Menu
▾
▴
[Jsbml-svn] SF.net SVN: jsbml:[2267] branches/astnode2-merging-alternate
|
From: <nik...@us...> - 2015-05-01 09:44:23
|
Revision: 2267
http://sourceforge.net/p/jsbml/code/2267
Author: niko-rodrigue
Date: 2015-05-01 09:44:19 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2217
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2217
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.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/GeneProduct.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/xml/parsers/FBCParser.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
branches/astnode2-merging-alternate/src/
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate 2015-05-01 09:44:19 UTC (rev 2267)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Added: svn:mergeinfo
## -0,0 +1 ##
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2217
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -1743,6 +1743,8 @@
"Cannot register {0}.", sbase.getElementName()));
}
+ // TODO - set package version and namespace if needed
+
/*
* Now, we can add all previous listeners. The next change will
* be fired after registering all ids.
@@ -1772,6 +1774,8 @@
private void registerChild(SBasePlugin sbasePlugin) {
// Could/Should be used by the method #firePropertyChange
+ // TODO - set package version and namespace if needed
+
int childCount = sbasePlugin.getChildCount();
if (childCount > 0) {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -157,9 +157,8 @@
*
*/
public Annotation(String annotation) throws XMLStreamException {
- this();
// parse the String as an XMLNode
- nonRDFannotation = XMLNode.convertStringToXMLNode(annotation);
+ this(XMLNode.convertStringToXMLNode(annotation));
}
/**
@@ -182,6 +181,15 @@
}
/**
+ *
+ * @param annotation
+ */
+ public Annotation(XMLNode annotation) {
+ this();
+ nonRDFannotation = annotation;
+ }
+
+ /**
* Adds a {@link CVTerm}.
*
* @param cvTerm
@@ -201,6 +209,23 @@
}
/**
+ * Adds an additional namespace to the set of declared namespaces of this
+ * {@link SBase}.
+ *
+ * @param prefix the prefix of the namespace to add
+ * @param uri the namespace uri
+ *
+ */
+ public void addDeclaredNamespace(String prefix, String uri)
+ {
+ if (!isSetNonRDFannotation()) {
+ nonRDFannotation = new XMLNode(new XMLTriple("annotation", null, null), new XMLAttributes());
+ }
+
+ nonRDFannotation.addNamespace(uri, prefix);
+ }
+
+ /**
* Appends some 'annotation' to the non RDF annotation {@link XMLNode} of this object.
*
* @param annotation some non RDF annotations.
@@ -246,6 +271,18 @@
return new Annotation(this);
}
+ /**
+ * @see org.sbml.jsbml.SBase#getHistory()
+ * @return
+ */
+ private History createHistory() {
+ history = new History();
+ history.parent = this;
+ history.addAllChangeListeners(getListOfTreeNodeChangeListeners());
+
+ return history;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#equals(java.lang.Object)
*/
@@ -301,6 +338,7 @@
return l;
}
+
/**
* Returns the about String of this object.
*
@@ -310,6 +348,7 @@
return about == null ? "" : about;
}
+
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@@ -318,7 +357,6 @@
return true;
}
-
/**
* Returns the {@link XMLNode} representing non RDF annotations.
*
@@ -330,58 +368,6 @@
return nonRDFannotation;
}
-
- /**
- *
- *
- * @return
- */
- public XMLNode getFullAnnotation() {
-
- XMLNode nonRdfAnnotationClone = null;
-
- if (isSetNonRDFannotation()) {
- nonRdfAnnotationClone = nonRDFannotation.clone();
- }
-
- // TODO - get the list of AnnotationWriter from the manager
- List<AnnotationWriter> annotationParsers = new ArrayList<AnnotationWriter>();
- // hack to delete
- annotationParsers.add(new SBMLRDFAnnotationParser());
-
- // calling the annotation parsers so that they update the XMLNode before returning it to the user
- for (AnnotationWriter annoWriter : annotationParsers) {
- nonRdfAnnotationClone = annoWriter.writeAnnotation((SBase) getParent(), nonRdfAnnotationClone);
- }
-
- return nonRdfAnnotationClone;
- }
-
- /**
- *
- *
- * @return
- */
- public String getFullAnnotationString() {
-
- XMLNode fullAnnotation = getFullAnnotation();
-
- // System.out.println("getFullAnnotationString - " + fullAnnotation);
-
- if (fullAnnotation != null) {
- try {
- return fullAnnotation.toXMLString();
- } catch (XMLStreamException e) {
- Logger logger = Logger.getLogger(Annotation.class);
- if (logger.isDebugEnabled()) {
- e.printStackTrace();
- }
- }
- }
-
- return "";
- }
-
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getChildAt(int)
*/
@@ -414,7 +400,7 @@
// }
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
@@ -447,27 +433,84 @@
/**
- * Returns the {@link History} of the Annotation.
+ * Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
- * @return the {@link History} of the Annotation.
+ * @return the number of controlled vocabulary terms in this {@link Annotation}.
*/
- public History getHistory() {
- if (!isSetHistory()) {
- createHistory();
+ public int getCVTermCount() {
+ return isSetListOfCVTerms() ? listOfCVTerms.size() : 0;
+ }
+
+ /**
+ *
+ * @return
+ */
+ public XMLNamespaces getDeclaredNamespaces() {
+ return isSetNonRDFannotation() ? nonRDFannotation.getNamespaces() : null;
+ }
+
+ /**
+ *
+ *
+ * @return
+ */
+ public XMLNode getFullAnnotation() {
+
+ XMLNode nonRdfAnnotationClone = null;
+
+ if (isSetNonRDFannotation()) {
+ nonRdfAnnotationClone = nonRDFannotation.clone();
}
- return history;
+ // TODO - get the list of AnnotationWriter from the manager
+ List<AnnotationWriter> annotationParsers = new ArrayList<AnnotationWriter>();
+ // hack to delete
+ annotationParsers.add(new SBMLRDFAnnotationParser());
+
+ // calling the annotation parsers so that they update the XMLNode before returning it to the user
+ for (AnnotationWriter annoWriter : annotationParsers) {
+ nonRdfAnnotationClone = annoWriter.writeAnnotation((SBase) getParent(), nonRdfAnnotationClone);
+ }
+
+ return nonRdfAnnotationClone;
}
+
/**
- * @see org.sbml.jsbml.SBase#getHistory()
+ *
+ *
* @return
*/
- private History createHistory() {
- history = new History();
- history.parent = this;
- history.addAllChangeListeners(getListOfTreeNodeChangeListeners());
+ public String getFullAnnotationString() {
+ XMLNode fullAnnotation = getFullAnnotation();
+
+ // System.out.println("getFullAnnotationString - " + fullAnnotation);
+
+ if (fullAnnotation != null) {
+ try {
+ return fullAnnotation.toXMLString();
+ } catch (XMLStreamException e) {
+ Logger logger = Logger.getLogger(Annotation.class);
+ if (logger.isDebugEnabled()) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ return "";
+ }
+
+ /**
+ * Returns the {@link History} of the Annotation.
+ *
+ * @return the {@link History} of the Annotation.
+ */
+ public History getHistory() {
+ if (!isSetHistory()) {
+ createHistory();
+ }
+
return history;
}
@@ -483,6 +526,19 @@
return listOfCVTerms;
}
+ /**
+ * Returns the {@link XMLNode} containing annotations other than
+ * the official RDF annotation, as defined in the SBML specifications.
+ *
+ * @return the {@link XMLNode} containing annotations other than RDF
+ * annotation. Return null if there are none.
+ */
+ public XMLNode getNonRDFannotation() {
+ if (nonRDFannotation != null) {
+ return nonRDFannotation;
+ }
+ return null;
+ }
/**
* Returns the String containing annotations other than RDF
@@ -503,21 +559,6 @@
}
/**
- * Returns the {@link XMLNode} containing annotations other than
- * the official RDF annotation, as defined in the SBML specifications.
- *
- * @return the {@link XMLNode} containing annotations other than RDF
- * annotation. Return null if there are none.
- */
- public XMLNode getNonRDFannotation() {
- if (nonRDFannotation != null) {
- return nonRDFannotation;
- }
- return null;
- }
-
-
- /**
* Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
* @return the number of controlled vocabulary terms in this {@link Annotation}.
@@ -527,13 +568,13 @@
return getCVTermCount();
}
+
/**
- * Gives the number of {@link CVTerm}s in this {@link Annotation}.
*
- * @return the number of controlled vocabulary terms in this {@link Annotation}.
+ * @return
*/
- public int getCVTermCount() {
- return isSetListOfCVTerms() ? listOfCVTerms.size() : 0;
+ public XMLNode getXMLNode() {
+ return getNonRDFannotation();
}
/* (non-Javadoc)
@@ -552,7 +593,6 @@
return hashCode;
}
-
/**
*
* @return
@@ -572,6 +612,7 @@
return about != null;
}
+
/**
* Checks if the {@link Annotation} is initialized.
*
@@ -613,7 +654,6 @@
return history != null && !history.isEmpty();
}
-
/**
* Checks if the list of {@link CVTerm} is not empty.
*
@@ -653,6 +693,7 @@
return isSetNonRDFannotation();
}
+
/**
* Checks if the RDF part of the Annotation is initialized.
*
@@ -699,7 +740,6 @@
return false;
}
-
/**
* Removes the given {@link CVTerm}.
*
@@ -718,6 +758,8 @@
return success;
}
+
+
/**
* Removes the {@link CVTerm} at the given index.
*
@@ -748,8 +790,6 @@
firePropertyChange(TreeNodeChangeEvent.about, oldAbout, this.about);
}
-
-
/**
* Changes the {@link History} instance to 'history'
*
@@ -766,6 +806,18 @@
/**
* Sets the value of the non RDF annotations
*
+ * @param nonRDFAnnotationStr
+ * @throws XMLStreamException
+ */
+ public void setNonRDFAnnotation(String nonRDFAnnotationStr) throws XMLStreamException {
+ if (nonRDFAnnotationStr != null) {
+ setNonRDFAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotationStr)));
+ }
+ }
+
+ /**
+ * Sets the value of the non RDF annotations
+ *
* @param nonRDFAnnotation
*/
public void setNonRDFAnnotation(XMLNode nonRDFAnnotation) {
@@ -791,18 +843,6 @@
}
/**
- * Sets the value of the non RDF annotations
- *
- * @param nonRDFAnnotationStr
- * @throws XMLStreamException
- */
- public void setNonRDFAnnotation(String nonRDFAnnotationStr) throws XMLStreamException {
- if (nonRDFAnnotationStr != null) {
- setNonRDFAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotationStr)));
- }
- }
-
- /**
* Clears the {@link List} of {@link CVTerm}s.
*/
public void unsetCVTerms() {
@@ -841,29 +881,4 @@
}
}
- /**
- * Adds an additional namespace to the set of declared namespaces of this
- * {@link SBase}.
- *
- * @param prefix the prefix of the namespace to add
- * @param uri the namespace uri
- *
- */
- public void addDeclaredNamespace(String prefix, String uri)
- {
- if (!isSetNonRDFannotation()) {
- nonRDFannotation = new XMLNode(new XMLTriple("annotation", null, null), new XMLAttributes());
- }
-
- nonRDFannotation.addNamespace(uri, prefix);
- }
-
- /**
- *
- * @return
- */
- public XMLNamespaces getDeclaredNamespaces() {
- return isSetNonRDFannotation() ? nonRDFannotation.getNamespaces() : null;
- }
-
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -332,6 +332,18 @@
return t;
}
+ /**
+ * Creates a new {@link Trigger} instance and sets it to this {@link Event}.
+ *
+ * @param math math the math expression for the new {@link Trigger}
+ * @return the new {@link Trigger} instance.
+ */
+ public Trigger createTrigger(ASTNode math) {
+ Trigger t = createTrigger();
+ t.setMath(math);
+ return t;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBaseWithUnit#equals(java.lang.Object)
*/
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLError.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -131,6 +131,8 @@
*/
public SBMLError(String message) {
super(message);
+ this.message = new Message();
+ this.message.setMessage(message);
}
/**
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -198,6 +198,20 @@
return isSetStoichiometry() ? false : true;
}
+ /**
+ *
+ * @param math
+ * @return
+ * @deprecated since SBML Level 3 this should not be used anymore.
+ */
+ @Deprecated
+ public StoichiometryMath createStoichiometryMath(ASTNode math) {
+ StoichiometryMath sm = new StoichiometryMath(getLevel(), getVersion());
+ sm.setMath(math);
+ setStoichiometryMath(sm);
+ return sm;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SimpleSpeciesReference#equals(java.lang.Object)
*/
@@ -345,8 +359,8 @@
/**
*
- * @return the stoichiometryMath of this SpeciesReference. Can be null if
- * the stoichiometryMath is not set.
+ * @return the stoichiometryMath of this SpeciesReference. Can be {@code null}
+ * if the stoichiometryMath is not set.
* @deprecated since SBML Level 3 this should not be used anymore.
*/
@Deprecated
Modified: 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/FBCConstants.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -178,6 +178,36 @@
*/
public static final String or = "or";
+ /**
+ * Introduced to FBC in version 2.
+ */
+ public static final String associatedSpecies = "associatedSpecies";
+
+ /**
+ *
+ */
+ public static final String fluxObjective = "fluxObjective";
+
+ /**
+ *
+ */
+ public static final String objective = "objective";
+
+ /**
+ *
+ */
+ public static final String fluxBound = "fluxBound";
+
+ /**
+ *
+ */
+ public static final String listOfFluxObjectives = "listOfFluxObjectives";
+
+ /**
+ *
+ */
+ public static final String listOfFluxes = "listOfFluxes";
+
static {
namespaces = new ArrayList<String>();
namespaces.add(namespaceURI_L3V1V1);
Modified: 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/GeneProduct.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -23,6 +23,7 @@
import java.util.Map;
import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.UniqueNamedSBase;
/**
@@ -48,6 +49,65 @@
/**
*
*/
+ private String associatedSpecies;
+
+
+ /**
+ * Returns the value of {@link #associatedSpecies}.
+ *
+ * @return the value of {@link #associatedSpecies}.
+ */
+ public String getAssociatedSpecies() {
+ //TODO: if variable is boolean, create an additional "isVar"
+ //TODO: return primitive data type if possible (e.g., int instead of Integer)
+ if (isSetAssociatedSpecies()) {
+ return associatedSpecies;
+ }
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(FBCConstants.associatedSpecies, this);
+ }
+
+
+ /**
+ * Returns whether {@link #associatedSpecies} is set.
+ *
+ * @return whether {@link #associatedSpecies} is set.
+ */
+ public boolean isSetAssociatedSpecies() {
+ return associatedSpecies != null;
+ }
+
+
+ /**
+ * Sets the value of associatedSpecies
+ *
+ * @param associatedSpecies the value of associatedSpecies to be set.
+ */
+ public void setAssociatedSpecies(String associatedSpecies) {
+ String oldAssociatedSpecies = this.associatedSpecies;
+ this.associatedSpecies = associatedSpecies;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, this.associatedSpecies);
+ }
+
+
+ /**
+ * Unsets the variable associatedSpecies.
+ *
+ * @return {@code true} if associatedSpecies was set before, otherwise {@code false}.
+ */
+ public boolean unsetAssociatedSpecies() {
+ if (isSetAssociatedSpecies()) {
+ String oldAssociatedSpecies = associatedSpecies;
+ associatedSpecies = null;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, associatedSpecies);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ */
public GeneProduct() {
super();
initDefaults();
@@ -186,6 +246,8 @@
if (attributeName.equals(FBCConstants.geneProductIdentifier) || attributeName.equals(FBCConstants.label)) {
setLabel(value);
+ } else if (attributeName.equals(FBCConstants.associatedSpecies)) {
+ setAssociatedSpecies(value);
} else {
isAttributeRead = false;
}
@@ -260,6 +322,9 @@
if (isSetLabel()) {
attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.label, getLabel());
}
+ if (isSetAssociatedSpecies()) {
+ attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.associatedSpecies, getAssociatedSpecies());
+ }
return attributes;
}
Modified: 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/Objective.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -313,7 +313,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -69,6 +69,7 @@
* @since 1.0
* @version $Rev$
*/
+@SuppressWarnings("deprecation")
@ProviderFor(ReadingParser.class)
public class FBCParser extends AbstractReaderWriter implements PackageParser {
@@ -191,7 +192,7 @@
*/
// Create the proper object and link it to his parent.
@Override
- @SuppressWarnings({"unchecked", "deprecation"})
+ @SuppressWarnings({"unchecked"})
public Object processStartElement(String elementName, String uri, String prefix,
boolean hasAttributes, boolean hasNamespaces, Object contextObject)
{
@@ -226,7 +227,7 @@
} else if (contextObject instanceof Objective) {
Objective objective = (Objective) contextObject;
- if (elementName.equals("listOfFluxObjectives") || elementName.equals("listOfFluxes")) {
+ if (elementName.equals(FBCConstants.listOfFluxObjectives) || elementName.equals(FBCConstants.listOfFluxes)) {
// listOfFluxes was the first name of listOfFluxObjectives in the preliminary specifications
ListOf<FluxObjective> listOfFluxObjectives = objective.getListOfFluxObjectives();
groupList = FBCList.listOfFluxObjectives;
@@ -285,7 +286,7 @@
else if (contextObject instanceof ListOf<?>) {
ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
- if (elementName.equals("fluxBound")
+ if (elementName.equals(FBCConstants.fluxBound)
&& groupList.equals(FBCList.listOfFluxBounds)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -294,7 +295,7 @@
extendeModel.addFluxBound(fluxBound);
return fluxBound;
- } else if (elementName.equals("objective")
+ } else if (elementName.equals(FBCConstants.objective)
&& groupList.equals(FBCList.listOfObjectives)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -303,7 +304,7 @@
extendeModel.addObjective(objective);
return objective;
- } else if (elementName.equals("fluxObjective")
+ } else if (elementName.equals(FBCConstants.fluxObjective)
&& groupList.equals(FBCList.listOfFluxObjectives)) {
Objective objective = (Objective) listOf.getParentSBMLObject();
@@ -311,7 +312,7 @@
objective.addFluxObjective(fluxObjective);
return fluxObjective;
- } else if (elementName.equals("geneProduct")
+ } else if (elementName.equals(FBCConstants.geneProduct)
&& groupList.equals(FBCList.listOfGeneProducts)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -329,12 +330,13 @@
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.WritingParser#writeElement(org.sbml.jsbml.xml.stax.SBMLObjectForXML, java.lang.Object)
*/
- @SuppressWarnings("deprecation")
@Override
public void writeElement(SBMLObjectForXML xmlObject,
Object sbmlElementToWrite) {
- logger.debug("FBCParser: writeElement");
+ if (logger.isDebugEnabled()) {
+ logger.debug("FBCParser: writeElement");
+ }
if (sbmlElementToWrite instanceof SBase) {
SBase sbase = (SBase) sbmlElementToWrite;
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -33,7 +33,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -103,6 +104,9 @@
this.spatialId = spatialId;
}
+ @Override
+ public abstract AbstractSpatialNamedSBase clone();
+
/**
* Initializes the default values using the namespace.
*/
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -1,143 +1,152 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.spatial;
-
-import java.util.Map;
-
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Alex Thomas
- * @version $Rev$
- * @since 1.0
- * @date Jan 22, 2014
- */
-public abstract class AbstractSpatialSBasePlugin extends AbstractSBasePlugin {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -75143209163226722L;
-
- /**
- *
- */
- public AbstractSpatialSBasePlugin() {
- super();
- initDefaults();
- }
-
- /**
- * @param plugin
- */
- public AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin plugin) {
- super(plugin);
- }
-
- /**
- * @param extendedSBase
- */
- public AbstractSpatialSBasePlugin(SBase extendedSBase) {
- super(extendedSBase);
- initDefaults();
- }
-
- /**
- * 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)
- * @see org.sbml.jsbml.AbstractTreeNode#getParent()
- */
- @Override
- public SBase getParent() {
- if (isSetExtendedSBase()) {
- return (SBase) getExtendedSBase().getParent();
- }
-
- return null;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
- */
- @Override
- public SBase getParentSBMLObject() {
- return getParent();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
- */
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- return super.writeXMLAttributes();
- }
-
- /**
- * @return
- */
- public Model getModel() {
- SBMLDocument doc = getSBMLDocument();
- return doc != null ? doc.getModel() : null;
- }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+import java.util.Map;
+
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+
+/**
+ *
+ * @author Alex Thomas
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date Jan 22, 2014
+ */
+public abstract class AbstractSpatialSBasePlugin extends AbstractSBasePlugin {
+
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -75143209163226722L;
+
+ /**
+ *
+ */
+ public AbstractSpatialSBasePlugin() {
+ super();
+ initDefaults();
+ }
+
+ /**
+ * @param plugin
+ */
+ public AbstractSpatialSBasePlugin(AbstractSpatialSBasePlugin plugin) {
+ super(plugin);
+ }
+
+ /**
+ * @param extendedSBase
+ */
+ public AbstractSpatialSBasePlugin(SBase extendedSBase) {
+ super(extendedSBase);
+ initDefaults();
+ }
+
+ @Override
+ public abstract AbstractSpatialSBasePlugin clone();
+
+ /**
+ * 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)
+ * @see org.sbml.jsbml.AbstractTreeNode#getParent()
+ */
+ @Override
+ public SBase getParent() {
+ if (isSetExtendedSBase()) {
+ return (SBase) getExtendedSBase().getParent();
+ }
+
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
+ */
+ @Override
+ public SBase getParentSBMLObject() {
+ return getParent();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
+ */
+ @Override
+ public String getPackageName() {
+ return SpatialConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
+ */
+ @Override
+ public String getPrefix() {
+ return SpatialConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
+ */
+ @Override
+ public String getURI() {
+ return getElementNamespace();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
+ */
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#writeXMLAttributes()
+ */
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ return super.writeXMLAttributes();
+ }
+
+ /**
+ * @return
+ */
+ public Model getModel() {
+ SBMLDocument doc = getSBMLDocument();
+ return doc != null ? doc.getModel() : null;
+ }
+
+ @Override
+ public String toString() {
+ return super.toString();
+ }
+
+}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -39,14 +39,13 @@
/**
* Generated serial version identifier.
*/
- private static final long serialVersionUID = 8982184068116596444L;
-
+ private static final long serialVersionUID = 8982184068116596444L;
+
/**
*
*/
private CoordinateKind coordinate;
-
/**
*
*/
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -33,7 +33,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -283,5 +284,16 @@
}
return equal;
}
+
+ @Override
+ public int hashCode() {
+ final int prime = 1039;//Change this prime number
+ int hashCode = super.hashCode();
+ if (isSetListOfAnalyticVolumes()) {
+ hashCode += prime * getListOfAnalyticVolumes().hashCode();
+ }
+ return hashCode;
+ }
+
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -35,7 +35,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -102,14 +103,17 @@
public AnalyticVolume(AnalyticVolume node) {
super(node);
if (node.isSetSpatialId()) {
- spatialId = new String(node.getSpatialId());
+ setSpatialId(node.getSpatialId());
}
if (node.isSetOrdinal()) {
- ordinal = new Integer(node.getOrdinal());
+ setOrdinal(node.getOrdinal());
}
if (node.isSetFunctionType()) {
- functionType = node.getFunctionType();
+ setFunctionType(node.getFunctionType());
}
+ if (node.isSetDomainType()) {
+ setDomainType(node.getDomainType());
+ }
}
/**
@@ -302,7 +306,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -315,7 +319,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
@@ -372,7 +376,7 @@
*/
@Override
public int hashCode() {
- final int prime = 431;//Change this prime number
+ final int prime = 1093;//Changed. It was 431
int hashCode = super.hashCode();
if (isSetSpatialId()) {
hashCode += prime * getSpatialId().hashCode();
@@ -411,14 +415,7 @@
attributes.remove("functionType");
attributes.put(SpatialConstants.shortLabel + ":functionType", getFunctionType().toString());
}
- if (isSetSBOTerm()) {
- attributes.remove(TreeNodeChangeEvent.sboTerm);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.sboTerm, getSBOTermID());
- }
- if (isSetMetaId()) {
- attributes.remove(TreeNodeChangeEvent.metaId);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.metaId, getMetaId());
- }
+
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -126,7 +126,7 @@
* @param value
*/
public void setValue(double value) {
- double oldValue = this.value;
+ Double oldValue = this.value;
this.value = value;
firePropertyChange(SpatialConstants.value, oldValue, this.value);
}
@@ -140,7 +140,7 @@
*/
public boolean unsetValue() {
if (isSetValue()) {
- double oldValue = value;
+ Double oldValue = value;
value = null;
firePropertyChange(SpatialConstants.value, oldValue, value);
return true;
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -99,8 +100,20 @@
return new CSGHomogeneousTransformation(this);
}
-
@Override
+ public int hashCode() {
+ final int prime = 1697;
+ int hashCode = super.hashCode();
+ if (isSetForwardTransformation()) {
+ hashCode += prime * getForwardTransformation().hashCode();
+ }
+ if (isSetReverseTransformation()) {
+ hashCode += prime * getReverseTransformation().hashCode();
+ }
+ return hashCode;
+ }
+
+ @Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -79,19 +79,15 @@
*/
public CSGObject(CSGObject csgo) {
super(csgo);
-
if (csgo.isSetDomainType()) {
- domainType = new String(csgo.getDomainType());
+ setDomainType(csgo.getDomainType());
}
-
if (csgo.isSetOrdinal()) {
- ordinal = new Integer(csgo.getOrdinal());
+ setOrdinal(csgo.getOrdinal());
}
-
if (csgo.isSetCSGNode()) {
setCSGNode((CSGNode) csgo.getCSGNode().clone());
}
-
}
@@ -228,7 +224,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -242,7 +238,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
@@ -303,7 +299,7 @@
@Override
public int hashCode() {
- final int prime = 1999;//Change this prime number
+ final int prime = 1669;
int hashCode = super.hashCode();
if (isSetOrdinal()) {
hashCode += prime * getOrdinal();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -103,12 +103,9 @@
*/
public CSGPrimitive(CSGPrimitive csgp) {
super(csgp);
-
-
if (csgp.isSetPrimitiveType()) {
- primitiveType = csgp.getPrimitiveType();
+ setPrimitiveType(csgp.getPrimitiveType());
}
-
}
@@ -213,7 +210,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1081;
int hashCode = super.hashCode();
if (isSetPrimitiveType()) {
hashCode += prime * getPrimitiveType().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -64,11 +64,9 @@
*/
public CSGPseudoPrimitive(CSGPseudoPrimitive csgp) {
super(csgp);
-
if (csgp.isSetCsgObjectRef()) {
- csgObjectRef = new String(csgp.getCsgObjectRef());
+ setCsgObjectRef(csgp.getCsgObjectRef());
}
-
}
@@ -166,7 +164,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1741;
int hashCode = super.hashCode();
if (isSetCsgObjectRef()) {
hashCode += prime * getCsgObjectRef().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -70,17 +71,19 @@
public CSGRotation(CSGRotation csgt) {
super(csgt);
if (csgt.isSetRotateAxisX()) {
- rotateAxisX = new Double(csgt.getRotateAxisX());
+ setRotateAxisX(csgt.getRotateAxisX());
}
if (csgt.isSetRotateAxisY()) {
- rotateAxisY = new Double(csgt.getRotateAxisY());
+ setRotateAxisY(csgt.getRotateAxisY());
}
if (csgt.isSetRotateAxisZ()) {
- rotateAxisZ = new Double(csgt.getRotateAxisZ());
+ setRotateAxisZ(csgt.getRotateAxisZ());
}
+ if (csgt.isSetRotateAngleInRadians()) {
+ setRotateAngleInRadians(csgt.getRotateAngleInRadians());
+ }
}
-
/**
* @param level
* @param version
@@ -165,7 +168,7 @@
* @param rotateAxisX
*/
public void setRotateAxisX(double rotateAxisX) {
- double oldRotateAxisX = this.rotateAxisX;
+ Double oldRotateAxisX = this.rotateAxisX;
this.rotateAxisX = rotateAxisX;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, this.rotateAxisX);
}
@@ -179,7 +182,7 @@
*/
public boolean unsetRotateAxisX() {
if (isSetRotateAxisX()) {
- double oldRotateAxisX = rotateAxisX;
+ Double oldRotateAxisX = rotateAxisX;
rotateAxisX = null;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, rotateAxisX);
return true;
@@ -217,7 +220,7 @@
* @param rotateAxisY
*/
public void setRotateAxisY(double rotateAxisY) {
- double oldRotateAxisY = this.rotateAxisY;
+ Double oldRotateAxisY = this.rotateAxisY;
this.rotateAxisY = rotateAxisY;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, this.rotateAxisY);
}
@@ -231,7 +234,7 @@
*/
public boolean unsetRotateAxisY() {
if (isSetRotateAxisY()) {
- double oldRotateAxisY = rotateAxisY;
+ Double oldRotateAxisY = rotateAxisY;
rotateAxisY = null;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, rotateAxisY);
return true;
@@ -269,7 +272,7 @@
* @param rotateAxisZ
*/
public void setRotateAxisZ(double rotateAxisZ) {
- double oldRotateAxisZ = this.rotateAxisZ;
+ Double oldRotateAxisZ = this.rotateAxisZ;
this.rotateAxisZ = rotateAxisZ;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, this.rotateAxisZ);
}
@@ -283,7 +286,7 @@
*/
public boolean unsetRotateAxisZ() {
if (isSetRotateAxisZ()) {
- double oldRotateAxisZ = rotateAxisZ;
+ Double oldRotateAxisZ = rotateAxisZ;
rotateAxisZ = null;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, rotateAxisZ);
return true;
@@ -321,7 +324,7 @@
* @param rotateAngleInRadians
*/
public void setRotateAngleInRadians(double rotateAngleInRadians) {
- double oldRotateAngleInRadians = this.rotateAngleInRadians;
+ Double oldRotateAngleInRadians = this.rotateAngleInRadians;
this.rotateAngleInRadians = rotateAngleInRadians;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, this.rotateAngleInRadians);
}
@@ -335,7 +338,7 @@
*/
public boolean unsetRotateAngleInRadians() {
if (isSetRotateAngleInRadians()) {
- double oldRotateAngleInRadians = rotateAngleInRadians;
+ Double oldRotateAngleInRadians = rotateAngleInRadians;
rotateAngleInRadians = null;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, rotateAngleInRadians);
return true;
@@ -345,7 +348,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1787;
int hashCode = super.hashCode();
if (isSetRotateAxisX()) {
hashCode += prime * getRotateAxisX();
@@ -367,20 +370,16 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetRotateAxisX()) {
- attributes.remove("rotateAxisX");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", String.valueOf(getRotateAxisX()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", rotateAxisX.toString());
}
if (isSetRotateAxisY()) {
- attributes.remove("rotateAxisY");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", String.valueOf(getRotateAxisY()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", rotateAxisY.toString());
}
if (isSetRotateAxisZ()) {
- attributes.remove("rotateAxisZ");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", String.valueOf(getRotateAxisZ()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", rotateAxisZ.toString());
}
if (isSetRotateAngleInRadians()) {
- attributes.remove("rotateAngleInRadians");
- attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", String.valueOf(getRotateAngleInRadians()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", rotateAngleInRadians.toString());
}
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -30,6 +30,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -68,13 +69,13 @@
public CSGScale(CSGScale csgt) {
super(csgt);
if (csgt.isSetScaleX()) {
- scaleX = new Double(csgt.getScaleX());
+ setScaleX(csgt.getScaleX());
}
if (csgt.isSetScaleY()) {
- scaleY = new Double(csgt.getScaleY());
+ setScaleY(csgt.getScaleY());
}
if (csgt.isSetScaleZ()) {
- scaleZ = new Double(csgt.getScaleZ());
+ setScaleZ(csgt.getScaleZ());
}
}
@@ -159,7 +160,7 @@
* @param scaleX
*/
public void setScaleX(double scaleX) {
- double oldScaleX = this.scaleX;
+ Double oldScaleX = this.scaleX;
this.scaleX = scaleX;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, this.scaleX);
}
@@ -173,7 +174,7 @@
*/
public boolean unsetScaleX() {
if (isSetScaleX()) {
- double oldScaleX = scaleX;
+ Double oldScaleX = scaleX;
scaleX = null;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, scaleX);
return true;
@@ -211,7 +212,7 @@
* @param scaleY
*/
public void setScaleY(double scaleY) {
- double oldScaleY = this.scaleY;
+ Double oldScaleY = this.scaleY;
this.scaleY = scaleY;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, this.scaleY);
}
@@ -225,7 +226,7 @@
*/
public boolean unsetScaleY() {
if (isSetScaleY()) {
- double oldScaleY = scaleY;
+ Double oldScaleY = scaleY;
scaleY = null;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, scaleY);
return true;
@@ -263,7 +264,7 @@
* @param scaleZ
*/
public void setScaleZ(double scaleZ) {
- double oldScaleZ = this.scaleZ;
+ Double oldScaleZ = this.scaleZ;
this.scaleZ = scaleZ;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, this.scaleZ);
}
@@ -277,7 +278,7 @@
*/
public boolean unsetScaleZ() {
if (isSetScaleZ()) {
- double oldScaleZ = scaleZ;
+ Double oldScaleZ = scaleZ;
scaleZ = null;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, scaleZ);
return true;
@@ -288,7 +289,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1777;
int hashCode = super.hashCode();
if (isSetScaleX()) {
hashCode += prime * getScaleX();
@@ -307,16 +308,13 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetScaleX()) {
- attributes.remove("scaleX");
- attributes.put(SpatialConstants.shortLabel + ":scaleX", String.valueOf(getScaleX()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleX", scaleX.toString());
}
if (isSetScaleY()) {
- attributes.remove("scaleY");
- attributes.put(SpatialConstants.shortLabel + ":scaleY", String.valueOf(getScaleY()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleY", scaleY.toString());
}
if (isSetScaleZ()) {
- attributes.remove("scaleZ");
- attributes.put(SpatialConstants.shortLabel + ":scaleZ", String.valueOf(getScaleZ()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleZ", scaleZ.toString());
}
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -36,6 +36,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -105,15 +106,15 @@
}
if (csgso.isSetOperationType()) {
- operationType = csgso.getOperationType();
+ setOperationType(csgso.getOperationType());
}
if (csgso.isSetComplementA()) {
- complementA = new String(csgso.getComplementA());
+ setComplementA(csgso.getComplementA());
}
if (csgso.isSetComplementB()) {
- complementB = new String(csgso.getComplementB());
+ setComplementB(csgso.getComplementB());
}
}
@@ -638,7 +639,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1861;
int hashCode = super.hashCode();
if (isSetOperationType()) {
hashCode += prime * getOperationType().hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-04-30 15:40:25 UTC (rev 2266)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-05-01 09:44:19 UTC (rev 2267)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
Modified: branches/astnode2-merging-...
[truncated message content] |
