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[Jsbml-svn] SF.net SVN: jsbml:[2401] trunk/extensions
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From: <nik...@us...> - 2015-11-17 11:57:15
|
Revision: 2401
http://sourceforge.net/p/jsbml/code/2401
Author: niko-rodrigue
Date: 2015-11-17 11:57:12 +0000 (Tue, 17 Nov 2015)
Log Message:
-----------
first batch of packages updates to remove the setNamepace that is not necessary any more
Modified Paths:
--------------
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.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/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialParameterPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -135,7 +135,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -308,7 +308,6 @@
} else {
listOfPorts = new ListOf<Port>();
}
- listOfPorts.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
@@ -335,7 +334,6 @@
} else {
listOfSubmodels = new ListOf<Submodel>();
}
- listOfSubmodels.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
@@ -568,7 +566,6 @@
if ((this.listOfPorts != null)) {
this.listOfPorts.setSBaseListType(ListOf.Type.other);
listOfPorts.unsetNamespace();
- listOfPorts.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
@@ -590,8 +587,6 @@
this.listOfSubmodels = listOfSubmodels;
if ((this.listOfSubmodels != null)) {
this.listOfSubmodels.setSBaseListType(ListOf.Type.other);
- listOfSubmodels.unsetNamespace();
- listOfSubmodels.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -141,7 +141,6 @@
} else {
listOfExternalModelDefinitions = new ListOf<ExternalModelDefinition>();
}
- listOfExternalModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfExternalModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfExternalModelDefinitions.setPackageName(null);
@@ -243,8 +242,6 @@
this.listOfExternalModelDefinitions = listOfExternalModelDefinitions;
if (listOfExternalModelDefinitions != null) {
- listOfExternalModelDefinitions.unsetNamespace();
- listOfExternalModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfExternalModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfExternalModelDefinitions.setPackageName(null);
@@ -431,7 +428,6 @@
} else {
listOfModelDefinitions = new ListOf<ModelDefinition>();
}
- listOfModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfModelDefinitions.setPackageName(null);
@@ -459,8 +455,6 @@
this.listOfModelDefinitions = listOfModelDefinitions;
if (listOfModelDefinitions != null) {
- listOfModelDefinitions.unsetNamespace();
- listOfModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfModelDefinitions.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -344,7 +344,6 @@
} else {
listOfReplacedElements = new ListOf<ReplacedElement>();
}
- listOfReplacedElements.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
@@ -379,8 +378,6 @@
this.listOfReplacedElements = listOfReplacedElements;
if (listOfReplacedElements != null) {
- listOfReplacedElements.unsetNamespace();
- listOfReplacedElements.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -120,7 +120,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -100,7 +100,6 @@
*/
public void init()
{
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -108,7 +108,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -89,7 +89,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -109,7 +109,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -162,7 +162,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
@@ -452,7 +451,6 @@
public ListOf<Deletion> getListOfDeletions() {
if (!isSetListOfDeletions()) {
listOfDeletions = new ListOf<Deletion>(getLevel(), getVersion());
- listOfDeletions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
@@ -479,8 +477,6 @@
if ((listOfDeletions != null)) {
listOfDeletions.setSBaseListType(ListOf.Type.other);
- listOfDeletions.unsetNamespace();
- listOfDeletions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -763,7 +763,6 @@
this.listOfFluxBounds = listOfFluxBounds;
if (listOfFluxBounds != null) {
- listOfFluxBounds.unsetNamespace();
listOfFluxBounds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfFluxBounds.setPackageName(null);
@@ -787,7 +786,6 @@
this.listOfGeneProducts = listOfGeneProducts;
if (listOfGeneProducts != null) {
- listOfGeneProducts.unsetNamespace();
listOfGeneProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfGeneProducts.setPackageName(null);
@@ -813,7 +811,7 @@
*
* @param listOfObjectives
*/
- public void setListOfObjectives(ListOf<Objective> listOfObjectives) { // TODO - fix the listOfObjectives methods
+ public void setListOfObjectives(ListOf<Objective> listOfObjectives) {
if (listOfObjectives instanceof ListOfObjectives) {
setListOfObjectives((ListOfObjectives) listOfObjectives);
} else {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -28,6 +28,7 @@
/**
* Unlike other SBML {@link ListOf} classes, {@link ListOfObjectives} adds an additional
* required attribute activeObjective.
+ *
* @author Nicolas Rodriguez
* @since 1.0
* @version $Rev$
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -261,7 +261,6 @@
public ListOf<Member> getListOfMembers() {
if (!isSetListOfMembers()) {
listOfMembers = new ListOf<Member>();
- listOfMembers.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMembers.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMembers.setPackageName(null);
@@ -297,8 +296,6 @@
this.listOfMembers = listOfMembers;
if (listOfMembers != null) {
- listOfMembers.unsetNamespace();
- listOfMembers.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMembers.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMembers.setPackageName(null);
@@ -489,7 +486,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
@@ -529,7 +525,6 @@
public ListOfMemberConstraint getListOfMemberConstraints() {
if (!isSetListOfMemberConstraints()) {
listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
- listOfMemberConstraints.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMemberConstraints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMemberConstraints.setPackageName(null);
@@ -551,8 +546,6 @@
this.listOfMemberConstraints = listOfMemberConstraints;
if (listOfMemberConstraints != null) {
- listOfMemberConstraints.unsetNamespace();
- listOfMemberConstraints.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMemberConstraints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMemberConstraints.setPackageName(null);
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -221,7 +221,6 @@
if (!isSetListOfGroups()) {
listOfGroups = new ListOf<Group>();
- listOfGroups.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGroups.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfGroups.setPackageName(null);
@@ -294,7 +293,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
}
@@ -325,7 +323,6 @@
this.listOfGroups = listOfGroups;
if (listOfGroups != null) {
- listOfGroups.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGroups.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfGroups.setPackageName(null);
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -77,7 +77,6 @@
super();
setPackageVersion(-1);
packageName = GroupsConstants.shortLabel;
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -88,7 +87,6 @@
super(level, version);
setPackageVersion(-1);
packageName = GroupsConstants.shortLabel;
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -65,7 +65,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -180,7 +180,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -161,8 +161,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- // TODO - removed once the mechanism are in place to set package version and namespace
- setNamespace(MultiConstants.namespaceURI);
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -88,7 +88,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -107,7 +107,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -116,7 +115,7 @@
*/
@Override
public String getPackageName() {
- return MultiConstants.packageName;
+ return MultiConstants.shortLabel;
}
@@ -180,7 +179,6 @@
public ListOf<CompartmentReference> getListOfCompartmentReferences() {
if (listOfCompartmentReferences == null) {
listOfCompartmentReferences = new ListOf<CompartmentReference>();
- listOfCompartmentReferences.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
@@ -208,8 +206,6 @@
this.listOfCompartmentReferences = listOfCompartmentReferences;
if (listOfCompartmentReferences != null) {
- listOfCompartmentReferences.unsetNamespace();
- listOfCompartmentReferences.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -95,7 +95,6 @@
*/
public MultiModelPlugin(Model model) {
super(model);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -136,7 +135,6 @@
public ListOf<SpeciesType> getListOfSpeciesTypes() {
if (listOfSpeciesTypes == null) {
listOfSpeciesTypes = new ListOf<SpeciesType>();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypes.setPackageName(null);
@@ -234,8 +232,6 @@
this.listOfSpeciesTypes = listOfSpeciesTypes;
if (listOfSpeciesTypes != null) {
- listOfSpeciesTypes.unsetNamespace();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypes.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -93,7 +93,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -94,7 +94,6 @@
*/
public MultiSpeciesPlugin(Species species) {
super(species);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -148,7 +147,6 @@
public ListOf<OutwardBindingSite> getListOfOutwardBindingSites() {
if (listOfOutwardBindingSites == null) {
listOfOutwardBindingSites = new ListOf<OutwardBindingSite>();
- listOfOutwardBindingSites.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutwardBindingSites.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfOutwardBindingSites.setPackageName(null);
@@ -175,8 +173,6 @@
this.listOfOutwardBindingSites = listOfOutwardBindingSites;
if (listOfOutwardBindingSites != null) {
- listOfOutwardBindingSites.unsetNamespace();
- listOfOutwardBindingSites.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutwardBindingSites.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfOutwardBindingSites.setPackageName(null);
@@ -333,7 +329,6 @@
public ListOf<SpeciesFeature> getListOfSpeciesFeatures() {
if (listOfSpeciesFeatures == null) {
listOfSpeciesFeatures = new ListOf<SpeciesFeature>();
- listOfSpeciesFeatures.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatures.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatures.setPackageName(null);
@@ -360,8 +355,6 @@
this.listOfSpeciesFeatures = listOfSpeciesFeatures;
if (listOfSpeciesFeatures != null) {
- listOfSpeciesFeatures.unsetNamespace();
- listOfSpeciesFeatures.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatures.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatures.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -94,7 +94,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -173,7 +172,6 @@
public ListOf<SpeciesTypeComponentMapInProduct> getListOfSpeciesTypeComponentMapInProducts() {
if (listOfSpeciesTypeComponentMapInProducts == null) {
listOfSpeciesTypeComponentMapInProducts = new ListOf<SpeciesTypeComponentMapInProduct>();
- listOfSpeciesTypeComponentMapInProducts.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentMapInProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentMapInProducts.setPackageName(null);
@@ -200,8 +198,6 @@
this.listOfSpeciesTypeComponentMapInProducts = listOfSpeciesTypeComponentMapInProducts;
if (listOfSpeciesTypeComponentMapInProducts != null) {
- listOfSpeciesTypeComponentMapInProducts.unsetNamespace();
- listOfSpeciesTypeComponentMapInProducts.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentMapInProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentMapInProducts.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -92,7 +92,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -147,7 +147,6 @@
*
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -163,7 +163,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -261,7 +260,6 @@
public ListOf<SpeciesFeatureValue> getListOfSpeciesFeatureValues() {
if (listOfSpeciesFeatureValues == null) {
listOfSpeciesFeatureValues = new ListOf<SpeciesFeatureValue>();
- listOfSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureValues.setPackageName(null);
@@ -286,8 +284,6 @@
this.listOfSpeciesFeatureValues = listOfSpeciesFeatureValues;
if (listOfSpeciesFeatureValues != null) {
- listOfSpeciesFeatureValues.unsetNamespace();
- listOfSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureValues.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -136,7 +136,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -155,7 +155,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -245,7 +244,6 @@
public ListOf<PossibleSpeciesFeatureValue> getListOfPossibleSpeciesFeatureValues() {
if (listOfPossibleSpeciesFeatureValues == null) {
listOfPossibleSpeciesFeatureValues = new ListOf<PossibleSpeciesFeatureValue>();
- listOfPossibleSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPossibleSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfPossibleSpeciesFeatureValues.setPackageName(null);
@@ -270,8 +268,6 @@
this.listOfPossibleSpeciesFeatureValues = listOfPossibleSpeciesFeatureValues;
if (listOfPossibleSpeciesFeatureValues != null) {
- listOfPossibleSpeciesFeatureValues.unsetNamespace();
- listOfPossibleSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPossibleSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfPossibleSpeciesFeatureValues.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -89,7 +89,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -568,7 +568,6 @@
public ListOf<InSpeciesTypeBond> getListOfInSpeciesTypeBonds() {
if (listOfInSpeciesTypeBonds == null) {
listOfInSpeciesTypeBonds = new ListOf<InSpeciesTypeBond>();
- listOfInSpeciesTypeBonds.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInSpeciesTypeBonds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfInSpeciesTypeBonds.setPackageName(null);
@@ -590,7 +589,6 @@
public ListOf<SpeciesFeatureType> getListOfSpeciesFeatureTypes() {
if (listOfSpeciesFeatureTypes == null) {
listOfSpeciesFeatureTypes = new ListOf<SpeciesFeatureType>();
- listOfSpeciesFeatureTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureTypes.setPackageName(null);
@@ -612,7 +610,6 @@
public ListOf<SpeciesTypeComponentIndex> getListOfSpeciesTypeComponentIndexes() {
if (listOfSpeciesTypeComponentIndexes == null) {
listOfSpeciesTypeComponentIndexes = new ListOf<SpeciesTypeComponentIndex>();
- listOfSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentIndexes.setPackageName(null);
@@ -634,7 +631,6 @@
public ListOf<SpeciesTypeInstance> getListOfSpeciesTypeInstances() {
if (listOfSpeciesTypeInstances == null) {
listOfSpeciesTypeInstances = new ListOf<SpeciesTypeInstance>();
- listOfSpeciesTypeInstances.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeInstances.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeInstances.setPackageName(null);
@@ -861,7 +857,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -1204,8 +1199,6 @@
unsetListOfInSpeciesTypeBonds();
this.listOfInSpeciesTypeBonds = listOfInSpeciesTypeBonds;
if (listOfInSpeciesTypeBonds != null) {
- listOfInSpeciesTypeBonds.unsetNamespace();
- listOfInSpeciesTypeBonds.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInSpeciesTypeBonds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfInSpeciesTypeBonds.setPackageName(null);
@@ -1228,8 +1221,6 @@
unsetListOfSpeciesFeatureTypes();
this.listOfSpeciesFeatureTypes = listOfSpeciesFeatureTypes;
if (listOfSpeciesFeatureTypes != null) {
- listOfSpeciesFeatureTypes.unsetNamespace();
- listOfSpeciesFeatureTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureTypes.setPackageName(null);
@@ -1253,8 +1244,6 @@
this.listOfSpeciesTypeComponentIndexes = listOfSpeciesTypeComponentIndexes;
if (listOfSpeciesTypeComponentIndexes != null) {
- listOfSpeciesTypeComponentIndexes.unsetNamespace();
- listOfSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentIndexes.setPackageName(null);
@@ -1277,8 +1266,6 @@
unsetListOfSpeciesTypeInstances();
this.listOfSpeciesTypeInstances = listOfSpeciesTypeInstances;
if (listOfSpeciesTypeInstances != null) {
- listOfSpeciesTypeInstances.unsetNamespace();
- listOfSpeciesTypeInstances.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeInstances.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeInstances.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -164,7 +164,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -278,7 +277,6 @@
public ListOf<DenotedSpeciesTypeComponentIndex> getListOfDenotedSpeciesTypeComponentIndexes() {
if (listOfDenotedSpeciesTypeComponentIndexes == null) {
listOfDenotedSpeciesTypeComponentIndexes = new ListOf<DenotedSpeciesTypeComponentIndex>();
- listOfDenotedSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDenotedSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfDenotedSpeciesTypeComponentIndexes.setPackageName(null);
@@ -302,8 +300,6 @@
unsetListOfDenotedSpeciesTypeComponentIndexes();
listOfDenotedSpeciesTypeComponentIndexes = listOfDenotedSpeciesTypeComponentIndices;
if (listOfDenotedSpeciesTypeComponentIndices != null) {
- listOfDenotedSpeciesTypeComponentIndices.unsetNamespace();
- listOfDenotedSpeciesTypeComponentIndices.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDenotedSpeciesTypeComponentIndices.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfDenotedSpeciesTypeComponentIndices.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -117,7 +117,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -226,7 +225,6 @@
public ListOf<SpeciesFeatureChange> getListOfSpeciesFeatureChanges() {
if (listOfSpeciesFeatureChanges == null) {
listOfSpeciesFeatureChanges = new ListOf<SpeciesFeatureChange>();
- listOfSpeciesFeatureChanges.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureChanges.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureChanges.setPackageName(null);
@@ -250,8 +248,6 @@
unsetListOfSpeciesFeatureChanges();
this.listOfSpeciesFeatureChanges = listOfSpeciesFeatureChanges;
if (listOfSpeciesFeatureChanges != null) {
- listOfSpeciesFeatureChanges.unsetNamespace();
- listOfSpeciesFeatureChanges.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureChanges.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureChanges.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -152,7 +152,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -579,7 +579,6 @@
this.listOfQualitativeSpecies = listOfQualitativeSpecies;
if (listOfQualitativeSpecies != null) {
- listOfQualitativeSpecies.unsetNamespace();
listOfQualitativeSpecies.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfQualitativeSpecies.setPackageName(null);
@@ -603,7 +602,6 @@
this.listOfTransitions = listOfTransitions;
if (listOfTransitions != null) {
- listOfTransitions.unsetNamespace();
listOfTransitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfTransitions.setPackageName(null);
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -666,7 +666,6 @@
listOfFunctionTerms = loft;
if (listOfFunctionTerms != null) {
- listOfFunctionTerms.unsetNamespace();
listOfFunctionTerms.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfFunctionTerms.setPackageName(null);
@@ -685,7 +684,6 @@
listOfInputs = loi;
if (listOfInputs != null) {
- listOfInputs.unsetNamespace();
listOfInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfInputs.setPackageName(null);
@@ -705,7 +703,6 @@
listOfOutputs = loo;
if (listOfOutputs != null) {
- listOfOutputs.unsetNamespace();
listOfOutputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfOutputs.setPackageName(null);
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -117,7 +117,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = SpatialConstants.shortLabel;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -73,7 +73,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -120,7 +120,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = SpatialConstants.shortLabel;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -25,14 +25,12 @@
import java.util.Collection;
import java.util.List;
import java.util.Map;
-import java.util.regex.Pattern;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.util.filters.NameFilter;
/**
@@ -340,7 +338,6 @@
if (!isSetListOfCSGNodes()) {
listOfCSGNodes = new ListOf<CSGNode>(getLevel(),
getVersion());
- listOfCSGNodes.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGNodes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGNodes.setPackageName(null);
@@ -363,7 +360,6 @@
this.listOfCSGNodes = listOfCSGNodes;
if (listOfCSGNodes != null) {
- listOfCSGNodes.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGNodes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGNodes.setPackageName(null);
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
if (!isSetListOfCSGObjects()) {
listOfCSGObjects = new ListOf<CSGObject>(getLevel(),
getVersion());
- listOfCSGObjects.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGObjects.setPackageName(null);
@@ -162,8 +161,6 @@
this.listOfCSGObjects = listOfCSGObjects;
if (listOfCSGObjects != null) {
- listOfCSGObjects.unsetNamespace();
- listOfCSGObjects.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGObjects.setPackageName(null);
@@ -242,13 +239,6 @@
}
- /*
- * TODO: if the ID is mandatory for CSGObject objects,
- * one should also add this methods
- */
- //public void removeCSGObject(String id) {
- // getListOfCSGObjects().removeFirst(new NameFilter(id));
- //}
/**
* Creates a new CSGObject element and adds it to the ListOfCSGObjects list
* @return
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-...
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