[Jsbml-svn] SF.net SVN: jsbml:[2352] trunk/extensions/fbc/src/org/sbml/jsbml

[<nik...@us...>]

Revision: 2352
          http://sourceforge.net/p/jsbml/code/2352
Author:   niko-rodrigue
Date:     2015-07-30 15:28:48 +0000 (Thu, 30 Jul 2015)
Log Message:
-----------
added the possiblity to parse fbc sbml file that use geneProteinAssociation so that we can read them and convert them using JSBML as the element was used for a very long time

Modified Paths:
--------------
    trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
    trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java

Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java	2015-07-30 15:10:43 UTC (rev 2351)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java	2015-07-30 15:28:48 UTC (rev 2352)
@@ -84,6 +84,12 @@
   public static final String geneProduct = "geneProduct";
 
   /**
+   * Used only in some of the FBC v2 release candidates
+   */
+  @Deprecated
+  public static final String       geneProteinAssociation = "geneProteinAssociation";
+
+  /**
    * 
    * @since jsbml 1.1, introduced in FBC version 2
    */

Modified: trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java	2015-07-30 15:10:43 UTC (rev 2351)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java	2015-07-30 15:28:48 UTC (rev 2352)
@@ -224,6 +224,14 @@
       if (elementName.equals(FBCConstants.geneProductAssociation)) {
         GeneProductAssociation gPA = fbcReaction.createGeneProductAssociation();
         return gPA;
+      } 
+      else if (elementName.equals(FBCConstants.geneProteinAssociation)) {
+        // FBCConstants.geneProteinAssociation has been used for a very long time in the FBC v2 release candidates
+        // so we are keeping it here in case some files still use it.
+        logger.warn("You are using an invalid element name '" + FBCConstants.geneProteinAssociation 
+          + "'. It was only used for few FBC V2 release candidates.");
+        GeneProductAssociation gPA = fbcReaction.createGeneProductAssociation();
+        return gPA;
       }
     } else if (contextObject instanceof GeneProductAssociation) {
       GeneProductAssociation gPA = (GeneProductAssociation) contextObject;

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