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[Jsbml-svn] SF.net SVN: jsbml:[2270] branches/astnode2-merging-alternate
|
From: <nik...@us...> - 2015-05-01 09:56:21
|
Revision: 2270
http://sourceforge.net/p/jsbml/code/2270
Author: niko-rodrigue
Date: 2015-05-01 09:56:17 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2227
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2227
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.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/CVTerm.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/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/util/compilers/MathMLXMLStreamCompiler.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/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/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/MultiModelPlugin.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/SpeciesFeatureType.java
branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.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/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/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/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/SampledField.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
branches/astnode2-merging-alternate/modules/celldesigner/src/org/sbml/jsbml/celldesigner/SBMLLayoutVisualizer.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate 2015-05-01 09:56:17 UTC (rev 2270)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2226
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2227
\ No newline at end of property
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -151,7 +151,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -397,7 +397,7 @@
}
/* (non-Javadoc)
- * @see org.sbml.jlibsbml.SBase#appendNotes(java.lang.String)
+ * @see org.sbml.jsbml.SBase#appendNotes(java.lang.String)
*/
@Override
public void appendNotes(String notes) throws XMLStreamException {
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Annotation.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -577,6 +577,14 @@
return getNonRDFannotation();
}
+ /**
+ *
+ * @param nonRDFannotation
+ */
+ public void setXMLNode(XMLNode nonRDFannotation) {
+ setNonRDFAnnotation(nonRDFannotation);
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#hashCode()
*/
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -29,7 +29,6 @@
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;
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Constraint.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -126,7 +126,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Event.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -405,7 +405,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/KineticLaw.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -289,7 +289,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Model.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1877,7 +1877,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/Reaction.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -512,7 +512,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBMLDocument.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -663,7 +663,7 @@
}
}
throw new IndexOutOfBoundsException(MessageFormat.format("Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SpeciesReference.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -280,7 +280,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -114,6 +114,25 @@
}
/**
+ *
+ * @param indent
+ * @throws XMLStreamException
+ */
+ public MathMLXMLStreamCompiler(String indent) throws XMLStreamException {
+ SMOutputFactory smFactory = new SMOutputFactory(XMLOutputFactory.newInstance());
+ writer = smFactory.createStax2Writer(new StringWriter());
+ this.indent = indent;
+ }
+
+ /**
+ * @throws XMLStreamException
+ *
+ */
+ public MathMLXMLStreamCompiler() throws XMLStreamException {
+ this("");
+ }
+
+ /**
* Writes an {@link ASTNode} the mathML.
*
* @param astNode the {@link ASTNode} to serialize as mathML
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -273,7 +273,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -601,7 +601,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
+ childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -536,7 +536,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ 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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -486,7 +486,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -616,7 +616,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
/* (non-Javadoc)
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -178,7 +178,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
@Override
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,208 +1,208 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * 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 javax.swing.tree.TreeNode;
-
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.1
- * @date 26.03.2015
- */
-public class DistribSBasePlugin extends AbstractSBasePlugin {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -1732369832900356125L;
- /**
- *
- */
- private Uncertainty uncertainty;
-
- /**
- * Creates a new {@link DistribSBasePlugin} instance.
- *
- * @param sbase the {@link SBase} to be extended.
- */
- public DistribSBasePlugin(SBase sbase) {
- super(sbase);
- setPackageVersion(-1);
- }
-
- /**
- * Creates a new {@link DistribSBasePlugin} instance, cloned from
- * the input parameter.
- *
- * @param obj the {@link DistribSBasePlugin} to clone
- */
- public DistribSBasePlugin(DistribSBasePlugin obj) {
- super(obj);
-
- if (obj.isSetUncertainty()) {
- setUncertainty(obj.getUncertainty().clone());
- }
- }
-
-
- /**
- * Creates and Sets a new {@link Uncertainty} instance.
- *
- * @return the newly created {@link Uncertainty} instance.
- */
- public Uncertainty createUncertainty() {
- Uncertainty uncert = new Uncertainty();
- setUncertainty(uncert);
- return uncert;
- }
-
-
- /**
- * Returns the value of {@link #uncertainty}.
- *
- * @return the value of {@link #uncertainty}.
- */
- public Uncertainty getUncertainty() {
- if (isSetUncertainty()) {
- return uncertainty;
- }
-
- return null;
- }
-
-
- /**
- * Returns whether {@link #uncertainty} is set.
- *
- * @return whether {@link #uncertainty} is set.
- */
- public boolean isSetUncertainty() {
- return uncertainty != null;
- }
-
-
- /**
- * Sets the value of uncertainty
- *
- * @param uncertainty the value of uncertainty to be set.
- */
- public void setUncertainty(Uncertainty uncertainty) {
- Uncertainty oldUncertainty = this.uncertainty;
- this.uncertainty = uncertainty;
- if (getExtendedSBase() != null) {
- getExtendedSBase().registerChild(uncertainty);
- }
- firePropertyChange(DistribConstants.uncertainty, oldUncertainty, this.uncertainty);
- }
-
-
- /**
- * Unsets the variable uncertainty.
- *
- * @return {@code true} if uncertainty was set before, otherwise {@code false}.
- */
- public boolean unsetUncertainty() {
- if (isSetUncertainty()) {
- Uncertainty oldUncertainty = uncertainty;
- uncertainty = null;
- firePropertyChange(DistribConstants.uncertainty, oldUncertainty, uncertainty);
- return true;
- }
- return false;
- }
-
-
- @Override
- public String getElementNamespace() {
- return DistribConstants.namespaceURI_L3V1V1; // TODO - change to return a String attribute that can be changed
- }
-
- @Override
- public String getPackageName() {
- return DistribConstants.shortLabel;
- }
-
- @Override
- public String getPrefix() {
- return DistribConstants.shortLabel;
- }
-
- @Override
- public String getURI() {
- return DistribConstants.namespaceURI; // TODO - change to return a String attribute that can be changed
- }
-
-
- @Override
- public int getChildCount() {
- int count = 0;
-
- if (isSetUncertainty()) {
- count++;
- }
-
- return count;
- }
-
-
- @Override
- public TreeNode getChildAt(int index) {
- if (index < 0) {
- throw new IndexOutOfBoundsException(index + " < 0");
- }
- int pos = 0;
-
- if (isSetUncertainty()) {
- if (pos == index) {
- return getUncertainty();
- }
- pos++;
- }
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
- }
-
- @Override
- public boolean getAllowsChildren() {
- return true;
- }
-
- @Override
- public AbstractSBasePlugin clone() {
- return new DistribSBasePlugin(this);
- }
-
- @Override
- public boolean readAttribute(String attributeName, String prefix,
- String value) {
- return false;
- }
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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 javax.swing.tree.TreeNode;
+
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+
+/**
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ * @date 26.03.2015
+ */
+public class DistribSBasePlugin extends AbstractSBasePlugin {
+
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -1732369832900356125L;
+ /**
+ *
+ */
+ private Uncertainty uncertainty;
+
+ /**
+ * Creates a new {@link DistribSBasePlugin} instance.
+ *
+ * @param sbase the {@link SBase} to be extended.
+ */
+ public DistribSBasePlugin(SBase sbase) {
+ super(sbase);
+ setPackageVersion(-1);
+ }
+
+ /**
+ * Creates a new {@link DistribSBasePlugin} instance, cloned from
+ * the input parameter.
+ *
+ * @param obj the {@link DistribSBasePlugin} to clone
+ */
+ public DistribSBasePlugin(DistribSBasePlugin obj) {
+ super(obj);
+
+ if (obj.isSetUncertainty()) {
+ setUncertainty(obj.getUncertainty().clone());
+ }
+ }
+
+
+ /**
+ * Creates and Sets a new {@link Uncertainty} instance.
+ *
+ * @return the newly created {@link Uncertainty} instance.
+ */
+ public Uncertainty createUncertainty() {
+ Uncertainty uncert = new Uncertainty();
+ setUncertainty(uncert);
+ return uncert;
+ }
+
+
+ /**
+ * Returns the value of {@link #uncertainty}.
+ *
+ * @return the value of {@link #uncertainty}.
+ */
+ public Uncertainty getUncertainty() {
+ if (isSetUncertainty()) {
+ return uncertainty;
+ }
+
+ return null;
+ }
+
+
+ /**
+ * Returns whether {@link #uncertainty} is set.
+ *
+ * @return whether {@link #uncertainty} is set.
+ */
+ public boolean isSetUncertainty() {
+ return uncertainty != null;
+ }
+
+
+ /**
+ * Sets the value of uncertainty
+ *
+ * @param uncertainty the value of uncertainty to be set.
+ */
+ public void setUncertainty(Uncertainty uncertainty) {
+ Uncertainty oldUncertainty = this.uncertainty;
+ this.uncertainty = uncertainty;
+ if (getExtendedSBase() != null) {
+ getExtendedSBase().registerChild(uncertainty);
+ }
+ firePropertyChange(DistribConstants.uncertainty, oldUncertainty, this.uncertainty);
+ }
+
+
+ /**
+ * Unsets the variable uncertainty.
+ *
+ * @return {@code true} if uncertainty was set before, otherwise {@code false}.
+ */
+ public boolean unsetUncertainty() {
+ if (isSetUncertainty()) {
+ Uncertainty oldUncertainty = uncertainty;
+ uncertainty = null;
+ firePropertyChange(DistribConstants.uncertainty, oldUncertainty, uncertainty);
+ return true;
+ }
+ return false;
+ }
+
+
+ @Override
+ public String getElementNamespace() {
+ return DistribConstants.namespaceURI_L3V1V1; // TODO - change to return a String attribute that can be changed
+ }
+
+ @Override
+ public String getPackageName() {
+ return DistribConstants.shortLabel;
+ }
+
+ @Override
+ public String getPrefix() {
+ return DistribConstants.shortLabel;
+ }
+
+ @Override
+ public String getURI() {
+ return DistribConstants.namespaceURI; // TODO - change to return a String attribute that can be changed
+ }
+
+
+ @Override
+ public int getChildCount() {
+ int count = 0;
+
+ if (isSetUncertainty()) {
+ count++;
+ }
+
+ return count;
+ }
+
+
+ @Override
+ public TreeNode getChildAt(int index) {
+ if (index < 0) {
+ throw new IndexOutOfBoundsException(index + " < 0");
+ }
+ int pos = 0;
+
+ if (isSetUncertainty()) {
+ if (pos == index) {
+ return getUncertainty();
+ }
+ pos++;
+ }
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ "Index {0,number,integer} >= {1,number,integer}", index,
+ Math.min(pos, 0)));
+ }
+
+ @Override
+ public boolean getAllowsChildren() {
+ return true;
+ }
+
+ @Override
+ public AbstractSBasePlugin clone() {
+ return new DistribSBasePlugin(this);
+ }
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix,
+ String value) {
+ return false;
+ }
+
+}
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 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -480,7 +480,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ Math.min(pos, 0)));
}
Modified: 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/BoundingBox.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -230,7 +230,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/CubicBezier.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/CubicBezier.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -238,7 +238,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/Curve.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -172,7 +172,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/GeneralGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -526,7 +526,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/GraphicalObject.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -250,7 +250,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/Layout.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -623,7 +623,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/LineSegment.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/LineSegment.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -219,7 +219,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/ReactionGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -228,7 +228,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/ReferenceGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/ReferenceGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -180,7 +180,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/layout/src/org/sbml/jsbml/ext/layout/SpeciesReferenceGlyph.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -179,7 +179,7 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: 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/MultiModelPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,321 +1,321 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * 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) 2009-2015 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.multi;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-import org.sbml.jsbml.util.filters.NameFilter;
-
-/**
- * In order to encode the structures needed to define and use multistate and multi-component
- * complexes, the element model is extended to be linked to a list of {@link SpeciesType}s.
- *
- * @author Nicolas Rodriguez
- * @version $Rev$
- * @since 1.0
- */
-public class MultiModelPlugin extends AbstractSBasePlugin {
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return MultiConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return MultiConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractTreeNode#getParent()
- */
- @Override
- public SBMLDocument getParent() {
- return (SBMLDocument) getExtendedSBase().getParent();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
- */
- @Override
- public SBMLDocument getParentSBMLObject() {
- return getParent();
- }
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -2875299722787282885L;
- /**
- *
- */
- ListOf<SpeciesType> listOfSpeciesTypes;
-
- /**
- *
- * @param model
- */
- public MultiModelPlugin(Model model) {
- super(model);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- }
-
- /**
- *
- * @param multiModel
- */
- public MultiModelPlugin(MultiModelPlugin multiModel) {
- super(multiModel);
-
- if (multiModel == null) {
- return;
- }
- if (multiModel.isSetListOfSpeciesTypes()) {
- setListOfSpeciesTypes(multiModel.getListOfSpeciesTypes().clone());
- }
- }
-
- @Override
- public MultiModelPlugin clone() {
- return new MultiModelPlugin(this);
- }
-
- /**
- * Returns the {@link Model}
- *
- * @return the {@link Model}
- */
- public Model getModel() {
- return (Model) extendedSBase;
- }
-
-
- /**
- * Returns the listOfSpeciesTypes.
- *
- * @return the listOfSpeciesTypes
- */
- public ListOf<SpeciesType> getListOfSpeciesTypes() {
- if (listOfSpeciesTypes == null) {
- listOfSpeciesTypes = new ListOf<SpeciesType>();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- listOfSpeciesTypes.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'multi'
- listOfSpeciesTypes.setPackageName(null);
- listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
- listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
-
- if (isSetExtendedSBase()) {
- extendedSBase.registerChild(listOfSpeciesTypes);
- }
- }
-
- return listOfSpeciesTypes;
- }
-
- /**
- * Adds a {@link SpeciesType}.
- *
- * @param speciesType the speciesType to add
- * @return
- */
- public boolean addSpeciesType(SpeciesType speciesType) {
- return getListOfSpeciesTypes().add(speciesType);
- }
-
- /**
- * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
- * <p>
- *
- * @return the {@link SpeciesType} object created
- * <p>
- * @see #addSpeciesType(SpeciesType r)
- */
- public SpeciesType createSpeciesType() {
- return createSpeciesType(null);
- }
-
- /**
- * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
- *
- * @param id
- * the id of the new element to create
- * @return the {@link SpeciesType} object created
- */
- public SpeciesType createSpeciesType(String id) {
- SpeciesType speciesType = new SpeciesType();
- speciesType.setId(id);
- addSpeciesType(speciesType);
-
- return speciesType;
- }
-
- /**
- * Gets the ith {@link SpeciesType}.
- *
- * @param i
- *
- * @return the ith {@link SpeciesType}
- * @throws IndexOutOfBoundsException if the index is invalid.
- */
- public SpeciesType getSpeciesType(int i) {
- return getListOfSpeciesTypes().get(i);
- }
-
- /**
- * Gets the {@link SpeciesType} that has the given id.
- *
- * @param id
- * @return the {@link SpeciesType} that has the given id or null if
- * no {@link SpeciesType} are found that match {@code id}.
- */
- public SpeciesType getSpeciesType(String id) {
- if (isSetListOfSpeciesTypes()) {
- return listOfSpeciesTypes.firstHit(new NameFilter(id));
- }
- return null;
- }
-
- /**
- * Returns {@code true} if the listOfSpeciesType is set.
- *
- * @return {@code true} if the listOfSpeciesType is set.
- */
- public boolean isSetListOfSpeciesTypes() {
- return listOfSpeciesTypes != null;
- }
-
- /**
- * Sets the listOfSpeciesTypes. If there was already some elements defined
- * on listOfSpeciesTypes, they will be unset beforehand.
- *
- * @param listOfSpeciesTypes
- */
- public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes) {
- unsetListOfSpeciesTypes();
- this.listOfSpeciesTypes = listOfSpeciesTypes;
-
- if (listOfSpeciesTypes != null) {
- listOfSpeciesTypes.unsetNamespace();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- listOfSpeciesTypes.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'multi'
- listOfSpeciesTypes.setPackageName(null);
- listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
- listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
- }
- if (extendedSBase != null) {
- extendedSBase.registerChild(this.listOfSpeciesTypes);
- }
- }
-
-
- /**
- * Sets the listOfSpeciesTypes to null
- *
- * @return {@code true} is successful
- */
- public boolean unsetListOfSpeciesTypes() {
- if (isSetListOfSpeciesTypes()) {
- ListOf<SpeciesType> oldSpeciesTypeElements = listOfSpeciesTypes;
- listOfSpeciesTypes = null;
- oldSpeciesTypeElements.fireNodeRemovedEvent();
- return true;
- }
- return false;
- }
-
-
-
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- // no attribute to read
- return false;
- }
-
- /* (non-Javadoc)
- * @see javax.swing.tree.TreeNode#getChildAt(int)
- */
- @Override
- public SBase getChildAt(int childIndex) {
- if (childIndex < 0) {
- throw new IndexOutOfBoundsException(childIndex + " < 0");
- }
-
- int pos = 0;
- if (isSetListOfSpeciesTypes()) {
- if (pos == childIndex) {
- return getListOfSpeciesTypes();
- }
- pos++;
- }
-
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}",
- childIndex, +Math.min(pos, 0)));
- }
-
- /* (non-Javadoc)
- * @see javax.swing.tree.TreeNode#getChildCount()
- */
- @Override
- public int getChildCount() {
- int count = 0;
- if (isSetListOfSpeciesTypes()) {
- count++;
- }
-
- return count;
- }
-
- @Override
- public boolean getAllowsChildren() {
- return true;
- }
-
- @Override
- public Map<String, String> writeXMLAttributes() {
- // no attribute to write
- return null;
- }
-
-
-}
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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) 2009-2015 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.multi;
+
+import java.text.MessageFormat;
+import java.util.Map;
+
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.ext.AbstractSBasePlugin;
+import org.sbml.jsbml.util.filters.NameFilter;
+
+/**
+ * In order to encode the structures needed to define and use multistate and multi-component
+ * complexes, the element model is extended to be linked to a list of {@link SpeciesType}s.
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.0
+ */
+public class MultiModelPlugin extends AbstractSBasePlugin {
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
+ */
+ @Override
+ public String getPackageName() {
+ return MultiConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
+ */
+ @Override
+ public String getPrefix() {
+ return MultiConstants.shortLabel;
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
+ */
+ @Override
+ public String getURI() {
+ return getElementNamespace();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.AbstractTreeNode#getParent()
+ */
+ @Override
+ public SBMLDocument getParent() {
+ return (SBMLDocument) getExtendedSBase().getParent();
+ }
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
+ */
+ @Override
+ public SBMLDocument getParentSBMLObject() {
+ return getParent();
+ }
+ /**
+ * Generated serial version identifier.
+ */
+ private static final long serialVersionUID = -2875299722787282885L;
+ /**
+ *
+ */
+ ListOf<SpeciesType> listOfSpeciesTypes;
+
+ /**
+ *
+ * @param model
+ */
+ public MultiModelPlugin(Model model) {
+ super(model);
+ setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ }
+
+ /**
+ *
+ * @param multiModel
+ */
+ public MultiModelPlugin(MultiModelPlugin multiModel) {
+ super(multiModel);
+
+ if (multiModel == null) {
+ return;
+ }
+ if (multiModel.isSetListOfSpeciesTypes()) {
+ setListOfSpeciesTypes(multiModel.getListOfSpeciesTypes().clone());
+ }
+ }
+
+ @Override
+ public MultiModelPlugin clone() {
+ return new MultiModelPlugin(this);
+ }
+
+ /**
+ * Returns the {@link Model}
+ *
+ * @return the {@link Model}
+ */
+ public Model getModel() {
+ return (Model) extendedSBase;
+ }
+
+
+ /**
+ * Returns the listOfSpeciesTypes.
+ *
+ * @return the listOfSpeciesTypes
+ */
+ public ListOf<SpeciesType> getListOfSpeciesTypes() {
+ if (listOfSpeciesTypes == null) {
+ listOfSpeciesTypes = new ListOf<SpeciesType>();
+ listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ listOfSpeciesTypes.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'multi'
+ listOfSpeciesTypes.setPackageName(null);
+ listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
+ listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
+
+ if (isSetExtendedSBase()) {
+ extendedSBase.registerChild(listOfSpeciesTypes);
+ }
+ }
+
+ return listOfSpeciesTypes;
+ }
+
+ /**
+ * Adds a {@link SpeciesType}.
+ *
+ * @param speciesType the speciesType to add
+ * @return
+ */
+ public boolean addSpeciesType(SpeciesType speciesType) {
+ return getListOfSpeciesTypes().add(speciesType);
+ }
+
+ /**
+ * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
+ * <p>
+ *
+ * @return the {@link SpeciesType} object created
+ * <p>
+ * @see #addSpeciesType(SpeciesType r)
+ */
+ public SpeciesType createSpeciesType() {
+ return createSpeciesType(null);
+ }
+
+ /**
+ * Creates a new {@link SpeciesType} inside this {@link MultiModelPlugin} and returns it.
+ *
+ * @param id
+ * the id of the new element to create
+ * @return the {@link SpeciesType} object created
+ */
+ public SpeciesType createSpeciesType(String id) {
+ SpeciesType speciesType = new SpeciesType();
+ speciesType.setId(id);
+ addSpeciesType(speciesType);
+
+ return speciesType;
+ }
+
+ /**
+ * Gets the ith {@link SpeciesType}.
+ *
+ * @param i
+ *
+ * @return the ith {@link SpeciesType}
+ * @throws IndexOutOfBoundsException if the index is invalid.
+ */
+ public SpeciesType getSpeciesType(int i) {
+ return getListOfSpeciesTypes().get(i);
+ }
+
+ /**
+ * Gets the {@link SpeciesType} that has the given id.
+ *
+ * @param id
+ * @return the {@link SpeciesType} that has the given id or null if
+ * no {@link SpeciesType} are found that match {@code id}.
+ */
+ public SpeciesType getSpeciesType(String id) {
+ if (isSetListOfSpeciesTypes()) {
+ return listOfSpeciesTypes.firstHit(new NameFilter(id));
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@code true} if the listOfSpeciesType is set.
+ *
+ * @return {@code true} if the listOfSpeciesType is set.
+ */
+ public boolean isSetListOfSpeciesTypes() {
+ return listOfSpeciesTypes != null;
+ }
+
+ /**
+ * Sets the listOfSpeciesTypes. If there was already some elements defined
+ * on listOfSpeciesTypes, they will be unset beforehand.
+ *
+ * @param listOfSpeciesTypes
+ */
+ public void setListOfSpeciesTypes(ListOf<SpeciesType> listOfSpeciesTypes) {
+ unsetListOfSpeciesTypes();
+ this.listOfSpeciesTypes = listOfSpeciesTypes;
+
+ if (listOfSpeciesTypes != null) {
+ listOfSpeciesTypes.unsetNamespace();
+ listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ listOfSpeciesTypes.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'multi'
+ listOfSpeciesTypes.setPackageName(null);
+ listOfSpeciesTypes.setPackageName(MultiConstants.shortLabel);
+ listOfSpeciesTypes.setSBaseListType(ListOf.Type.other);
+ }
+ if (extendedSBase != null) {
+ extendedSBase.registerChild(this.listOfSpeciesTypes);
+ }
+ }
+
+
+ /**
+ * Sets the listOfSpeciesTypes to null
+ *
+ * @return {@code true} is successful
+ */
+ public boolean unsetListOfSpeciesTypes() {
+ if (isSetListOfSpeciesTypes()) {
+ ListOf<SpeciesType> oldSpeciesTypeElements = listOfSpeciesTypes;
+ listOfSpeciesTypes = null;
+ oldSpeciesTypeElements.fireNodeRemovedEvent();
+ return true;
+ }
+ return false;
+ }
+
+
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ // no attribute to read
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.tree.TreeNode#getChildAt(int)
+ */
+ @Override
+ public SBase getChildAt(int childIndex) {
+ if (childIndex < 0) {
+ throw new IndexOutOfBoundsException(childIndex + " < 0");
+ }
+
+ int pos = 0;
+ if (isSetListOfSpeciesTypes()) {
+ if (pos == childIndex) {
+ return getListOfSpeciesTypes();
+ }
+ pos++;
+ }
+
+ throw new IndexOutOfBoundsException(MessageFormat.format(
+ "Index {0,number,integer} >= {1,number,integer}",
+ childIndex, Math.min(pos, 0)));
+ }
+
+ /* (non-Javadoc)
+ * @see javax.swing.tree.TreeNode#getChildCount()
+ */
+ @Override
+ public int getChildCount() {
+ int count = 0;
+ if (isSetListOfSpeciesTypes()) {
+ count++;
+ }
+
+ return count;
+ }
+
+ @Override
+ public boolean getAllowsChildren() {
+ return true;
+ }
+
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ // no attribute to write
+ return null;
+ }
+
+
+}
Modified: 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/MultiSpeciesPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
+++ branches/astnode2-merging-alternate/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-05-01 09:56:17 UTC (rev 2270)
@@ -1,672 +1,672 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * 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) 2009-2015 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.multi;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.ListOf;
-import org.sbml.jsbml.SBase;
-import org.sbml.jsbml.Species;
-import org.sbml.jsbml.ext.AbstractSBasePlugin;
-
-/**
- *
- * @author Nicolas Rodriguez
- * @author Marine Dumousseau
- * @since 1.0
- * @version $Rev$
- */
-public class MultiSpeciesPlugin extends AbstractSBasePlugin {
-
- // TODO - implements IdManager: SpeciesFeature are id unique within one Species
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
- */
- @Override
- public String getPackageName() {
- return MultiConstants.shortLabel;
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
- */
- @Override
- public String getPrefix() {
- return MultiConstants.shortLabel;
- }
-
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.SBasePlugin#getURI()
- */
- @Override
- public String getURI() {
- return getElementNamespace();
- }
-
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -5396837209115412420L;
-
- /**
- *
- */
- private ListOf<OutwardBindingSite> listOfOutwardBindingSites;
-
- /**
- *
- */
- private ListOf<SpeciesFeature> listOfSpeciesFeatures;
-
- /**
- *
- */
- private String speciesType;
-
- /**
- *
- * @param species
- */
- public MultiSpeciesPlugin(Species species) {
- super(species);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
- }
-
-
- /**
- * @param multiSpecies
- */
- public MultiSpeciesPlugin(MultiSpeciesPlugin multiSpecies) {
- super(multiSpecies);
-
- // c...
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