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[Jsbml-svn] SF.net SVN: jsbml:[1301] trunk
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From: <and...@us...> - 2012-06-12 06:21:38
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Revision: 1301
http://jsbml.svn.sourceforge.net/jsbml/?rev=1301&view=rev
Author: andreas-draeger
Date: 2012-06-12 06:21:26 +0000 (Tue, 12 Jun 2012)
Log Message:
-----------
Added several convenient methods and avoided null pointer exceptions when dealing with user objects.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
trunk/core/src/org/sbml/jsbml/SBO.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/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
Modified: trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -61,6 +61,7 @@
* @return the index of the child in the parent's list of children or -1 if no
* such child can be found.
*/
+ @SuppressWarnings("unchecked")
public static int indexOf(TreeNode parent, TreeNode child) {
if (child == null) {
throw new IllegalArgumentException("Argument is null.");
@@ -249,7 +250,7 @@
*/
//@Override
public boolean containsUserObjectKey(Object key) {
- return userObjects.containsKey(key);
+ return isSetUserObjects() ? userObjects.containsKey(key) : false;
}
/* (non-Javadoc)
Modified: trunk/core/src/org/sbml/jsbml/SBO.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBO.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/core/src/org/sbml/jsbml/SBO.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -700,6 +700,15 @@
return 534;
}
+ /**
+ * Physical compartment.
+ *
+ * @return
+ */
+ public static int getCompartment() {
+ return 290;
+ }
+
/**
*
* @return
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CompartmentGlyph.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -94,14 +94,6 @@
public String getCompartment() {
return getNamedSBase();
}
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.layout.NamedSBaseGlyph#getNamedSBaseInstance()
- */
- @Override
- public Compartment getNamedSBaseInstance() {
- return (Compartment) super.getNamedSBaseInstance();
- }
/**
* @return
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -479,6 +479,14 @@
return null;
}
+ /**
+ *
+ * @return
+ */
+ public int getAdditionalGraphicalObjectCount() {
+ return isSetListOfAdditionalGraphicalObjects() ? listOfAdditionalGraphicalObjects.size() : 0;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
*/
@@ -531,7 +539,7 @@
throw new IndexOutOfBoundsException(String.format("Index %d >= %d",
index, +((int) Math.min(pos, 0))));
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildCount()
*/
@@ -558,7 +566,7 @@
}
return count;
}
-
+
/**
*
* @param i
@@ -567,7 +575,7 @@
public CompartmentGlyph getCompartmentGlyph(int i) {
return getListOfCompartmentGlyphs().get(i);
}
-
+
/**
*
* @param id
@@ -584,10 +592,19 @@
*
* @return
*/
+ public int getCompartmentGlyphCount() {
+ return isSetListOfCompartmentGlyphs() ? listOfCompartmentGlyphs.size() : 0;
+ }
+
+ /**
+ *
+ * @return
+ */
public Dimensions getDimensions() {
return dimensions;
}
-
+
+
/**
*
* @return
@@ -599,7 +616,7 @@
}
return listOfAdditionalGraphicalObjects;
}
-
+
/**
*
* @return
@@ -611,7 +628,6 @@
}
return listOfCompartmentGlyphs;
}
-
/**
*
@@ -624,7 +640,7 @@
}
return listOfReactionGlyphs;
}
-
+
/**
*
* @return
@@ -669,16 +685,24 @@
}
return null;
}
-
+
/**
*
+ * @return
+ */
+ public int getReactionGlyphCount() {
+ return isSetListOfReactionGlyphs() ? listOfReactionGlyphs.size() : 0;
+ }
+
+ /**
+ *
* @param i
* @return
*/
public SpeciesGlyph getSpeciesGlyph(int i) {
return getListOfSpeciesGlyphs().get(i);
}
-
+
/**
*
* @param id
@@ -690,16 +714,24 @@
}
return null;
}
-
+
/**
*
+ * @return
+ */
+ public int getSpeciesGlyphCount() {
+ return isSetListOfSpeciesGlyphs() ? listOfSpeciesGlyphs.size() : 0;
+ }
+
+ /**
+ *
* @param i
* @return
*/
public TextGlyph getTextGlyph(int i) {
return getListOfTextGlyphs().get(i);
}
-
+
/**
*
* @param id
@@ -711,14 +743,22 @@
}
return null;
}
-
+
/**
*
+ * @return
*/
+ public int getTextGlyphCount() {
+ return isSetListOfTextGlyphs() ? listOfTextGlyphs.size() : 0;
+ }
+
+ /**
+ *
+ */
private void initDefault() {
addNamespace(LayoutConstants.namespaceURI);
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@@ -726,21 +766,21 @@
// See "Including Layout Information in SBML Files" Version 2.2, p. 6
return true;
}
-
+
/**
* @return
*/
public boolean isSetAddGraphicalObjects() {
return (listOfAdditionalGraphicalObjects != null) && (listOfAdditionalGraphicalObjects.size() > 0);
}
-
+
/**
* @return
*/
public boolean isSetDimensions() {
return dimensions != null;
}
-
+
/**
* @return
*/
@@ -769,14 +809,14 @@
public boolean isSetListOfSpeciesGlyphs() {
return (listOfSpeciesGlyphs != null) && (listOfSpeciesGlyphs.size() > 0);
}
-
+
/**
* @return
*/
public boolean isSetListOfTextGlyphs() {
return (listOfTextGlyphs != null) && (listOfTextGlyphs.size() > 0);
}
-
+
/**
* @param attributeName
* @param prefix
@@ -814,7 +854,7 @@
this.dimensions = dimensions;
registerChild(this.dimensions);
}
-
+
/**
*
* @param AdditionalGraphicalObjects
@@ -827,7 +867,7 @@
registerChild(this.listOfAdditionalGraphicalObjects);
}
}
-
+
/**
*
* @param compartmentGlyphs
@@ -840,7 +880,7 @@
}
registerChild(this.listOfCompartmentGlyphs);
}
-
+
/**
*
* @param reactionGlyphs
@@ -853,7 +893,7 @@
registerChild(this.listOfReactionGlyphs);
}
}
-
+
/**
*
* @param speciesGlyphs
@@ -870,7 +910,7 @@
registerChild(this.listOfSpeciesGlyphs);
}
}
-
+
/**
*
* @param textGlyphs
@@ -883,7 +923,7 @@
registerChild(this.listOfTextGlyphs);
}
}
-
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#toString()
*/
@@ -891,7 +931,7 @@
public String toString() {
return getElementName();
}
-
+
/**
* Removes the {@link #listOfAdditionalGraphicalObjects} from this {@link Model} and notifies
* all registered instances of {@link TreeNodeChangeListener}.
@@ -925,7 +965,7 @@
}
return false;
}
-
+
/**
* Removes the {@link #listOfReactionGlyphs} from this {@link Model} and notifies
* all registered instances of {@link TreeNodeChangeListener}.
@@ -959,7 +999,7 @@
}
return false;
}
-
+
/**
* Removes the {@link #listOfTextGlyphs} from this {@link Model} and notifies
* all registered instances of {@link TreeNodeChangeListener}.
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -205,14 +205,6 @@
return listOfSpeciesReferencesGlyph;
}
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.layout.NamedSBaseGlyph#getNamedSBaseInstance()
- */
- @Override
- public Reaction getNamedSBaseInstance() {
- return (Reaction) super.getNamedSBaseInstance();
- }
-
/**
*
* @return
@@ -331,7 +323,7 @@
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetReaction()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.reaction, getReaction());
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesGlyph.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -87,14 +87,6 @@
public SpeciesGlyph clone() {
return new SpeciesGlyph(this);
}
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.layout.NamedSBaseGlyph#getNamedSBaseInstance()
- */
- @Override
- public Species getNamedSBaseInstance() {
- return (Species) super.getNamedSBaseInstance();
- }
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -179,14 +179,6 @@
return curve;
}
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.layout.NamedSBaseGlyph#getNamedSBaseInstance()
- */
- @Override
- public SimpleSpeciesReference getNamedSBaseInstance() {
- return (SimpleSpeciesReference) super.getNamedSBaseInstance();
- }
-
/**
*
* @return
@@ -356,15 +348,15 @@
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetSpeciesGlyph()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.speciesGlyph, speciesGlyph);
}
if (isSetSpeciesReference()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.speciesReference, getSpeciesReference());
}
if (isSetSpeciesReferenceRole()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.role, role.toString().toLowerCase());
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2012-06-11 19:29:10 UTC (rev 1300)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/TextGlyph.java 2012-06-12 06:21:26 UTC (rev 1301)
@@ -285,15 +285,15 @@
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetGraphicalObject()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.graphicalObject, graphicalObject);
}
if (isSetText()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.text, text);
}
if (isSetOriginOfText()) {
- attributes.put(LayoutConstants.shortLabel + ":"
+ attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.originOfText, getOriginOfText());
}
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