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[Jsbml-svn] SF.net SVN: jsbml:[2456] trunk/core/src/org/sbml/jsbml/ASTNode.java
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From: <nik...@us...> - 2015-12-15 11:58:09
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Revision: 2456
http://sourceforge.net/p/jsbml/code/2456
Author: niko-rodrigue
Date: 2015-12-15 11:58:07 +0000 (Tue, 15 Dec 2015)
Log Message:
-----------
added a field and some methods in ASTNode to handle the semantics annotations
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-15 11:56:29 UTC (rev 2455)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-15 11:58:07 UTC (rev 2456)
@@ -48,6 +48,7 @@
import org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler;
import org.sbml.jsbml.util.compilers.UnitsCompiler;
import org.sbml.jsbml.util.filters.Filter;
+import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.stax.SBMLReader;
/**
@@ -1391,6 +1392,12 @@
private String encoding;
/**
+ * XMLNode that will hold the content of the 'semantics' mathML element.
+ */
+ private List<XMLNode> semanticsAnnotationList;
+
+
+ /**
* Tells if the type attribute of the cn element was set and we need to
* write it back or if it is set to the default (REAL).
*
@@ -1498,6 +1505,14 @@
listOfNodes.add(c);
}
}
+
+ if (astNode.semanticsAnnotationList != null) {
+ semanticsAnnotationList = new ArrayList<XMLNode>();
+
+ for (XMLNode semanticsAnnotation : astNode.semanticsAnnotationList) {
+ semanticsAnnotationList.add(semanticsAnnotation.clone());
+ }
+ }
}
/**
@@ -2272,6 +2287,8 @@
if (equal && isSetUnits()) {
equal &= getUnits().equals(ast.getUnits());
}
+
+ // TODO - semanticsAnnotationList not part of equals or hashcode ?
}
return equal;
}
@@ -2355,6 +2372,8 @@
@Override
public TreeNode getChildAt(int i) {
return getChild(i);
+
+ // TODO - add semantics XMLNode ??
}
/* (non-Javadoc)
@@ -2363,6 +2382,8 @@
@Override
public int getChildCount() {
return listOfNodes == null ? 0 : listOfNodes.size();
+
+ // TODO - add semantics XMLNode ??
}
/**
@@ -2803,6 +2824,12 @@
if (isSetClassName()) {
hashCode += prime * getClassName().hashCode();
}
+ if (isSetUnits()) {
+ hashCode += prime * getUnits().hashCode();
+ }
+ // TODO - semanticsAnnotationList not part of equals or hashcode ?
+
+
return hashCode;
}
@@ -4356,4 +4383,102 @@
return tree;
}
+ /**
+ * Adds the given {@link XMLNode} as a MathML <code><semantics></code> element to this {@link ASTNode}.
+ *
+ * <p>
+ * The {@code <semantics>} element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more {@code <annotation>} or
+ * {@code <annotation-xml>} elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @param semanticsAnnotation the annotation to add.
+ * @return the added {@link XMLNode}.
+ */
+ public XMLNode addSemanticsAnnotation(XMLNode semanticsAnnotation) {
+ if (semanticsAnnotation == null) {
+ return null;
+ }
+ if (semanticsAnnotationList == null) {
+ semanticsAnnotationList = new ArrayList<XMLNode>();
+ }
+
+ semanticsAnnotationList.add(semanticsAnnotation);
+
+ return semanticsAnnotation;
+ }
+
+ /**
+ * Gets the number of <em>semantic annotation</em> elements inside this node.
+ *
+ * <p>
+ * The <code><semantics></code> element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more <code><annotation></code> or
+ * <code><annotation-xml></code> elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @return the number of annotations of this {@link ASTNode}.
+ * @see ASTNode#addSemanticsAnnotation(XMLNode semanticsAnnotation)
+ */
+ public int getNumSemanticsAnnotations() {
+ if (semanticsAnnotationList == null) {
+ return 0;
+ }
+
+ return semanticsAnnotationList.size();
+ }
+
+ /**
+ * Gets the nth <code><semantics></code> annotation of this node.
+ *
+ * <p>
+ * The <code><semantics></code> element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more <code><annotation></code> or
+ * <code><annotation-xml></code> elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @return the nth annotation of this {@link ASTNode}, or <code>null</code> if this node has
+ * no nth annotation (<code>n ></code>
+ * {@link ASTNode#getNumSemanticsAnnotations()}
+ * <code>- 1</code> or n < 0).
+ * @see ASTNode#addSemanticsAnnotation(XMLNode sAnnotation)
+ */
+ public XMLNode getSemanticsAnnotation(int n) {
+ if (semanticsAnnotationList == null || n < 0 || (n > (getNumSemanticsAnnotations() -1))) {
+ return null;
+ }
+
+ return semanticsAnnotationList.get(n);
+ }
+
+ /**
+ * Returns the list of semantics annotations of this node.
+ *
+ * @return the list of semantics annotations of this node or null if no semantics annotation are present.
+ */
+ public List<XMLNode> getListOfSemanticsAnnotations() {
+ return semanticsAnnotationList;
+ }
+
+ // TODO - removeSemanticsAnnotation
+ // TODO - unsetsemanticsAnnotation
+
}
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