[Jsbml-svn] SF.net SVN: jsbml:[2271] branches/astnode2-merging-alternate

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

Revision: 2271
          http://sourceforge.net/p/jsbml/code/2271
Author:   niko-rodrigue
Date:     2015-05-01 10:01:31 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2232

Revision Links:
--------------
    http://sourceforge.net/p/jsbml/code/2232

Modified Paths:
--------------
    branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
    branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
    branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
    branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
    branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
    branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
    branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
    branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
    branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
    branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
    branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
    branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
    branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
    branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
    branches/astnode2-merging-alternate/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java
    branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
    branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
    branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
    branches/astnode2-merging-alternate/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Image.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LineEnding.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LinearGradient.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Rectangle.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderCubicBezier.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
    branches/astnode2-merging-alternate/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
    branches/astnode2-merging-alternate/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialParameterPlugin.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java

Added Paths:
-----------
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java

Property Changed:
----------------
    branches/astnode2-merging-alternate/

Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate	2015-05-01 10:01:31 UTC (rev 2271)

Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2227
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2232
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/resources/org/sbml/jsbml/resources/Messages.xml	2015-05-01 10:01:31 UTC (rev 2271)
@@ -31,8 +31,6 @@
   
   <entry key="IndexExceedsBoundsException">Index {0,number,integer} >= {1,number,integer}</entry>
   <entry key="IndexExceedsBoundsException2">Node {0} has no children.</entry>
-  <entry key="IndexSurpassesBoundsException">Index {0,number,integer} &#60; {0,number,integer}</entry>
-  <entry key="NullArgument">Argument is null.</entry>
   
   <entry key="AbstractMathContainer.toFormula">Could not create infix formula from syntax tree.</entry>
   <entry key="AbstractMathContainer.inclusion">{0} in {1}</entry>
@@ -60,42 +58,5 @@
   <entry key="AbstractSBase.emptyNotes">The notes to append are empty!</entry>
   <entry key="AbstractSBase.invalidNotesStructure">The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.</entry>
   <entry key="AbstractSBase.problemAddingXMLNode">There was a problem adding the given XMLNode: ''{0}'' to the ''body'' XMLNode.</entry>
-  
-  <entry key="Assignment.ILLEGAL_CONSTANT_VARIABLE_MSG">Cannot set the constant variable {0} as the target of this {1}.</entry>
-  <entry key="Assignment.ILLEGAL_VARIABLE_EXCEPTION_MSG">Cannot set SpeciesReference {0} as the Variable in {1} for SBML Level &#60; 3</entry>
-  <entry key="Assignment.NO_SUCH_VARIABLE_EXCEPTION_MSG">Model {0} does not contain any variable with identifier {1}.</entry>
-  
-  <entry key="ASTNode.INVALID_OPERATOR_MSG">Invalid operator {0}. The operator must be one of the following constants: PLUS, MINUS, TIMES, DIVIDE, or POWER.</entry>
-  <entry key="ASTNode.log">logarithm cannot be created for null values</entry>
-  <entry key="ASTNode.relational">Cannot create a relational node with null arguments.</entry>
-  <entry key="ASTNode1">Clone constructor: Origin type = {0}</entry>
-  <entry key="ASTNode.arithmeticOperation">Cannot divide by zero.</entry>
-  <entry key="ASTNode.compile1">Fractions must have one numerator and one denominator, here {0,number,integer} elements are given.</entry>
-  <entry key="ASTNode.compile2">ASTNode of type FUNCTION but the variable is not a FunctionDefinition! ({0}, {1})</entry>
-  <entry key="ASTNode.compile3">ASTNode of type FUNCTION but the variable is null: ({0}, {1})! Check that your object is linked to a Model.</entry>
-  <entry key="ASTNode.compile4">getCharacter() should be called only when isOperator().</entry>
-  <entry key="ASTNode.getDenominator">getDenominator() should be called only when getType() == RATIONAL.</entry>
-  <entry key="ASTNode.getExponent">getExponent() should be called only when getType() == REAL_E or REAL</entry>
-  <entry key="ASTNode.getInteger">getInteger() should be called only when getType() == INTEGER</entry>
-  <entry key="ASTNode.getMantissa">getMantissa() should be called only when getType() == REAL or REAL_E</entry>
-  <entry key="ASTNode.getName">getName() should be called only when !isNumber() &#38;&#38; !isOperator()</entry>
-  <entry key="ASTNode.getNumerator">getNumerator() should be called only when isRational()</entry>
-  <entry key="ASTNode.getReal">getReal() should be called only when isReal() returns true.</entry>
-  <entry key="ASTNode.getReferencedNamedSBases">Name of this node is {0}  but no variable is set.</entry>
-  <entry key="ASTNode.getVariable1">The name \"{0}\" represented by this node is an argument in a function call, i.e., a placeholder for some other element. No corresponding CallableSBase exists in the model</entry>
-  <entry key="ASTNode.getVariable2">Cannot find any element with id \"{0}\" in the model.</entry>
-  <entry key="ASTNode.getVariable3">This ASTNode is not yet linked to a model and can therefore not determine its variable \"{0}\".</entry>
-  <entry key="ASTNode.getVariable4">getVariable() should be called only when isVariable() == true.</entry>
-  <entry key="ASTNode.initDefaults">initDefaults called! type was {0}</entry>
-  <entry key="ASTNode.reduceToBinary1">MINUS node with {0,number,integer} children left unchanged</entry>
-  <entry key="ASTNode.reduceToBinary2">DIVIDE node with {0,number,integer} children left unchanged</entry>
-  <entry key="ASTNode.reduceToBinary3">NOT node with {0,number,integer} children left unchanged</entry>
-  <entry key="ASTNode.reduceToBinary4">XOR node with {0,number,integer} children left unchanged</entry>
-  <entry key="ASTNode.reduceToBinary5">{0} node with {1,number,integer} children left unchanged</entry>
-  <entry key="ASTNode.setType">setType called: typeBefore={0} typeAfter={1}</entry>
-  <entry key="ASTNode.setUnits1">Unexpected attribute {0}, a unit can only be assigned to literal numbers.</entry>
-  <entry key="ASTNode.setUnits2">Unexpected attribute {0}, only a valid unit kind or the identifier of a unit definition are allowed here.</entry>
-  <entry key="ASTNode.setUnits3">Cannot set unit {0} for a numbers in an ASTNode before SBML Level 3.</entry>
-  <entry key="ASTNode.toString">Could not compile ASTNode to formula: {0}</entry>
 
 </properties>
\ No newline at end of file

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -150,7 +150,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 
@@ -180,12 +180,14 @@
           name = getElementName();
           SBase parent = getParentSBMLObject();
           if ((parent != null) && (parent instanceof NamedSBase)) {
-            name += " in " + parent.toString();
+            name = MessageFormat.format(
+              resourceBundle.getString("AbstractMathContainer.inclusion"),
+              name, parent.toString());
           }
         }
         logger.warn(MessageFormat.format(
-          "Could not derive unit from syntax tree of {0}: {1}", name,
-          exc.getLocalizedMessage()));
+          resourceBundle.getString("AbstractMathContainer.getDerivedUnitDefinition"),
+          name, exc.getLocalizedMessage()));
         logger.debug(exc.getLocalizedMessage(), exc);
       }
     }
@@ -233,8 +235,8 @@
   public String getFormula() {
     try {
       return isSetMath() ? getMath().toFormula() : "";
-    } catch (Throwable e) {
-      logger.warn("Could not create infix formula from syntax tree.", e);
+    } catch (Throwable exc) {
+      logger.warn(resourceBundle.getString("AbstractMathContainer.toFormula"), exc);
       return "invalid";
     }
   }
@@ -352,4 +354,5 @@
     }
     return attributes;
   }
+
 }

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractNamedSBase.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -162,7 +162,8 @@
   boolean checkIdentifier(String sID) {
     if ((sID == null) || !SyntaxChecker.isValidId(sID, getLevel(), getVersion())) {
       throw new IllegalArgumentException(MessageFormat.format(
-        "\"{0}\" is not a valid identifier for this {1}.", sID, getElementName()));
+        resourceBundle.getString("AbstractNamedSBase.checkIdentifier"),
+        sID, getElementName()));
     }
     return true;
   }

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -689,7 +689,9 @@
           for (i=0; i < addedNotes.getChildCount(); i++)
           {
             if (curBody.addChild(addedNotes.getChildAt(i)) < 0) {
-              logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+              logger.warn(MessageFormat.format(
+                resourceBundle.getString("AbstractSBase.appendNotes"),
+                SBMLtools.toXML(addedNotes.getChildAt(i))));
               return;
             }
           }
@@ -731,7 +733,9 @@
           for (i = 0; i < addedNotes.getChildCount(); i++)
           {
             if (curNotes.addChild(addedNotes.getChildAt(i)) < 0) {
-              logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+              logger.warn(MessageFormat.format(
+                resourceBundle.getString("AbstractSBase.appendNotes"),
+                SBMLtools.toXML(addedNotes.getChildAt(i))));
               return;
             }
           }
@@ -760,7 +764,7 @@
    *             Level/Version combination than this current {@link SBase}, an
    *             {@link LevelVersionError} is thrown. This method is only
    *             package-wide visible because it is not intended to be a
-   *             "real" check, rather than to indicate potential errors.
+   *             <i>real</i> check, rather than to indicate potential errors.
    */
   protected boolean checkLevelAndVersionCompatibility(SBase sbase) {
     if (sbase.getLevelAndVersion().equals(getLevelAndVersion())) {
@@ -812,7 +816,7 @@
     }
 
     throw new IllegalArgumentException(MessageFormat.format(
-      "The package namespace or name ''{0}'' is unknown!",
+      resourceBundle.getString("AbstractSBase.createPlugin"),
       nameOrUri));
   }
 
@@ -843,13 +847,12 @@
    */
   @Override
   public void enablePackage(String packageURIOrName, boolean enabled) {
-
     SBMLDocument doc = getSBMLDocument();
 
     if (doc != null) {
       doc.enablePackage(packageURIOrName, enabled);
-    } else {
-      logger.debug("Package not enabled, could not find the SBMLDocument.");
+    } else if (logger.isDebugEnabled()) {
+      logger.debug(resourceBundle.getString("AbstractSBase.enablePackage"));
     }
   }
 
@@ -998,7 +1001,9 @@
     TreeNode parent = getParent();
 
     if (logger.isDebugEnabled()) {
-      logger.debug("fireNodeRemovedEvent called on " + this + " (parent = " + parent + ")");
+      logger.debug(MessageFormat.format(
+        resourceBundle.getString("AbstractSBase.fireNodeRemovedEvent"),
+        this, parent));
     }
 
     if ((parent != null) && (parent instanceof SBase)) {
@@ -1076,10 +1081,10 @@
       }
     }
 
-    throw new IndexOutOfBoundsException(isLeaf() ? MessageFormat.format(
-      "Node {0} has no children.", getElementName()) : MessageFormat.format(
-        "Index {0,number,integer} >= {1,number,integer}",
-        childIndex, Math.min(pos, 0)));
+    throw new IndexOutOfBoundsException(isLeaf() ?
+      MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException2"), getElementName()) :
+        MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
+          childIndex, Math.min(pos, 0)));
   }
 
   /* (non-Javadoc)
@@ -1111,7 +1116,7 @@
       return annotation.getCVTerm(index);
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "No such controlled vocabulary term with index {0,number,integer}.", index));
+      resourceBundle.getString("AbstractSBase.getCVTerm"), index));
   }
 
   /* (non-Javadoc)
@@ -1154,16 +1159,15 @@
    */
   @Override
   public SBasePlugin getExtension(String nameOrUri) {
-
     // use always the package name in the map
     PackageParser packageParser = ParserManager.getManager().getPackageParser(nameOrUri);
 
     if (packageParser != null) {
-
       return extensions.get(packageParser.getPackageName());
     }
 
-    throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+    throw new IllegalArgumentException(MessageFormat.format(
+      resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
   }
 
   /* (non-Javadoc)
@@ -1383,7 +1387,8 @@
       }
     }
 
-    throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+    throw new IllegalArgumentException(MessageFormat.format(
+      resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
   }
 
   /* (non-Javadoc)
@@ -1616,7 +1621,8 @@
       //      return false;
     }
 
-    throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+    throw new IllegalArgumentException(MessageFormat.format(
+      resourceBundle.getString("AbstractSBase.createPlugin"), nameOrUri));
   }
 
   /* (non-Javadoc)
@@ -1691,11 +1697,11 @@
     if ((sbase != null) && (sbase.getParent() != null)) {
       if (sbase.getParent() == this) {
         logger.warn(MessageFormat.format(
-          "Trying to register {0} ''{1}'', which is already registered under {2} ''{3}''.",
+          resourceBundle.getString("AbstractSBase.registerChild1"),
           sbase.getElementName(), sbase, getElementName(), this));
       } else {
         logger.warn(MessageFormat.format(
-          "{0} ''{1}'' is associated to the different parent ''{2}''. Please remove it there before adding it to this ''{3}'' or add a clone of it to this element.",
+          resourceBundle.getString("AbstractSBase.registerChild2"),
           sbase.getClass().getSimpleName(), sbase, sbase.getParent(), this));
       }
       return false;
@@ -1743,7 +1749,8 @@
         sbase.addAllChangeListeners(listeners);
 
         throw new IllegalArgumentException(MessageFormat.format(
-          "Cannot register {0}.", sbase.getElementName()));
+          resourceBundle.getString("AbstractSBase.registerChild3"),
+          sbase.getElementName()));
       }
 
       // TODO - set package version and namespace if needed
@@ -1918,7 +1925,7 @@
         throw new PropertyNotAvailableException(TreeNodeChangeEvent.metaId, this);
       } else if (!SyntaxChecker.isValidMetaId(metaId)) {
         throw new IllegalArgumentException(MessageFormat.format(
-          "\"{0}\" is not a valid meta-identifier for this {1}.",
+          resourceBundle.getString("AbstractSBase.setMetaId"),
           metaId, getElementName()));
       }
     }
@@ -2031,7 +2038,7 @@
     }
     if (!SBO.checkTerm(term)) {
       throw new IllegalArgumentException(MessageFormat.format(
-        "Cannot set invalid SBO term {0,number,integer} because it must not be smaller than zero or larger than 9999999.",
+        resourceBundle.getString("AbstractSBase.setSBOTerm"),
         term));
     }
     Integer oldTerm = Integer.valueOf(sboTerm);
@@ -2086,8 +2093,10 @@
   public void unregisterChild(SBase sbase) {
 
     if (logger.isDebugEnabled()) {
-      logger.debug("unregister called! " + sbase.getElementName() + " "
-          + (sbase instanceof NamedSBase ? ((NamedSBase) sbase).getId() : ""));
+      logger.debug(MessageFormat.format(
+        resourceBundle.getString("AbstractSBase.unregisterChild1"),
+        sbase.getElementName(),
+        (sbase instanceof NamedSBase ? ((NamedSBase) sbase).getId() : "")));
     }
 
     if ((sbase != null)) {
@@ -2103,7 +2112,8 @@
       // If possible, recursively unregister all ids of the SBase in our model:
       if ((idManager != null)
           && !idManager.unregister(sbase)) {
-        throw new IllegalArgumentException(MessageFormat.format("Cannot unregister {0}.",
+        throw new IllegalArgumentException(MessageFormat.format(
+          resourceBundle.getString("AbstractSBase.unregisterChild2"),
           sbase.getElementName()));
       }
 
@@ -2125,7 +2135,9 @@
   private void unregisterChild(SBasePlugin sbasePlugin)  {
 
     if (logger.isDebugEnabled()) {
-      logger.debug("AbstractSBase - #unregisterChild(SBasePlugin) - called on '" + sbasePlugin + "'");
+      logger.debug(MessageFormat.format(
+        resourceBundle.getString("AbstractSBase.unregisterChild3"),
+        sbasePlugin));
     }
 
     int childCount = sbasePlugin.getChildCount();
@@ -2223,7 +2235,9 @@
       return;
     }
 
-    throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
+    throw new IllegalArgumentException(MessageFormat.format(
+      resourceBundle.getString("AbstractSBase.createPlugin"),
+      nameOrUri));
   }
 
   @Override

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -399,7 +399,7 @@
     //			pos++;
     //		}
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       childIndex, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -125,7 +125,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -404,7 +404,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/History.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -184,7 +184,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       childIndex, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -288,7 +288,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -1876,7 +1876,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -511,7 +511,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -662,7 +662,7 @@
         return getModel();
       }
     }
-    throw new IndexOutOfBoundsException(MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+    throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -279,7 +279,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/UnitDefinition.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -697,7 +697,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       + Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -176,7 +176,7 @@
       }
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       childIndex, getChildCount()));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -272,7 +272,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       childIndex, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -600,7 +600,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       childIndex, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -535,7 +535,7 @@
     }
 
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -485,7 +485,7 @@
     }
 
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -615,7 +615,7 @@
     }
 
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -177,7 +177,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -185,7 +185,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -479,7 +479,7 @@
     }
 
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}", index,
+      resourceBundle.getString("IndexExceedsBoundsException"), index,
       Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -1,262 +1,262 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2014 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- * 
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.distrib;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import javax.swing.tree.TreeNode;
-
-import org.sbml.jsbml.AbstractNamedSBase;
-import org.sbml.jsbml.xml.XMLNode;
-
-/**
- * 
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.1
- * @date 26.03.2015
- */
-public class Uncertainty extends AbstractNamedSBase {
-
-  /**
-   * Generated serial version identifier.
-   */
-  private static final long serialVersionUID = -904719821379100471L;
-  /**
-   * 
-   */
-  private XMLNode uncertML;
-
-  /**
-   * Creates an Uncertainty instance
-   */
-  public Uncertainty() {
-    super();
-    initDefaults();
-  }
-
-
-  /**
-   * Creates a Uncertainty instance with an id.
-   * 
-   * @param id the identifier for the new element.
-   */
-  public Uncertainty(String id) {
-    super(id);
-    initDefaults();
-  }
-
-
-  /**
-   * Creates a Uncertainty instance with a level and version.
-   * 
-   * @param level SBML Level
-   * @param version SBML Version
-   */
-  public Uncertainty(int level, int version) {
-    this(null, null, level, version);
-  }
-
-
-  /**
-   * Creates a Uncertainty instance with an id, level, and version.
-   * 
-   * @param id the identifier for this element.
-   * @param level the SBML Level
-   * @param version the SBML Version
-   */
-  public Uncertainty(String id, int level, int version) {
-    this(id, null, level, version);
-  }
-
-
-  /**
-   * Creates a Uncertainty instance with an id, name, level, and version.
-   * 
-   * @param id the identifier for this element.
-   * @param name a human-readable name for this element that can be used for display purposes.
-   * @param level the SBML Level
-   * @param version the SBML Version
-   */
-  public Uncertainty(String id, String name, int level, int version) {
-    super(id, name, level, version);
-    initDefaults();
-  }
-
-
-  /**
-   * Clone constructor
-   * @param obj
-   */
-  public Uncertainty(Uncertainty obj) {
-    super(obj);
-  }
-
-  /**
-   * Initializes the default values using the namespace.
-   */
-  public void initDefaults() {
-    setNamespace(DistribConstants.namespaceURI);  // TODO - removed once the mechanism are in place to set package version and namespace
-    setPackageVersion(-1);
-    packageName = DistribConstants.shortLabel;
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
-   */
-  @Override
-  public boolean isIdMandatory() {
-    return false;
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.AbstractSBase#clone()
-   */
-  @Override
-  public Uncertainty clone() {
-    return new Uncertainty(this);
-  }
-
-
-  /**
-   * Returns the value of {@link #uncertML}.
-   *
-   * @return the value of {@link #uncertML}.
-   */
-  public XMLNode getUncertML() {
-    if (isSetUncertML()) {
-      return uncertML;
-    }
-
-    return null;
-  }
-
-
-  /**
-   * Returns whether {@link #uncertML} is set.
-   *
-   * @return whether {@link #uncertML} is set.
-   */
-  public boolean isSetUncertML() {
-    return uncertML != null;
-  }
-
-
-  /**
-   * Sets the value of uncertML
-   *
-   * @param uncertML the value of uncertML to be set.
-   */
-  public void setUncertML(XMLNode uncertML) {
-    XMLNode oldUncertML = this.uncertML;
-    this.uncertML = uncertML;
-    this.uncertML.setParent(this);
-    firePropertyChange(DistribConstants.uncertML, oldUncertML, this.uncertML);
-  }
-
-
-  /**
-   * Unsets the variable uncertML.
-   *
-   * @return {@code true} if uncertML was set before, otherwise {@code false}.
-   */
-  public boolean unsetUncertML() {
-    if (isSetUncertML()) {
-      XMLNode oldUncertML = uncertML;
-      uncertML = null;
-      firePropertyChange(DistribConstants.uncertML, oldUncertML, uncertML);
-      return true;
-    }
-    return false;
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.AbstractSBase#getAllowsChildren()
-   */
-  @Override
-  public boolean getAllowsChildren() {
-    return true;
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.AbstractSBase#getChildCount()
-   */
-  @Override
-  public int getChildCount() {
-    int count = super.getChildCount();
-
-    if (isSetUncertML()) {
-      count++;
-    }
-
-    return count;
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
-   */
-  @Override
-  public TreeNode getChildAt(int index) {
-    if (index < 0) {
-      throw new IndexOutOfBoundsException(index + " < 0");
-    }
-    int count = super.getChildCount(), pos = 0;
-
-    if (index < count) {
-      return super.getChildAt(index);
-    } else {
-      index -= count;
-    }
-
-    if (isSetUncertML()) {
-      if (pos == index) {
-        return getUncertML();
-      }
-      pos++;
-    }
-
-    throw new IndexOutOfBoundsException(
-      MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
-        index, Math.min(pos, 0)));
-  }
-
-  /* (non-Javadoc)
-   * @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
-   */
-  @Override
-  public Map<String, String> writeXMLAttributes() {
-    Map<String, String> attributes = super.writeXMLAttributes();
-
-    if (isSetId()) {
-      attributes.remove("id");
-      attributes.put(DistribConstants.shortLabel + ":id", getId());
-    }
-    if (isSetName()) {
-      attributes.remove("name");
-      attributes.put(DistribConstants.shortLabel + ":name", getId());
-    }
-
-    return attributes;
-  }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.distrib;
+
+import java.text.MessageFormat;
+import java.util.Map;
+
+import javax.swing.tree.TreeNode;
+
+import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.xml.XMLNode;
+
+/**
+ * 
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ * @date 26.03.2015
+ */
+public class Uncertainty extends AbstractNamedSBase {
+
+  /**
+   * Generated serial version identifier.
+   */
+  private static final long serialVersionUID = -904719821379100471L;
+  /**
+   * 
+   */
+  private XMLNode uncertML;
+
+  /**
+   * Creates an Uncertainty instance
+   */
+  public Uncertainty() {
+    super();
+    initDefaults();
+  }
+
+
+  /**
+   * Creates a Uncertainty instance with an id.
+   * 
+   * @param id the identifier for the new element.
+   */
+  public Uncertainty(String id) {
+    super(id);
+    initDefaults();
+  }
+
+
+  /**
+   * Creates a Uncertainty instance with a level and version.
+   * 
+   * @param level SBML Level
+   * @param version SBML Version
+   */
+  public Uncertainty(int level, int version) {
+    this(null, null, level, version);
+  }
+
+
+  /**
+   * Creates a Uncertainty instance with an id, level, and version.
+   * 
+   * @param id the identifier for this element.
+   * @param level the SBML Level
+   * @param version the SBML Version
+   */
+  public Uncertainty(String id, int level, int version) {
+    this(id, null, level, version);
+  }
+
+
+  /**
+   * Creates a Uncertainty instance with an id, name, level, and version.
+   * 
+   * @param id the identifier for this element.
+   * @param name a human-readable name for this element that can be used for display purposes.
+   * @param level the SBML Level
+   * @param version the SBML Version
+   */
+  public Uncertainty(String id, String name, int level, int version) {
+    super(id, name, level, version);
+    initDefaults();
+  }
+
+
+  /**
+   * Clone constructor
+   * @param obj
+   */
+  public Uncertainty(Uncertainty obj) {
+    super(obj);
+  }
+
+  /**
+   * Initializes the default values using the namespace.
+   */
+  public void initDefaults() {
+    setNamespace(DistribConstants.namespaceURI);  // TODO - removed once the mechanism are in place to set package version and namespace
+    setPackageVersion(-1);
+    packageName = DistribConstants.shortLabel;
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.NamedSBase#isIdMandatory()
+   */
+  @Override
+  public boolean isIdMandatory() {
+    return false;
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.AbstractSBase#clone()
+   */
+  @Override
+  public Uncertainty clone() {
+    return new Uncertainty(this);
+  }
+
+
+  /**
+   * Returns the value of {@link #uncertML}.
+   *
+   * @return the value of {@link #uncertML}.
+   */
+  public XMLNode getUncertML() {
+    if (isSetUncertML()) {
+      return uncertML;
+    }
+
+    return null;
+  }
+
+
+  /**
+   * Returns whether {@link #uncertML} is set.
+   *
+   * @return whether {@link #uncertML} is set.
+   */
+  public boolean isSetUncertML() {
+    return uncertML != null;
+  }
+
+
+  /**
+   * Sets the value of uncertML
+   *
+   * @param uncertML the value of uncertML to be set.
+   */
+  public void setUncertML(XMLNode uncertML) {
+    XMLNode oldUncertML = this.uncertML;
+    this.uncertML = uncertML;
+    this.uncertML.setParent(this);
+    firePropertyChange(DistribConstants.uncertML, oldUncertML, this.uncertML);
+  }
+
+
+  /**
+   * Unsets the variable uncertML.
+   *
+   * @return {@code true} if uncertML was set before, otherwise {@code false}.
+   */
+  public boolean unsetUncertML() {
+    if (isSetUncertML()) {
+      XMLNode oldUncertML = uncertML;
+      uncertML = null;
+      firePropertyChange(DistribConstants.uncertML, oldUncertML, uncertML);
+      return true;
+    }
+    return false;
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.AbstractSBase#getAllowsChildren()
+   */
+  @Override
+  public boolean getAllowsChildren() {
+    return true;
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.AbstractSBase#getChildCount()
+   */
+  @Override
+  public int getChildCount() {
+    int count = super.getChildCount();
+
+    if (isSetUncertML()) {
+      count++;
+    }
+
+    return count;
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
+   */
+  @Override
+  public TreeNode getChildAt(int index) {
+    if (index < 0) {
+      throw new IndexOutOfBoundsException(index + " < 0");
+    }
+    int count = super.getChildCount(), pos = 0;
+
+    if (index < count) {
+      return super.getChildAt(index);
+    } else {
+      index -= count;
+    }
+
+    if (isSetUncertML()) {
+      if (pos == index) {
+        return getUncertML();
+      }
+      pos++;
+    }
+
+    throw new IndexOutOfBoundsException(
+      MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
+        index, Math.min(pos, 0)));
+  }
+
+  /* (non-Javadoc)
+   * @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
+   */
+  @Override
+  public Map<String, String> writeXMLAttributes() {
+    Map<String, String> attributes = super.writeXMLAttributes();
+
+    if (isSetId()) {
+      attributes.remove("id");
+      attributes.put(DistribConstants.shortLabel + ":id", getId());
+    }
+    if (isSetName()) {
+      attributes.remove("name");
+      attributes.put(DistribConstants.shortLabel + ":name", getId());
+    }
+
+    return attributes;
+  }
+
+}

Modified: branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -267,7 +267,7 @@
   public TreeNode getChildAt(int childIndex) {
     if (childIndex < 0 || childIndex >= 1) {
       throw new IndexOutOfBoundsException(MessageFormat.format(
-        "Index {0,number,integer} >= {1,number,integer}",
+        resourceBundle.getString("IndexExceedsBoundsException"),
         childIndex, +Math.min(getChildCount(), 0)));
     }
 

Modified: branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -293,7 +293,7 @@
   public TreeNode getChildAt(int childIndex) {
     if (childIndex < 0 || childIndex >= 1) {
       throw new IndexOutOfBoundsException(MessageFormat.format(
-        "Index {0,number,integer} >= {1,number,integer}",
+        resourceBundle.getString("IndexExceedsBoundsException"),
         childIndex, +Math.min(getChildCount(), 0)));
     }
 

Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -259,7 +259,7 @@
     }
 
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCReactionPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -179,7 +179,7 @@
     }
 
     throw new IndexOutOfBoundsException(
-      MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+      MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
         index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCSpeciesPlugin.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -166,7 +166,7 @@
     }
     int pos = 0;
     throw new IndexOutOfBoundsException(MessageFormat.format(
-      "Index {0,number,integer} >= {1,number,integer}",
+      resourceBundle.getString("IndexExceedsBoundsException"),
       index, + Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProteinAssociation.java	2015-05-01 10:01:31 UTC (rev 2271)
@@ -158,7 +158,7 @@
       pos++;
     }
     throw new IndexOutOfBoundsException(
-      MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
+      MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
         index, Math.min(pos, 0)));
   }
 

Modified: branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java	2015-05-01 09:56:17 UTC (rev 2270)
+++ branches/astnode2-merging-alternate/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOpera...
 
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