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[Jsbml-svn] SF.net SVN: jsbml:[2276] branches/astnode2-merging-alternate/core/src/org/ sbml/jsbml
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From: <nik...@us...> - 2015-05-01 15:12:13
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Revision: 2276
http://sourceforge.net/p/jsbml/code/2276
Author: niko-rodrigue
Date: 2015-05-01 15:12:11 +0000 (Fri, 01 May 2015)
Log Message:
-----------
corrected a bug in SBMLReader that was removing child ASTNode when a cn element with a type attribute was not the first child. I removed the block of code as I don't think we need it any more.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java.oldASTNode 2015-05-01 15:12:11 UTC (rev 2276)
@@ -1670,6 +1670,10 @@
* the node to add as child.
*/
public void addChild(ASTNode child) {
+ if (logger.isDebugEnabled()) {
+ logger.debug(" adding child current node: \n" + astNodeToTree(this, "", ""));
+ logger.debug(" adding child: \n" + astNodeToTree(child, "", ""));
+ }
listOfNodes.add(child);
setParentSBMLObject(child, parentSBMLObject, 0);
child.setParent(this);
@@ -3791,6 +3795,10 @@
*/
public void setType(String typeStr) {
// System.out.println("ASTNode: setType(String) called.");
+ if (logger.isDebugEnabled()) {
+ logger.debug("ASTNode: setType(String) called: " + typeStr);
+ }
+
Type type = Type.getTypeFor(typeStr);
setType(type);
if (type != Type.UNKNOWN) {
@@ -3848,7 +3856,7 @@
setValue(Maths.AVOGADRO_L3V1);
definitionURL = URI_AVOGADRO_DEFINITION;
}
- Type oldValue = getType();
+ Type oldValue = this.type;
this.type = type;
firePropertyChange(TreeNodeChangeEvent.type, oldValue, type);
}
@@ -4223,4 +4231,24 @@
}
}
+ /**
+ * Returns a simple tree view of the ASTNode internal, including mainly
+ * node type and hierarchy.
+ *
+ * @param n
+ * @param tree
+ * @param indent
+ * @return a simple tree view of the ASTNode internal
+ */
+ public static String astNodeToTree(ASTNode n, String tree, String indent) {
+ tree = tree + indent + n.getType() + " " +
+ (n.isInteger() ? n.getInteger() : "") + (n.isReal() ? n.getReal() : "") + "\n";
+
+ for (ASTNode child : n.getChildren()) {
+ tree = astNodeToTree(child, tree, indent + " ");
+ }
+
+ return tree;
+ }
+
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -126,9 +126,9 @@
ASTNode astNode = (ASTNode) contextObject;
// NOTE: By default cn ASTNodes are of type REAL
- if (value.equals("integer")) {
- astNode.setType(Type.INTEGER);
- }
+// if (value.equals("integer")) {
+// astNode.setType(Type.INTEGER);
+// }
// System.out.println("MathMLStaxParser : processAttribute called");
// System.out.println("MathMLStaxParser : processAttribute : element name = " + elementName + ", attribute name = " + attributeName +
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -923,12 +923,13 @@
hasNamespace, sbmlElements.peek());
if (processedElement != null) {
+ /* // TODO - I don't think we need this code any more!?
if (processedElement instanceof ASTNode) {
ASTNode astNode = (ASTNode) processedElement;
if (currentNode.getLocalPart().equals("cn") && hasAttributes) {
- Object object = sbmlElements.peek();
- if (object != null && object instanceof ASTNode) {
- ASTNode parent = (ASTNode) object;
+ // Object object = sbmlElements.peek();
+ // if (object != null && object instanceof ASTNode) {
+ // ASTNode parent = (ASTNode) object;
if (att.next().getValue().equals("integer")) {
astNode.setType(Type.INTEGER);
} else if(att.next().getValue().equals("e-notation")) {
@@ -936,11 +937,13 @@
} else if(att.next().getValue().equals("rational")) {
astNode.setType(Type.RATIONAL);
}
- parent.removeChild(0);
- parent.addChild(astNode);
+ // TODO - wrong, we need to remove the last one! in fact, we don't need to remove and add it again the ASTNode as it's the same
+ // parent.removeChild(0);
+ // parent.addChild(astNode);
}
- }
+ // }
}
+ */
sbmlElements.push(processedElement);
} else {
// It is normal to have sometimes null returned as some of the
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 11:41:21 UTC (rev 2275)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-05-01 15:12:11 UTC (rev 2276)
@@ -178,7 +178,9 @@
// testDocument.checkConsistency();
// System.out.println(XMLNode.convertXMLNodeToString(testDocument.getModel().getAnnotation().getNonRDFannotation()));
-
+
+ System.out.println(ASTNode.astNodeToTree(testDocument.getModel().getReaction(0).getKineticLaw().getMath(), "", ""));
+
System.out.println("Going to check package version and namespace for all elements.");
PackageUtil.checkPackages(testDocument);
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