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[Jsbml-svn] SF.net SVN: jsbml:[2269] branches/astnode2-merging-alternate
|
From: <nik...@us...> - 2015-05-01 09:53:15
|
Revision: 2269
http://sourceforge.net/p/jsbml/code/2269
Author: niko-rodrigue
Date: 2015-05-01 09:53:13 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2226
Revision Links:
--------------
http://sourceforge.net/p/jsbml/code/2226
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
Added Paths:
-----------
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate 2015-05-01 09:53:13 UTC (rev 2269)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2217
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2226
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/AbstractSBase.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -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 +1831,22 @@
}
/* (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#setAnnotation(java.lang.String)
+ */
+ @Override
+ public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException {
+ setAnnotation(XMLNode.convertStringToXMLNode(StringTools.toXMLAnnotationString(nonRDFAnnotation)));
+ }
+
+ /* (non-Javadoc)
* @see org.sbml.jsbml.SBase#setHistory(org.sbml.jsbml.History)
*/
@Override
@@ -2204,7 +2223,7 @@
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: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/CVTerm.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -29,10 +29,13 @@
import java.util.regex.Pattern;
import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.util.TreeNodeAdapter;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
+import org.sbml.jsbml.xml.XMLAttributes;
+import org.sbml.jsbml.xml.XMLNode;
/**
* Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
@@ -507,6 +510,42 @@
}
/**
+ *
+ * @param miriam
+ */
+ public CVTerm(XMLNode miriam) {
+ this();
+ if (miriam.getName().equals("annotation")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("RDF")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("Description")) {
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getURI().equals("http://biomodels.net/biology-qualifiers/")) {
+ if (miriam.getPrefix().equals("bqbiol")) {
+ setQualifier(Qualifier.getBiologicalQualifierFor(miriam.getName()));
+ } else {
+ setQualifier(Qualifier.getModelQualifierFor(miriam.getName()));
+ }
+ miriam = miriam.getChildAt(0);
+ }
+ if (miriam.getName().equals("Bag")) {
+ for (int j = 0; j < miriam.getChildCount(); j++) {
+ XMLNode child = miriam.getChildAt(j);
+ if (child.getName().equals("li")) {
+ XMLAttributes attributes = child.getAttributes();
+ for (int i = 0; i < attributes.size(); i++) {
+ addResource(attributes.getValue(i));
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Creates a {@link CVTerm} instance from a given {@link CVTerm}.
*
* @param term the {@link CVTerm} to clone
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/SBase.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -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 +858,19 @@
public void setAnnotation(Annotation annotation);
/**
+ *
+ * @param nonRDFAnnotation
+ */
+ public void setAnnotation(XMLNode nonRDFAnnotation);
+
+ /**
+ *
+ * @param nonRDFAnnotation
+ * @throws XMLStreamException
+ */
+ public void setAnnotation(String nonRDFAnnotation) throws XMLStreamException;
+
+ /**
* Sets the history.
*
* @param history the history of this {@link SBase}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/XMLAttributes.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -510,11 +510,18 @@
* @return the number of attributes in this {@link XMLAttributes} set.
*/
public int getLength() {
+ return attributeNames.size();
+ }
+ /**
+ *
+ * @return
+ * @see #getLength()
+ */
+ public int size() {
return attributeNames.size();
}
-
/**
* Returns the local name of an attribute in this {@link XMLAttributes} set (by position).
* <p>
Copied: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java (from rev 2226, trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -0,0 +1,44 @@
+/*
+ * $Id: CompressionKind.java 2206 2015-04-23 09:57:59Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java $
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+/**
+ * This enum type was created following the specifications defined in Spatial Package v0.90.
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date 23 Apr 2015
+ */
+public enum CompressionKind {
+ /**
+ * If no compression is used
+ */
+ UNCOMPRESSED,
+ /**
+ * If the deflation algorithm was used to compress the text version of the data
+ */
+ DEFLATED,
+ /**
+ * If the base 64 algorithm was used to transform the binary form of the actual members into text
+ */
+ BASE64;
+}
\ No newline at end of file
Copied: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java (from rev 2226, trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -0,0 +1,53 @@
+/*
+ * $Id: DataKind.java 2206 2015-04-23 09:57:59Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java $
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.ext.spatial;
+
+
+/**
+ * This enum type was created following the specifications defined in Spatial Package v0.90.
+ * @author Piero Dalle Pezze
+ * @version $Rev$
+ * @since 1.0
+ * @date 23 Apr 2015
+ */
+public enum DataKind {
+ /**
+ * To indicate 8-bit unsigned integer
+ */
+ UINT8,
+ /**
+ * To indicate 16-bit unsigned integer
+ */
+ UINT16,
+ /**
+ * To indicate 32-bit unsigned integer
+ */
+ UINT32,
+ /**
+ * To indicate single-precision (32-bit) floating point values
+ */
+ FLOAT,
+ /**
+ * To indicate double-precision (64-bit) floating point values
+ */
+ DOUBLE;
+}
\ No newline at end of file
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -28,6 +28,7 @@
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.PropertyUndefinedError;
/**
* @author Alex Thomas
@@ -41,7 +42,7 @@
/**
*
*/
- ListOf<SpatialPoints> listOfSpatialPoints;
+ SpatialPoints spatialPoints;
/**
*
*/
@@ -69,8 +70,8 @@
setListOfParametricObjects(pg.getListOfParametricObjects().clone());
}
- if (pg.isSetListOfSpatialPoints()) {
- setListOfSpatialPoints(pg.getListOfSpatialPoints().clone());
+ if (pg.isSetSpatialPoints()) {
+ setSpatialPoints(pg.getSpatialPoints().clone());
}
}
@@ -113,9 +114,9 @@
equal &= pg.getListOfParametricObjects().equals(getListOfParametricObjects());
}
- equal &= pg.isSetListOfSpatialPoints() == isSetListOfSpatialPoints();
- if (equal && isSetListOfSpatialPoints()) {
- equal &= pg.getListOfSpatialPoints().equals(getListOfSpatialPoints());
+ equal &= pg.isSetSpatialPoints() == isSetSpatialPoints();
+ if (equal && isSetSpatialPoints()) {
+ equal &= pg.getSpatialPoints().equals(getSpatialPoints());
}
}
@@ -129,8 +130,8 @@
if (isSetListOfParametricObjects()) {
hashCode += prime * getListOfParametricObjects().hashCode();
}
- if (isSetListOfSpatialPoints()) {
- hashCode += prime * getListOfSpatialPoints().hashCode();
+ if (isSetSpatialPoints()) {
+ hashCode += prime * getSpatialPoints().hashCode();
}
return hashCode;
}
@@ -251,7 +252,7 @@
//}
/**
* Creates a new ParametricObject element and adds it to the ListOfParametricObjects list
- * @return
+ * @return a new {@link ParametricObject} element
*/
public ParametricObject createParametricObject() {
return createParametricObject(null);
@@ -270,146 +271,60 @@
return parametricObject;
}
- /**
- *
- */
-
+
/**
- * Returns {@code true}, if listOfSpatialPoints contains at least one element.
+ * Returns the value of {@link #spatialPoints}.
*
- * @return {@code true}, if listOfSpatialPoints contains at least one element,
- * otherwise {@code false}
+ * @return the value of {@link #spatialPoints}.
*/
- public boolean isSetListOfSpatialPoints() {
- if ((listOfSpatialPoints == null) || listOfSpatialPoints.isEmpty()) {
- return false;
+ public SpatialPoints getSpatialPoints() {
+ if (isSetSpatialPoints()) {
+ return spatialPoints;
}
- return true;
+ // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+ throw new PropertyUndefinedError(SpatialConstants.spatialPoints, this);
}
/**
- * Returns the listOfSpatialPoints. Creates it if it is not already existing.
+ * Returns whether {@link #spatialPoints} is set.
*
- * @return the listOfSpatialPoints
+ * @return whether {@link #spatialPoints} is set.
*/
- public ListOf<SpatialPoints> getListOfSpatialPoints() {
- if (!isSetListOfSpatialPoints()) {
- listOfSpatialPoints = new ListOf<SpatialPoints>(getLevel(),
- getVersion());
- listOfSpatialPoints.setNamespace(SpatialConstants.namespaceURI);
- listOfSpatialPoints.setSBaseListType(ListOf.Type.other);
- registerChild(listOfSpatialPoints);
- }
- return listOfSpatialPoints;
+ public boolean isSetSpatialPoints() {
+ return this.spatialPoints != null;
}
/**
- * Sets the given {@code ListOf<SpatialPoint>}. If listOfSpatialPoints
- * was defined before and contains some elements, they are all unset.
+ * Sets the value of spatialPoints
*
- * @param listOfSpatialPoints
+ * @param spatialPoints the value of spatialPoints to be set.
*/
- public void setListOfSpatialPoints(ListOf<SpatialPoints> listOfSpatialPoints) {
- unsetListOfSpatialPoints();
- this.listOfSpatialPoints = listOfSpatialPoints;
- registerChild(this.listOfSpatialPoints);
+ public void setSpatialPoints(SpatialPoints spatialPoints) {
+ SpatialPoints oldSpatialPoints = this.spatialPoints;
+ this.spatialPoints = spatialPoints;
+ firePropertyChange(SpatialConstants.spatialPoints, oldSpatialPoints, this.spatialPoints);
}
/**
- * Returns {@code true}, if listOfSpatialPoints contain at least one element,
- * otherwise {@code false}
+ * Unsets the variable spatialPoints.
*
- * @return {@code true}, if listOfSpatialPoints contain at least one element,
- * otherwise {@code false}
+ * @return {@code true} if spatialPoints was set before, otherwise {@code false}.
*/
- public boolean unsetListOfSpatialPoints() {
- if (isSetListOfSpatialPoints()) {
- ListOf<SpatialPoints> oldSpatialPoints = listOfSpatialPoints;
- listOfSpatialPoints = null;
- oldSpatialPoints.fireNodeRemovedEvent();
+ public boolean unsetSpatialPoints() {
+ if (isSetSpatialPoints()) {
+ SpatialPoints oldSpatialPoints = this.spatialPoints;
+ this.spatialPoints = null;
+ firePropertyChange(SpatialConstants.spatialPoints, oldSpatialPoints, this.spatialPoints);
return true;
}
return false;
}
- /**
- * Adds a new {@link SpatialPoints} to the listOfSpatialPoints.
- * <p>The listOfSpatialPoints is initialized if necessary.
- *
- * @param spatialPoints the element to add to the list
- * @return true (as specified by {@link Collection#add})
- */
- public boolean addSpatialPoints(SpatialPoints spatialPoints) {
- return getListOfSpatialPoints().add(spatialPoints);
- }
-
-
- /**
- * Removes an element from the listOfSpatialPoints.
- *
- * @param spatialPoints the element to be removed from the list
- * @return true if the list contained the specified element
- * @see List#remove(Object)
- */
- public boolean removeSpatialPoints(SpatialPoints spatialPoints) {
- if (isSetListOfSpatialPoints()) {
- return getListOfSpatialPoints().remove(spatialPoints);
- }
- return false;
- }
-
-
- /**
- * Removes an element from the listOfSpatialPoints at the given index.
- *
- * @param i the index where to remove the {@link SpatialPoint}
- * @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
- */
- public void removeSpatialPoints(int i) {
- if (!isSetListOfSpatialPoints()) {
- throw new IndexOutOfBoundsException(Integer.toString(i));
- }
- // if (getListOfSpatialPoints().size() == 1) {
- // throw new SBMLException("There must be at least one SpatialPoint defined for this list");
- // }
- getListOfSpatialPoints().remove(i);
- }
-
-
- /*
- * TODO: if the ID is mandatory for SpatialPoints objects,
- * one should also add this methods
- */
- //public void removeSpatialPoints(String id) {
- // getListOfSpatialPoints().removeFirst(new NameFilter(id));
- //}
- /**
- * Creates a new SpatialPoints element and adds it to the ListOfSpatialPoints list
- * @return
- */
- public SpatialPoints createSpatialPoints() {
- return createSpatialPoints(null);
- }
-
-
- /**
- * Creates a new {@link SpatialPoints} element and adds it to the ListOfSpatialPoints list
- * @param id
- *
- * @return a new {@link SpatialPoints} element
- */
- public SpatialPoints createSpatialPoints(String id) {
- SpatialPoints spatialPoints = new SpatialPoints(getLevel(), getVersion());
- addSpatialPoints(spatialPoints);
- return spatialPoints;
- }
-
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#getAllowsChildren()
*/
@@ -427,7 +342,7 @@
if (isSetListOfParametricObjects()) {
count++;
}
- if (isSetListOfSpatialPoints()) {
+ if (isSetSpatialPoints()) {
count++;
}
return count;
@@ -453,9 +368,9 @@
}
pos++;
}
- if (isSetListOfSpatialPoints()) {
+ if (isSetSpatialPoints()) {
if (pos == index) {
- return getListOfSpatialPoints();
+ return getSpatialPoints();
}
pos++;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -330,5 +330,34 @@
return success;
}
+
+ /*
+ * (non-Javadoc)
+ * @see org.sbml.jsbml.ext.AbstractSBasePlugin#hashCode()
+ */
+ @Override
+ public int hashCode() {
+ final int prime = 2039;
+ int hashCode = super.hashCode();
+ if (isSetGeometry()) {
+ hashCode += prime * getGeometry().hashCode();
+ }
+ return hashCode;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("SpatialModelPlugin [geometry=");
+ builder.append(geometry);
+ builder.append(", spatialIdMap=");
+ builder.append(spatialIdMap);
+ builder.append("]");
+ return builder.toString();
+ }
+
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -197,7 +197,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 2039;
int hashCode = super.hashCode();
if (isSetIsLocal()) {
hashCode += prime * isLocal.hashCode();
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -29,7 +29,6 @@
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
-import org.sbml.jsbml.util.TreeNodeChangeEvent;
/**
* @author Alex Thomas
@@ -112,6 +111,9 @@
if (equal && isSetComponents()) {
equal &= tc.getComponents().equals(getComponents());
}
+ if (equal && isSetComponentsLength()) {
+ equal &= tc.getComponentsLength() == getComponentsLength();
+ }
}
return equal;
}
@@ -178,7 +180,7 @@
*/
public int getComponentsLength() {
if (isSetComponentsLength()) {
- return componentsLength;
+ return componentsLength.intValue();
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.componentsLength, this);
@@ -204,6 +206,9 @@
if (isSetComponents()) {
hashCode += prime * getComponents().hashCode();
}
+ if (isSetComponentsLength()) {
+ hashCode += prime * getComponentsLength();
+ }
return hashCode;
}
@@ -223,15 +228,6 @@
attributes.put(SpatialConstants.shortLabel + ":componentsLength",
String.valueOf(getComponentsLength()));
}
-
- if (isSetSBOTerm()) {
- attributes.remove(TreeNodeChangeEvent.sboTerm);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.sboTerm, getSBOTermID());
- }
- if (isSetMetaId()) {
- attributes.remove(TreeNodeChangeEvent.metaId);
- attributes.put(SpatialConstants.shortLabel + ":" + TreeNodeChangeEvent.metaId, getMetaId());
- }
return attributes;
}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 09:46:00 UTC (rev 2268)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-05-01 09:53:13 UTC (rev 2269)
@@ -378,9 +378,9 @@
}
} else if (contextObject instanceof ParametricGeometry) {
ParametricGeometry pg = (ParametricGeometry) contextObject;
- if (elementName.equals(SpatialConstants.listOfSpatialPoints)){
- ListOf<SpatialPoints> listOfSpatialPoints = pg.getListOfSpatialPoints();
- return listOfSpatialPoints;
+ if (elementName.equals(SpatialConstants.spatialPoints)){
+ SpatialPoints spatialPoints = pg.getSpatialPoints();
+ return spatialPoints;
} else if (elementName.equals(SpatialConstants.listOfParametricObjects)){
ListOf<ParametricObject> listOfParametricObjects = pg.getListOfParametricObjects();
return listOfParametricObjects;
@@ -497,7 +497,7 @@
} else if (elementName.equals(SpatialConstants.spatialPoints)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
SpatialPoints elem = new SpatialPoints();
- pg.addSpatialPoints(elem);
+ pg.setSpatialPoints(elem);
return elem;
} else if (elementName.equals(SpatialConstants.parametricObject)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
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