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[Jsbml-svn] SF.net SVN: jsbml:[1305] trunk
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From: <nik...@us...> - 2012-06-12 16:01:27
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Revision: 1305
http://jsbml.svn.sourceforge.net/jsbml/?rev=1305&view=rev
Author: niko-rodrigue
Date: 2012-06-12 16:01:16 +0000 (Tue, 12 Jun 2012)
Log Message:
-----------
corrected AbstractSBase.addExtension to not add the extension namespace to the list of namespaces and stax/SBMLWriter to use the namespaces from the extensions Map instead of the SBase list of namespaces (which should a single namespace in fact) + cleaned a bit the RenderParser
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java
trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2012-06-12 13:15:01 UTC (rev 1304)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2012-06-12 16:01:16 UTC (rev 1305)
@@ -280,7 +280,6 @@
*/
public void addExtension(String namespace, SBasePlugin sbase) {
this.extensions.put(namespace, sbase);
- addNamespace(namespace);
firePropertyChange(TreeNodeChangeEvent.addExtension, null, sbase);
}
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java 2012-06-12 13:15:01 UTC (rev 1304)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java 2012-06-12 16:01:16 UTC (rev 1305)
@@ -175,6 +175,9 @@
listOfElementsToWrite.add(children.nextElement());
}
+ logger.debug("getListOfSBMLElementsToWrite : nb children = " + listOfElementsToWrite.size());
+ logger.debug("getListOfSBMLElementsToWrite : children = " + listOfElementsToWrite);
+
if (listOfElementsToWrite.isEmpty()) {
listOfElementsToWrite = null;
}
@@ -223,6 +226,14 @@
if (sbmlElementToWrite instanceof SBase) {
SBase sbase = (SBase) sbmlElementToWrite;
+ logger.debug("writeElement : sbase.namespaces size = " + sbase.getNamespaces().size());
+ logger.debug("writeElement : sbase.namespaces = " + sbase.getNamespaces());
+
+ if (!sbase.getNamespaces().contains(getNamespaceURI())) {
+ logger.debug("writeElement : rejected element");
+ return;
+ }
+
if (!xmlObject.isSetName()) {
if (sbase instanceof ListOf<?>) {
ListOf<?> listOf = (ListOf<?>) sbase;
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2012-06-12 13:15:01 UTC (rev 1304)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2012-06-12 16:01:16 UTC (rev 1305)
@@ -290,7 +290,7 @@
if (object instanceof SBase) {
SBase sbase = (SBase) object;
- packageNamespaces = sbase.getNamespaces();
+ packageNamespaces = sbase.getExtensionPackages().keySet();
} else if (object instanceof Annotation) {
Annotation annotation = (Annotation) object;
packageNamespaces = annotation.getNamespaces();
Modified: trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java 2012-06-12 13:15:01 UTC (rev 1304)
+++ trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java 2012-06-12 16:01:16 UTC (rev 1305)
@@ -58,67 +58,7 @@
*/
private Logger logger = Logger.getLogger(RenderParser.class);
- /* (non-Javadoc)
- * @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getListOfSBMLElementsToWrite(java.lang.Object)
- */
- @Override
- public ArrayList<Object> getListOfSBMLElementsToWrite(Object sbase) {
- if (logger.isDebugEnabled()) {
- logger.debug("getListOfSBMLElementsToWrite : " + sbase.getClass().getCanonicalName());
- }
-
- ArrayList<Object> listOfElementsToWrite = new ArrayList<Object>();
-
- if (sbase instanceof SBMLDocument) {
- // nothing to do
- // TODO : the 'required' attribute is written even if there is no plugin class for the SBMLDocument, so I am not totally sure how this is done.
- }
- else if (sbase instanceof ListOf<?>) {
- // if the sbase is a ListOf, we could have a RenderModelPlugin attached to it
- ListOf<?> listOf = (ListOf<?>)sbase;
- if (listOf.getSBaseListType() == Type.other) {
-
- SBasePlugin plugin = listOf.getExtension(RenderConstants.namespaceURI);
-
- if (plugin != null) {
- RenderModelPlugin rmp = (RenderModelPlugin) plugin;
-
- // then add its extension children to the list of elements to write
- Enumeration<TreeNode> children = rmp.children();
- while (children.hasMoreElements()) {
- listOfElementsToWrite.add(children.nextElement());
- }
- }
- }
- }
- else if (sbase instanceof Layout) {
- // if the sbase is a Layout get its extension
- RenderLayoutPlugin rlp = (RenderLayoutPlugin)((Layout)sbase).getExtension(RenderConstants.namespaceURI);
-
- // then add its extension children to the list of elements to write
- Enumeration<TreeNode> children = rlp.children();
- while (children.hasMoreElements()) {
- listOfElementsToWrite.add(children.nextElement());
- }
- }
- else if (sbase instanceof TreeNode) {
- Enumeration<TreeNode> children = ((TreeNode) sbase).children();
-
- while (children.hasMoreElements()) {
- listOfElementsToWrite.add(children.nextElement());
- }
- }
-
- if (listOfElementsToWrite.isEmpty()) {
- listOfElementsToWrite = null;
- } else if (logger.isDebugEnabled()) {
- logger.debug("getListOfSBMLElementsToWrite size = " + listOfElementsToWrite.size());
- }
-
- return listOfElementsToWrite;
- }
-
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#processStartElement(java.lang.String, java.lang.String, boolean, boolean, java.lang.Object)
*/
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