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From: <nik...@us...> - 2016-01-11 14:48:00
|
Revision: 2463
http://sourceforge.net/p/jsbml/code/2463
Author: niko-rodrigue
Date: 2016-01-11 14:47:58 +0000 (Mon, 11 Jan 2016)
Log Message:
-----------
sorting the input files to have them in the right order compared to the input
Modified Paths:
--------------
trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
Modified: trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java 2016-01-11 14:38:00 UTC (rev 2462)
+++ trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java 2016-01-11 14:47:58 UTC (rev 2463)
@@ -26,6 +26,7 @@
import java.io.FileFilter;
import java.nio.file.Files;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
import java.util.List;
@@ -72,6 +73,8 @@
files = new File[1];
files[0] = argsAsFile;
}
+
+ Arrays.sort(files);
long init = Calendar.getInstance().getTimeInMillis();
List<String> differences = new ArrayList<String>();
@@ -83,7 +86,6 @@
for (File file : files)
{
String fileName = file.getAbsolutePath();
-
// read the mathml, infix math input and expected output.
byte[] encoded = null;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2016-01-11 14:38:03
|
Revision: 2462
http://sourceforge.net/p/jsbml/code/2462
Author: niko-rodrigue
Date: 2016-01-11 14:38:00 +0000 (Mon, 11 Jan 2016)
Log Message:
-----------
modified the output produce by the infix formula reading/writing test class
Modified Paths:
--------------
trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
Modified: trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java 2016-01-10 16:05:51 UTC (rev 2461)
+++ trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java 2016-01-11 14:38:00 UTC (rev 2462)
@@ -25,7 +25,9 @@
import java.io.File;
import java.io.FileFilter;
import java.nio.file.Files;
+import java.util.ArrayList;
import java.util.Calendar;
+import java.util.List;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.xml.XMLNode;
@@ -72,7 +74,11 @@
}
long init = Calendar.getInstance().getTimeInMillis();
+ List<String> differences = new ArrayList<String>();
+ List<String> difference2s = new ArrayList<String>();
int nbEquals = 0;
+ int nbEqualsIgnoreSpace = 0;
+ int nbTests = 0;
for (File file : files)
{
@@ -98,6 +104,8 @@
continue;
}
+ nbTests++;
+
for (int i = 0; i < 2; i++)
{
XMLNode xmlNode = astNode.getSemanticsAnnotation(i);
@@ -122,13 +130,28 @@
System.out.println("Infix input = '" + infixInput + "'");
System.out.println("Infix output = '" + infixOutput + "'");
- System.out.println("Infix expected output = '" + infixExpectedOutput + "'");
+ System.out.print("Infix expected output = '" + infixExpectedOutput + "'");
+ boolean different = true;
+
if (infixOutput != null && infixOutput.equals(infixExpectedOutput)) {
nbEquals++;
- System.out.println("#########################################################");
+ System.out.print(" ###");
+ different = false;
}
-
+ if (infixOutput != null && infixOutput.replace(" ", "").equals(infixExpectedOutput.replace(" ", ""))) {
+ nbEqualsIgnoreSpace++;
+ System.out.println(" @@@");
+ different = false;
+ }
+ System.out.println("\n");
+
+ if (different) {
+ differences.add("input= '" + infixInput + "', output = '" + infixOutput + "' (expected output = '" + infixExpectedOutput + "')");
+ }
+ if (different && (infixInput.indexOf("%") == -1) && (infixExpectedOutput.indexOf("arc") == -1)) {
+ difference2s.add("input= '" + infixInput + "', output = '" + infixOutput + "' (expected output = '" + infixExpectedOutput + "')");
+ }
}
catch (Exception e)
{
@@ -138,7 +161,9 @@
}
- System.out.println("Nb test where we have the same output = " + nbEquals);
+ System.out.println("Nb tests where we have the same output without considering spaces = " + nbEqualsIgnoreSpace + " / " + nbTests
+ + " (" + (nbTests - nbEqualsIgnoreSpace) + " failed tests)");
+ System.out.println("Nb tests where we have the same output, including spaces = " + nbEquals + " (nb tests = " + nbTests + ")");
long end = Calendar.getInstance().getTimeInMillis();
long nbSecondes = (end - init)/1000;
@@ -148,5 +173,18 @@
} else {
System.out.println("It took " + nbSecondes + " secondes.");
}
+
+ if (differences.size() > 0) {
+ System.out.println("\n\n List of differences: \n");
+
+ for (String difference : differences) {
+ System.out.println(difference);
+ }
+ }
+
+ if (difference2s.size() > 0) {
+ System.out.println("\n\nNb tests where we don't have the same output (excluding modulo and trigonometric operators) = " + difference2s.size()
+ + " (nb tests = " + nbTests + ")");
+ }
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2016-01-10 16:05:54
|
Revision: 2461
http://sourceforge.net/p/jsbml/code/2461
Author: andreas-draeger
Date: 2016-01-10 16:05:51 +0000 (Sun, 10 Jan 2016)
Log Message:
-----------
* Improved an error message.
* Added convenient functions to Curve in Layout and to Group in Groups.
* Added static function parseMathML in ASTNode as requested by Jason Zwolak.
* Removed Java 8 dependency in TestSemanticsMathML because JSBML should be compatible with Java 6 for now.
* Added a type hierarchy graph for Multi.
Modified Paths:
--------------
trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml
trunk/core/src/org/sbml/jsbml/ASTNode.java
trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
Added Paths:
-----------
trunk/extensions/multi/doc/img/type_hierarchy.pdf
Modified: trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml
===================================================================
--- trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/core/resources/org/sbml/jsbml/resources/cfg/Messages.xml 2016-01-10 16:05:51 UTC (rev 2461)
@@ -34,7 +34,7 @@
<entry key="SBMLCoreParser.instanciationError">The element ''{0}'' could not be instanciated as a Java object!</entry>
<entry key="SBMLCoreParser.namespaceIgnored">Namespace ignored on ''{0}''! {1} = {2}</entry>
- <entry key="SBMLCoreParser.reactionWithoutParticipantsError">The reaction ''{0}'' does not contain any reactants or products.</entry>
+ <entry key="SBMLCoreParser.reactionWithoutParticipantsError">The reaction ''{0}'' does neither contain any reactants nor products.</entry>
<entry key="SBMLCoreParser.unknownAttributeOnElement">Could not recognize the attribute ''{0}'' on the element {1}. Please check the specification for SBML.</entry>
<entry key="SBMLCoreParser.unknownElement">The element ''{0}'' is not recognized.</entry>
<entry key="SBMLCoreParser.unknownReferenceError1">No {0} matches the {1} ''{2}'' of {3} ''{4}''.</entry>
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2016-01-10 16:05:51 UTC (rev 2461)
@@ -374,10 +374,12 @@
*/
TIMES,
/**
- * MathML markup can be combined with other markup languages, and these mixing constructions are realized by the semantic
- * annotation elements. The semantic annotation elements provide an important tool for making associations between
- * alternate representations of an expression, and for associating semantic properties and other attributions with
- * a MathML expression.
+ * MathML markup can be combined with other markup languages, and these
+ * mixing constructions are realized by the semantic annotation elements.
+ * The semantic annotation elements provide an important tool for making
+ * associations between alternate representations of an expression, and for
+ * associating semantic properties and other attributions with a MathML
+ * expression.
*/
SEMANTICS,
/**
@@ -1091,6 +1093,15 @@
}
/**
+ * @param mathML a {@link String} in MathML format.
+ * @return An {@link ASTNode} representation of the given MathML {@link String}.
+ * @see #readMathMLFromString(String)
+ */
+ public static ASTNode parseMathML(String mathML) {
+ return readMathMLFromString(mathML);
+ }
+
+ /**
* Creates a piecewise {@link ASTNode}.
*
* <p>At least one {@link ASTNode} must be given
@@ -1402,8 +1413,8 @@
* XMLNode that will hold the content of the 'semantics' mathML element.
*/
private List<XMLNode> semanticsAnnotationList;
-
-
+
+
/**
* Tells if the type attribute of the cn element was set and we need to
* write it back or if it is set to the default (REAL).
@@ -1504,7 +1515,7 @@
className = astNode.className;
encoding = astNode.encoding;
style = astNode.style;
-
+
if (astNode.getChildCount() > 0) {
for (ASTNode child : astNode.listOfNodes) {
ASTNode c = child.clone();
@@ -1512,10 +1523,10 @@
listOfNodes.add(c);
}
}
-
+
if (astNode.semanticsAnnotationList != null) {
semanticsAnnotationList = new ArrayList<XMLNode>();
-
+
for (XMLNode semanticsAnnotation : astNode.semanticsAnnotationList) {
semanticsAnnotationList.add(semanticsAnnotation.clone());
}
@@ -2294,7 +2305,7 @@
if (equal && isSetUnits()) {
equal &= getUnits().equals(ast.getUnits());
}
-
+
// TODO - semanticsAnnotationList not part of equals or hashcode ?
}
return equal;
@@ -2379,7 +2390,7 @@
@Override
public TreeNode getChildAt(int i) {
return getChild(i);
-
+
// TODO - add semantics XMLNode ??
}
@@ -2389,8 +2400,8 @@
@Override
public int getChildCount() {
return listOfNodes == null ? 0 : listOfNodes.size();
-
- // TODO - add semantics XMLNode ??
+
+ // TODO - add semantics XMLNode ??
}
/**
@@ -2836,7 +2847,7 @@
}
// TODO - semanticsAnnotationList not part of equals or hashcode ?
-
+
return hashCode;
}
@@ -3152,7 +3163,7 @@
|| type == Type.RELATIONAL_LT || type == Type.RELATIONAL_NEQ;
}
-
+
/**
* Return true if this node contain some semantics annotations.
*
@@ -3162,8 +3173,8 @@
public boolean isSemantics() {
return getNumSemanticsAnnotations() > 0;
}
-
-
+
+
/**
* @return
*/
@@ -4403,7 +4414,8 @@
}
/**
- * Adds the given {@link XMLNode} as a MathML <code><semantics></code> element to this {@link ASTNode}.
+ * Adds the given {@link XMLNode} as a MathML {@code <semantics>}
+ * element to this {@link ASTNode}.
*
* <p>
* The {@code <semantics>} element is a MathML 2.0 construct
@@ -4427,12 +4439,12 @@
if (semanticsAnnotationList == null) {
semanticsAnnotationList = new ArrayList<XMLNode>();
}
-
+
semanticsAnnotationList.add(semanticsAnnotation);
-
+
return semanticsAnnotation;
}
-
+
/**
* Gets the number of <em>semantic annotation</em> elements inside this node.
*
@@ -4450,7 +4462,7 @@
*
* @return the number of annotations of this {@link ASTNode}.
* @see ASTNode#addSemanticsAnnotation(XMLNode semanticsAnnotation)
- */
+ */
public int getNumSemanticsAnnotations() {
if (semanticsAnnotationList == null) {
return 0;
@@ -4479,7 +4491,7 @@
* {@link ASTNode#getNumSemanticsAnnotations()}
* <code>- 1</code> or n < 0).
* @see ASTNode#addSemanticsAnnotation(XMLNode sAnnotation)
- */
+ */
public XMLNode getSemanticsAnnotation(int n) {
if (semanticsAnnotationList == null || n < 0 || (n > (getNumSemanticsAnnotations() -1))) {
return null;
@@ -4487,7 +4499,7 @@
return semanticsAnnotationList.get(n);
}
-
+
/**
* Returns the list of semantics annotations of this node.
*
@@ -4496,8 +4508,8 @@
public List<XMLNode> getListOfSemanticsAnnotations() {
return semanticsAnnotationList;
}
-
+
// TODO - removeSemanticsAnnotation
// TODO - unsetsemanticsAnnotation
-
+
}
Modified: trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java 2016-01-10 16:05:51 UTC (rev 2461)
@@ -19,7 +19,27 @@
* and also available online as <http://sbml.org/Software/JSBML/License>.
* ----------------------------------------------------------------------------
*/
-
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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.test;
import javax.xml.stream.XMLStreamException;
@@ -29,10 +49,19 @@
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLWriter;
-
+/**
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ */
public class TestSemanticsMathML {
- public static void main(String[] args)
+ /**
+ *
+ * @param args
+ */
+ public static void main(String[] args)
{
String mathml = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ " <semantics>"
@@ -45,25 +74,28 @@
ASTNode node = ASTNode.readMathMLFromString(mathml);
-
+
System.out.println("nb semantic annotations = " + node.getNumSemanticsAnnotations());
-
+
System.out.println(node.toMathML());
-
+
SBMLDocument doc = new SBMLDocument(3, 1);
-
+
doc.createModel().createReaction().createKineticLaw().setMath(node);
-
+
try {
System.out.println(new SBMLWriter().writeSBMLToString(doc));
- } catch (SBMLException | XMLStreamException e) {
- e.printStackTrace();
+ } catch (SBMLException exc) {
+ exc.printStackTrace();
+ } catch (XMLStreamException exc) {
+ exc.printStackTrace();
}
-
+
int n = doc.checkConsistency();
-
+
if (n > 0) {
doc.printErrors(System.out);
}
}
+
}
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2016-01-10 16:05:51 UTC (rev 2461)
@@ -28,7 +28,9 @@
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.SBase;
import org.sbml.jsbml.UniqueNamedSBase;
/**
@@ -42,13 +44,13 @@
/**
* This is a collection of possible values for the {@code kind} attribute within
- * a {@link Group}.
+ * a {@link Group}.
*
*/
public enum Kind {
/**
- * The group represents a class, and its members have an <i>is-a</i> relationship to the group. For example, the
- * group could represent a type of molecule such as ATP, and the members could be species located in different
+ * The group represents a class, and its members have an <i>is-a</i> relationship to the group. For example, the
+ * group could represent a type of molecule such as ATP, and the members could be species located in different
* compartments, thereby establishing that the species are pools of the same molecule in different locations.
*/
classification,
@@ -59,9 +61,9 @@
*/
partonomy,
/**
- * The grouping is merely a collection for convenience, without an implied relationship between the members.
+ * The grouping is merely a collection for convenience, without an implied relationship between the members.
* For example, the group could be used to collect together multiple disparate components of a model—species,
- * reactions, events—involved in a particular phenotype, and apply a common annotation rather than having to
+ * reactions, events—involved in a particular phenotype, and apply a common annotation rather than having to
* copy the same annotation to each component individually.
*/
collection
@@ -85,7 +87,7 @@
/**
*
*/
-// removed as unsupported but could be added again in the future private ListOfMemberConstraint listOfMemberConstraints = null;
+ // removed as unsupported but could be added again in the future private ListOfMemberConstraint listOfMemberConstraints = null;
/**
*
@@ -109,10 +111,10 @@
setKind(group.getKind());
}
- // removed as unsupported but could be added again in the future
+ // removed as unsupported but could be added again in the future
// if (group.isSetListOfMemberConstraints()) {
-// setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
-// }
+ // setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
+ // }
}
/**
@@ -172,7 +174,9 @@
*/
public Member createMemberWithIdRef(String id, String idRef) {
Member m = new Member();
- m.setId(id);
+ if (id != null) {
+ m.setId(id);
+ }
m.setIdRef(idRef);
addMember(m);
return m;
@@ -187,12 +191,49 @@
*/
public Member createMemberWithMetaIdRef(String id, String metaIdRef) {
Member m = new Member();
- m.setId(id);
+ if (id != null) {
+ m.setId(id);
+ }
m.setMetaIdRef(metaIdRef);
addMember(m);
return m;
}
+ /**
+ * @param sbase
+ * the element that should be referenced as a new member of this
+ * {@link Group}.
+ * @return the newly created {@link Member} or {@code null} if the given
+ * {@link SBase} neither has a metaId nor an id.
+ * @see #createMember(String, SBase)
+ */
+ public Member creteMember(SBase sbase) {
+ return createMember(null, sbase);
+ }
+
+ /**
+ * @param id
+ * the identifier to be set for the new {@link Member}, can be
+ * {@code null}.
+ * @param sbase
+ * the element that should be referenced as a new member of this
+ * {@link Group}.
+ * @return the newly created {@link Member} or {@code null} if the given
+ * {@link SBase} neither has a metaId nor an id.
+ */
+ public Member createMember(String id, SBase sbase) {
+ if (sbase instanceof NamedSBase) {
+ NamedSBase nsb = (NamedSBase) sbase;
+ if (nsb.isSetId()) {
+ return createMemberWithIdRef(id, nsb.getId());
+ }
+ }
+ if (sbase.isSetMetaId()) {
+ return createMemberWithMetaIdRef(id, sbase.getMetaId());
+ }
+ return null;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
*/
@@ -219,13 +260,13 @@
position++;
}
- // removed as unsupported but could be added again in the future
-// if (isSetListOfMemberConstraints()) {
-// if (position == index) {
-// return getListOfMemberConstraints();
-// }
-// position++;
-// }
+ // removed as unsupported but could be added again in the future
+ // if (isSetListOfMemberConstraints()) {
+ // if (position == index) {
+ // return getListOfMemberConstraints();
+ // }
+ // position++;
+ // }
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
@@ -243,10 +284,10 @@
if (isSetListOfMembers()) {
childCount++;
}
- // removed as unsupported but could be added again in the future
-// if (isSetListOfMemberConstraints()) {
-// childCount++;
-// }
+ // removed as unsupported but could be added again in the future
+ // if (isSetListOfMemberConstraints()) {
+ // childCount++;
+ // }
return childCount;
}
@@ -460,15 +501,15 @@
return isSetListOfMembers() ? getListOfMembers().size() : 0;
}
- // removed as unsupported but could be added again in the future
-// /**
-// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
-// *
-// * @return the number of {@link MemberConstraint}s of this {@link Group}.
-// */
-// public int getMemberConstraintCount() {
-// return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
-// }
+ // removed as unsupported but could be added again in the future
+ // /**
+ // * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+ // *
+ // * @return the number of {@link MemberConstraint}s of this {@link Group}.
+ // */
+ // public int getMemberConstraintCount() {
+ // return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
+ // }
/**
* Returns the number of {@link Member}s of this {@link Group}.
@@ -480,16 +521,16 @@
return getMemberCount();
}
- // removed as unsupported but could be added again in the future
-// /**
-// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
-// *
-// * @return the number of {@link MemberConstraint}s of this {@link Group}.
-// * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
-// */
-// public int getNumMemberConstraints() {
-// return getMemberConstraintCount();
-// }
+ // removed as unsupported but could be added again in the future
+ // /**
+ // * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+ // *
+ // * @return the number of {@link MemberConstraint}s of this {@link Group}.
+ // * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
+ // */
+ // public int getNumMemberConstraints() {
+ // return getMemberConstraintCount();
+ // }
/**
*
@@ -515,142 +556,142 @@
public boolean isSetKind() {
return kind!=null;
}
-
-
-//
-// /**
-// * Returns {@code true}, if listOfMemberConstraints is not null.
-// *
-// * @return {@code true}, if listOfMemberConstraints is not null,
-// * otherwise {@code false}
-// */
-// public boolean isSetListOfMemberConstraints() {
-// return listOfMemberConstraints != null;
-// }
-//
-// /**
-// * Returns the listOfMemberConstraints. Creates it if it is not already existing.
-// *
-// * @return the listOfMemberConstraints
-// */
-// public ListOfMemberConstraint getListOfMemberConstraints() {
-// if (!isSetListOfMemberConstraints()) {
-// listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
-// listOfMemberConstraints.setPackageVersion(-1);
-// // changing the ListOf package name from 'core' to 'groups'
-// listOfMemberConstraints.setPackageName(null);
-// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
-// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
-// registerChild(listOfMemberConstraints);
-// }
-// return listOfMemberConstraints;
-// }
-//
-// /**
-// * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
-// * was defined before and contains some elements, they are all unset.
-// *
-// * @param listOfMemberConstraints
-// */
-// public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
-// unsetListOfMemberConstraints();
-// this.listOfMemberConstraints = listOfMemberConstraints;
-//
-// if (listOfMemberConstraints != null) {
-// listOfMemberConstraints.setPackageVersion(-1);
-// // changing the ListOf package name from 'core' to 'groups'
-// listOfMemberConstraints.setPackageName(null);
-// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
-// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
-//
-// registerChild(this.listOfMemberConstraints);
-// }
-// }
-//
-// /**
-// * Returns {@code true}, if listOfMemberConstraints contain at least one element,
-// * otherwise {@code false}
-// *
-// * @return {@code true}, if listOfMemberConstraints contain at least one element,
-// * otherwise {@code false}
-// */
-// public boolean unsetListOfMemberConstraints() {
-// if (isSetListOfMemberConstraints()) {
-// ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
-// listOfMemberConstraints = null;
-// oldMemberConstraints.fireNodeRemovedEvent();
-// return true;
-// }
-// return false;
-// }
-//
-// /**
-// * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
-// * <p>The listOfMemberConstraints is initialized if necessary.
-// *
-// * @param memberConstraint the element to add to the list
-// * @return true (as specified by {@link java.util.Collection#add})
-// */
-// public boolean addMemberConstraint(MemberConstraint memberConstraint) {
-// return getListOfMemberConstraints().add(memberConstraint);
-// }
-//
-// /**
-// * Removes an element from the listOfMemberConstraints.
-// *
-// * @param memberConstraint the element to be removed from the list
-// * @return true if the list contained the specified element
-// * @see java.util.List#remove(Object)
-// */
-// public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
-// if (isSetListOfMemberConstraints()) {
-// return getListOfMemberConstraints().remove(memberConstraint);
-// }
-// return false;
-// }
-//
-// /**
-// * Removes an element from the listOfMemberConstraints at the given index.
-// *
-// * @param i the index where to remove the {@link MemberConstraint}
-// * @throws IndexOutOfBoundsException if the listOf is not set or
-// * if the index is out of bound (index < 0 || index > list.size)
-// */
-// public void removeMemberConstraint(int i) {
-// if (!isSetListOfMemberConstraints()) {
-// throw new IndexOutOfBoundsException(Integer.toString(i));
-// }
-// getListOfMemberConstraints().remove(i);
-// }
-//
-// /**
-// * @param id
-// */
-// public void removeMemberConstraint(String id) {
-// getListOfMemberConstraints().removeFirst(new NameFilter(id));
-// }
-//
-// /**
-// * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
-// * @return
-// */
-// public MemberConstraint createMemberConstraint() {
-// return createMemberConstraint(null);
-// }
-//
-// /**
-// * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
-// * @param id
-// *
-// * @return a new {@link MemberConstraint} element
-// */
-// public MemberConstraint createMemberConstraint(String id) {
-// MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
-// addMemberConstraint(MemberConstraint);
-// return MemberConstraint;
-// }
+ //
+ // /**
+ // * Returns {@code true}, if listOfMemberConstraints is not null.
+ // *
+ // * @return {@code true}, if listOfMemberConstraints is not null,
+ // * otherwise {@code false}
+ // */
+ // public boolean isSetListOfMemberConstraints() {
+ // return listOfMemberConstraints != null;
+ // }
+ //
+ // /**
+ // * Returns the listOfMemberConstraints. Creates it if it is not already existing.
+ // *
+ // * @return the listOfMemberConstraints
+ // */
+ // public ListOfMemberConstraint getListOfMemberConstraints() {
+ // if (!isSetListOfMemberConstraints()) {
+ // listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
+ // listOfMemberConstraints.setPackageVersion(-1);
+ // // changing the ListOf package name from 'core' to 'groups'
+ // listOfMemberConstraints.setPackageName(null);
+ // listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+ // listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+ // registerChild(listOfMemberConstraints);
+ // }
+ // return listOfMemberConstraints;
+ // }
+ //
+ // /**
+ // * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
+ // * was defined before and contains some elements, they are all unset.
+ // *
+ // * @param listOfMemberConstraints
+ // */
+ // public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
+ // unsetListOfMemberConstraints();
+ // this.listOfMemberConstraints = listOfMemberConstraints;
+ //
+ // if (listOfMemberConstraints != null) {
+ // listOfMemberConstraints.setPackageVersion(-1);
+ // // changing the ListOf package name from 'core' to 'groups'
+ // listOfMemberConstraints.setPackageName(null);
+ // listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+ // listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+ //
+ // registerChild(this.listOfMemberConstraints);
+ // }
+ // }
+ //
+ // /**
+ // * Returns {@code true}, if listOfMemberConstraints contain at least one element,
+ // * otherwise {@code false}
+ // *
+ // * @return {@code true}, if listOfMemberConstraints contain at least one element,
+ // * otherwise {@code false}
+ // */
+ // public boolean unsetListOfMemberConstraints() {
+ // if (isSetListOfMemberConstraints()) {
+ // ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
+ // listOfMemberConstraints = null;
+ // oldMemberConstraints.fireNodeRemovedEvent();
+ // return true;
+ // }
+ // return false;
+ // }
+ //
+ // /**
+ // * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
+ // * <p>The listOfMemberConstraints is initialized if necessary.
+ // *
+ // * @param memberConstraint the element to add to the list
+ // * @return true (as specified by {@link java.util.Collection#add})
+ // */
+ // public boolean addMemberConstraint(MemberConstraint memberConstraint) {
+ // return getListOfMemberConstraints().add(memberConstraint);
+ // }
+ //
+ // /**
+ // * Removes an element from the listOfMemberConstraints.
+ // *
+ // * @param memberConstraint the element to be removed from the list
+ // * @return true if the list contained the specified element
+ // * @see java.util.List#remove(Object)
+ // */
+ // public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
+ // if (isSetListOfMemberConstraints()) {
+ // return getListOfMemberConstraints().remove(memberConstraint);
+ // }
+ // return false;
+ // }
+ //
+ // /**
+ // * Removes an element from the listOfMemberConstraints at the given index.
+ // *
+ // * @param i the index where to remove the {@link MemberConstraint}
+ // * @throws IndexOutOfBoundsException if the listOf is not set or
+ // * if the index is out of bound (index < 0 || index > list.size)
+ // */
+ // public void removeMemberConstraint(int i) {
+ // if (!isSetListOfMemberConstraints()) {
+ // throw new IndexOutOfBoundsException(Integer.toString(i));
+ // }
+ // getListOfMemberConstraints().remove(i);
+ // }
+ //
+ // /**
+ // * @param id
+ // */
+ // public void removeMemberConstraint(String id) {
+ // getListOfMemberConstraints().removeFirst(new NameFilter(id));
+ // }
+ //
+ // /**
+ // * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
+ // * @return
+ // */
+ // public MemberConstraint createMemberConstraint() {
+ // return createMemberConstraint(null);
+ // }
+ //
+ // /**
+ // * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
+ // * @param id
+ // *
+ // * @return a new {@link MemberConstraint} element
+ // */
+ // public MemberConstraint createMemberConstraint(String id) {
+ // MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
+ // addMemberConstraint(MemberConstraint);
+ // return MemberConstraint;
+ // }
+
+
/* (non-Javadoc)
* @see org.sbml.jsbml.element.SBase#readAttribute(String attributeName, String prefix, String value)
*/
@@ -714,7 +755,6 @@
// TODO - add methods to get/set/... the attribute from the ListOfMemberConstraint
-
@Override
public boolean getAllowsChildren() {
return true;
@@ -728,11 +768,11 @@
final int prime = 31;
int result = super.hashCode();
result = prime * result + ((kind == null) ? 0 : kind.hashCode());
- // removed as unsupported but could be added again in the future
-// result = prime
-// * result
-// + ((listOfMemberConstraints == null) ? 0
-// : listOfMemberConstraints.hashCode());
+ // removed as unsupported but could be added again in the future
+ // result = prime
+ // * result
+ // + ((listOfMemberConstraints == null) ? 0
+ // : listOfMemberConstraints.hashCode());
result = prime * result
+ ((listOfMembers == null) ? 0 : listOfMembers.hashCode());
return result;
@@ -756,14 +796,14 @@
if (kind != other.kind) {
return false;
}
- // removed as unsupported but could be added again in the future
-// if (listOfMemberConstraints == null) {
-// if (other.listOfMemberConstraints != null) {
-// return false;
-// }
-// } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
-// return false;
-// }
+ // removed as unsupported but could be added again in the future
+ // if (listOfMemberConstraints == null) {
+ // if (other.listOfMemberConstraints != null) {
+ // return false;
+ // }
+ // } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
+ // return false;
+ // }
if (listOfMembers == null) {
if (other.listOfMembers != null) {
return false;
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2016-01-10 16:05:51 UTC (rev 2461)
@@ -123,8 +123,22 @@
}
/**
- * Creates a new {@link CubicBezier} instance, adds it to this {@link Curve} and returns it.
*
+ * @param start
+ * @param end
+ * @return
+ */
+ public LineSegment createLineSegment(Point start, Point end) {
+ LineSegment cs = createLineSegment();
+ cs.setStart(start);
+ cs.setEnd(end);
+ return cs;
+ }
+
+ /**
+ * Creates a new {@link CubicBezier} instance, adds it to this {@link Curve}.
+ * and returns it.
+ *
* @return the new {@link CubicBezier} instance
*/
public CubicBezier createCubicBezier() {
@@ -133,6 +147,22 @@
return cs;
}
+ /**
+ *
+ * @param start
+ * @param basePoint1
+ * @param basePoint2
+ * @param end
+ * @return
+ */
+ public CubicBezier createCubicBezier(Point start, Point basePoint1, Point basePoint2, Point end) {
+ CubicBezier cs = createCubicBezier();
+ cs.setStart(start);
+ cs.setBasePoint1(basePoint1);
+ cs.setBasePoint2(basePoint2);
+ cs.setEnd(end);
+ return cs;
+ }
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
Added: trunk/extensions/multi/doc/img/type_hierarchy.pdf
===================================================================
(Binary files differ)
Index: trunk/extensions/multi/doc/img/type_hierarchy.pdf
===================================================================
--- trunk/extensions/multi/doc/img/type_hierarchy.pdf 2015-12-18 16:01:20 UTC (rev 2460)
+++ trunk/extensions/multi/doc/img/type_hierarchy.pdf 2016-01-10 16:05:51 UTC (rev 2461)
Property changes on: trunk/extensions/multi/doc/img/type_hierarchy.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-18 16:01:23
|
Revision: 2460
http://sourceforge.net/p/jsbml/code/2460
Author: niko-rodrigue
Date: 2015-12-18 16:01:20 +0000 (Fri, 18 Dec 2015)
Log Message:
-----------
added a test class to test the expected infix outputs developed by Lucian
Added Paths:
-----------
trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
Added: trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java (rev 0)
+++ trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java 2015-12-18 16:01:20 UTC (rev 2460)
@@ -0,0 +1,152 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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.test;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.nio.file.Files;
+import java.util.Calendar;
+
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.xml.XMLNode;
+
+
+public class TestInfixReadingWriting {
+
+
+ public static void main(String[] args) {
+
+ if (args.length < 1) {
+ System.out.println(
+ "Usage: java org.sbml.jsbml.test.TestInfixReadingWriting folder|file");
+ System.exit(0);
+ }
+
+ // this JOptionPane is added here to be able to start visualVM profiling
+ // before the reading or writing is started.
+ // JOptionPane.showMessageDialog(null, "Eggs are not supposed to be green.");
+
+ File argsAsFile = new File(args[0]);
+ File[] files = null;
+
+ if (argsAsFile.isDirectory())
+ {
+ files = argsAsFile.listFiles(new FileFilter() {
+
+ @Override
+ public boolean accept(File pathname)
+ {
+ if (pathname.getName().endsWith(".xml"))
+ {
+ return true;
+ }
+
+ return false;
+ }
+ });
+ }
+ else
+ {
+ files = new File[1];
+ files[0] = argsAsFile;
+ }
+
+ long init = Calendar.getInstance().getTimeInMillis();
+ int nbEquals = 0;
+
+ for (File file : files)
+ {
+ String fileName = file.getAbsolutePath();
+
+ // read the mathml, infix math input and expected output.
+
+ byte[] encoded = null;
+ String mathMLString = null;
+ String infixInput = null;
+ String infixExpectedOutput = null;
+
+ try
+ {
+ encoded = Files.readAllBytes(file.toPath());
+ mathMLString = new String(encoded, "UTF-8");
+
+ ASTNode astNode = ASTNode.readMathMLFromString(mathMLString);
+ String infixOutput = astNode.toFormula();
+
+ if (astNode.getNumSemanticsAnnotations() != 2) {
+ System.out.println("!!!!!!!!!! ERROR: for file '" + fileName + "' we found " + astNode.getNumSemanticsAnnotations() + " semantics annotations !");
+ continue;
+ }
+
+ for (int i = 0; i < 2; i++)
+ {
+ XMLNode xmlNode = astNode.getSemanticsAnnotation(i);
+ String encoding = "";
+
+ if (xmlNode.getName().equals("annotation") && xmlNode.hasAttr("encoding"))
+ {
+ encoding = xmlNode.getAttrValue("encoding");
+
+ if (encoding.equals("infix-input"))
+ {
+ infixInput = xmlNode.getChild(0).getCharacters();
+ }
+ else if (encoding.equals("infix-output"))
+ {
+ infixExpectedOutput = xmlNode.getChild(0).getCharacters();
+ }
+ }
+ }
+
+ // compare the different output
+
+ System.out.println("Infix input = '" + infixInput + "'");
+ System.out.println("Infix output = '" + infixOutput + "'");
+ System.out.println("Infix expected output = '" + infixExpectedOutput + "'");
+
+ if (infixOutput != null && infixOutput.equals(infixExpectedOutput)) {
+ nbEquals++;
+ System.out.println("#########################################################");
+ }
+
+ }
+ catch (Exception e)
+ {
+ System.out.println(fileName);
+ e.printStackTrace();
+ }
+
+ }
+
+ System.out.println("Nb test where we have the same output = " + nbEquals);
+
+ long end = Calendar.getInstance().getTimeInMillis();
+ long nbSecondes = (end - init)/1000;
+
+ if (nbSecondes > 120) {
+ System.out.println("It took " + nbSecondes/60 + " minutes.");
+ } else {
+ System.out.println("It took " + nbSecondes + " secondes.");
+ }
+ }
+}
Property changes on: trunk/core/test/org/sbml/jsbml/test/TestInfixReadingWriting.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-18 15:12:03
|
Revision: 2459
http://sourceforge.net/p/jsbml/code/2459
Author: niko-rodrigue
Date: 2015-12-18 15:12:01 +0000 (Fri, 18 Dec 2015)
Log Message:
-----------
implemented the writting of the semantics mathML element for the top level ASTNode
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
Added Paths:
-----------
trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java
Modified: trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-12-17 14:53:38 UTC (rev 2458)
+++ trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-12-18 15:12:01 UTC (rev 2459)
@@ -39,6 +39,8 @@
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.xml.XMLNode;
+import org.sbml.jsbml.xml.parsers.XMLNodeWriter;
import com.ctc.wstx.stax.WstxOutputFactory;
@@ -161,9 +163,27 @@
writer.writeCharacters("\n");
writer.setPrefix("math", ASTNode.URI_MATHML_DEFINITION);
-
+
+ // if an ASTNode.isSemantics we need to write the enclosing 'semantics' element !!
+ if (astNode.isSemantics()) {
+ writer.writeCharacters(compiler.indent);
+ compiler.indent += " ";
+ writer.writeStartElement("semantics");
+ writer.writeCharacters("\n");
+ }
+
compiler.compile(astNode);
+ // writing the semantics annotation elements here to write them only for the top level element.
+ if (astNode.isSemantics()) {
+
+ compiler.compileSemanticAnnotations(astNode);
+
+ writer.writeCharacters(" ");
+ writer.writeEndElement();
+ writer.writeCharacters("\n");
+ }
+
writer.writeEndElement();
writer.writeEndDocument();
writer.close();
@@ -357,6 +377,9 @@
case VECTOR:
compileVector(astNode);
break;
+// case SEMANTICS:
+// compileSemantics(astNode);
+// break;
default: // UNKNOWN:
logger.warn("!!!!! I don't know what to do with the node of type " + astNode.getType());
break;
@@ -446,7 +469,7 @@
writer.writeCharacters(indent);
writer.writeEmptyElement(ASTNode.URI_MATHML_DEFINITION, "exponentiale");
writer.writeCharacters("\n");
-
+
} catch (XMLStreamException e) {
e.printStackTrace();
}
@@ -1002,7 +1025,42 @@
}
}
+
/**
+ * @param node
+ */
+ public void compileSemanticAnnotations(ASTNode node) {
+
+ try {
+
+ if (node.getNumSemanticsAnnotations() > 0)
+ {
+ // TODO - use the current 'indent' value to initialize the XMLNodeWriter
+ XMLNodeWriter xmlNodeWriter = new XMLNodeWriter(writer, 0, 2, ' ');
+
+ for (int i = 0; i < node.getNumSemanticsAnnotations(); i++)
+ {
+ XMLNode xmlNode = node.getSemanticsAnnotation(i);
+
+ writer.writeCharacters(indent);
+ xmlNodeWriter.write(xmlNode);
+ writer.writeCharacters("\n");
+ }
+ }
+ } catch (XMLStreamException e) {
+ e.printStackTrace();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+// private void compileSemantics(ASTNode astNode) {
+// // would be needed for ASTNode2 may be ?
+// }
+
+
+ /**
* @param args
*/
public static void main(String[] args) {
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-12-17 14:53:38 UTC (rev 2458)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-12-18 15:12:01 UTC (rev 2459)
@@ -886,12 +886,15 @@
// All the element should have a namespace.
if (elementNamespace != null) {
+ // TODO - change the way we deal with notes, message and annotation and just use the context object ! If XMLNode, we use the 'anyXML' parser
+ // it will allow us to deal easily with unknowns XML elements.
+
parser = initializedParsers.get(elementNamespace);
// if the current node is a notes or message element
// and the matching ReadingParser is a XMLNodeReader,
// we need to set the typeOfNotes variable of the
// XMLNodeReader instance.
- if (currentNode.getLocalPart().equals("notes")
+ if (currentNode.getLocalPart().equals("notes")
|| currentNode.getLocalPart().equals("message")
|| currentNode.getLocalPart().equals("annotation"))
{
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-12-17 14:53:38 UTC (rev 2458)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-12-18 15:12:01 UTC (rev 2459)
@@ -786,6 +786,7 @@
// Creating an SMOutputElement to be sure that the previous nested element tag is closed properly.
SMNamespace mathMLNamespace = element.getNamespace(ASTNode.URI_MATHML_DEFINITION, ASTNode.URI_MATHML_PREFIX);
SMOutputElement mathElement = element.addElement(mathMLNamespace, "math");
+
MathMLXMLStreamCompiler compiler = new MathMLXMLStreamCompiler(
writer, createIndentationString(indent + indentCount));
boolean isSBMLNamespaceNeeded = compiler.isSBMLNamespaceNeeded(m.getMath());
@@ -817,8 +818,27 @@
writer.writeCharacters(whitespaces);
writer.writeCharacters("\n");
+ ASTNode astNode = m.getMath();
+
+ // if an ASTNode.isSemantics we need to write the enclosing 'semantics' element !!
+ if (astNode.isSemantics()) {
+ writer.writeCharacters(whitespaces);
+ writer.writeStartElement("semantics");
+ writer.writeCharacters("\n");
+ }
+
compiler.compile(m.getMath());
+ // writing the semantics annotation elements here to write them only for the top level element.
+ if (astNode.isSemantics()) {
+
+ compiler.compileSemanticAnnotations(astNode);
+
+ writer.writeCharacters(whitespaces);
+ writer.writeEndElement();
+ writer.writeCharacters("\n");
+ }
+
writer.writeCharacters(whitespaces);
}
}
Added: trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java (rev 0)
+++ trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java 2015-12-18 15:12:01 UTC (rev 2459)
@@ -0,0 +1,69 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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.test;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.SBMLWriter;
+
+
+public class TestSemanticsMathML {
+
+ public static void main(String[] args)
+ {
+ String mathml = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ + " <semantics>"
+ + " <exponentiale/>"
+ + " <annotation encoding=\"infix-input\">ExponentialE</annotation>"
+ + " <annotation encoding=\"infix-output\">exponentiale</annotation>"
+ + " <annotation-xml encoding=\"infix-output\">exponentiale</annotation-xml>"
+ + " </semantics>"
+ + "</math>";
+
+
+ ASTNode node = ASTNode.readMathMLFromString(mathml);
+
+ System.out.println("nb semantic annotations = " + node.getNumSemanticsAnnotations());
+
+ System.out.println(node.toMathML());
+
+ SBMLDocument doc = new SBMLDocument(3, 1);
+
+ doc.createModel().createReaction().createKineticLaw().setMath(node);
+
+ try {
+ System.out.println(new SBMLWriter().writeSBMLToString(doc));
+ } catch (SBMLException | XMLStreamException e) {
+ e.printStackTrace();
+ }
+
+ int n = doc.checkConsistency();
+
+ if (n > 0) {
+ doc.printErrors(System.out);
+ }
+ }
+}
Property changes on: trunk/core/test/org/sbml/jsbml/test/TestSemanticsMathML.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-17 14:53:41
|
Revision: 2458
http://sourceforge.net/p/jsbml/code/2458
Author: niko-rodrigue
Date: 2015-12-17 14:53:38 +0000 (Thu, 17 Dec 2015)
Log Message:
-----------
modified a bit the reading of semantics mathml annotations to comply to the expected structure
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-15 15:04:43 UTC (rev 2457)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-17 14:53:38 UTC (rev 2458)
@@ -374,6 +374,13 @@
*/
TIMES,
/**
+ * MathML markup can be combined with other markup languages, and these mixing constructions are realized by the semantic
+ * annotation elements. The semantic annotation elements provide an important tool for making associations between
+ * alternate representations of an expression, and for associating semantic properties and other attributions with
+ * a MathML expression.
+ */
+ SEMANTICS,
+ /**
*
*/
UNKNOWN,
@@ -3145,7 +3152,19 @@
|| type == Type.RELATIONAL_LT || type == Type.RELATIONAL_NEQ;
}
+
/**
+ * Return true if this node contain some semantics annotations.
+ *
+ * @return true if this node contain some semantics annotations.
+ * @see #getNumSemanticsAnnotations()
+ */
+ public boolean isSemantics() {
+ return getNumSemanticsAnnotations() > 0;
+ }
+
+
+ /**
* @return
*/
public boolean isSetClassName() {
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-15 15:04:43 UTC (rev 2457)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-17 14:53:38 UTC (rev 2458)
@@ -26,7 +26,6 @@
import java.util.List;
import javax.swing.tree.TreeNode;
-import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
@@ -273,29 +272,15 @@
}
// if elementName.equals(semantics) add all child elements as semanticsAnnotation to the parent ASTNode !
- if (elementName.equals("semantics"))
+ if (elementName.equals("annotation") || elementName.equals("annotation-xml"))
{
TreeNode parentNode = xmlNode.getParent();
if (parentNode instanceof ASTNode)
{
- // we are at the end of the top level 'semantics' element.
- // adding all child elements that are not empty as semanticAnnotation // TODO - keep the top level 'semantics' element if not empty.
+ // we are at the end of the annotation or annotation-xml elements.
+ ((ASTNode) parentNode).addSemanticsAnnotation(xmlNode);
- for (XMLNode childNode : xmlNode.getChildElements(null, null))
- {
- if (childNode.isText() && childNode.getCharacters().trim().length() == 0) {
- continue;
- }
- ((ASTNode) parentNode).addSemanticsAnnotation(childNode);
-
-// try {
-// System.out.println("MathMLStaxParser - processEndElement - semantic annotation = \n" + childNode.toXMLString());
-// } catch (XMLStreamException e) {
-// e.printStackTrace();
-// }
- }
-
// System.out.println("MathMLStaxParser - processEndElement - num semantic annotation = " + ((ASTNode) parentNode).getNumSemanticsAnnotations());
}
@@ -321,7 +306,8 @@
// add other type of ASTNode in the test ??
if ((astNode.isFunction() || astNode.isOperator() || astNode.isRelational() ||
astNode.isLogical()) && !elementName.equals("apply") && !elementName.equals("piecewise")
- && !elementName.equals("lamdba") && !astNode.getType().equals(ASTNode.Type.LAMBDA))
+ && !elementName.equals("lamdba") && !astNode.getType().equals(ASTNode.Type.LAMBDA)
+ && !elementName.equals("semantics"))
{
if (logger.isDebugEnabled()) {
logger.debug("processEndElement : stack stay the same. ASTNode type = " + astNode.getType());
@@ -381,7 +367,8 @@
if (elementName.equals("math") || elementName.equals("apply") || elementName.equals("sep")
|| elementName.equals("piece") || elementName.equals("otherwise")
- || elementName.equals("bvar") || elementName.equals("degree") || elementName.equals("logbase"))
+ || elementName.equals("bvar") || elementName.equals("degree") || elementName.equals("logbase")
+ || elementName.equals("semantics"))
{
if (elementName.equals("apply"))
{
@@ -420,7 +407,7 @@
// System.out.println("MathMLStaxParser: processStartElement parent type: " + parentASTNode.getType());
}
- if (elementName.equals("semantics"))
+ if (elementName.equals("annotation") || elementName.equals("annotation-xml"))
{
// Creating a StartElement XMLNode !!
XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
@@ -437,7 +424,7 @@
// if semantics, create a new XMLNode and return it. Set the ASTNode as the parent so that
// we can add the semanticsAnnotation element in the #processEndElement method.
- if (elementName.equals("semantics"))
+ if (elementName.equals("annotation") || elementName.equals("annotation-xml"))
{
// Creating a StartElement XMLNode !!
XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-15 15:04:46
|
Revision: 2457
http://sourceforge.net/p/jsbml/code/2457
Author: niko-rodrigue
Date: 2015-12-15 15:04:43 +0000 (Tue, 15 Dec 2015)
Log Message:
-----------
implement reading of mathML semantics annotations
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-15 11:58:07 UTC (rev 2456)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-15 15:04:43 UTC (rev 2457)
@@ -26,6 +26,7 @@
import java.util.List;
import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
@@ -35,6 +36,10 @@
import org.sbml.jsbml.MathContainer;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.xml.XMLAttributes;
+import org.sbml.jsbml.xml.XMLNamespaces;
+import org.sbml.jsbml.xml.XMLNode;
+import org.sbml.jsbml.xml.XMLTriple;
/**
* A MathMLStaxParser is used to parse the MathML expressions injected into a SBML
@@ -66,7 +71,7 @@
* otherwise the XML version will appear at the beginning of the output.
*/
private boolean omitXMLDeclaration;
-
+
/**
* A {@link Logger} for this class.
*/
@@ -117,6 +122,13 @@
// Process the possible attributes.
// the sbml:units attribute is handle by the SBMLCoreParser.
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+ xmlNode.addAttr(attributeName, value, uri, prefix);
+ return;
+ }
+
if (! (contextObject instanceof ASTNode)) {
logger.debug("processAttribute : !!!!!!!!! context is not an ASTNode (" +
contextObject.getClass());
@@ -162,6 +174,15 @@
logger.debug("processCharactersOf : element name = " + elementName + ", characters = " + characters);
}
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ XMLNode textNode = new XMLNode(characters);
+ xmlNode.addChild(textNode);
+ return;
+ }
+
// Depending of the type of ASTNode, we need to do different things
if (! (contextObject instanceof ASTNode)) {
logger.debug("processCharactersOf : !!!!!!!!! context is not an ASTNode (" +
@@ -243,6 +264,47 @@
logger.debug("processEndElement : element name = " + elementName);
}
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ if (xmlNode.getChildCount() == 0) {
+ xmlNode.setEnd();
+ }
+
+ // if elementName.equals(semantics) add all child elements as semanticsAnnotation to the parent ASTNode !
+ if (elementName.equals("semantics"))
+ {
+ TreeNode parentNode = xmlNode.getParent();
+
+ if (parentNode instanceof ASTNode)
+ {
+ // we are at the end of the top level 'semantics' element.
+ // adding all child elements that are not empty as semanticAnnotation // TODO - keep the top level 'semantics' element if not empty.
+
+ for (XMLNode childNode : xmlNode.getChildElements(null, null))
+ {
+ if (childNode.isText() && childNode.getCharacters().trim().length() == 0) {
+ continue;
+ }
+ ((ASTNode) parentNode).addSemanticsAnnotation(childNode);
+
+// try {
+// System.out.println("MathMLStaxParser - processEndElement - semantic annotation = \n" + childNode.toXMLString());
+// } catch (XMLStreamException e) {
+// e.printStackTrace();
+// }
+ }
+
+ // System.out.println("MathMLStaxParser - processEndElement - num semantic annotation = " + ((ASTNode) parentNode).getNumSemanticsAnnotations());
+ }
+
+ }
+
+ // always remove the XMLNode from the stack.
+ return true;
+ }
+
if (elementName.equals("sep")) {
return false;
} else if (contextObject instanceof MathContainer) {
@@ -276,12 +338,29 @@
* @see org.sbml.jsbml.xml.ReadingParser#processNamespace(String elementName, String URI, String prefix, String localName, boolean hasAttributes, boolean isLastNamespace, Object contextObject)
*/
@Override
- public void processNamespace(String elementName, String URI, String prefix,
+ public void processNamespace(String elementName, String uri, String prefix,
String localName, boolean hasAttributes, boolean isLastNamespace,
Object contextObject)
{
- // TODO
+
+ if (contextObject instanceof XMLNode) {
+ XMLNode xmlNode = (XMLNode) contextObject;
+
+ if (!xmlNode.isStart()) {
+ logger.debug(MessageFormat.format(
+ "processNamespace: context Object is not a start node! {0}",
+ contextObject));
+ }
+ if (localName == null || localName.trim().length() == 0) {
+ localName = "xmlns";
+ }
+
+ xmlNode.addNamespace(uri, localName);
+ }
+
+ // TODO - store namespaces on mathML elements !
+
logger.debug("processNamespace called");
}
@@ -306,7 +385,7 @@
{
if (elementName.equals("apply"))
{
- lastElementWasApply = true;
+ lastElementWasApply = true; // TODO - write the booleans inside a user object to make the parser multi-thread safe ?
}
else
{
@@ -340,12 +419,46 @@
parentASTNode = mathContainer.getMath();
// System.out.println("MathMLStaxParser: processStartElement parent type: " + parentASTNode.getType());
}
+
+ if (elementName.equals("semantics"))
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ xmlNode.setParent(parentASTNode);
+
+ return xmlNode;
+ }
+
} else if (contextObject instanceof ASTNode) {
parentASTNode = ((ASTNode) contextObject);
mathContainer = parentASTNode.getParentSBMLObject();
// System.out.println("MathMLStaxParser: processStartElement parent type: " + parentASTNode.getType());
- } else {
+
+ // if semantics, create a new XMLNode and return it. Set the ASTNode as the parent so that
+ // we can add the semanticsAnnotation element in the #processEndElement method.
+ if (elementName.equals("semantics"))
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ xmlNode.setParent(parentASTNode);
+
+ return xmlNode;
+ }
+ }
+ // We are inside a mathML 'semantics' element, everything is read into an XMLNode
+ else if (contextObject instanceof XMLNode)
+ {
+ // Creating a StartElement XMLNode !!
+ XMLNode xmlNode = new XMLNode(new XMLTriple(elementName, uri, prefix), new XMLAttributes(), new XMLNamespaces());
+ XMLNode parentNode = (XMLNode) contextObject;
+
+ parentNode.addChild(xmlNode);
+
+ return xmlNode;
+ }
+ else
+ {
// Should never happen
logger.debug("processStartElement: !!!!!!!!!!! Should not have been here !!!!!!!!!!!");
logger.debug("processStartElement: contextObject.classname = " + contextObject.getClass().getName());
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-15 11:58:09
|
Revision: 2456
http://sourceforge.net/p/jsbml/code/2456
Author: niko-rodrigue
Date: 2015-12-15 11:58:07 +0000 (Tue, 15 Dec 2015)
Log Message:
-----------
added a field and some methods in ASTNode to handle the semantics annotations
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-15 11:56:29 UTC (rev 2455)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-15 11:58:07 UTC (rev 2456)
@@ -48,6 +48,7 @@
import org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler;
import org.sbml.jsbml.util.compilers.UnitsCompiler;
import org.sbml.jsbml.util.filters.Filter;
+import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.stax.SBMLReader;
/**
@@ -1391,6 +1392,12 @@
private String encoding;
/**
+ * XMLNode that will hold the content of the 'semantics' mathML element.
+ */
+ private List<XMLNode> semanticsAnnotationList;
+
+
+ /**
* Tells if the type attribute of the cn element was set and we need to
* write it back or if it is set to the default (REAL).
*
@@ -1498,6 +1505,14 @@
listOfNodes.add(c);
}
}
+
+ if (astNode.semanticsAnnotationList != null) {
+ semanticsAnnotationList = new ArrayList<XMLNode>();
+
+ for (XMLNode semanticsAnnotation : astNode.semanticsAnnotationList) {
+ semanticsAnnotationList.add(semanticsAnnotation.clone());
+ }
+ }
}
/**
@@ -2272,6 +2287,8 @@
if (equal && isSetUnits()) {
equal &= getUnits().equals(ast.getUnits());
}
+
+ // TODO - semanticsAnnotationList not part of equals or hashcode ?
}
return equal;
}
@@ -2355,6 +2372,8 @@
@Override
public TreeNode getChildAt(int i) {
return getChild(i);
+
+ // TODO - add semantics XMLNode ??
}
/* (non-Javadoc)
@@ -2363,6 +2382,8 @@
@Override
public int getChildCount() {
return listOfNodes == null ? 0 : listOfNodes.size();
+
+ // TODO - add semantics XMLNode ??
}
/**
@@ -2803,6 +2824,12 @@
if (isSetClassName()) {
hashCode += prime * getClassName().hashCode();
}
+ if (isSetUnits()) {
+ hashCode += prime * getUnits().hashCode();
+ }
+ // TODO - semanticsAnnotationList not part of equals or hashcode ?
+
+
return hashCode;
}
@@ -4356,4 +4383,102 @@
return tree;
}
+ /**
+ * Adds the given {@link XMLNode} as a MathML <code><semantics></code> element to this {@link ASTNode}.
+ *
+ * <p>
+ * The {@code <semantics>} element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more {@code <annotation>} or
+ * {@code <annotation-xml>} elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @param semanticsAnnotation the annotation to add.
+ * @return the added {@link XMLNode}.
+ */
+ public XMLNode addSemanticsAnnotation(XMLNode semanticsAnnotation) {
+ if (semanticsAnnotation == null) {
+ return null;
+ }
+ if (semanticsAnnotationList == null) {
+ semanticsAnnotationList = new ArrayList<XMLNode>();
+ }
+
+ semanticsAnnotationList.add(semanticsAnnotation);
+
+ return semanticsAnnotation;
+ }
+
+ /**
+ * Gets the number of <em>semantic annotation</em> elements inside this node.
+ *
+ * <p>
+ * The <code><semantics></code> element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more <code><annotation></code> or
+ * <code><annotation-xml></code> elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @return the number of annotations of this {@link ASTNode}.
+ * @see ASTNode#addSemanticsAnnotation(XMLNode semanticsAnnotation)
+ */
+ public int getNumSemanticsAnnotations() {
+ if (semanticsAnnotationList == null) {
+ return 0;
+ }
+
+ return semanticsAnnotationList.size();
+ }
+
+ /**
+ * Gets the nth <code><semantics></code> annotation of this node.
+ *
+ * <p>
+ * The <code><semantics></code> element is a MathML 2.0 construct
+ * that can be used to associate additional information with a MathML
+ * construct. The construct can be used to decorate a MathML expressions with
+ * a sequence of one or more <code><annotation></code> or
+ * <code><annotation-xml></code> elements. Each such element contains a
+ * pair of items; the first is a symbol that acts as an attribute or key, and
+ * the second is the value associated with the attribute or key. Please refer
+ * to the MathML 2.0 documentation, particularly the <a target="_blank"
+ * href="http://www.w3.org/TR/2007/WD-MathML3-20071005/chapter5.html#mixing.semantic.annotations">Section
+ * 5.2, Semantic Annotations</a> for more information about these constructs.
+ *
+ * @return the nth annotation of this {@link ASTNode}, or <code>null</code> if this node has
+ * no nth annotation (<code>n ></code>
+ * {@link ASTNode#getNumSemanticsAnnotations()}
+ * <code>- 1</code> or n < 0).
+ * @see ASTNode#addSemanticsAnnotation(XMLNode sAnnotation)
+ */
+ public XMLNode getSemanticsAnnotation(int n) {
+ if (semanticsAnnotationList == null || n < 0 || (n > (getNumSemanticsAnnotations() -1))) {
+ return null;
+ }
+
+ return semanticsAnnotationList.get(n);
+ }
+
+ /**
+ * Returns the list of semantics annotations of this node.
+ *
+ * @return the list of semantics annotations of this node or null if no semantics annotation are present.
+ */
+ public List<XMLNode> getListOfSemanticsAnnotations() {
+ return semanticsAnnotationList;
+ }
+
+ // TODO - removeSemanticsAnnotation
+ // TODO - unsetsemanticsAnnotation
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-15 11:56:32
|
Revision: 2455
http://sourceforge.net/p/jsbml/code/2455
Author: niko-rodrigue
Date: 2015-12-15 11:56:29 +0000 (Tue, 15 Dec 2015)
Log Message:
-----------
improved the TestSBMLDocumentClone class to test as well serialisation and de-serialisation of whole documents
Modified Paths:
--------------
trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java
Modified: trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java
===================================================================
--- trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java 2015-12-11 16:09:34 UTC (rev 2454)
+++ trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java 2015-12-15 11:56:29 UTC (rev 2455)
@@ -22,14 +22,22 @@
package org.sbml.jsbml.test;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
+import java.io.NotSerializableException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Base64;
import java.util.Calendar;
import java.util.List;
+import javax.swing.tree.TreeNode;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.SBMLDocument;
@@ -39,6 +47,7 @@
import org.sbml.jsbml.util.filters.Filter;
+
/**
* Test class used to check that jsbml SBMLDocument equals method return true when passed it's clone.
*
@@ -129,6 +138,26 @@
System.out.println(notEqualSBases);
}
+
+
+ String docString = toSerializedString(doc);
+ SBMLDocument serializedDoc = (SBMLDocument) fromSerializedString(docString);
+
+ boolean equalsSerialized = doc.equals(serializedDoc);
+
+ // System.out.println("Equals serialized = " + equalsSerialized);
+
+ if (!equalsSerialized) {
+ nbNotEquals++;
+ fileNotEquals.add(file);
+
+ List<SBase> notEqualSBases = checkEquals(doc, serializedDoc, new ArrayList<SBase>());
+
+ System.out.println("SBases not equals after serialization: " + notEqualSBases);
+ }
+
+ // TODO - write to String with SBMLWriter and compare again the result with equals !!
+
}
catch (XMLStreamException e)
{
@@ -178,6 +207,38 @@
}
}
+ /**
+ * @param sbase
+ * @param serializedSBase
+ * @param notEqualsList
+ * @return
+ */
+ private static List<SBase> checkEquals(SBase sbase, SBase serializedSBase, ArrayList<SBase> notEqualsList)
+ {
+ if (!sbase.equals(serializedSBase)) {
+ notEqualsList.add(sbase);
+ }
+
+ if (sbase.getChildCount() > 0) {
+
+ for (int i = 0; i < sbase.getChildCount(); i++) {
+ TreeNode child = sbase.getChildAt(i);
+
+ if (child instanceof SBase) {
+ checkEquals((SBase) child, (SBase) serializedSBase.getChildAt(i), notEqualsList);
+ }
+ }
+ }
+
+
+ return notEqualsList;
+ }
+
+ /**
+ * @param argsAsFile
+ * @param filesList
+ * @return
+ */
private static List<File> findAllXMLFiles(File argsAsFile, List<File> filesList)
{
// System.out.println("Analyzing directory '" + argsAsFile.getAbsolutePath() + "'");
@@ -224,5 +285,29 @@
return filesList;
}
-
+ /** Read the object from Base64 string. */
+ private static Object fromSerializedString(String s) throws IOException , ClassNotFoundException {
+ byte [] data = Base64.getDecoder().decode(s);
+ ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(data));
+ Object o = ois.readObject();
+ ois.close();
+ return o;
+ }
+
+ /** Write the object to a Base64 string. */
+ private static String toSerializedString(Serializable o) throws IOException {
+
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ ObjectOutputStream oos = new ObjectOutputStream(baos);
+
+ try {
+ oos.writeObject(o);
+ oos.close();
+ return Base64.getEncoder().encodeToString(baos.toByteArray());
+
+ } catch (NotSerializableException e) {
+ System.out.println("ERROR !! current content of the serialization : \n" + new String(baos.toByteArray()));
+ throw e;
+ }
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-11 16:09:36
|
Revision: 2454
http://sourceforge.net/p/jsbml/code/2454
Author: niko-rodrigue
Date: 2015-12-11 16:09:34 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
updated version in the ant build files
Modified Paths:
--------------
trunk/build.xml
trunk/core/build.xml
trunk/jsbml-build.properties
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-12-11 15:48:48 UTC (rev 2453)
+++ trunk/build.xml 2015-12-11 16:09:34 UTC (rev 2454)
@@ -46,8 +46,8 @@
<property name="Name" value="JSBML" />
<property name="name" value="jsbml" />
- <property name="version" value="1.1" />
- <property name="api.version" value="1.1" />
+ <property name="version" value="1.2-SNAPSHOT" />
+ <property name="api.version" value="1.2" />
<property name="year" value="${YEAR}" />
Modified: trunk/core/build.xml
===================================================================
--- trunk/core/build.xml 2015-12-11 15:48:48 UTC (rev 2453)
+++ trunk/core/build.xml 2015-12-11 16:09:34 UTC (rev 2454)
@@ -43,8 +43,8 @@
<property name="Name" value="JSBML"/>
<property name="name" value="jsbml"/>
- <property name="version" value="1.1"/>
- <property name="api.version" value="1.1"/>
+ <property name="version" value="1.2-SNAPSHOT"/>
+ <property name="api.version" value="1.2"/>
<property name="year" value="${YEAR}"/>
Modified: trunk/jsbml-build.properties
===================================================================
--- trunk/jsbml-build.properties 2015-12-11 15:48:48 UTC (rev 2453)
+++ trunk/jsbml-build.properties 2015-12-11 16:09:34 UTC (rev 2454)
@@ -1,7 +1,7 @@
jsbml.Name=JSBML
jsbml.name=jsbml
-jsbml.version=1.1
-jsbml.api.version=1.1
+jsbml.version=1.2-SNAPSHOT
+jsbml.api.version=1.2
jsbml.groupId=org.sbml.jsbml
jsbml.artifactId=jsbml-parent
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-11 15:48:52
|
Revision: 2453
http://sourceforge.net/p/jsbml/code/2453
Author: niko-rodrigue
Date: 2015-12-11 15:48:48 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
put most log4j Logger as transient (and static final) so that they do not prevent serialization + removed some unused ResourceBundle in the spatial package
Modified Paths:
--------------
trunk/NEWS.txt
trunk/core/src/org/sbml/jsbml/AbstractMathContainer.java
trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
trunk/core/src/org/sbml/jsbml/ListOf.java
trunk/core/src/org/sbml/jsbml/Species.java
trunk/core/src/org/sbml/jsbml/UnitDefinition.java
trunk/core/src/org/sbml/jsbml/ext/AbstractSBasePlugin.java
trunk/core/src/org/sbml/jsbml/util/CobraUtil.java
trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java
trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java
trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java
trunk/core/src/org/sbml/jsbml/xml/parsers/XMLNodeReader.java
trunk/core/src/org/sbml/jsbml/xml/stax/DateProcessor.java
trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
trunk/core/src/org/sbml/jsbml/xml/stax/XMLLogger.java
trunk/extensions/arrays/src/org/sbml/jsbml/xml/parsers/ArraysParser.java
trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
trunk/extensions/comp/src/org/sbml/jsbml/xml/parsers/CompParser.java
trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/DistribParser.java
trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/UncertMLXMLNodeReader.java
trunk/extensions/dyn/src/org/sbml/jsbml/xml/parsers/DynParser.java
trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java
trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/L3LayoutParser.java
trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/LayoutParser.java
trunk/extensions/qual/src/org/sbml/jsbml/xml/parsers/QualParser.java
trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java
trunk/extensions/req/src/org/sbml/jsbml/xml/parsers/ReqParser.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/NEWS.txt 2015-12-11 15:48:48 UTC (rev 2453)
@@ -17,6 +17,16 @@
- The clone constructor for SBaseRef was not cloning properly it's child
SBaseRef.
+ - The equals method of ASTNode was failing when one of the double values
+ was set to NaN.
+
+ - Corrected several potential NullPointerExceptions that could occur
+ during the cloning of an SBMLDocument that contain plugins.
+
+ - Corrected a potential NullPointerException in the
+ TreeNodeAdapter(Object, TreeNode) constructor.
+
+
===========================================================================
Version 1.1 (09-12-2015)
===========================================================================
Modified: trunk/core/src/org/sbml/jsbml/AbstractMathContainer.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/AbstractMathContainer.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -49,7 +49,7 @@
/**
* A logger for user-messages.
*/
- private static final Logger logger = Logger.getLogger(AbstractMathContainer.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractMathContainer.class);
/**
* The math formula as an abstract syntax tree.
Modified: trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -79,7 +79,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(AbstractTreeNode.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractTreeNode.class);
/**
Modified: trunk/core/src/org/sbml/jsbml/ListOf.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ListOf.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/ListOf.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -261,7 +261,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(ListOf.class);
+ private static final transient Logger logger = Logger.getLogger(ListOf.class);
/**
* Helper method to initialize newly created lists.
Modified: trunk/core/src/org/sbml/jsbml/Species.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/Species.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/Species.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -42,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(Species.class);
+ private static final transient Logger logger = Logger.getLogger(Species.class);
/**
* Generated serial version identifier.
Modified: trunk/core/src/org/sbml/jsbml/UnitDefinition.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/UnitDefinition.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/UnitDefinition.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -63,7 +63,7 @@
/**
* The logger for this class.
*/
- private static final Logger logger = Logger.getLogger(UnitDefinition.class);
+ private static final transient Logger logger = Logger.getLogger(UnitDefinition.class);
/**
* Generated serial version identifier.
*/
Modified: trunk/core/src/org/sbml/jsbml/ext/AbstractSBasePlugin.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ext/AbstractSBasePlugin.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/ext/AbstractSBasePlugin.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -51,7 +51,7 @@
/**
*
*/
- private Logger logger = Logger.getLogger(AbstractSBasePlugin.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractSBasePlugin.class);
/**
*
Modified: trunk/core/src/org/sbml/jsbml/util/CobraUtil.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/CobraUtil.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/util/CobraUtil.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -40,7 +40,7 @@
*/
public class CobraUtil {
- private static Logger logger = Logger.getLogger(CobraUtil.class);
+ private static final transient Logger logger = Logger.getLogger(CobraUtil.class);
/**
* Parses the notes of the given {@link SBase} element.
Modified: trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -44,7 +44,7 @@
/**
* A {@link Logger} for this class.
*/
- private static transient Logger logger;
+ private static final transient Logger logger = Logger.getLogger(SimpleTreeNodeChangeListener.class);
/**
* Creates an {@link TreeNodeChangeListener} that writes all events to the
@@ -52,7 +52,6 @@
*/
public SimpleTreeNodeChangeListener() {
super();
- logger = Logger.getLogger(SimpleTreeNodeChangeListener.class);
}
/**
Modified: trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/util/compilers/MathMLXMLStreamCompiler.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -64,7 +64,7 @@
/**
* A {@link Logger} for this class.
*/
- private final Logger logger = Logger.getLogger(MathMLXMLStreamCompiler.class);
+ private static final transient Logger logger = Logger.getLogger(MathMLXMLStreamCompiler.class);
/**
*
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/AbstractReaderWriter.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -53,7 +53,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(AbstractReaderWriter.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractReaderWriter.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.ReadingParser#processAttribute(String
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/MathMLStaxParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -70,7 +70,7 @@
/**
* A {@link Logger} for this class.
*/
- private transient Logger logger = Logger.getLogger(MathMLStaxParser.class);
+ private static final transient Logger logger = Logger.getLogger(MathMLStaxParser.class);
/**
*
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -66,7 +66,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(ParserManager.class);
+ private static final transient Logger logger = Logger.getLogger(ParserManager.class);
private String[] parserDefaults =
{"org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader", "org.sbml.jsbml.xml.parsers.SBMLCoreParser",
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLRDFAnnotationParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -90,7 +90,7 @@
* Logger to be able to send informative, debug, warning or error messages.
*
*/
- private Logger logger = Logger.getLogger(getClass());
+ private static final transient Logger logger = Logger.getLogger(SBMLRDFAnnotationParser.class);
@Override
public XMLNode writeAnnotation(SBase contextObject, XMLNode xmlNode)
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/XMLNodeReader.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/XMLNodeReader.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/XMLNodeReader.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -60,7 +60,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(XMLNodeReader.class);
+ private static final transient Logger logger = Logger.getLogger(XMLNodeReader.class);
/**
*
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/DateProcessor.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/DateProcessor.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/DateProcessor.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -48,7 +48,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(DateProcessor.class);
+ private static final transient Logger logger = Logger.getLogger(DateProcessor.class);
static {
instance = new DateProcessor();
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -119,7 +119,7 @@
/**
* A {@link Logger} for this class.
*/
- private transient Logger logger = Logger.getLogger(SBMLReader.class);
+ private static final transient Logger logger = Logger.getLogger(SBMLReader.class);
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -260,7 +260,7 @@
/**
* A {@link Logger} for this class.
*/
- Logger logger = Logger.getLogger(SBMLWriter.class);
+ private static final transient Logger logger = Logger.getLogger(SBMLWriter.class);
/**
Modified: trunk/core/src/org/sbml/jsbml/xml/stax/XMLLogger.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/stax/XMLLogger.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/core/src/org/sbml/jsbml/xml/stax/XMLLogger.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -36,7 +36,7 @@
/**
* logger
*/
- private Logger logger = Logger.getLogger(XMLLogger.class);
+ private static final transient Logger logger = Logger.getLogger(XMLLogger.class);
/**
*
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/xml/parsers/ArraysParser.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/xml/parsers/ArraysParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/xml/parsers/ArraysParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -47,7 +47,7 @@
/**
* A {@link Logger} for this class.
*/
- private final Logger logger = Logger.getLogger(ArraysParser.class);
+ private static final transient Logger logger = Logger.getLogger(ArraysParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.ReadingParser#getNamespaces()
Modified: trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -61,7 +61,7 @@
*/
public class FlatteningTest {
- private static Logger logger = Logger.getLogger(FlatteningTest.class);
+ private static final transient Logger logger = Logger.getLogger(FlatteningTest.class);
@Test
public void sizeZeroTest() {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/xml/parsers/CompParser.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/xml/parsers/CompParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/comp/src/org/sbml/jsbml/xml/parsers/CompParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -63,7 +63,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CompParser.class);
+ private static final transient Logger logger = Logger.getLogger(CompParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getNamespaceURI()
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/DistribParser.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/DistribParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/DistribParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -80,7 +80,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(DistribParser.class);
+ private static final transient Logger logger = Logger.getLogger(DistribParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#getListOfSBMLElementsToWrite(Object sbase)
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/UncertMLXMLNodeReader.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/UncertMLXMLNodeReader.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/xml/parsers/UncertMLXMLNodeReader.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -53,7 +53,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(UncertMLXMLNodeReader.class);
+ private static final transient Logger logger = Logger.getLogger(UncertMLXMLNodeReader.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.ReadingParser#processCharactersOf(String elementName, String characters, Object contextObject)
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/xml/parsers/DynParser.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/xml/parsers/DynParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/xml/parsers/DynParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -61,7 +61,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(DynParser.class);
+ private static final transient Logger logger = Logger.getLogger(DynParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.ReadingParser#getNamespaces()
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -99,7 +99,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(FBCParser.class);
+ private static final transient Logger logger = Logger.getLogger(FBCParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#getListOfSBMLElementsToWrite(Object sbase)
Modified: trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -53,7 +53,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(GroupsParser.class);
+ private static final transient Logger logger = Logger.getLogger(GroupsParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#getListOfSBMLElementsToWrite(Object sbase)
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -53,7 +53,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(BoundingBox.class);
+ private static final transient Logger logger = Logger.getLogger(BoundingBox.class);
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -116,7 +116,7 @@
/**
*
*/
- private Logger logger = Logger.getLogger(CurveSegment.class);
+ private static final transient Logger logger = Logger.getLogger(CurveSegment.class);
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -60,7 +60,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(Dimensions.class);
+ private static final transient Logger logger = Logger.getLogger(Dimensions.class);
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -60,7 +60,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(GraphicalObject.class);
+ private static final transient Logger logger = Logger.getLogger(GraphicalObject.class);
/**
*
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -57,7 +57,7 @@
/**
* A {@link Logger} for this class.
*/
- private static final Logger logger = Logger.getLogger(Point.class);
+ private static final transient Logger logger = Logger.getLogger(Point.class);
/**
* the x coordinate
Modified: trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/L3LayoutParser.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/L3LayoutParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/L3LayoutParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -115,7 +115,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(L3LayoutParser.class);
+ private static final transient Logger logger = Logger.getLogger(L3LayoutParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#getListOfSBMLElementsToWrite(Object sbase)
Modified: trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/LayoutParser.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/LayoutParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/layout/src/org/sbml/jsbml/xml/parsers/LayoutParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -80,7 +80,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(LayoutParser.class);
+ private static final transient Logger logger = Logger.getLogger(LayoutParser.class);
/**
*
Modified: trunk/extensions/qual/src/org/sbml/jsbml/xml/parsers/QualParser.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/xml/parsers/QualParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/qual/src/org/sbml/jsbml/xml/parsers/QualParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -65,7 +65,7 @@
/**
*
*/
- private Logger logger = Logger.getLogger(QualParser.class);
+ private static final transient Logger logger = Logger.getLogger(QualParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#getListOfSBMLElementsToWrite(Object sbase)
Modified: trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/render/src/org/sbml/jsbml/xml/parsers/RenderParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -64,7 +64,7 @@
/**
* The logger for this RenderParser
*/
- private static final Logger logger = Logger.getLogger(RenderParser.class);
+ private static final transient Logger logger = Logger.getLogger(RenderParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getShortLabel()
Modified: trunk/extensions/req/src/org/sbml/jsbml/xml/parsers/ReqParser.java
===================================================================
--- trunk/extensions/req/src/org/sbml/jsbml/xml/parsers/ReqParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/req/src/org/sbml/jsbml/xml/parsers/ReqParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -52,7 +52,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(ReqParser.class);
+ private static final transient Logger logger = Logger.getLogger(ReqParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getNamespaceURI()
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,14 +23,12 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
/**
* @author Alex Thomas
@@ -44,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(AbstractSpatialNamedSBase.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractSpatialNamedSBase.class);
/**
* Generated serial version identifier.
@@ -59,11 +57,6 @@
/**
*
*/
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
- /**
- *
- */
public AbstractSpatialNamedSBase() {
super();
initDefaults();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
/**
* @author Alex Thomas
@@ -41,7 +39,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(AdjacentDomains.class);
+ private static final transient Logger logger = Logger.getLogger(AdjacentDomains.class);
/**
*
@@ -51,12 +49,7 @@
*
*/
private String domain2;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
* Generated serial version identifier.
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -40,7 +40,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(AdvectionCoefficient.class);
+ private static final transient Logger logger = Logger.getLogger(AdvectionCoefficient.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,16 +23,11 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
-import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractMathContainer;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.SBMLException;
-import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
-import org.sbml.jsbml.util.TreeNodeChangeEvent;
/**
* @author Alex Thomas
@@ -47,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(AnalyticVolume.class);
+ private static final transient Logger logger = Logger.getLogger(AnalyticVolume.class);
/**
*
@@ -71,12 +66,7 @@
*/
private static final long serialVersionUID = 1757917501241390228L;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
/**
@@ -42,7 +40,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(Boundary.class);
+ private static final transient Logger logger = Logger.getLogger(Boundary.class);
/**
* Generated serial version identifier.
@@ -54,12 +52,7 @@
*/
private Double value;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.SBMLException;
/**
* @author Alex Thomas
@@ -41,7 +39,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(BoundaryCondition.class);
+ private static final transient Logger logger = Logger.getLogger(BoundaryCondition.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,13 +23,11 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
@@ -45,7 +43,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGObject.class);
+ private static final transient Logger logger = Logger.getLogger(CSGObject.class);
/**
* Generated serial version identifier.
@@ -67,12 +65,7 @@
*/
private CSGNode csgNode;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
/**
* @author Alex Thomas
@@ -41,7 +39,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGPrimitive.class);
+ private static final transient Logger logger = Logger.getLogger(CSGPrimitive.class);
/**
*
@@ -53,12 +51,7 @@
*/
private PrimitiveKind primitiveType;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
/**
* @author Alex Thomas
@@ -41,7 +39,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGPseudoPrimitive.class);
+ private static final transient Logger logger = Logger.getLogger(CSGPseudoPrimitive.class);
/**
*
@@ -53,12 +51,7 @@
*/
private String csgObjectRef;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -41,7 +41,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGRotation.class);
+ private static final transient Logger logger = Logger.getLogger(CSGRotation.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -42,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGScale.class);
+ private static final transient Logger logger = Logger.getLogger(CSGScale.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -46,7 +46,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGSetOperator.class);
+ private static final transient Logger logger = Logger.getLogger(CSGSetOperator.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -41,7 +41,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CSGTranslation.class);
+ private static final transient Logger logger = Logger.getLogger(CSGTranslation.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -42,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CompartmentMapping.class);
+ private static final transient Logger logger = Logger.getLogger(CompartmentMapping.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -48,7 +48,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CoordinateComponent.class);
+ private static final transient Logger logger = Logger.getLogger(CoordinateComponent.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -44,7 +44,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(CoordinateReference.class);
+ private static final transient Logger logger = Logger.getLogger(CoordinateReference.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -26,7 +26,6 @@
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.xml.parsers.SpatialParser;
/**
@@ -53,7 +52,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(DiffusionCoefficient.class);
+ private static final transient Logger logger = Logger.getLogger(DiffusionCoefficient.class);
/**
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -46,7 +46,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(Domain.class);
+ private static final transient Logger logger = Logger.getLogger(Domain.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -42,7 +42,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(DomainType.class);
+ private static final transient Logger logger = Logger.getLogger(DomainType.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -46,7 +46,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(Geometry.class);
+ private static final transient Logger logger = Logger.getLogger(Geometry.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -40,7 +40,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(GeometryDefinition.class);
+ private static final transient Logger logger = Logger.getLogger(GeometryDefinition.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -44,7 +44,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(InteriorPoint.class);
+ private static final transient Logger logger = Logger.getLogger(InteriorPoint.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -43,7 +43,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(OrdinalMapping.class);
+ private static final transient Logger logger = Logger.getLogger(OrdinalMapping.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -45,7 +45,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(ParameterType.class);
+ private static final transient Logger logger = Logger.getLogger(ParameterType.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -41,7 +41,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(ParametricObject.class);
+ private static final transient Logger logger = Logger.getLogger(ParametricObject.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -46,7 +46,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SampledField.class);
+ private static final transient Logger logger = Logger.getLogger(SampledField.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -47,7 +47,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SampledFieldGeometry.class);
+ private static final transient Logger logger = Logger.getLogger(SampledFieldGeometry.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -23,11 +23,9 @@
import java.text.MessageFormat;
import java.util.Map;
-import java.util.ResourceBundle;
import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
/**
@@ -43,7 +41,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SampledVolume.class);
+ private static final transient Logger logger = Logger.getLogger(SampledVolume.class);
/**
* Generated serial version identifier.
@@ -67,12 +65,7 @@
*/
private Double maxValue;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -40,7 +40,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SpatialPoints.class);
+ private static final transient Logger logger = Logger.getLogger(SpatialPoints.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -44,7 +44,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SpatialReactionPlugin.class);
+ private static final transient Logger logger = Logger.getLogger(SpatialReactionPlugin.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -39,7 +39,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SpatialSymbolReference.class);
+ private static final transient Logger logger = Logger.getLogger(SpatialSymbolReference.class);
/**
* Generated serial version identifier.
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -43,7 +43,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(TransformationComponent.class);
+ private static final transient Logger logger = Logger.getLogger(TransformationComponent.class);
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-12-11 14:05:22 UTC (rev 2452)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-12-11 15:48:48 UTC (rev 2453)
@@ -60,7 +60,6 @@
import org.sbml.jsbml.ext.spatial.InteriorPoint;
import org.sbml.jsbml.ext.spatial.ParametricGeometry;
import org.sbml.jsbml.ext.spatial.ParametricObject;
-import org.sbml.jsbml.ext.spatial.PolygonObject;
import org.sbml.jsbml.ext.spatial.SampledField;
import org.sbml.jsbml.ext.spatial.SampledFieldGeometry;
import org.sbml.jsbml.ext.spatial.SampledVolume;
@@ -89,7 +88,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(SpatialParser.class);
+ private static final transient Logger logger = Logger.getLogger(SpatialParser.class);
/**
* The name space of required elements.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-11 14:05:24
|
Revision: 2452
http://sourceforge.net/p/jsbml/code/2452
Author: niko-rodrigue
Date: 2015-12-11 14:05:22 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
renamed the log4j Logger field to logger in SBMLCoreParser.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-12-11 14:02:33 UTC (rev 2451)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-12-11 14:05:22 UTC (rev 2452)
@@ -98,7 +98,7 @@
/**
* Log4j logger
*/
- private static final transient Logger log4jLogger = Logger.getLogger(SBMLCoreParser.class);
+ private static final transient Logger logger = Logger.getLogger(SBMLCoreParser.class);
/**
* Localization support.
@@ -158,8 +158,8 @@
Object contextObject)
{
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"processing the attribute: ''{0}'' (value = {1}) on element ''{2}'' ({3}).",
attributeName, value, elementName, contextObject));
}
@@ -174,8 +174,8 @@
try {
isAttributeRead = sbase.readAttribute(attributeName, prefix, value);
} catch (Throwable exc) {
- log4jLogger.error(exc.getMessage());
- log4jLogger.info("Attribute = " + attributeName + ", element = " + elementName);
+ logger.error(exc.getMessage());
+ logger.info("Attribute = " + attributeName + ", element = " + elementName);
}
}
// A SBMLCoreParser can modify a contextObject which is an instance of
@@ -193,16 +193,16 @@
isAttributeRead = true;
} catch (IllegalArgumentException e) {
// TODO: Write from which element the error is coming from: astNode.getParentSBMLObject();
- log4jLogger.warn(e.getMessage());
+ logger.warn(e.getMessage());
// Log the error to the ErrorLog object ??
}
- log4jLogger.debug("SBMLCoreParser: processAttribute: adding an unit to an ASTNode");
+ logger.debug("SBMLCoreParser: processAttribute: adding an unit to an ASTNode");
}
if (!isAttributeRead) {
// TODO: Here we should add a hint which SBML Level/Version combination is used.
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownAttributeOnElement"), // Level {2,number,integer} Version {3,number,integer}
attributeName, elementName));
// Log the error to the ErrorLog object ??
@@ -225,8 +225,8 @@
if ((elementName != null) && elementName.equals("notes")) {
} else if ((characters != null) && (characters.trim().length() != 0)) {
- // log4jLogger.warn("The SBML core XML element should not have any content, everything should be stored as attribute.");
- // log4jLogger.warn("The Characters are: @" + characters.trim() + "@");
+ // logger.warn("The SBML core XML element should not have any content, everything should be stored as attribute.");
+ // logger.warn("The Characters are: @" + characters.trim() + "@");
}
}
@@ -236,51 +236,51 @@
@Override
public void processEndDocument(SBMLDocument sbmlDocument) {
- log4jLogger.debug("SBMLCoreParser: processEndDocument");
+ logger.debug("SBMLCoreParser: processEndDocument");
if (sbmlDocument.isSetModel()) {
Model model = sbmlDocument.getModel();
if (model.isSetAreaUnits() && !model.isSetAreaUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "areaUnitsID", model.getAreaUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetConversionFactor()
&& !model.isSetConversionFactorInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Parameter", "conversionFactorID", model.getConversionFactor(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetExtentUnits() && !model.isSetExtentUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "extentUnitsID", model.getExtentUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetLengthUnits() && !model.isSetLengthUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "lengthUnitsID", model.getLengthUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetSubstanceUnits()
&& !model.isSetSubstanceUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "substanceUnitsID", model.getSubstanceUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetTimeUnits() && !model.isSetTimeUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "timeUnitsID", model.getTimeUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
}
if (model.isSetVolumeUnits() && !model.isSetVolumeUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "volumeUnitsID", model.getVolumeUnits(),
model.getElementName(), SBMLtools.getIdOrName(model)));
@@ -290,7 +290,7 @@
if (model.getLevel() == 1) {
- log4jLogger.debug("Transformed SBMLLevel1Rule: processEndDocument: model is level 1");
+ logger.debug("Transformed SBMLLevel1Rule: processEndDocument: model is level 1");
int i = 0;
for (Rule rule : model.getListOfRules().clone()) {
@@ -299,22 +299,22 @@
if (((SBMLLevel1Rule) rule).isScalar()) {
realRule = ((SBMLLevel1Rule) rule).cloneAsAssignmentRule();
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"Transformed SBMLLevel1Rule: {0} into AssignmentRule.",
((SBMLLevel1Rule) rule).getVariable()));
}
} else {
realRule = ((SBMLLevel1Rule) rule).cloneAsRateRule();
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"Transformed SBMLLevel1Rule: {0} into RateRule.",
((SBMLLevel1Rule) rule).getVariable()));
}
}
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"Transformed SBMLLevel1Rule: realRule = {0}",
realRule));
}
@@ -332,7 +332,7 @@
AssignmentRule assignmentRule = (AssignmentRule) rule;
if (assignmentRule.isSetVariable()
&& !assignmentRule.isSetVariableInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError2"),
"Symbol", "variableID", assignmentRule.getVariable(),
assignmentRule.getElementName()));
@@ -340,7 +340,7 @@
if (assignmentRule.isSetUnits()
&& !assignmentRule.isSetUnitsInstance()
&& assignmentRule.isParameter()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError2"),
"UnitDefinition", "unitsID", assignmentRule.getUnits(),
assignmentRule.getElementName()));
@@ -349,7 +349,7 @@
RateRule rateRule = (RateRule) rule;
if (rateRule.isSetVariable()
&& !rateRule.isSetVariableInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError3"),
"Symbol", "variableID", rateRule.getVariable(),
rateRule.getElementName()));
@@ -362,20 +362,20 @@
Compartment compartment = model.getCompartment(i);
if (compartment.isSetCompartmentType()
&& !compartment.isSetCompartmentTypeInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"CompartmentType", "compartmentTypeID", compartment.getCompartmentType(),
compartment.getElementName(), SBMLtools.getIdOrName(compartment)));
}
if (compartment.isSetOutside()
&& !compartment.isSetOutsideInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Compartment", "outsideID", compartment.getOutside(),
compartment.getElementName(), SBMLtools.getIdOrName(compartment)));
}
if (compartment.isSetUnits() && !compartment.isSetUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "unitsID", compartment.getUnits(),
compartment.getElementName(), SBMLtools.getIdOrName(compartment)));
@@ -387,7 +387,7 @@
Event event = model.getEvent(i);
if (event.isSetTimeUnits() && !event.isSetTimeUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "timeUnitsID", event.getTimeUnits(),
event.getElementName(), SBMLtools.getIdOrName(event)));
@@ -401,7 +401,7 @@
if (eventAssignment.isSetVariable()
&& !eventAssignment.isSetVariableInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError4"),
"Symbol", "variableID", eventAssignment.getVariable(),
eventAssignment.getElementName(), event.getElementName(),
@@ -418,7 +418,7 @@
if (initialAssignment.isSetVariable()
&& !initialAssignment.isSetVariableInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError5"),
"Symbol", "symbolID",
initialAssignment.getVariable(),
@@ -431,7 +431,7 @@
Reaction reaction = model.getReaction(i);
if (reaction.isSetCompartment()
&& !reaction.isSetCompartmentInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Compartment", "compartmentID", reaction.getCompartment(),
reaction.getElementName(), SBMLtools.getIdOrName(reaction)));
@@ -445,7 +445,7 @@
if (speciesReference.isSetSpecies()
&& !speciesReference.isSetSpeciesInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Species", "speciesID", speciesReference.getSpecies(),
speciesReference.getElementName(),
@@ -460,7 +460,7 @@
if (speciesReference.isSetSpecies()
&& !speciesReference.isSetSpeciesInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Species", "speciesID",
speciesReference.getSpecies(), speciesReference.getElementName(),
@@ -469,7 +469,7 @@
}
}
if (neitherReactantsNorProducts) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.reactionWithoutParticipantsError"),
SBMLtools.getIdOrName(reaction)));
}
@@ -481,7 +481,7 @@
if (modifierSpeciesReference.isSetSpecies()
&& !modifierSpeciesReference
.isSetSpeciesInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Species", "speciesID",
modifierSpeciesReference.getSpecies(),
@@ -493,7 +493,7 @@
KineticLaw kineticLaw = reaction.getKineticLaw();
if (kineticLaw.isSetTimeUnits()
&& !kineticLaw.isSetTimeUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError6"),
"UnitDefinition", "timeUnitsID", kineticLaw.getTimeUnits(),
kineticLaw.getElementName(), reaction.getElementName(),
@@ -501,7 +501,7 @@
}
if (kineticLaw.isSetSubstanceUnits()
&& !kineticLaw.isSetSubstanceUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError6"),
"UnitDefinition", "substanceUnitsID",
kineticLaw.getSubstanceUnits(), kineticLaw.getElementName(),
@@ -513,7 +513,7 @@
.getLocalParameter(j);
if (parameter.isSetUnits()
&& !parameter.isSetUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "unitsID",
parameter.getUnits(), parameter.getElementName(),
@@ -530,7 +530,7 @@
if (species.isSetSubstanceUnits()
&& !species.isSetSubstanceUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "subtsanceUnitsID",
species.getSubstanceUnits(), species.getElementName(),
@@ -538,28 +538,28 @@
}
if (species.isSetSpeciesType()
&& !species.isSetSpeciesTypeInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"SpeciesType", "speciesTypeID", species.getSpeciesType(),
species.getElementName(), SBMLtools.getIdOrName(species)));
}
if (species.isSetConversionFactor()
&& !species.isSetConversionFactorInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Parameter", "conversionFactorID", species.getConversionFactor(),
species.getElementName(), SBMLtools.getIdOrName(species)));
}
if (species.isSetCompartment()
&& !species.isSetCompartmentInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"Compartment", "compartmentID", species.getCompartment(),
species.getElementName(), SBMLtools.getIdOrName(species)));
}
if (species.isSetSpatialSizeUnits()
&& !species.isSetSpatialSizeUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "spatialSizeUnitsID",
species.getSpatialSizeUnits(), species.getElementName(),
@@ -572,7 +572,7 @@
Parameter parameter = model.getParameter(i);
if (parameter.isSetUnits()
&& !parameter.isSetUnitsInstance()) {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownReferenceError1"),
"UnitDefinition", "unitsID", parameter.getUnits(),
parameter.getElementName(), SBMLtools.getIdOrName(parameter)));
@@ -581,10 +581,10 @@
}
} else {
- log4jLogger.error("The Model element has not been created.");
+ logger.error("The Model element has not been created.");
}
- log4jLogger.debug("Starting to check the package version and namespace for all package elements");
+ logger.debug("Starting to check the package version and namespace for all package elements");
// checks silently package version and namespace and try to fix any problems encountered.
PackageUtil.checkPackages(sbmlDocument, true, true);
}
@@ -615,8 +615,8 @@
} else {
sbase.addDeclaredNamespace(localName, URI);
}
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"processNamespace: {0} = {1}",
prefix, URI));
}
@@ -630,15 +630,15 @@
} else {
annotation.addDeclaredNamespace(localName, URI);
}
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format(
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format(
"processNamespace: {0} = {1}",
prefix, URI));
}
}
else
{
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.namespaceIgnored"),
elementName, localName, URI));
// TODO - store into the XMLNode for unknown things
@@ -763,12 +763,12 @@
return listOfSpeciesTypes;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"),
elementName));
}
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"),
elementName));
}
@@ -938,7 +938,7 @@
return speciesType;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"),
elementName));
}
@@ -955,7 +955,7 @@
return unit;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (list.getParentSBMLObject() instanceof Reaction) {
@@ -979,7 +979,7 @@
return speciesReference;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (elementName.equals("specieReference")
@@ -998,7 +998,7 @@
return speciesReference;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (elementName
@@ -1011,7 +1011,7 @@
return modifierSpeciesReference;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (list.getParentSBMLObject() instanceof KineticLaw) {
@@ -1038,7 +1038,7 @@
return localParameter;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (list.getParentSBMLObject() instanceof Event) {
@@ -1053,11 +1053,11 @@
return eventAssignment;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (contextObject instanceof UnitDefinition) {
@@ -1093,7 +1093,7 @@
return priority;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (contextObject instanceof Reaction) {
@@ -1120,7 +1120,7 @@
return kineticLaw;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (contextObject instanceof SpeciesReference) {
@@ -1132,7 +1132,7 @@
return stoichiometryMath;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (contextObject instanceof KineticLaw) {
@@ -1153,7 +1153,7 @@
return listOfLocalParameters;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else if (contextObject instanceof Constraint) {
@@ -1167,26 +1167,26 @@
return constraint;
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} else {
- log4jLogger.warn(MessageFormat.format(
+ logger.warn(MessageFormat.format(
bundle.getString("SBMLCoreParser.unknownElement"), elementName));
}
} catch (InstantiationException exc) {
- log4jLogger.error(MessageFormat.format(
+ logger.error(MessageFormat.format(
bundle.getString("SBMLCoreParser.instanciationError"), elementName));
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(exc.getMessage());
- log4jLogger.debug(exc.getStackTrace());
+ if (logger.isDebugEnabled()) {
+ logger.debug(exc.getMessage());
+ logger.debug(exc.getStackTrace());
}
} catch (IllegalAccessException exc) {
- log4jLogger.error(MessageFormat.format(
+ logger.error(MessageFormat.format(
bundle.getString("SBMLCoreParser.instanciationError"), elementName));
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(exc.getMessage());
- log4jLogger.debug(exc.getStackTrace());
+ if (logger.isDebugEnabled()) {
+ logger.debug(exc.getMessage());
+ logger.debug(exc.getStackTrace());
}
}
}
@@ -1239,8 +1239,8 @@
if (sbmlElementToWrite instanceof SBase) {
SBase sbase = (SBase) sbmlElementToWrite;
- if (log4jLogger.isDebugEnabled()) {
- log4jLogger.debug(MessageFormat.format("writeElement: {0}", sbase.getElementName()));
+ if (logger.isDebugEnabled()) {
+ logger.debug(MessageFormat.format("writeElement: {0}", sbase.getElementName()));
}
// dealing with level 1 rules
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|
|
From: <nik...@us...> - 2015-12-11 14:02:35
|
Revision: 2451
http://sourceforge.net/p/jsbml/code/2451
Author: niko-rodrigue
Date: 2015-12-11 14:02:33 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
removed the XMLLogger field in SBMLCoreParser with its associated methods as it was never used
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-12-11 13:51:54 UTC (rev 2450)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java 2015-12-11 14:02:33 UTC (rev 2451)
@@ -71,7 +71,6 @@
import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.XMLTriple;
import org.sbml.jsbml.xml.stax.SBMLObjectForXML;
-import org.sbml.jsbml.xml.stax.XMLLogger;
/**
* Parses the SBML core elements of an SBML file. It can read and write SBML
@@ -97,11 +96,6 @@
private Map<String, Class<? extends Object>> sbmlCoreElements;
/**
- * The logger of this parser
- */
- private XMLLogger logger;
-
- /**
* Log4j logger
*/
private static final transient Logger log4jLogger = Logger.getLogger(SBMLCoreParser.class);
@@ -148,13 +142,6 @@
}
/**
- * @return the logger
- */
- public XMLLogger getLogger() {
- return logger;
- }
-
- /**
*
* @return the namespace URI of this parser.
*/
@@ -1223,14 +1210,6 @@
}
}
- /**
- * @param logger
- * the logger to set
- */
- public void setLogger(XMLLogger logger) {
- this.logger = logger;
- }
-
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.WritingParser#writeAttributes(SBMLObjectForXML xmlObject, Object sbmlElementToWrite)
*/
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|
|
From: <nik...@us...> - 2015-12-11 13:51:56
|
Revision: 2450
http://sourceforge.net/p/jsbml/code/2450
Author: niko-rodrigue
Date: 2015-12-11 13:51:54 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
corrected the AbstractSBase.equals method to make sure to use '.equals' to compare the namespace attribute and not '==' as '==' can return false even when the two String are identicals, in some circumstances
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-12-11 13:47:06 UTC (rev 2449)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-12-11 13:51:54 UTC (rev 2450)
@@ -84,7 +84,7 @@
/**
* A logger for this class.
*/
- private static final Logger logger = Logger.getLogger(AbstractSBase.class);
+ private static final transient Logger logger = Logger.getLogger(AbstractSBase.class);
/**
* Generated serial version identifier.
@@ -954,6 +954,7 @@
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
+
if (equals) {
/*
* Casting will be no problem because the super class has just
@@ -965,6 +966,7 @@
if (equals && sbase.isSetMetaId()) {
equals &= sbase.getMetaId().equals(getMetaId());
}
+
/*
* All child nodes are already checked by the recursive method in
* AbstractTreeNode. We here have to check the following own items
@@ -978,7 +980,8 @@
if (equals && sbase.isSetLevelAndVersion()) {
equals &= sbase.getLevelAndVersion().equals(getLevelAndVersion());
}
- equals &= sbase.getNamespace() == getNamespace();
+
+ equals &= getNamespace() != null ? getNamespace().equals(sbase.getNamespace()) : sbase.getNamespace() == null ;
if (declaredNamespaces == null) {
if (sbase.getDeclaredNamespaces() != null) {
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|
|
From: <nik...@us...> - 2015-12-11 13:47:09
|
Revision: 2449
http://sourceforge.net/p/jsbml/code/2449
Author: niko-rodrigue
Date: 2015-12-11 13:47:06 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
corrected a potential NullPointerException in the TreeNodeAdapter(Object, TreeNode) constructor
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
Modified: trunk/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-12-11 13:43:13 UTC (rev 2448)
+++ trunk/core/src/org/sbml/jsbml/util/TreeNodeAdapter.java 2015-12-11 13:47:06 UTC (rev 2449)
@@ -87,9 +87,13 @@
super();
this.userObject = userObject;
this.parent = parent;
+
if (parent instanceof TreeNodeWithChangeSupport) {
- addAllChangeListeners(((TreeNodeWithChangeSupport) parent)
- .getListOfTreeNodeChangeListeners());
+ TreeNodeWithChangeSupport parentTreeNode = (TreeNodeWithChangeSupport) parent;
+
+ if (parentTreeNode.getListOfTreeNodeChangeListeners() != null) {
+ addAllChangeListeners(parentTreeNode.getListOfTreeNodeChangeListeners());
+ }
}
}
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|
|
From: <nik...@us...> - 2015-12-11 13:43:16
|
Revision: 2448
http://sourceforge.net/p/jsbml/code/2448
Author: niko-rodrigue
Date: 2015-12-11 13:43:13 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
corrected several potential NullPointerExceptions that could occur during the cloning of an SBMLDocument
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/SBMLDocument.java
Modified: trunk/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-12-11 13:38:49 UTC (rev 2447)
+++ trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-12-11 13:43:13 UTC (rev 2448)
@@ -117,7 +117,7 @@
/**
* logger used to print messages
*/
- private transient Logger logger = Logger.getLogger(getClass());
+ private static final transient Logger logger = Logger.getLogger(SBMLDocument.class);
/**
* Stores all the meta identifiers within this {@link SBMLDocument} to avoid
@@ -489,7 +489,8 @@
}
metaIds.put(sbase.getMetaId(), sbase);
- if (logger.isDebugEnabled()) {
+ // logger can be null during cloning apparently
+ if (logger != null && logger.isDebugEnabled()) {
logger.debug("SBMLDocument - #collectMetaIds - node = '" + sbase + "'");
}
}
@@ -513,6 +514,11 @@
* @return
*/
public boolean containsMetaId(String metaId) {
+
+ if (mappingFromMetaId2SBase == null) {
+ mappingFromMetaId2SBase = new HashMap<String, SBase>();
+ }
+
return mappingFromMetaId2SBase.containsKey(metaId);
}
@@ -1162,6 +1168,11 @@
*
*/
boolean registerMetaId(SBase sbase, boolean add) {
+
+ if (mappingFromMetaId2SBase == null) {
+ mappingFromMetaId2SBase = new HashMap<String, SBase>();
+ }
+
if (sbase.isSetMetaId()) {
if (add) {
// We should call checkMetaid if we want to throw IllegalArgumentException here when metaid already present
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|
|
From: <nik...@us...> - 2015-12-11 13:38:51
|
Revision: 2447
http://sourceforge.net/p/jsbml/code/2447
Author: niko-rodrigue
Date: 2015-12-11 13:38:49 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
the ASTNode.equals method was failing when one of the double values was set to NaN. We should probably check all other equals methods for this problem
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/ASTNode.java
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-11 13:10:22 UTC (rev 2446)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-12-11 13:38:49 UTC (rev 2447)
@@ -2242,10 +2242,10 @@
&& ast.getDenominator() == getDenominator();
}
if ((ast.getType() == Type.REAL_E) && (type == Type.REAL_E)) {
- equal &= ast.getMantissa() == getMantissa()
+ equal &= Double.isNaN(getMantissa()) ? Double.isNaN(ast.getMantissa()) : ast.getMantissa() == getMantissa()
&& ast.getExponent() == getExponent();
} else if (isReal() && ast.isReal()) {
- equal &= ast.getReal() == getReal();
+ equal &= Double.isNaN(getReal()) ? Double.isNaN(ast.getReal()) : ast.getReal() == getReal();
}
equal &= isSetClassName() == ast.isSetClassName();
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|
|
From: <nik...@us...> - 2015-12-11 13:10:25
|
Revision: 2446
http://sourceforge.net/p/jsbml/code/2446
Author: niko-rodrigue
Date: 2015-12-11 13:10:22 +0000 (Fri, 11 Dec 2015)
Log Message:
-----------
corrected the MultiParser to properly write listOfSpeciesTypes and IntraSpeciesReaction
Modified Paths:
--------------
trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java
Modified: trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java 2015-12-10 15:51:11 UTC (rev 2445)
+++ trunk/extensions/multi/src/org/sbml/jsbml/xml/parsers/MultiParser.java 2015-12-11 13:10:22 UTC (rev 2446)
@@ -30,7 +30,9 @@
import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
+import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.Compartment;
+import org.sbml.jsbml.JSBML;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
@@ -39,6 +41,7 @@
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.ext.SBasePlugin;
+import org.sbml.jsbml.ext.multi.IntraSpeciesReaction;
import org.sbml.jsbml.ext.multi.MultiCompartmentPlugin;
import org.sbml.jsbml.ext.multi.MultiConstants;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
@@ -68,7 +71,7 @@
/**
* A {@link Logger} for this class.
*/
- private Logger logger = Logger.getLogger(MultiParser.class);
+ private static final transient Logger logger = Logger.getLogger(MultiParser.class);
/**
*
@@ -111,7 +114,20 @@
listOfElementsToWrite = super.getListOfSBMLElementsToWrite(treeNode);
}
- // TODO - IntraSpeciesReaction child
+ // IntraSpeciesReaction children
+ if (treeNode instanceof IntraSpeciesReaction) {
+ String sbmlNamespace = JSBML.getNamespaceFrom(((IntraSpeciesReaction) treeNode).getLevel(), ((IntraSpeciesReaction) treeNode).getVersion());
+
+ for (Object child : listOfElementsToWrite) {
+ if (child instanceof AbstractSBase && ((AbstractSBase) child).getNamespace() == null) {
+ AbstractSBase sbase = (AbstractSBase) child;
+ logger.debug("Found one suspect Model child: " + sbase.getElementName() + ". Setting the SBML namespace to it.");
+ sbase.setNamespace(sbmlNamespace);
+ }
+ }
+ }
+
+
return listOfElementsToWrite;
}
@@ -257,6 +273,13 @@
{
super.writeElement(xmlObject, sbmlElementToWrite);
+ // listOfBindingSiteSpeciesTypes if a BindingSpeciesType is the first element of the list of SpeciesTypes.
+ if (xmlObject.isSetName() && xmlObject.getName().equals("listOfBindingSiteSpeciesTypes")) {
+ xmlObject.setName(MultiConstants.listOfSpeciesTypes);
+ }
+
+ // listOfIntraSpeciesReactions cannot happen as core ListOf don't depend on the first element for their name.
+
if (logger.isDebugEnabled()) {
logger.debug("writeElement: " + sbmlElementToWrite.getClass().getSimpleName());
}
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|
|
From: <nik...@us...> - 2015-12-10 15:51:13
|
Revision: 2445
http://sourceforge.net/p/jsbml/code/2445
Author: niko-rodrigue
Date: 2015-12-10 15:51:11 +0000 (Thu, 10 Dec 2015)
Log Message:
-----------
added a class to test SBMLDocument.clone and .equals on the whole sbml-test-suite + corrected the clone constructor of SBaseRef that was not cloning it's child SBaseRef
Modified Paths:
--------------
trunk/NEWS.txt
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
Added Paths:
-----------
trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-12-10 15:08:42 UTC (rev 2444)
+++ trunk/NEWS.txt 2015-12-10 15:51:11 UTC (rev 2445)
@@ -12,10 +12,11 @@
- The whole SBMLDocument was not serializable, few classes were not
implementing the Serializable class. This should be fixed now. Thanks
- to Jens Thargor who reported the problem.
+ to Jens Einloft who reported the problem.
+ - The clone constructor for SBaseRef was not cloning properly it's child
+ SBaseRef.
-
===========================================================================
Version 1.1 (09-12-2015)
===========================================================================
Added: trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java
===================================================================
--- trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java (rev 0)
+++ trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java 2015-12-10 15:51:11 UTC (rev 2445)
@@ -0,0 +1,228 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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.test;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Calendar;
+import java.util.List;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLException;
+import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.util.filters.Filter;
+
+
+/**
+ * Test class used to check that jsbml SBMLDocument equals method return true when passed it's clone.
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.2
+ */
+public class TestSBMLDocumentClone {
+
+ public TestSBMLDocumentClone() {
+ }
+
+ /**
+ * Checks that jsbml {@link SBMLDocument#equals(Object)} method return true against it's clone.
+ *
+ * <p>If passed a folder, it will look recursively for all xml files. Particularly setup to go through
+ * the sbml-test-suite folders and test all valid models there.
+ *
+ * @param args the file or folder to test
+ * @throws SBMLException
+ */
+ public static void main(String[] args) throws SBMLException {
+
+ if (args.length < 1) {
+ System.out.println("Usage: java org.sbml.jsbml.test.TestSBMLDocumentClone sbmlFileName|folder");
+ System.exit(0);
+ }
+
+ // this JOptionPane is added here to be able to start visualVM profiling
+ // before the reading or writing is started.
+ // JOptionPane.showMessageDialog(null, "Eggs are not supposed to be green.");
+
+ File argsAsFile = new File(args[0]);
+ List<File> files = null;
+
+ if (argsAsFile.isDirectory())
+ {
+ files = findAllXMLFiles(argsAsFile, new ArrayList<File>());
+ }
+ else
+ {
+ files = new ArrayList<File>();
+ files.add(argsAsFile);
+ }
+
+ double globalInit = Calendar.getInstance().getTimeInMillis();
+ double globalEnd = 0;
+ int nbNotEquals = 0;
+ List<File> fileNotEquals = new ArrayList<File>();
+
+ System.out.println("Going to test '" + files.size() + "' files !");
+
+ for (File file : files)
+ {
+
+ double init = Calendar.getInstance().getTimeInMillis();
+ // System.out.println(Calendar.getInstance().getTime());
+
+ String fileName = file.getAbsolutePath();
+
+ System.out.printf("Reading %s\n", fileName);
+
+ try {
+
+ SBMLDocument doc = new SBMLReader().readSBML(file, null);
+
+ boolean equals = doc.equals(doc.clone());
+
+ if (!equals) {
+ nbNotEquals++;
+ fileNotEquals.add(file);
+ System.out.printf("Reading %s\n", fileName);
+ System.out.println(file.getAbsolutePath() + " is not equals to it's clone !!!!!!!!!!!!!!!!!!!!!!!!!!");
+
+ @SuppressWarnings("unchecked")
+ List<SBase> notEqualSBases = (List<SBase>) doc.filter(new Filter() {
+
+ @Override
+ public boolean accepts(Object o) {
+ if (o instanceof SBase) {
+ SBase s = (SBase) o;
+
+ return ! s.equals(s.clone());
+ }
+ return false;
+ }
+ });
+
+ System.out.println(notEqualSBases);
+ }
+ }
+ catch (XMLStreamException e)
+ {
+ e.printStackTrace();
+ }
+ catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ catch (Exception e)
+ {
+ System.out.printf("Reading %s\n", fileName);
+ nbNotEquals++;
+ fileNotEquals.add(file);
+ e.printStackTrace();
+ }
+
+ // System.out.println(Calendar.getInstance().getTime());
+ double end = Calendar.getInstance().getTimeInMillis();
+ globalEnd = end;
+ double nbMilliseconds = end - init;
+
+ if (files.size() == 1)
+ {
+ System.out.println((int)nbMilliseconds);
+ }
+ }
+
+ if (nbNotEquals > 0) {
+ System.out.println("Found " + nbNotEquals + " documents not equals to their clone or failing to clone.");
+
+ for (File file : fileNotEquals) {
+ System.out.println(file.getAbsolutePath());
+
+ }
+ }
+
+ if (files.size() > 1)
+ {
+ double globalNbMilliseconds = globalEnd - globalInit;
+ double globalSeconds = globalNbMilliseconds / 1000;
+
+ System.out.println("Reading and writing " + files.size() + " models took : " + globalSeconds + " seconds.");
+ System.out.println("Mean per model = " + globalSeconds / files.size() + " seconds (" + globalNbMilliseconds / files.size() + " ms).");
+
+ System.out.println((int)globalNbMilliseconds);
+ }
+ }
+
+ private static List<File> findAllXMLFiles(File argsAsFile, List<File> filesList)
+ {
+ // System.out.println("Analyzing directory '" + argsAsFile.getAbsolutePath() + "'");
+
+ File[] xmlFiles = argsAsFile.listFiles(new FileFilter() {
+
+ @Override
+ public boolean accept(File pathname)
+ {
+ if (pathname.getName().contains("-jsbml.xml") || pathname.getName().contains("fail")
+ || pathname.getName().contains("sedml"))
+ {
+ return false;
+ }
+
+ if (pathname.getName().endsWith(".xml"))
+ {
+ return true;
+ }
+
+ return false;
+ }
+ });
+
+ File[] directories = argsAsFile.listFiles(new FileFilter() {
+
+ @Override
+ public boolean accept(File pathname)
+ {
+ return pathname.isDirectory();
+ }
+ });
+
+ if (xmlFiles.length > 0) {
+ filesList.addAll(Arrays.asList(xmlFiles));
+ }
+
+ if (directories.length > 0) {
+ for(File directory : directories) {
+ findAllXMLFiles(directory, filesList);
+ }
+ }
+
+ return filesList;
+ }
+
+
+}
Property changes on: trunk/examples/test/src/org/sbml/jsbml/test/TestSBMLDocumentClone.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-12-10 15:08:42 UTC (rev 2444)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-12-10 15:51:11 UTC (rev 2445)
@@ -126,7 +126,7 @@
setMetaIdRef(obj.getMetaIdRef());
}
if (obj.isSetSBaseRef()) {
- setSBaseRef(obj.getSBaseRef());
+ setSBaseRef(obj.getSBaseRef().clone());
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-10 15:08:44
|
Revision: 2444
http://sourceforge.net/p/jsbml/code/2444
Author: niko-rodrigue
Date: 2015-12-10 15:08:42 +0000 (Thu, 10 Dec 2015)
Log Message:
-----------
we decided to put the list of listeners as transient in AbstractTreeNode so that they don't need to implements serializable
Modified Paths:
--------------
trunk/NEWS.txt
trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-12-10 14:45:31 UTC (rev 2443)
+++ trunk/NEWS.txt 2015-12-10 15:08:42 UTC (rev 2444)
@@ -2,6 +2,21 @@
===========================================================================
+Version 1.2-X (XX-XX-2016)
+===========================================================================
+
+ * New Features:
+
+
+ * Bug Fixes:
+
+ - The whole SBMLDocument was not serializable, few classes were not
+ implementing the Serializable class. This should be fixed now. Thanks
+ to Jens Thargor who reported the problem.
+
+
+
+===========================================================================
Version 1.1 (09-12-2015)
===========================================================================
Modified: trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-12-10 14:45:31 UTC (rev 2443)
+++ trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-12-10 15:08:42 UTC (rev 2444)
@@ -110,7 +110,7 @@
/**
* {@link List} of listeners for this component
*/
- protected List<TreeNodeChangeListener> listOfListeners;
+ protected transient List<TreeNodeChangeListener> listOfListeners;
/**
* The parent element of this {@link Annotation}.
Modified: trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java 2015-12-10 14:45:31 UTC (rev 2443)
+++ trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java 2015-12-10 15:08:42 UTC (rev 2444)
@@ -22,7 +22,6 @@
package org.sbml.jsbml.util;
import java.beans.PropertyChangeListener;
-import java.io.Serializable;
import javax.swing.tree.TreeNode;
@@ -36,7 +35,7 @@
* @since 0.8
* @version $Rev$
*/
-public interface TreeNodeChangeListener extends PropertyChangeListener, Serializable {
+public interface TreeNodeChangeListener extends PropertyChangeListener {
/**
* The {@link TreeNode} passed to this method has just been added to the
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-10 14:45:33
|
Revision: 2443
http://sourceforge.net/p/jsbml/code/2443
Author: niko-rodrigue
Date: 2015-12-10 14:45:31 +0000 (Thu, 10 Dec 2015)
Log Message:
-----------
making sure that the whole SBMLDocument is serializable. Few classes were missing and were not serializable before.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java
trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java
trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java
trunk/core/src/org/sbml/jsbml/xml/XMLNamespaces.java
trunk/core/src/org/sbml/jsbml/xml/XMLTriple.java
Modified: trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java 2015-12-10 10:07:57 UTC (rev 2442)
+++ trunk/core/src/org/sbml/jsbml/util/SimpleTreeNodeChangeListener.java 2015-12-10 14:45:31 UTC (rev 2443)
@@ -22,6 +22,7 @@
package org.sbml.jsbml.util;
import java.beans.PropertyChangeEvent;
+import java.io.Serializable;
import java.text.MessageFormat;
import javax.swing.tree.TreeNode;
@@ -38,12 +39,12 @@
* @since 0.8
* @version $Rev$
*/
-public class SimpleTreeNodeChangeListener implements TreeNodeChangeListener {
+public class SimpleTreeNodeChangeListener implements TreeNodeChangeListener, Serializable {
/**
* A {@link Logger} for this class.
*/
- private Logger logger;
+ private static transient Logger logger;
/**
* Creates an {@link TreeNodeChangeListener} that writes all events to the
Modified: trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java 2015-12-10 10:07:57 UTC (rev 2442)
+++ trunk/core/src/org/sbml/jsbml/util/TreeNodeChangeListener.java 2015-12-10 14:45:31 UTC (rev 2443)
@@ -22,6 +22,7 @@
package org.sbml.jsbml.util;
import java.beans.PropertyChangeListener;
+import java.io.Serializable;
import javax.swing.tree.TreeNode;
@@ -35,7 +36,7 @@
* @since 0.8
* @version $Rev$
*/
-public interface TreeNodeChangeListener extends PropertyChangeListener {
+public interface TreeNodeChangeListener extends PropertyChangeListener, Serializable {
/**
* The {@link TreeNode} passed to this method has just been added to the
Modified: trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-12-10 10:07:57 UTC (rev 2442)
+++ trunk/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-12-10 14:45:31 UTC (rev 2443)
@@ -21,6 +21,7 @@
*/
package org.sbml.jsbml.xml;
+import java.io.Serializable;
import java.util.ArrayList;
import org.sbml.jsbml.JSBML;
@@ -39,7 +40,7 @@
* @since 0.8
* @version $Rev$
*/
-public class XMLAttributes {
+public class XMLAttributes implements Serializable {
/**
*
Modified: trunk/core/src/org/sbml/jsbml/xml/XMLNamespaces.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/XMLNamespaces.java 2015-12-10 10:07:57 UTC (rev 2442)
+++ trunk/core/src/org/sbml/jsbml/xml/XMLNamespaces.java 2015-12-10 14:45:31 UTC (rev 2443)
@@ -21,6 +21,7 @@
*/
package org.sbml.jsbml.xml;
+import java.io.Serializable;
import java.util.LinkedHashMap;
import java.util.Map;
@@ -61,7 +62,7 @@
* @since 0.8
* @version $Rev$
*/
-public class XMLNamespaces {
+public class XMLNamespaces implements Serializable {
/**
* HashMap<Prefix, URI>
Modified: trunk/core/src/org/sbml/jsbml/xml/XMLTriple.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/XMLTriple.java 2015-12-10 10:07:57 UTC (rev 2442)
+++ trunk/core/src/org/sbml/jsbml/xml/XMLTriple.java 2015-12-10 14:45:31 UTC (rev 2443)
@@ -21,6 +21,7 @@
*/
package org.sbml.jsbml.xml;
+import java.io.Serializable;
import java.text.MessageFormat;
/**
@@ -61,7 +62,7 @@
* @since 0.8
* @version $Rev$
*/
-public class XMLTriple {
+public class XMLTriple implements Serializable {
/**
*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-10 10:08:00
|
Revision: 2442
http://sourceforge.net/p/jsbml/code/2442
Author: niko-rodrigue
Date: 2015-12-10 10:07:57 +0000 (Thu, 10 Dec 2015)
Log Message:
-----------
updated pom files to 1.2-SNAPSHOT
Modified Paths:
--------------
trunk/core/pom.xml
trunk/dev/maven/pom.xml
trunk/extensions/arrays/pom.xml
trunk/extensions/comp/pom.xml
trunk/extensions/distrib/pom.xml
trunk/extensions/dyn/pom.xml
trunk/extensions/fbc/pom.xml
trunk/extensions/groups/pom.xml
trunk/extensions/layout/pom.xml
trunk/extensions/multi/pom.xml
trunk/extensions/pom.xml
trunk/extensions/qual/pom.xml
trunk/extensions/render/pom.xml
trunk/extensions/req/pom.xml
trunk/extensions/spatial/pom.xml
trunk/modules/android/pom.xml
trunk/modules/celldesigner/pom.xml
trunk/modules/compare/pom.xml
trunk/modules/libSBMLcompat/pom.xml
trunk/modules/libSBMLio/pom.xml
trunk/modules/pom.xml
trunk/modules/tidy/pom.xml
trunk/pom.xml
Property Changed:
----------------
trunk/modules/tidy/
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/core/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -30,7 +30,7 @@
<parent>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml-parent</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<!--
Modified: trunk/dev/maven/pom.xml
===================================================================
--- trunk/dev/maven/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/dev/maven/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
Modified: trunk/extensions/arrays/pom.xml
===================================================================
--- trunk/extensions/arrays/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/arrays/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/comp/pom.xml
===================================================================
--- trunk/extensions/comp/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/comp/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/distrib/pom.xml
===================================================================
--- trunk/extensions/distrib/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/distrib/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/dyn/pom.xml
===================================================================
--- trunk/extensions/dyn/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/dyn/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/fbc/pom.xml
===================================================================
--- trunk/extensions/fbc/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/fbc/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/groups/pom.xml
===================================================================
--- trunk/extensions/groups/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/groups/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/layout/pom.xml
===================================================================
(Binary files differ)
Modified: trunk/extensions/multi/pom.xml
===================================================================
--- trunk/extensions/multi/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/multi/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/pom.xml
===================================================================
--- trunk/extensions/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -32,7 +32,7 @@
<parent>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml-parent</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/qual/pom.xml
===================================================================
--- trunk/extensions/qual/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/qual/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/render/pom.xml
===================================================================
--- trunk/extensions/render/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/render/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
@@ -40,7 +40,7 @@
<dependency>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>jsbml-layout</artifactId>
- <version>1.1-b1</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: trunk/extensions/req/pom.xml
===================================================================
--- trunk/extensions/req/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/req/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/extensions/spatial/pom.xml
===================================================================
--- trunk/extensions/spatial/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/extensions/spatial/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>ext</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Modified: trunk/modules/android/pom.xml
===================================================================
--- trunk/modules/android/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/android/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1-b1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
Modified: trunk/modules/celldesigner/pom.xml
===================================================================
--- trunk/modules/celldesigner/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/celldesigner/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -27,7 +27,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1-b1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@@ -44,15 +44,15 @@
<dependency>
<groupId>org</groupId>
<artifactId>libsbmlj</artifactId>
- <version>3.4.1</version>
+ <version>3.4.1</version> <!-- TODO: versions are not up to date -->
</dependency>
<dependency>
<groupId>org</groupId>
- <artifactId>sbmlj</artifactId>
+ <artifactId>sbmlj</artifactId> <!-- what is sbmlj ? -->
<version>1.0.0</version>
</dependency>
</dependencies>
-</project>
\ No newline at end of file
+</project>
Modified: trunk/modules/compare/pom.xml
===================================================================
--- trunk/modules/compare/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/compare/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -27,7 +27,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1-b1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@@ -51,14 +51,6 @@
<artifactId>libsbmlj</artifactId>
<version>5.0.0</version>
</dependency>
- <!--
- <dependency>
- <groupId>org.sbml.jsbml</groupId>
- <artifactId>jsbml-.8-rc1-with-dependencies</artifactId>
- <version>0.8.0</version>
- </dependency>
- -->
-
</dependencies>
</project>
Modified: trunk/modules/libSBMLcompat/pom.xml
===================================================================
--- trunk/modules/libSBMLcompat/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/libSBMLcompat/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1-b1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
Modified: trunk/modules/libSBMLio/pom.xml
===================================================================
--- trunk/modules/libSBMLio/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/libSBMLio/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -27,7 +27,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1-b1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@@ -42,4 +42,4 @@
<version>5.4.1</version>
</dependency>
</dependencies>
-</project>
\ No newline at end of file
+</project>
Modified: trunk/modules/pom.xml
===================================================================
--- trunk/modules/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -33,7 +33,7 @@
<parent>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml-parent</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
Index: trunk/modules/tidy
===================================================================
--- trunk/modules/tidy 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/tidy 2015-12-10 10:07:57 UTC (rev 2442)
Property changes on: trunk/modules/tidy
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/modules/tidy/pom.xml
===================================================================
--- trunk/modules/tidy/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/modules/tidy/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<parent>
<groupId>org.sbml.jsbml.modules</groupId>
<artifactId>modules</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-12-08 13:43:58 UTC (rev 2441)
+++ trunk/pom.xml 2015-12-10 10:07:57 UTC (rev 2442)
@@ -28,7 +28,7 @@
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml-parent</artifactId>
- <version>1.1</version>
+ <version>1.2-SNAPSHOT</version>
<packaging>pom</packaging>
<name>JSBML</name>
<inceptionYear>2009</inceptionYear>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-08 13:44:02
|
Revision: 2441
http://sourceforge.net/p/jsbml/code/2441
Author: niko-rodrigue
Date: 2015-12-08 13:43:58 +0000 (Tue, 08 Dec 2015)
Log Message:
-----------
put back the escapeinside option for the listings, so that we can add some Latex code inside the exmaples as before
Modified Paths:
--------------
trunk/core/doc/user_guide/User_Guide.pdf
trunk/core/doc/user_guide/User_Guide.tex
Modified: trunk/core/doc/user_guide/User_Guide.pdf
===================================================================
--- trunk/core/doc/user_guide/User_Guide.pdf 2015-12-08 13:10:33 UTC (rev 2440)
+++ trunk/core/doc/user_guide/User_Guide.pdf 2015-12-08 13:43:58 UTC (rev 2441)
@@ -25,7 +25,7 @@
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This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-12-08 13:10:36
|
Revision: 2440
http://sourceforge.net/p/jsbml/code/2440
Author: niko-rodrigue
Date: 2015-12-08 13:10:33 +0000 (Tue, 08 Dec 2015)
Log Message:
-----------
updated user guide with the latest extension graphs
Modified Paths:
--------------
trunk/core/doc/user_guide/User_Guide.pdf
Modified: trunk/core/doc/user_guide/User_Guide.pdf
===================================================================
--- trunk/core/doc/user_guide/User_Guide.pdf 2015-12-06 18:23:39 UTC (rev 2439)
+++ trunk/core/doc/user_guide/User_Guide.pdf 2015-12-08 13:10:33 UTC (rev 2440)
@@ -13462,7 +13462,7 @@
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@@ Diff output truncated at 100000 characters. @@
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|
From: <nik...@us...> - 2015-12-06 18:23:42
|
Revision: 2439
http://sourceforge.net/p/jsbml/code/2439
Author: niko-rodrigue
Date: 2015-12-06 18:23:39 +0000 (Sun, 06 Dec 2015)
Log Message:
-----------
tags release 1.1
Added Paths:
-----------
tags/jsbml-1.1/
Index: tags/jsbml-1.1
===================================================================
--- trunk 2015-12-06 18:19:00 UTC (rev 2438)
+++ tags/jsbml-1.1 2015-12-06 18:23:39 UTC (rev 2439)
Property changes on: tags/jsbml-1.1
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,11 ##
+.classpath
+.project
+dist
+build
+bin
+jsbml.log
+.apt_generated
+.factorypath
+.settings
+jsbmlTestResults.txt
+target
Added: LicenseHeader
## -0,0 +1,19 ##
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * 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) 2009-2011 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
+ *
+ * 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>.
+ * ----------------------------------------------------------------------------
+ */
\ No newline at end of property
Added: svn:mergeinfo
## -0,0 +1,2 ##
+/branches/astnode2-merging-alternate:2189-2376
+/tags/release-0.8-b1:588
\ No newline at end of property
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