Menu
▾
▴
[Jsbml-svn] SF.net SVN: jsbml:[2469] trunk/extensions/multi/src/org/sbml/jsbml
|
From: <nik...@us...> - 2016-01-21 16:28:11
|
Revision: 2469
http://sourceforge.net/p/jsbml/code/2469
Author: niko-rodrigue
Date: 2016-01-21 16:28:08 +0000 (Thu, 21 Jan 2016)
Log Message:
-----------
corrected the MultiParser class so that the ASTNode multi attributes are read properly and so that it write correctly 'listOfSpeciesTypeComponentIndexes' + made MultiASTNodePlugin extends AbstractASTNodePlugin
Modified Paths:
--------------
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiASTNodePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiASTNodePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiASTNodePlugin.java 2016-01-21 15:37:40 UTC (rev 2468)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiASTNodePlugin.java 2016-01-21 16:28:08 UTC (rev 2469)
@@ -5,7 +5,7 @@
* 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) 2009-2014 jointly by the following organizations:
+ * Copyright (C) 2009-2016 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
@@ -24,7 +24,11 @@
import java.util.HashMap;
import java.util.Map;
+import javax.swing.tree.TreeNode;
+
+import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.ext.AbstractASTNodePlugin;
/**
*
@@ -32,7 +36,7 @@
* @version $Rev$
* @since 1.1
*/
-public class MultiASTNodePlugin {
+public class MultiASTNodePlugin extends AbstractASTNodePlugin {
/**
*
@@ -48,9 +52,24 @@
*
*/
public MultiASTNodePlugin() {
- // TODO
+ super();
}
+ public MultiASTNodePlugin(MultiASTNodePlugin multiASTNodePlugin) {
+ super(multiASTNodePlugin);
+
+ if (multiASTNodePlugin.isSetRepresentationType()) {
+ setRepresentationType(multiASTNodePlugin.getRepresentationType());
+ }
+ if (multiASTNodePlugin.isSetSpeciesReference()) {
+ setSpeciesReference(multiASTNodePlugin.getSpeciesReference());
+ }
+ }
+
+ public MultiASTNodePlugin(ASTNode astNode) {
+ super(astNode);
+ }
+
/**
* Returns the value of {@link #speciesReference}.
*
@@ -84,7 +103,7 @@
public void setSpeciesReference(String speciesReference) {
String oldSpeciesReference = this.speciesReference;
this.speciesReference = speciesReference;
- // firePropertyChange(MultiConstants.speciesReference, oldSpeciesReference, this.speciesReference);
+ firePropertyChange(MultiConstants.speciesReference, oldSpeciesReference, this.speciesReference);
}
@@ -97,7 +116,7 @@
if (isSetSpeciesReference()) {
String oldSpeciesReference = speciesReference;
speciesReference = null;
- // firePropertyChange(MultiConstants.speciesReference, oldSpeciesReference, this.speciesReference);
+ firePropertyChange(MultiConstants.speciesReference, oldSpeciesReference, this.speciesReference);
return true;
}
return false;
@@ -111,13 +130,9 @@
* @return the value of {@link #representationType}.
*/
public RepresentationType getRepresentationType() {
- //TODO: if variable is boolean, create an additional "isVar"
- //TODO: return primitive data type if possible (e.g., int instead of Integer)
if (isSetRepresentationType()) {
return representationType;
}
- // 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(MultiConstants.representationType, this);
return null;
}
@@ -141,7 +156,7 @@
public void setRepresentationType(RepresentationType representationType) {
RepresentationType oldRepresentationType = this.representationType;
this.representationType = representationType;
- // firePropertyChange(MultiConstants.representationType, oldRepresentationType, this.representationType);
+ firePropertyChange(MultiConstants.representationType, oldRepresentationType, this.representationType);
}
@@ -154,7 +169,7 @@
if (isSetRepresentationType()) {
RepresentationType oldRepresentationType = representationType;
representationType = null;
- // firePropertyChange(MultiConstants.representationType, oldRepresentationType, this.representationType);
+ firePropertyChange(MultiConstants.representationType, oldRepresentationType, this.representationType);
return true;
}
return false;
@@ -209,8 +224,8 @@
*/
@Override
public int hashCode() {
- final int prime = 31;
- int result = 1;
+ final int prime = 857;
+ int result = super.hashCode();
result = prime * result
+ ((representationType == null) ? 0 : representationType.hashCode());
result = prime * result
@@ -227,12 +242,11 @@
if (this == obj) {
return true;
}
- if (obj == null) {
+
+ if (! super.equals(obj)) {
return false;
}
- if (getClass() != obj.getClass()) {
- return false;
- }
+
MultiASTNodePlugin other = (MultiASTNodePlugin) obj;
if (representationType != other.representationType) {
return false;
@@ -257,5 +271,40 @@
+ ", representationType=" + representationType + "]";
}
+ @Override
+ public String getPackageName() {
+ return MultiConstants.packageName;
+ }
+ @Override
+ public String getPrefix() {
+ return MultiConstants.packageName;
+ }
+
+ @Override
+ public String getURI() {
+ return getElementNamespace();
+ }
+
+ @Override
+ public TreeNode getChildAt(int childIndex) {
+ return null;
+ }
+
+ @Override
+ public int getChildCount() {
+ return 0;
+ }
+
+ @Override
+ public boolean getAllowsChildren() {
+ return false;
+ }
+
+ @Override
+ public MultiASTNodePlugin clone() {
+ return new MultiASTNodePlugin(this);
+ }
+
+
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java 2016-01-21 15:37:40 UTC (rev 2468)
+++ trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java 2016-01-21 16:28:08 UTC (rev 2469)
@@ -44,6 +44,7 @@
import org.sbml.jsbml.ext.ASTNodePlugin;
import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.multi.IntraSpeciesReaction;
+import org.sbml.jsbml.ext.multi.MultiASTNodePlugin;
import org.sbml.jsbml.ext.multi.MultiCompartmentPlugin;
import org.sbml.jsbml.ext.multi.MultiConstants;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
@@ -152,7 +153,7 @@
}
} else if (contextObject instanceof ASTNode) {
contextObject = ((ASTNode) contextObject).getPlugin(getShortLabel());
- } // TODO - ASTNode2 ?
+ } // TODO - ASTNode2 when it is used for reading.
super.processAttribute(elementName, attributeName, value, uri, prefix, isLastAttribute, contextObject);
}
@@ -281,7 +282,9 @@
if (xmlObject.isSetName() && xmlObject.getName().equals("listOfBindingSiteSpeciesTypes")) {
xmlObject.setName(MultiConstants.listOfSpeciesTypes);
}
-
+ else if (xmlObject.isSetName() && xmlObject.getName().equals("listOfSpeciesTypeComponentIndexs")) {
+ xmlObject.setName(MultiConstants.listOfSpeciesTypeComponentIndexes);
+ }
// listOfIntraSpeciesReactions cannot happen as core ListOf don't depend on the first element for their name.
if (logger.isDebugEnabled()) {
@@ -343,7 +346,7 @@
public ASTNodePlugin createPluginFor(ASTNode astNode) {
if (astNode != null) {
- return null; // TODO
+ return new MultiASTNodePlugin(astNode);
}
return null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
