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[Jsbml-svn] SF.net SVN: jsbml:[2218] trunk/core
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From: <and...@us...> - 2015-04-22 15:11:31
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Revision: 2218
http://sourceforge.net/p/jsbml/code/2218
Author: andreas-draeger
Date: 2015-04-22 15:11:23 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
* Started to extract user messages from AbstractSBase to an XML file.
* Implemented a new method to set the non-RDF annotation on SBase for libSBML compliance.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
trunk/core/src/org/sbml/jsbml/SBase.java
Added Paths:
-----------
trunk/core/resources/org/sbml/jsbml/resources/Messages.xml
Added: trunk/core/resources/org/sbml/jsbml/resources/Messages.xml
===================================================================
--- trunk/core/resources/org/sbml/jsbml/resources/Messages.xml (rev 0)
+++ trunk/core/resources/org/sbml/jsbml/resources/Messages.xml 2015-04-22 15:11:23 UTC (rev 2218)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
+<properties>
+ <comment>
+ $Id$
+ $URL$
+ ----------------------------------------------------------------------------
+ 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.
+ ----------------------------------------------------------------------------
+
+ A collection of text messages to be presented to uses upon certain events.
+
+ Author: Andreas Dräger
+ Version: $Rev$
+ Since: 1.1
+ </comment>
+
+ <entry key="IndexExceedsBoundsException">Index {0,number,integer} >= {1,number,integer}</entry>
+
+ <entry key="AbstractSBase.addDeclaredNamespace">The only allowed prefix for a namespace is 'xmlns:'.</entry>
+ <entry key="AbstractSBase.addExtensionExc">The package namespace or name ''{0}'' is unknown!</entry>
+ <entry key="AbstractSBase.setNamespaceExc">An SBase element cannot belong to two different namespaces! Current namespace = ''{0}'', new namespace = ''{1}''</entry>
+ <entry key="AbstractSBase.emptyNotes">The notes to append are empty!</entry>
+ <entry key="AbstractSBase.invalidNotesStructure">The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.</entry>
+ <entry key="AbstractSBase.problemAddingXMLNode">There was a problem adding the given XMLNode: ''{0}'' to the ''body'' XMLNode.</entry>
+
+</properties>
\ No newline at end of file
Property changes on: trunk/core/resources/org/sbml/jsbml/resources/Messages.xml
___________________________________________________________________
Added: svn:keywords
## -0,0 +1 ##
+Id URL Rev
\ No newline at end of property
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-22 15:01:44 UTC (rev 2217)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-22 15:11:23 UTC (rev 2218)
@@ -318,10 +318,9 @@
*/
@Override
public void addDeclaredNamespace(String prefix, String namespace) {
-
if ((!prefix.startsWith("xmlns:")) && (!prefix.equals("xmlns"))) {
if (prefix.indexOf(":") != -1) {
- throw new IllegalArgumentException("The only allowed prefix for a namespace is 'xmlns:'.");
+ throw new IllegalArgumentException(resourceBundle.getString("AbstractSBase.addDeclaredNamespace"));
}
prefix = "xmlns:" + prefix;
}
@@ -360,7 +359,7 @@
firePropertyChange(TreeNodeChangeEvent.addExtension, null, sbasePlugin);
} else {
throw new IllegalArgumentException(MessageFormat.format(
- "The package namespace or name ''{0}'' is unknown!", nameOrUri));
+ resourceBundle.getString("AbstractSBase.addExtensionExc"), nameOrUri));
}
}
@@ -384,12 +383,12 @@
* @param namespace the XML namespace to which this {@link SBase} belong.
*/
public void setNamespace(String namespace) {
-
if ((elementNamespace != null) && (!elementNamespace.equals(namespace))) {
// if we implement proper conversion some days, we need to unset the namespace before changing it.
- logger.error(MessageFormat.format("An SBase element cannot belong to two different namespaces! Current namespace = ''{0}'', new namespace = ''{1}''", elementNamespace, namespace));
- // throw new IllegalArgumentException(MessageFormat.format("An SBase element cannot belong to two different namespaces ! "
- // + "Current namespace = '{0}', new namespace = '{1}' ", elementNamespace, namespace));
+ logger.error(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.setNamespaceExc"),
+ elementNamespace, namespace));
+ // throw new IllegalArgumentException(MessageFormat.format(resourceBundle.getString("AbstractSBase.setNamespaceExc"), elementNamespace, namespace));
}
String old = elementNamespace;
elementNamespace = namespace;
@@ -496,7 +495,7 @@
else
{
// the given notes is empty
- logger.info("The notes to append are empty !!");
+ logger.info(resourceBundle.getString("AbstractSBase.emptyNotes"));
return;
}
}
@@ -533,7 +532,7 @@
// The given notes node needs to be added to a parent node
// if the node is neither "html" nor "body" element because the
// children of addedNotes will be added to the current notes later if the
- // node is neither "html" nor "body" (i.e. any XHTML element that
+ // node is neither "html" nor "body" (i.e., any XHTML element that
// would be permitted within a "body" element)
addedNotes.addChild(notes);
addedNotesType = NOTES_TYPE.NotesAny;
@@ -569,7 +568,7 @@
if (!headFound || !bodyFound || otherElementFound)
{
// TODO - throw an exception as well
- logger.warn("The given 'notes' String does not have the proper structure, excepting the children 'head' and 'body' to the 'html' element.");
+ logger.warn(resourceBundle.getString("AbstractSBase.invalidNotesStructure"));
return;
}
}
@@ -639,7 +638,9 @@
for (i=0; i < addedBody.getChildCount(); i++)
{
if (curBody.addChild(addedBody.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedBody.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.problemAddingXMLNode"),
+ SBMLtools.toXML(addedBody.getChildAt(i))));
return;
}
}
@@ -650,10 +651,12 @@
// adds the given body or other tag (permitted in the body) to the current
// html tag
- for (i=0; i < addedNotes.getChildCount(); i++)
+ for (i = 0; i < addedNotes.getChildCount(); i++)
{
if (curBody.addChild(addedNotes.getChildAt(i)) < 0) {
- logger.warn("There was a problem adding the given XMLNode: '" + SBMLtools.toXML(addedNotes.getChildAt(i)) + "' to the 'body' XMLNode.");
+ logger.warn(MessageFormat.format(
+ resourceBundle.getString("AbstractSBase.problemAddingXMLNode"),
+ SBMLtools.toXML(addedNotes.getChildAt(i))));
return;
}
}
@@ -1775,7 +1778,7 @@
// Could/Should be used by the method #firePropertyChange
// TODO - set package version and namespace if needed
-
+
int childCount = sbasePlugin.getChildCount();
if (childCount > 0) {
@@ -1828,6 +1831,14 @@
}
/* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#setAnnotation(org.sbml.jsbml.xml.XMLNode)
+ */
+ @Override
+ public void setAnnotation(XMLNode nonRDFAnnotation) {
+ getAnnotation().setNonRDFAnnotation(nonRDFAnnotation);
+ }
+
+ /* (non-Javadoc)
* @see org.sbml.jsbml.SBase#setHistory(org.sbml.jsbml.History)
*/
@Override
@@ -2204,7 +2215,7 @@
return;
}
- throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!!", nameOrUri));
+ throw new IllegalArgumentException(MessageFormat.format("The package namespace or name ''{0}'' is unknown!", nameOrUri));
}
@Override
Modified: trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-04-22 15:01:44 UTC (rev 2217)
+++ trunk/core/src/org/sbml/jsbml/AbstractTreeNode.java 2015-04-22 15:11:23 UTC (rev 2218)
@@ -32,11 +32,13 @@
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
+import java.util.ResourceBundle;
import java.util.Set;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
import org.sbml.jsbml.util.TreeNodeChangeListener;
@@ -60,6 +62,11 @@
private static final long serialVersionUID = 8629109724566600238L;
/**
+ * Localization support.
+ */
+ protected static final transient ResourceBundle resourceBundle = ResourceManager.getBundle("org.sbml.jsbml.resources.Messages");
+
+ /**
*
*/
public static final String UNKNOWN_ATTRIBUTES = "unknown.attributes"; //$NON-NLS-1$
Modified: trunk/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBase.java 2015-04-22 15:01:44 UTC (rev 2217)
+++ trunk/core/src/org/sbml/jsbml/SBase.java 2015-04-22 15:11:23 UTC (rev 2218)
@@ -503,15 +503,15 @@
public int getCVTermCount();
/**
- * Returns the name of the SBML Level 3 package in which this element is defined, as
+ * Returns the name of the SBML Level 3 package in which this element is defined, as
* defined in <a href="http://sbml.org/Community/Wiki"> the sbml.org community wiki</a>.
*
- * <p> For example, the string "core" will be returned if this element is defined in SBML Level 3 Core.
+ * <p> For example, the string "core" will be returned if this element is defined in SBML Level 3 Core.
*
* @return the name of the SBML Level 3 package in which this element is defined.
*/
public String getPackageName();
-
+
/**
* Returns the version of the SBML Level 3 package to which this element belongs.
*
@@ -522,7 +522,7 @@
* @return the version of the SBML Level 3 package to which this element belongs.
*/
public int getPackageVersion();
-
+
/**
* Returns the parent of this {@link SBase}.
*
@@ -584,16 +584,16 @@
/**
* Returns the namespace to which this {@link SBase} belong to. Same as {@link #getNamespace()}.
*
- * <p>For example, all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core
+ * <p>For example, all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core
* must have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
* <p>The elements that belong to SBML core might return null.
*
* @return the namespace to which this {@link SBase} belong to.
* @see SBase#getNamespace()
- * @libsbml.deprecated
+ * @libsbml.deprecated
*/
public String getURI();
-
+
/**
* Returns the Version within the SBML Level of the overall SBML document.
* Return -1 if it is not set.
@@ -858,6 +858,12 @@
public void setAnnotation(Annotation annotation);
/**
+ *
+ * @param nonRDFAnnotation
+ */
+ public void setAnnotation(XMLNode nonRDFAnnotation);
+
+ /**
* Sets the history.
*
* @param history the history of this {@link SBase}
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