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[Jsbml-svn] SF.net SVN: jsbml:[2457] trunk/core/src/org/sbml/jsbml/xml/parsers/ MathMLStaxParser.java
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From: <nik...@us...> - 2015-12-15 15:04:46
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Revision: 2457
http://sourceforge.net/p/jsbml/code/2457
Author: niko-rodrigue
Date: 2015-12-15 15:04:43 +0000 (Tue, 15 Dec 2015)
Log Message:
-----------
implement reading of mathML semantics annotations
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-15 11:58:07 UTC (rev 2456)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-15 15:04:43 UTC (rev 2457)
@@ -26,6 +26,7 @@
import java.util.List;
import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
@@ -35,6 +36,10 @@
import org.sbml.jsbml.MathContainer;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.xml.XMLAttributes;
+import org.sbml.jsbml.xml.XMLNamespaces;
+import org.sbml.jsbml.xml.XMLNode;
+import org.sbml.jsbml.xml.XMLTriple;
/**
* A MathMLStaxParser is used to parse the MathML expressions injected into a SBML
@@ -66,7 +71,7 @@
* otherwise the XML version will appear at the beginning of the output.
*/
private boolean omitXMLDeclaration;
-
+
/**
* A {@link Logger} for this class.
*/
@@ -117,6 +122,13 @@
// Process the possible attributes.
// the sbml:units attribute is handle by the SBMLCoreParser.
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+ xmlNode.addAttr(attributeName, value, uri, prefix);
+ return;
+ }
+
if (! (contextObject instanceof ASTNode)) {
logger.debug("processAttribute : !!!!!!!!! context is not an ASTNode (" +
contextObject.getClass());
@@ -162,6 +174,15 @@
logger.debug("processCharactersOf : element name = " + elementName + ", characters = " + characters);
}
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ XMLNode textNode = new XMLNode(characters);
+ xmlNode.addChild(textNode);
+ return;
+ }
+
// Depending of the type of ASTNode, we need to do different things
if (! (contextObject instanceof ASTNode)) {
logger.debug("processCharactersOf : !!!!!!!!! context is not an ASTNode (" +
@@ -243,6 +264,47 @@
logger.debug("processEndElement : element name = " + elementName);
}
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ if (xmlNode.getChildCount() == 0) {
+ xmlNode.setEnd();
+ }
+
+ // if elementName.equals(semantics) add all child elements as semanticsAnnotation to the parent ASTNode !
+ if (elementName.equals("semantics"))
+ {
+ TreeNode parentNode = xmlNode.getParent();
+
+ if (parentNode instanceof ASTNode)
+ {
+ // we are at the end of the top level 'semantics' element.
+ // adding all child elements that are not empty as semanticAnnotation // TODO - keep the top level 'semantics' element if not empty.
+
+ for (XMLNode childNode : xmlNode.getChildElements(null, null))
+ {
+ if (childNode.isText() && childNode.getCharacters().trim().length() == 0) {
+ continue;
+ }
+ ((ASTNode) parentNode).addSemanticsAnnotation(childNode);
+
+// try {
+// System.out.println("MathMLStaxParser - processEndElement - semantic annotation = \n" + childNode.toXMLString());
+// } catch (XMLStreamException e) {
+// e.printStackTrace();
+// }
+ }
+
+ // System.out.println("MathMLStaxParser - processEndElement - num semantic annotation = " + ((ASTNode) parentNode).getNumSemanticsAnnotations());
+ }
+
+ }
+
+ // always remove the XMLNode from the stack.
+ return true;
+ }
+
if (elementName.equals("sep")) {
return false;
} else if (contextObject instanceof MathContainer) {
@@ -276,12 +338,29 @@
* @see org.sbml.jsbml.xml.ReadingParser#processNamespace(String elementName, String URI, String prefix, String localName, boolean hasAttributes, boolean isLastNamespace, Object contextObject)
*/
@Override
- public void processNamespace(String elementName, String URI, String prefix,
+ public void processNamespace(String elementName, String uri, String prefix,
String localName, boolean hasAttributes, boolean isLastNamespace,
Object contextObject)
{
- // TODO
+
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ if (!xmlNode.isStart()) {
+ logger.debug(MessageFormat.format(
+ "processNamespace: context Object is not a start node! {0}",
+ contextObject));
+ }
+ if (localName == null || localName.trim().length() == 0) {
+ localName = "xmlns";
+ }
+
+ xmlNode.addNamespace(uri, localName);
+ }
+
+ // TODO - store namespaces on mathML elements !
+
logger.debug("processNamespace called");
}
@@ -306,7 +385,7 @@
{
if (elementName.equals("apply"))
{
- lastElementWasApply = true;
+ lastElementWasApply = true; // TODO - write the booleans inside a user object to make the parser multi-thread safe ?
}
else
{
@@ -340,12 +419,46 @@
parentASTNode = mathContainer.getMath();
// System.out.println("MathMLStaxParser: processStartElement parent type: " + parentASTNode.getType());
}
+
+ if (elementName.equals("semantics"))
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ xmlNode.setParent(parentASTNode);
+
+ return xmlNode;
+ }
+
} else if (contextObject instanceof ASTNode) {
parentASTNode = ((ASTNode) contextObject);
mathContainer = parentASTNode.getParentSBMLObject();
// System.out.println("MathMLStaxParser: processStartElement parent type: " + parentASTNode.getType());
- } else {
+
+ // if semantics, create a new XMLNode and return it. Set the ASTNode as the parent so that
+ // we can add the semanticsAnnotation element in the #processEndElement method.
+ if (elementName.equals("semantics"))
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ xmlNode.setParent(parentASTNode);
+
+ return xmlNode;
+ }
+ }
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ else if (contextObject instanceof XMLNode)
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ XMLNode parentNode = (XMLNode) contextObject;
+
+ parentNode.addChild(xmlNode);
+
+ return xmlNode;
+ }
+ else
+ {
// Should never happen
logger.debug("processStartElement: !!!!!!!!!!! Should not have been here !!!!!!!!!!!");
logger.debug("processStartElement: contextObject.classname = " + contextObject.getClass().getName());
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