[Jsbml-svn] SF.net SVN: jsbml:[2222] trunk/core/src/org/sbml/jsbml

[<and...@us...>]

Revision: 2222
          http://sourceforge.net/p/jsbml/code/2222
Author:   andreas-draeger
Date:     2015-04-22 15:57:10 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Implemented a new constructor for CVTerm that reads the content of XMLNode objects. This needs more testing, but it should work in principle.

Modified Paths:
--------------
    trunk/core/src/org/sbml/jsbml/CVTerm.java
    trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java

Modified: trunk/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/CVTerm.java	2015-04-22 15:54:01 UTC (rev 2221)
+++ trunk/core/src/org/sbml/jsbml/CVTerm.java	2015-04-22 15:57:10 UTC (rev 2222)
@@ -29,10 +29,13 @@
 import java.util.regex.Pattern;
 
 import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
 
 import org.sbml.jsbml.util.StringTools;
 import org.sbml.jsbml.util.TreeNodeAdapter;
 import org.sbml.jsbml.util.TreeNodeChangeEvent;
+import org.sbml.jsbml.xml.XMLAttributes;
+import org.sbml.jsbml.xml.XMLNode;
 
 /**
  * Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
@@ -507,6 +510,42 @@
   }
 
   /**
+   * 
+   * @param miriam
+   */
+  public CVTerm(XMLNode miriam) {
+    this();
+    if (miriam.getName().equals("annotation")) {
+      miriam = miriam.getChildAt(0);
+    }
+    if (miriam.getName().equals("RDF")) {
+      miriam = miriam.getChildAt(0);
+    }
+    if (miriam.getName().equals("Description")) {
+      miriam = miriam.getChildAt(0);
+    }
+    if (miriam.getURI().equals("http://biomodels.net/biology-qualifiers/")) {
+      if (miriam.getPrefix().equals("bqbiol")) {
+        setQualifier(Qualifier.getBiologicalQualifierFor(miriam.getName()));
+      } else {
+        setQualifier(Qualifier.getModelQualifierFor(miriam.getName()));
+      }
+      miriam = miriam.getChildAt(0);
+    }
+    if (miriam.getName().equals("Bag")) {
+      for (int j = 0; j < miriam.getChildCount(); j++) {
+        XMLNode child = miriam.getChildAt(j);
+        if (child.getName().equals("li")) {
+          XMLAttributes attributes = child.getAttributes();
+          for (int i = 0; i < attributes.size(); i++) {
+            addResource(attributes.getValue(i));
+          }
+        }
+      }
+    }
+  }
+
+  /**
    * Creates a {@link CVTerm} instance from a given {@link CVTerm}.
    * 
    * @param term the {@link CVTerm} to clone

Modified: trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java	2015-04-22 15:54:01 UTC (rev 2221)
+++ trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java	2015-04-22 15:57:10 UTC (rev 2222)
@@ -510,11 +510,18 @@
    * @return the number of attributes in this {@link XMLAttributes} set.
    */
   public int getLength() {
+    return attributeNames.size();
+  }
 
+  /**
+   * 
+   * @return
+   * @see #getLength()
+   */
+  public int size() {
     return attributeNames.size();
   }
 
-
   /**
    * Returns the local name of an attribute in this {@link XMLAttributes} set (by position).
    * <p>

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