectives.setPackageName(FBCConstants.shortLabel);
listOfFluxObjectives.setSBaseListType(ListOf.Type.other);
+
registerChild(listOfFluxObjectives);
}
return listOfFluxObjectives;
@@ -471,7 +475,15 @@
public void setListOfFluxObjectives(ListOf<FluxObjective> listOfFluxObjectives) {
unsetListOfFluxObjectives();
this.listOfFluxObjectives = listOfFluxObjectives;
- registerChild(this.listOfFluxObjectives);
+
+ if (listOfFluxObjectives != null) {
+ listOfFluxObjectives.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'fbc'
+ listOfFluxObjectives.setPackageName(null);
+ listOfFluxObjectives.setPackageName(FBCConstants.shortLabel);
+
+ registerChild(this.listOfFluxObjectives);
+ }
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -58,6 +58,7 @@
*/
public CompartmentGlyph() {
super();
+ initDefaults();
}
/**
@@ -66,6 +67,7 @@
*/
public CompartmentGlyph(CompartmentGlyph compartmentGlyph) {
super(compartmentGlyph);
+ initDefaults();
}
/**
@@ -75,6 +77,7 @@
*/
public CompartmentGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -83,6 +86,7 @@
*/
public CompartmentGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -93,6 +97,7 @@
*/
public CompartmentGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
/* (non-Javadoc)
@@ -103,6 +108,14 @@
return new CompartmentGlyph(this);
}
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#getCompartment()
*/
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -75,6 +75,7 @@
*/
public GeneralGlyph() {
super();
+ initDefaults();
}
/**
@@ -84,6 +85,7 @@
*/
public GeneralGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -110,6 +112,7 @@
*/
public GeneralGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -120,8 +123,16 @@
*/
public GeneralGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
/**
* Returns {@code true}, if listOfSubGlyphs contains at least one element.
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -71,6 +71,7 @@
*/
public ReactionGlyph() {
super();
+ initDefaults();
}
/**
@@ -80,6 +81,7 @@
*/
public ReactionGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -103,6 +105,7 @@
*/
public ReactionGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -113,7 +116,16 @@
*/
public ReactionGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
+
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
/**
* Appends the specified element to the end of the
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -71,6 +71,7 @@
*/
public ReferenceGlyph() {
super();
+ initDefaults();
}
/**
@@ -80,6 +81,7 @@
*/
public ReferenceGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -105,6 +107,7 @@
*/
public ReferenceGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -115,8 +118,17 @@
*/
public ReferenceGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#clone()
*/
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -51,6 +51,7 @@
*/
public SpeciesGlyph() {
super();
+ initDefaults();
}
/**
@@ -60,6 +61,7 @@
*/
public SpeciesGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -68,6 +70,7 @@
*/
public SpeciesGlyph(SpeciesGlyph speciesGlyph) {
super(speciesGlyph);
+ initDefaults();
}
/**
@@ -76,6 +79,7 @@
*/
public SpeciesGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -86,6 +90,7 @@
*/
public SpeciesGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
/* (non-Javadoc)
@@ -97,6 +102,14 @@
}
/**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
+
+ /**
*
* @return
*/
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -70,6 +70,7 @@
*/
public SpeciesReferenceGlyph() {
super();
+ initDefaults();
}
/**
@@ -79,6 +80,7 @@
*/
public SpeciesReferenceGlyph(int level, int version) {
super(level, version);
+ initDefaults();
}
/**
@@ -96,6 +98,7 @@
if (speciesReferenceGlyph.isSetSpeciesGlyph()) {
setSpeciesGlyph(new String(speciesReferenceGlyph.getSpeciesGlyph()));
}
+ initDefaults();
}
/**
@@ -104,6 +107,7 @@
*/
public SpeciesReferenceGlyph(String id) {
super(id);
+ initDefaults();
}
/**
@@ -114,6 +118,7 @@
*/
public SpeciesReferenceGlyph(String id, int level, int version) {
super(id, level, version);
+ initDefaults();
}
/* (non-Javadoc)
@@ -125,6 +130,14 @@
}
/**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
+
+ /**
*
* @return
*/
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2015-12-03 16:40:35 UTC (rev 2431)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2015-12-03 17:04:05 UTC (rev 2432)
@@ -60,7 +60,7 @@
*/
public TextGlyph() {
super();
- setNamespace(LayoutConstants.namespaceURI);
+ initDefaults();
}
/**
@@ -70,7 +70,7 @@
*/
public TextGlyph(int level, int version) {
super(level, version);
- setNamespace(LayoutConstants.namespaceURI);
+ initDefaults();
}
/**
@@ -79,7 +79,7 @@
*/
public TextGlyph(String id) {
super(id);
- setNamespace(LayoutConstants.namespaceURI);
+ initDefaults();
}
/**
@@ -90,7 +90,7 @@
*/
public TextGlyph(String id, int level, int version) {
super(id, level, version);
- setNamespace(LayoutConstants.namespaceURI);
+ initDefaults();
}
/**
@@ -115,6 +115,14 @@
return new TextGlyph(this);
}
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = LayoutConstants.shortLabel;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
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