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[Jsbml-svn] SF.net SVN: jsbml:[1294] trunk
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From: <and...@us...> - 2012-06-10 06:46:39
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Revision: 1294
http://jsbml.svn.sourceforge.net/jsbml/?rev=1294&view=rev
Author: andreas-draeger
Date: 2012-06-10 06:46:32 +0000 (Sun, 10 Jun 2012)
Log Message:
-----------
TextGlyph has now also become an instance of NamedSBaseGlyph. The methods returning an instance of core elements, e.g., getSpeciesInstance() in all derivatives of NamedSBaseGlyph have been removed because it is possible to let ids point to NamedSBases from other packages. Many classes that extend AbstractNamedSBase now have also become UniqueNamedSBase in order to better support their registration in the model.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/Model.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/NamedSBaseGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/ReactionRule.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeRestriction.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeState.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeature.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeatureInstance.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/SymbolicValue.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
Modified: trunk/core/src/org/sbml/jsbml/Model.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/Model.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/core/src/org/sbml/jsbml/Model.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -3929,8 +3929,9 @@
success &= registerId((UnitDefinition) newNsb, !delete);
} else {
// in L3 packages we might have different id namespaces
- logger.error("registerIds : the object " + newNsb.getClass().getCanonicalName() + " is neither " +
- "a UniqueNamedSBase, a LocalParameter or a UnitDefinition so it's id will not be registered in the Model.");
+ logger.error(MessageFormat.format(
+ "registerIds: the object {0} is neither a UniqueNamedSBase, a LocalParameter or a UnitDefinition so its id will not be registered in the Model.",
+ newNsb.getClass().getCanonicalName()));
}
} else if (!newNsb.isIdMandatory()) {
// do nothing
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -95,14 +95,6 @@
return getNamedSBase();
}
- /**
- *
- * @return
- */
- public Compartment getCompartmentInstance() {
- return getNamedSBaseInstance();
- }
-
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.NamedSBaseGlyph#getNamedSBaseInstance()
*/
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -31,6 +31,7 @@
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Species;
+import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.TreeNodeChangeListener;
import org.sbml.jsbml.util.filters.NameFilter;
@@ -43,7 +44,7 @@
* @since 1.0
* @version $Rev$
*/
-public class Layout extends AbstractNamedSBase {
+public class Layout extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
@@ -58,6 +59,7 @@
/**
*
*/
+ // TODO: Why are there methods called addGraphicalObjects and additionalGraphicalObjects?
private ListOf<GraphicalObject> listOfAdditionalGraphicalObjects;
/**
*
@@ -157,7 +159,7 @@
public void addAdditionalGraphical(GraphicalObject object) {
if (object != null) {
registerChild(object);
- listOfAdditionalGraphicalObjects.add(object);
+ getListOfAdditionalGraphicalObjects().add(object);
}
}
@@ -179,7 +181,7 @@
public void addReactionGlyph(ReactionGlyph reactionGlyph) {
if (reactionGlyph != null) {
registerChild(reactionGlyph);
- listOfReactionGlyphs.add(reactionGlyph);
+ getListOfReactionGlyphs().add(reactionGlyph);
}
}
@@ -190,7 +192,7 @@
public void addSpeciesGlyph(SpeciesGlyph speciesGlyph) {
if (speciesGlyph != null) {
registerChild(speciesGlyph);
- listOfSpeciesGlyphs.add(speciesGlyph);
+ getListOfSpeciesGlyphs().add(speciesGlyph);
}
}
@@ -201,7 +203,7 @@
public void addTextGlyph(TextGlyph TextGlyph) {
if (TextGlyph != null) {
registerChild(TextGlyph);
- listOfTextGlyphs.add(TextGlyph);
+ getListOfTextGlyphs().add(TextGlyph);
}
}
@@ -262,15 +264,11 @@
*
* @param id
* the identifier of the {@link CompartmentGlyph} to be created.
- * @param compartment
- * {@link Compartment} ID.
* @return a new {@link CompartmentGlyph}.
+ * @see #createCompartmentGlyph(String, String)
*/
- public CompartmentGlyph createCompartmentGlyph(String id, String compartment) {
- CompartmentGlyph glyph = new CompartmentGlyph(id, getLevel(), getVersion());
- glyph.setCompartment(compartment);
- addCompartmentGlyph(glyph);
- return glyph;
+ public CompartmentGlyph createCompartmentGlyph(String id) {
+ return createCompartmentGlyph(id, null);
}
/**
@@ -278,11 +276,15 @@
*
* @param id
* the identifier of the {@link CompartmentGlyph} to be created.
+ * @param compartment
+ * {@link Compartment} ID.
* @return a new {@link CompartmentGlyph}.
- * @see #createCompartmentGlyph(String, String)
*/
- public CompartmentGlyph createCompartmentGlyph(String id) {
- return createCompartmentGlyph(id, null);
+ public CompartmentGlyph createCompartmentGlyph(String id, String compartment) {
+ CompartmentGlyph glyph = new CompartmentGlyph(id, getLevel(), getVersion());
+ glyph.setCompartment(compartment);
+ addCompartmentGlyph(glyph);
+ return glyph;
}
/**
@@ -325,6 +327,18 @@
*
* @param id
* the identifier of the {@link ReactionGlyph} to be created.
+ * @return a new {@link ReactionGlyph}.
+ * @see #createReactionGlyph(String, String)
+ */
+ public ReactionGlyph createReactionGlyph(String id) {
+ return createReactionGlyph(id, null);
+ }
+
+ /**
+ * Creates and adds a new {@link ReactionGlyph}.
+ *
+ * @param id
+ * the identifier of the {@link ReactionGlyph} to be created.
* @param reaction
* {@link Reaction} ID.
* @return a new {@link ReactionGlyph}.
@@ -335,19 +349,19 @@
addReactionGlyph(glyph);
return glyph;
}
-
+
/**
- * Creates and adds a new {@link ReactionGlyph}.
+ * Creates and adds a new {@link SpeciesGlyph} with the given identifier.
*
* @param id
- * the identifier of the {@link ReactionGlyph} to be created.
- * @return a new {@link ReactionGlyph}.
- * @see #createReactionGlyph(String, String)
+ * the identifier for the {@link SpeciesGlyph} to be created.
+ * @return a new {@link SpeciesGlyph}.
+ * @see #createSpeciesGlyph(String, String)
*/
- public ReactionGlyph createReactionGlyph(String id) {
- return createReactionGlyph(id, null);
+ public SpeciesGlyph createSpeciesGlyph(String id) {
+ return createSpeciesGlyph(id, null);
}
-
+
/**
* Creates and adds a new {@link SpeciesGlyph}.
*
@@ -363,19 +377,19 @@
addSpeciesGlyph(glyph);
return glyph;
}
-
+
/**
- * Creates and adds a new {@link SpeciesGlyph} with the given identifier.
+ * Creates and adds a new {@link TextGlyph}.
*
* @param id
- * the identifier for the {@link SpeciesGlyph} to be created.
- * @return a new {@link SpeciesGlyph}.
- * @see #createSpeciesGlyph(String, String)
+ * the identifier for the {@link TextGlyph} to be created.
+ * @return a new {@link TextGlyph}.
+ * @see #createTextGlyph(String, String)
*/
- public SpeciesGlyph createSpeciesGlyph(String id) {
- return createSpeciesGlyph(id, null);
+ public TextGlyph createTextGlyph(String id) {
+ return createTextGlyph(id, null);
}
-
+
/**
* Creates and adds a new {@link TextGlyph}.
*
@@ -393,18 +407,6 @@
}
/**
- * Creates and adds a new {@link TextGlyph}.
- *
- * @param id
- * the identifier for the {@link TextGlyph} to be created.
- * @return a new {@link TextGlyph}.
- * @see #createTextGlyph(String, String)
- */
- public TextGlyph createTextGlyph(String id) {
- return createTextGlyph(id, null);
- }
-
- /**
* Searches all instances of {@link CompartmentGlyph} within this {@link Layout} that
* refer to the {@link Compartment} with the given id.
*
@@ -424,14 +426,14 @@
*/
@SuppressWarnings("unchecked")
private <T> List<T> findGlyphs(ListOf<? extends T> listOfGlyphs, String id) {
- if (isSetListOfReactionGlyphs()) {
+ if (isSetListOfReactionGlyphs() && (listOfGlyphs != null) && (!listOfGlyphs.isEmpty())) {
NamedSBaseReferenceFilter filter = new NamedSBaseReferenceFilter(id);
filter.setFilterForReference(true);
return (List<T>) listOfReactionGlyphs.filter(filter);
}
return new ArrayList<T>(0);
}
-
+
/**
* Searches all instances of {@link ReactionGlyph} within this {@link Layout} that
* refer to the {@link Reaction} with the given id.
@@ -443,7 +445,7 @@
public List<ReactionGlyph> findReactionGlyphs(String reactionID) {
return findGlyphs(listOfReactionGlyphs, reactionID);
}
-
+
/**
* Searches all instances of {@link SpeciesGlyph} within this {@link Layout} that
* refer to the {@link Species} with the given id.
@@ -455,6 +457,19 @@
public List<SpeciesGlyph> findSpeciesGlyphs(String speciesID) {
return findGlyphs(listOfSpeciesGlyphs, speciesID);
}
+
+ /**
+ * Searches within the {@link #listOfTextGlyphs} for {@link TextGlyph}s whose
+ * {@link TextGlyph#getOriginOfText()} points to the given id.
+ *
+ * @param id
+ * the identifier of the element for which {@link TextGlyph}s are to be
+ * found.
+ * @return all {@link TextGlyph}s associated to an element with the given id.
+ */
+ public List<TextGlyph> findTextGlyphs(String id) {
+ return findGlyphs(listOfTextGlyphs, id);
+ }
/**
*
@@ -683,7 +698,28 @@
/**
*
+ * @param i
+ * @return
*/
+ public TextGlyph getTextGlyph(int i) {
+ return getListOfTextGlyphs().get(i);
+ }
+
+ /**
+ *
+ * @param id
+ * @return
+ */
+ public TextGlyph getTextGlyph(String id) {
+ if (isSetListOfTextGlyphs()) {
+ return listOfTextGlyphs.firstHit(new NameFilter(id));
+ }
+ return null;
+ }
+
+ /**
+ *
+ */
private void initDefault() {
addNamespace(LayoutConstant.namespaceURI);
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/NamedSBaseGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/NamedSBaseGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/NamedSBaseGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -144,6 +144,14 @@
public boolean isSetNamedSBase() {
return (sbaseID != null) && (sbaseID.length() > 0);
}
+
+ /**
+ *
+ * @param namedSBase
+ */
+ public void setNamedSBase(NamedSBase namedSBase) {
+ setNamedSBase(namedSBase.getId());
+ }
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -222,16 +222,8 @@
}
/**
- *
* @return
*/
- public Reaction getReactionInstance() {
- return getNamedSBaseInstance();
- }
-
- /**
- * @return
- */
public boolean isSetCurve() {
return curve != null;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -103,14 +103,6 @@
public String getSpecies() {
return getNamedSBase();
}
-
- /**
- *
- * @return
- */
- public Species getSpeciesInstance() {
- return getNamedSBaseInstance();
- }
/**
* @return the {@link #speciesId}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -204,16 +204,8 @@
}
/**
- *
* @return
*/
- public SimpleSpeciesReference getSpeciesReferenceInstance() {
- return getNamedSBaseInstance();
- }
-
- /**
- * @return
- */
public SpeciesReferenceRole getSpeciesReferenceRole() {
return role;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -21,8 +21,10 @@
import java.util.Map;
+import org.sbml.jsbml.NamedSBase;
+
/**
* @author Nicolas Rodriguez
* @author Sebastian Frölich
@@ -30,7 +32,7 @@
* @since 1.0
* @version $Rev$
*/
-public class TextGlyph extends GraphicalObject {
+public class TextGlyph extends NamedSBaseGlyph {
/**
* Generated serial version identifier.
@@ -45,11 +47,6 @@
/**
*
*/
- private String originOfText;
-
- /**
- *
- */
private String text;
/**
@@ -96,12 +93,12 @@
*/
public TextGlyph(TextGlyph textGlyph) {
super(textGlyph);
-
- // TODO : use the iSet methods
-
- this.graphicalObject = new String(textGlyph.getGraphicalObject());
- this.originOfText = new String(textGlyph.getOriginOfText());
- this.text = new String(textGlyph.getText());
+ if (textGlyph.isSetGraphicalObject()) {
+ this.graphicalObject = new String(textGlyph.getGraphicalObject());
+ }
+ if (textGlyph.isSetText()) {
+ this.text = new String(textGlyph.getText());
+ }
}
/* (non-Javadoc)
@@ -149,7 +146,7 @@
* @return
*/
public String getOriginOfText() {
- return originOfText;
+ return getNamedSBase();
}
/**
@@ -191,7 +188,7 @@
* @return
*/
public boolean isSetOriginOfText() {
- return originOfText != null;
+ return isSetNamedSBase();
}
/**
@@ -250,10 +247,16 @@
*
* @param originOfText
*/
+ public void setOriginOfText(NamedSBase originOfText) {
+ setNamedSBase(originOfText);
+ }
+
+ /**
+ *
+ * @param originOfText
+ */
public void setOriginOfText(String originOfText) {
- String oldOriginOfText = this.originOfText;
- this.originOfText = originOfText;
- firePropertyChange(LayoutConstant.originOfText, oldOriginOfText, this.originOfText);
+ setNamedSBase(originOfText);
}
/**
@@ -283,7 +286,7 @@
}
if (isSetOriginOfText()) {
attributes.put(LayoutConstant.shortLabel + ":"
- + LayoutConstant.originOfText, originOfText);
+ + LayoutConstant.originOfText, getOriginOfText());
}
return attributes;
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/ReactionRule.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/ReactionRule.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/ReactionRule.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -8,7 +8,12 @@
public class ReactionRule extends AbstractNamedSBase {
- ListOf<SpeciesTypeRestrictionReference> listOfConditions;
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = 7757296070294814156L;
+
+ ListOf<SpeciesTypeRestrictionReference> listOfConditions;
ListOf<SpeciesTypeRestrictionReference> listOfResults;
// TODO : add a kineticLaw
@@ -113,10 +118,17 @@
return false;
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
+ */
+ //@Override
public boolean isIdMandatory() {
return false;
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#clone()
+ */
@Override
public AbstractSBase clone() {
// TODO
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -6,7 +6,12 @@
public class SpeciesTypeInstance extends AbstractNamedSBase {
- private double initialAmount;
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = 1775590492963078468L;
+
+ private double initialAmount;
private double initialConcentration;
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeRestriction.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeRestriction.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeRestriction.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -5,7 +5,11 @@
public class SpeciesTypeRestriction extends AbstractNamedSBase {
- private String speciesTypeInstance;
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -6703552149441215128L;
+ private String speciesTypeInstance;
/**
* Returns the speciesTypeInstance.
@@ -25,11 +29,17 @@
this.speciesTypeInstance = speciesTypeInstance;
}
-
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
+ */
+ //@Override
public boolean isIdMandatory() {
return false;
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#clone()
+ */
@Override
public AbstractSBase clone() {
// TODO
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeState.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeState.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeState.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -15,6 +15,11 @@
public class SpeciesTypeState extends AbstractNamedSBase implements UniqueNamedSBase {
/**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = 7110790636241167977L;
+
+ /**
*
*/
private String speciesType;
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeature.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeature.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeature.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -23,6 +23,10 @@
public class StateFeature extends AbstractNamedSBase implements UniqueNamedSBase {
/**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -1796119514784158560L;
+ /**
*
*/
ListOf<PossibleValue> listOfPossibleValues;
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeatureInstance.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeatureInstance.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/StateFeatureInstance.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -11,7 +11,12 @@
public class StateFeatureInstance extends AbstractNamedSBase {
- private String stateFeature;
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = 3961860838884568696L;
+
+ private String stateFeature;
private ListOf<StateFeatureValue> listOfStateFeatureValues;
@@ -23,10 +28,17 @@
initDefaults();
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
+ */
+ //@Override
public boolean isIdMandatory() {
return false;
}
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractSBase#clone()
+ */
@Override
public AbstractSBase clone() {
// TODO
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -40,7 +40,7 @@
* @since 1.0
* @date $Date$
*/
-public class QualitativeSpecies extends AbstractNamedSBase implements UniqueNamedSBase{
+public class QualitativeSpecies extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/SymbolicValue.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/SymbolicValue.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/SymbolicValue.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -35,7 +35,7 @@
* @since 1.0
* @date $Date$
*/
-public class SymbolicValue extends AbstractNamedSBase implements UniqueNamedSBase{
+public class SymbolicValue extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
@@ -210,6 +210,7 @@
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
+ @Override
public boolean readAttribute(String attributeName, String prefix, String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
@@ -230,6 +231,7 @@
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
*/
+ @Override
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -28,6 +28,7 @@
import org.sbml.jsbml.LevelVersionError;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.UniqueNamedSBase;
/**
@@ -39,7 +40,7 @@
* @since 1.0
* @date 08.05.2012
*/
-public class GradientBase extends AbstractNamedSBase {
+public class GradientBase extends AbstractNamedSBase implements UniqueNamedSBase {
/**
*
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -29,6 +29,7 @@
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.filters.NameFilter;
/**
@@ -40,7 +41,7 @@
* @since 1.0
* @date 04.05.2012
*/
-public class RenderInformationBase extends AbstractNamedSBase {
+public class RenderInformationBase extends AbstractNamedSBase implements UniqueNamedSBase {
/**
*
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java 2012-06-08 14:48:51 UTC (rev 1293)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java 2012-06-10 06:46:32 UTC (rev 1294)
@@ -26,6 +26,7 @@
import org.sbml.jsbml.LevelVersionError;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.UniqueNamedSBase;
/**
* @author Eugen Netz
@@ -36,7 +37,7 @@
* @since 1.0
* @date 08.05.2012
*/
-public class Style extends AbstractNamedSBase {
+public class Style extends AbstractNamedSBase implements UniqueNamedSBase {
/**
*
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