Menu
▾
▴
jsbml-svn
|
From: <nik...@us...> - 2014-12-10 14:08:00
|
Revision: 2101
http://sourceforge.net/p/jsbml/code/2101
Author: niko-rodrigue
Date: 2014-12-10 14:07:48 +0000 (Wed, 10 Dec 2014)
Log Message:
-----------
only the package shortlabel should be used to get extension/plugin objects.
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2014-12-09 19:27:27 UTC (rev 2100)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2014-12-10 14:07:48 UTC (rev 2101)
@@ -113,7 +113,7 @@
Model model = getModel();
- SpatialModelPlugin m = (SpatialModelPlugin) model.getExtension(SpatialConstants.packageName);
+ SpatialModelPlugin m = (SpatialModelPlugin) model.getExtension(SpatialConstants.shortLabel);
//TODO: Get the correct element in geometry using the spid
return m.getGeometry();
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java 2014-12-09 19:27:27 UTC (rev 2100)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java 2014-12-10 14:07:48 UTC (rev 2101)
@@ -268,7 +268,7 @@
//
// for (Parameter p: params) {
// SpatialParameterPlugin paramPlugin =
- // (SpatialParameterPlugin) p.getExtension(SpatialConstants.packageName);
+ // (SpatialParameterPlugin) p.getExtension(SpatialConstants.shortLabel);
//
// if (paramPlugin != null) {
// ParameterType paramType = paramPlugin.getParamType();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-21 13:00:39
|
Revision: 2194
http://sourceforge.net/p/jsbml/code/2194
Author: pdp10
Date: 2015-04-21 13:00:30 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Removed the String compartment from CompartmentMapping, as this class is now a field of SpatialCompartmentPluging in the package spatial, version 0.90.
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-04-21 12:59:30 UTC (rev 2193)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-04-21 13:00:30 UTC (rev 2194)
@@ -30,7 +30,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -44,11 +45,6 @@
/**
*
*/
- private String compartment;
-
- /**
- *
- */
private String domainType;
/**
@@ -70,9 +66,6 @@
public CompartmentMapping(CompartmentMapping cm) {
super(cm);
- if (cm.isSetCompartment()) {
- compartment = new String(cm.getCompartment());
- }
if (cm.isSetDomainType()) {
domainType = new String(cm.getDomainType());
}
@@ -117,10 +110,6 @@
if (equal) {
CompartmentMapping cm = (CompartmentMapping) object;
- equal &= cm.isSetCompartment() == isSetCompartment();
- if (equal && isSetCompartment()) {
- equal &= cm.getCompartment().equals(getCompartment());
- }
equal &= cm.isSetDomainType() == isSetDomainType();
if (equal && isSetDomainType()) {
equal &= cm.getDomainType().equals(getDomainType());
@@ -133,56 +122,8 @@
return equal;
}
- /**
- * Returns the value of compartment
- *
- * @return the value of compartment
- */
- public String getCompartment() {
- if (isSetCompartment()) {
- return compartment;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.compartment, this);
- }
/**
- * Returns whether compartment is set
- *
- * @return whether compartment is set
- */
- public boolean isSetCompartment() {
- return compartment != null;
- }
-
-
- /**
- * Sets the value of compartment
- * @param compartment
- */
- public void setCompartment(String compartment) {
- String oldCompartment = this.compartment;
- this.compartment = compartment;
- firePropertyChange(SpatialConstants.compartment, oldCompartment, this.compartment);
- }
-
- /**
- * Unsets the variable compartment
- *
- * @return {@code true}, if compartment was set before,
- * otherwise {@code false}
- */
- public boolean unsetCompartment() {
- if (isSetCompartment()) {
- String oldCompartment = compartment;
- compartment = null;
- firePropertyChange(SpatialConstants.compartment, oldCompartment, compartment);
- return true;
- }
- return false;
- }
-
- /**
* Returns the value of domainType
*
* @return the value of domainType
@@ -307,11 +248,8 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1319;//Changed, it was 983
int hashCode = super.hashCode();
- if (isSetCompartment()) {
- hashCode += prime * getCompartment().hashCode();
- }
if (isSetDomainType()) {
hashCode += prime * getDomainType().hashCode();
}
@@ -325,10 +263,6 @@
@Override
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetCompartment()) {
- attributes.remove("compartment");
- attributes.put(SpatialConstants.shortLabel + ":compartment", getCompartment());
- }
if (isSetDomainType()) {
attributes.remove("domainType");
attributes.put(SpatialConstants.shortLabel + ":domainType",
@@ -349,10 +283,7 @@
&& (SpatialConstants.shortLabel == prefix);
if (!isAttributeRead) {
isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.compartment)) {
- setCompartment(value);
- }
- else if (attributeName.equals(SpatialConstants.domainType)) {
+ if (attributeName.equals(SpatialConstants.domainType)) {
setDomainType(value);
}
else if (attributeName.equals(SpatialConstants.unitSize)) {
@@ -372,9 +303,7 @@
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
- builder.append("CompartmentMapping [compartment=");
- builder.append(compartment);
- builder.append(", domainType=");
+ builder.append("CompartmentMapping [domainType=");
builder.append(domainType);
builder.append(", unitSize=");
builder.append(unitSize);
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java 2015-04-21 12:59:30 UTC (rev 2193)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java 2015-04-21 13:00:30 UTC (rev 2194)
@@ -22,6 +22,7 @@
package org.sbml.jsbml.ext.spatial;
import java.text.MessageFormat;
+import java.util.Map;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.ListOf;
@@ -29,7 +30,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -198,5 +200,54 @@
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}", index,pos));
}
+
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ Map<String, String> attributes = super.writeXMLAttributes();
+ if (isSetCompartmentMapping()) {
+ attributes.remove("compartmentMapping");
+ attributes.put(SpatialConstants.shortLabel + ":compartmentMapping",
+ getCompartmentMapping());
+ }
+ return attributes;
+ }
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
+ && (SpatialConstants.shortLabel == prefix);
+ if (!isAttributeRead) {
+ isAttributeRead = true;
+ if (attributeName.equals(SpatialConstants.compartmentMapping)) {
+ setCompartmentMapping(value);
+ }
+ else {
+ isAttributeRead = false;
+ }
+ }
+ return isAttributeRead;
+ }
+
+ @Override
+ public int hashCode() {
+ final int prime = 1259;
+ int hashCode = super.hashCode();
+ if (isSetCompartmentMapping()) {
+ hashCode += prime * getCompartmentMapping().hashCode();
+ }
+ return hashCode;
+ }
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("SpatialCompartmentPlugin [compartmentMapping=");
+ builder.append(compartmentMapping);
+ builder.append("]");
+ return builder.toString();
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-21 13:25:57
|
Revision: 2197
http://sourceforge.net/p/jsbml/code/2197
Author: pdp10
Date: 2015-04-21 13:25:49 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
update for 0.90 spatial specs
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.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/ParameterType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -33,7 +33,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -103,6 +104,11 @@
this.spatialId = spatialId;
}
+ @Override
+ public AbstractSpatialNamedSBase clone() {
+ return new AbstractSpatialNamedSBase(this);
+ }
+
/**
* Initializes the default values using the namespace.
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -31,6 +31,7 @@
/**
*
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 22, 2014
@@ -65,6 +66,11 @@
initDefaults();
}
+ @Override
+ public AbstractSpatialSBasePlugin clone() {
+ return new AbstractSpatialSBasePlugin(this);
+ }
+
/**
* Initializes the default values using the namespace.
*/
@@ -139,5 +145,10 @@
SBMLDocument doc = getSBMLDocument();
return doc != null ? doc.getModel() : null;
}
+
+ @Override
+ public String toString() {
+ return super.toString();
+ }
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -39,14 +39,13 @@
/**
* Generated serial version identifier.
*/
- private static final long serialVersionUID = 8982184068116596444L;
-
+ private static final long serialVersionUID = 8982184068116596444L;
+
/**
*
*/
private CoordinateKind coordinate;
-
/**
*
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Collection;
import java.util.List;
+import java.util.Map;
import javax.swing.tree.TreeNode;
@@ -33,7 +34,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -283,5 +285,49 @@
}
return equal;
}
+
+ @Override
+ public int hashCode() {
+ final int prime = 1039;//Change this prime number
+ int hashCode = super.hashCode();
+ if (isSetListOfAnalyticVolumes()) {
+ hashCode += prime * getListOfAnalyticVolumes().hashCode();
+ }
+ return hashCode;
+ }
+
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ Map<String, String> attributes = super.writeXMLAttributes();
+ if (isSetListOfAnalyticVolumes()) {
+ attributes.put(SpatialConstants.shortLabel + ":listOfAnalyticVolumes", getListOfAnalyticVolumes().toString());
+ }
+ return attributes;
+ }
+
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
+ && (SpatialConstants.shortLabel == prefix);
+ if (!isAttributeRead) {
+ isAttributeRead = true;
+ if (attributeName.equals(SpatialConstants.listOfAnalyticVolumes)) {
+ try {
+ setListOfAnalyticVolumes(listOfAnalyticVolumes.valueOf(value));
+ } catch (Exception e) {
+ MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
+ SpatialConstants.listOfAnalyticVolumes);
+ }
+ }
+ else {
+ isAttributeRead = false;
+ }
+ }
+ return isAttributeRead;
+ }
+
+
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -35,7 +35,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -110,6 +111,9 @@
if (node.isSetFunctionType()) {
functionType = node.getFunctionType();
}
+ if (node.isSetDomainType()) {
+ domainType = node.getDomainType();
+ }
}
/**
@@ -372,7 +376,7 @@
*/
@Override
public int hashCode() {
- final int prime = 431;//Change this prime number
+ final int prime = 1093;//Changed. It was 431
int hashCode = super.hashCode();
if (isSetSpatialId()) {
hashCode += prime * getSpatialId().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -37,7 +37,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -451,7 +452,13 @@
}
if (isSetUnits()) {
hashCode += prime * getUnits().hashCode();
- }
+ }
+ if (isSetBoundaryMaximum()) {
+ hashCode += prime * getBoundaryMaximum()().hashCode();
+ }
+ if (isSetBoundaryMinimum()) {
+ hashCode += prime * getBoundaryMinimum()().hashCode();
+ }
return hashCode;
}
@@ -502,6 +509,14 @@
attributes.remove("unit");
attributes.put(SpatialConstants.shortLabel+":unit", getUnits());
}
+ if (isSetBoundaryMaximum()()) {
+ attributes.remove("boundaryMaximum");
+ attributes.put(SpatialConstants.shortLabel+":boundaryMaximum", getBoundaryMaximum()());
+ }
+ if (isSetBoundaryMinimum()()) {
+ attributes.remove("boundaryMinimum");
+ attributes.put(SpatialConstants.shortLabel+":boundaryMinimum", getBoundaryMinimum()());
+ }
return attributes;
}
@@ -532,6 +547,22 @@
SpatialConstants.unit);
}
}
+ else if (attributeName.equals(SpatialConstants.boundaryMaximum)) {
+ try {
+ setBoundaryMaximum(value);
+ } catch (Exception e) {
+ MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
+ SpatialConstants.boundaryMaximum);
+ }
+ }
+ else if (attributeName.equals(SpatialConstants.boundaryMinimum)) {
+ try {
+ setBoundaryMinimum(value);
+ } catch (Exception e) {
+ MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
+ SpatialConstants.boundaryMinimum);
+ }
+ }
else {
isAttributeRead = false;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -32,6 +32,7 @@
/**
* @author Alex Thomas
* @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date 09.09.2011
@@ -121,7 +122,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1373;//Changed, it was 983
int hashCode = super.hashCode();
if (isSetCoordinate()) {
hashCode += prime * getCoordinate().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -60,7 +60,7 @@
/**
* Refers to species object that the parameter is associated with
*/
- private String speciesRef;
+ private String speciesRef; // TODO Check whether this is the correct name.
/**
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-21 13:15:20 UTC (rev 2196)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-21 13:25:49 UTC (rev 2197)
@@ -352,10 +352,13 @@
*
*/
public static final String listOfGeometryDefinitions = "listOfGeometryDefinitions";
-
/**
*
*/
+ public static final String listOfAnalyticVolumes = "listOfAnalyticVolumes";
+ /**
+ *
+ */
public static final String coordinateComponent = "coordinateComponent";
/**
*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-21 15:40:07
|
Revision: 2203
http://sourceforge.net/p/jsbml/code/2203
Author: pdp10
Date: 2015-04-21 15:40:05 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
update for package spatial v0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.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/CSGTransformation.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.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
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGHomogeneousTransformation.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -99,8 +100,20 @@
return new CSGHomogeneousTransformation(this);
}
-
@Override
+ public int hashCode() {
+ final int prime = 1697;
+ int hashCode = super.hashCode();
+ if (isSetForwardTransformation()) {
+ hashCode += prime * getForwardTransformation().hashCode();
+ }
+ if (isSetReverseTransformation()) {
+ hashCode += prime * getReverseTransformation().hashCode();
+ }
+ return hashCode;
+ }
+
+ @Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -79,19 +79,15 @@
*/
public CSGObject(CSGObject csgo) {
super(csgo);
-
if (csgo.isSetDomainType()) {
- domainType = new String(csgo.getDomainType());
+ setDomainType(csgo.getDomainType());
}
-
if (csgo.isSetOrdinal()) {
- ordinal = new Integer(csgo.getOrdinal());
+ setOrdinal(csgo.getOrdinal());
}
-
if (csgo.isSetCSGNode()) {
setCSGNode((CSGNode) csgo.getCSGNode().clone());
}
-
}
@@ -303,7 +299,7 @@
@Override
public int hashCode() {
- final int prime = 1999;//Change this prime number
+ final int prime = 1669;
int hashCode = super.hashCode();
if (isSetOrdinal()) {
hashCode += prime * getOrdinal();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -103,12 +103,9 @@
*/
public CSGPrimitive(CSGPrimitive csgp) {
super(csgp);
-
-
if (csgp.isSetPrimitiveType()) {
- primitiveType = csgp.getPrimitiveType();
+ setPrimitiveType(csgp.getPrimitiveType());
}
-
}
@@ -213,7 +210,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1081;
int hashCode = super.hashCode();
if (isSetPrimitiveType()) {
hashCode += prime * getPrimitiveType().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -64,11 +64,9 @@
*/
public CSGPseudoPrimitive(CSGPseudoPrimitive csgp) {
super(csgp);
-
if (csgp.isSetCsgObjectRef()) {
- csgObjectRef = new String(csgp.getCsgObjectRef());
+ setCsgObjectRef(csgp.getCsgObjectRef());
}
-
}
@@ -166,7 +164,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1741;
int hashCode = super.hashCode();
if (isSetCsgObjectRef()) {
hashCode += prime * getCsgObjectRef().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -29,6 +29,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -70,17 +71,19 @@
public CSGRotation(CSGRotation csgt) {
super(csgt);
if (csgt.isSetRotateAxisX()) {
- rotateAxisX = new Double(csgt.getRotateAxisX());
+ setRotateAxisX(csgt.getRotateAxisX());
}
if (csgt.isSetRotateAxisY()) {
- rotateAxisY = new Double(csgt.getRotateAxisY());
+ setRotateAxisY(csgt.getRotateAxisY());
}
if (csgt.isSetRotateAxisZ()) {
- rotateAxisZ = new Double(csgt.getRotateAxisZ());
+ setRotateAxisZ(csgt.getRotateAxisZ());
}
+ if (csgt.isSetRotateAngleInRadians()) {
+ setRotateAngleInRadians(csgt.getRotateAngleInRadians());
+ }
}
-
/**
* @param level
* @param version
@@ -345,7 +348,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1787;
int hashCode = super.hashCode();
if (isSetRotateAxisX()) {
hashCode += prime * getRotateAxisX();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -30,6 +30,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -68,13 +69,13 @@
public CSGScale(CSGScale csgt) {
super(csgt);
if (csgt.isSetScaleX()) {
- scaleX = new Double(csgt.getScaleX());
+ setScaleX(csgt.getScaleX());
}
if (csgt.isSetScaleY()) {
- scaleY = new Double(csgt.getScaleY());
+ setScaleY(csgt.getScaleY());
}
if (csgt.isSetScaleZ()) {
- scaleZ = new Double(csgt.getScaleZ());
+ setScaleZ(csgt.getScaleZ());
}
}
@@ -288,7 +289,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1777;
int hashCode = super.hashCode();
if (isSetScaleX()) {
hashCode += prime * getScaleX();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -36,6 +36,7 @@
/**
* @author Alex Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -105,15 +106,15 @@
}
if (csgso.isSetOperationType()) {
- operationType = csgso.getOperationType();
+ setOperationType(csgso.getOperationType());
}
if (csgso.isSetComplementA()) {
- complementA = new String(csgso.getComplementA());
+ setComplementA(csgso.getComplementA());
}
if (csgso.isSetComplementB()) {
- complementB = new String(csgso.getComplementB());
+ setComplementB(csgso.getComplementB());
}
}
@@ -638,7 +639,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1861;
int hashCode = super.hashCode();
if (isSetOperationType()) {
hashCode += prime * getOperationType().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTransformation.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -29,6 +29,7 @@
/**
* @author Alex-Thomas
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
* @date Jan 20, 2014
@@ -66,13 +67,13 @@
public CSGTranslation(CSGTranslation csgt) {
super(csgt);
if (csgt.isSetTranslateX()) {
- translateX = new Double(csgt.getTranslateX());
+ setTranslateX(csgt.getTranslateX());
}
if (csgt.isSetTranslateY()) {
- translateY = new Double(csgt.getTranslateY());
+ setTranslateY(csgt.getTranslateY());
}
if (csgt.isSetTranslateZ()) {
- translateZ = new Double(csgt.getTranslateZ());
+ setTranslateZ(csgt.getTranslateZ());
}
}
@@ -286,7 +287,7 @@
@Override
public int hashCode() {
- final int prime = 313;//Change this prime number
+ final int prime = 1693;
int hashCode = super.hashCode();
if (isSetTranslateX()) {
hashCode += prime * getTranslateX();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -92,15 +92,15 @@
super(diffCoeff);
if (diffCoeff.isSetDiffusionKind()) {
- diffusionKind = diffCoeff.getDiffusionKind();
+ setDiffusionKind(diffCoeff.getDiffusionKind());
}
if (diffCoeff.isSetCoordinateReference1()) {
- coordinateReference1 = diffCoeff.getCoordinateReference1();
+ setCoordinateReference1(diffCoeff.getCoordinateReference1());
}
if (diffCoeff.isSetCoordinateReference2()) {
- coordinateReference2 = diffCoeff.getCoordinateReference2();
+ setCoordinateReference2(diffCoeff.getCoordinateReference2());
}
}
@@ -314,7 +314,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1531;
int hashCode = super.hashCode();
if (isSetDiffusionKind()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -96,7 +96,7 @@
setListOfInteriorPoints(dm.getListOfInteriorPoints().clone());
}
if (dm.isSetDomainType()) {
- domainType = new String(dm.getDomainType());
+ setDomainType(dm.getDomainType());
}
}
@@ -359,11 +359,14 @@
*/
@Override
public int hashCode() {
- final int prime = 1531;//Change this prime number
+ final int prime = 1571;
int hashCode = super.hashCode();
if (isSetDomainType()) {
hashCode += prime * getDomainType().hashCode();
}
+ if (isSetListOfInteriorPoints()) {
+ hashCode += prime * getListOfInteriorPoints().hashCode();
+ }
return hashCode;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-04-21 15:04:20 UTC (rev 2202)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-04-21 15:40:05 UTC (rev 2203)
@@ -62,7 +62,7 @@
public DomainType(DomainType sb) {
super(sb);
if (sb.isSetSpatialDimensions()) {
- spatialDimensions = Integer.valueOf(sb.getSpatialDimensions());
+ setSpatialDimensions(sb.getSpatialDimensions());
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 08:09:46
|
Revision: 2204
http://sourceforge.net/p/jsbml/code/2204
Author: pdp10
Date: 2015-04-22 08:09:38 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
update for spatial package v0.90
Modified Paths:
--------------
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/ImageData.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -37,7 +37,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -112,25 +113,28 @@
* @param sb
*/
public Geometry(Geometry sb) {
- super(sb);
- if (sb.isSetCoordinateSystem()) {
- setCoordinateSystem(sb.getCoordinateSystem());
- }
+ super(sb);
+ if (sb.isSetListOfCoordinateComponents()) {
+ setListOfCoordinateComponents(sb.getListOfCoordinateComponents().clone());
+ }
+ if (sb.isSetListOfDomainTypes()) {
+ setListOfDomainTypes(sb.getListOfDomainTypes().clone());
+ }
+ if (sb.isSetListOfDomains()) {
+ setListOfDomains(sb.getListOfDomains().clone());
+ }
if (sb.isSetListOfAdjacentDomains()) {
setListOfAdjacentDomains(sb.getListOfAdjacentDomains().clone());
}
- if (sb.isSetListOfDomains()) {
- setListOfDomains(sb.getListOfDomains().clone());
- }
- if (sb.isSetListOfDomainTypes()) {
- setListOfDomainTypes(sb.getListOfDomainTypes().clone());
- }
if (sb.isSetListOfGeometryDefinitions()) {
setListOfGeometryDefinitions(sb.getListOfGeometryDefinitions().clone());
}
if (sb.isSetListOfSampledFields()) {
setListOfSampledFields(sb.getListOfSampledFields().clone());
}
+ if (sb.isSetCoordinateSystem()) {
+ setCoordinateSystem(sb.getCoordinateSystem());
+ }
}
/**
@@ -196,7 +200,6 @@
if (equal && isSetListOfSampledFields()) {
equal &= gm.getListOfSampledFields() == getListOfSampledFields();
}
-
}
return equal;
}
@@ -529,7 +532,7 @@
* Creates a new GeometryDefinition element and adds it to the ListOfGeometryDefinitions list
* @return
*/
- public SampledFieldGeometry createSampledFieldGeometryn() {
+ public SampledFieldGeometry createSampledFieldGeometry() {
return createSampledFieldGeometry(null);
}
@@ -1237,16 +1240,6 @@
attributes.remove("coordinateSystem");
attributes.put(SpatialConstants.shortLabel + ':' + SpatialConstants.coordinateSystem, coordinateSystem.toString());
}
- 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());
- }
- //TODO: Not sure why sboTerm and metaId are written here...?
-
return attributes;
}
@@ -1260,6 +1253,24 @@
if (isSetCoordinateSystem()) {
hashCode += prime * coordinateSystem.hashCode();
}
+ if (isSetListOfAdjacentDomains()) {
+ hashCode += prime * listOfAdjacentDomains.hashCode();
+ }
+ if (isSetListOfCoordinateComponents()) {
+ hashCode += prime * listOfCoordinateComponents.hashCode();
+ }
+ if (isSetListOfDomains()) {
+ hashCode += prime * listOfDomains.hashCode();
+ }
+ if (isSetListOfDomainTypes()) {
+ hashCode += prime * listOfDomainTypes.hashCode();
+ }
+ if (isSetListOfGeometryDefinitions()) {
+ hashCode += prime * listOfGeometryDefinitions.hashCode();
+ }
+ if (isSetListOfSampledFields()) {
+ hashCode += prime * listOfSampledFields.hashCode();
+ }
return hashCode;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -170,7 +170,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1559;
int hashCode = super.hashCode();
if (isSetIsActive()) {
hashCode += prime * getIsActive().hashCode();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -34,7 +34,8 @@
* @author Alex Thomas
* @author Andreas Dräger
* @since 1.0
- * @version $Rev$
+ * @version $Rev$
+ * @deprecated
*/
public class ImageData extends AbstractSBase {
@@ -46,11 +47,11 @@
/**
*
*/
- private Integer samplesLength;
+ private Integer samplesLength; // TODO: is this field really required??
/**
*
*/
- private Integer samples[];
+ private Integer[] samples;
/**
*
@@ -71,11 +72,11 @@
public ImageData(ImageData im) {
super(im);
if (im.isSetSamples()) {
- samples = im.getSamples().clone();
+ setSamples(im.getSamples().clone());
samplesLength = samples.length;
}
if (im.isSetDataType()) {
- dataType = new String(im.getDataType());
+ setDataType(im.getDataType());
}
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -35,7 +35,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -341,7 +342,7 @@
*/
@Override
public int hashCode() {
- final int prime = 509;//Change this prime number
+ final int prime = 1627;
int hashCode = super.hashCode();
if (isSetCoord1()) {
hashCode += prime * getCoord1();
@@ -360,25 +361,14 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetCoord1()) {
- attributes.remove("coord1");
attributes.put(SpatialConstants.shortLabel + ":coord1", String.valueOf(getCoord1()));
}
if (isSetCoord2()) {
- attributes.remove("coord2");
attributes.put(SpatialConstants.shortLabel + ":coord2", String.valueOf(getCoord2()));
}
if (isSetCoord3()) {
- attributes.remove("coord3");
attributes.put(SpatialConstants.shortLabel + ":coord3", String.valueOf(getCoord3()));
}
- 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: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -121,6 +121,19 @@
return equal;
}
+ @Override
+ public int hashCode() {
+ final int prime = 1543;
+ int hashCode = super.hashCode();
+ if (isSetListOfGeometryDefinitions()) {
+ hashCode += prime * getListOfGeometryDefinitions().hashCode();
+ }
+ if (isSetListOfOrdinalMappings()) {
+ hashCode += prime * getListOfOrdinalMappings().hashCode();
+ }
+ return hashCode;
+ }
+
/**
* Returns {@code true}, if listOfGeometryDefinitions contains at least one element.
*
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -67,7 +67,7 @@
super(om);
if (om.isSetGeometryDefinition()) {
- setGeometryDefinition(new String(om.getGeometryDefinition()));
+ setGeometryDefinition(om.getGeometryDefinition());
}
if (om.isSetOrdinal()) {
setOrdinal(om.getOrdinal());
@@ -228,7 +228,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 2039;
int hashCode = super.hashCode();
if (isSetOrdinal()) {
hashCode += prime * getOrdinal();
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-21 15:40:05 UTC (rev 2203)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-22 08:09:38 UTC (rev 2204)
@@ -87,10 +87,10 @@
public ParameterType(ParameterType ref) {
super(ref);
if (ref.isSetSpId()) {
- spId = new String(ref.getSpId());
+ setSpId(ref.getSpId());
}
if (ref.isSetSpeciesReference()) {
- speciesRef = new String(ref.getSpeciesReference());
+ setSpeciesReference(ref.getSpeciesReference());
}
}
@@ -280,7 +280,7 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1901;
int hashCode = super.hashCode();
if (isSetSpId()) {
hashCode += prime * getSpId().hashCode();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-22 09:58:02
|
Revision: 2206
http://sourceforge.net/p/jsbml/code/2206
Author: niko-rodrigue
Date: 2015-04-22 09:57:59 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
corrected the spatial package classes to avoid NullPointerException when setting int/Integer, double/Double or boolean/Boolean (because of the auto-boxing)
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.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/CSGTranslation.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.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
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -24,7 +24,6 @@
import java.text.MessageFormat;
import java.util.Collection;
import java.util.List;
-import java.util.Map;
import javax.swing.tree.TreeNode;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -126,7 +126,7 @@
* @param value
*/
public void setValue(double value) {
- double oldValue = this.value;
+ Double oldValue = this.value;
this.value = value;
firePropertyChange(SpatialConstants.value, oldValue, this.value);
}
@@ -140,7 +140,7 @@
*/
public boolean unsetValue() {
if (isSetValue()) {
- double oldValue = value;
+ Double oldValue = value;
value = null;
firePropertyChange(SpatialConstants.value, oldValue, value);
return true;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -224,7 +224,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -238,7 +238,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -168,7 +168,7 @@
* @param rotateAxisX
*/
public void setRotateAxisX(double rotateAxisX) {
- double oldRotateAxisX = this.rotateAxisX;
+ Double oldRotateAxisX = this.rotateAxisX;
this.rotateAxisX = rotateAxisX;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, this.rotateAxisX);
}
@@ -182,7 +182,7 @@
*/
public boolean unsetRotateAxisX() {
if (isSetRotateAxisX()) {
- double oldRotateAxisX = rotateAxisX;
+ Double oldRotateAxisX = rotateAxisX;
rotateAxisX = null;
firePropertyChange(SpatialConstants.rotateAxisX, oldRotateAxisX, rotateAxisX);
return true;
@@ -220,7 +220,7 @@
* @param rotateAxisY
*/
public void setRotateAxisY(double rotateAxisY) {
- double oldRotateAxisY = this.rotateAxisY;
+ Double oldRotateAxisY = this.rotateAxisY;
this.rotateAxisY = rotateAxisY;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, this.rotateAxisY);
}
@@ -234,7 +234,7 @@
*/
public boolean unsetRotateAxisY() {
if (isSetRotateAxisY()) {
- double oldRotateAxisY = rotateAxisY;
+ Double oldRotateAxisY = rotateAxisY;
rotateAxisY = null;
firePropertyChange(SpatialConstants.rotateAxisY, oldRotateAxisY, rotateAxisY);
return true;
@@ -272,7 +272,7 @@
* @param rotateAxisZ
*/
public void setRotateAxisZ(double rotateAxisZ) {
- double oldRotateAxisZ = this.rotateAxisZ;
+ Double oldRotateAxisZ = this.rotateAxisZ;
this.rotateAxisZ = rotateAxisZ;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, this.rotateAxisZ);
}
@@ -286,7 +286,7 @@
*/
public boolean unsetRotateAxisZ() {
if (isSetRotateAxisZ()) {
- double oldRotateAxisZ = rotateAxisZ;
+ Double oldRotateAxisZ = rotateAxisZ;
rotateAxisZ = null;
firePropertyChange(SpatialConstants.rotateAxisZ, oldRotateAxisZ, rotateAxisZ);
return true;
@@ -324,7 +324,7 @@
* @param rotateAngleInRadians
*/
public void setRotateAngleInRadians(double rotateAngleInRadians) {
- double oldRotateAngleInRadians = this.rotateAngleInRadians;
+ Double oldRotateAngleInRadians = this.rotateAngleInRadians;
this.rotateAngleInRadians = rotateAngleInRadians;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, this.rotateAngleInRadians);
}
@@ -338,7 +338,7 @@
*/
public boolean unsetRotateAngleInRadians() {
if (isSetRotateAngleInRadians()) {
- double oldRotateAngleInRadians = rotateAngleInRadians;
+ Double oldRotateAngleInRadians = rotateAngleInRadians;
rotateAngleInRadians = null;
firePropertyChange(SpatialConstants.rotateAngleInRadians, oldRotateAngleInRadians, rotateAngleInRadians);
return true;
@@ -370,20 +370,16 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetRotateAxisX()) {
- attributes.remove("rotateAxisX");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", String.valueOf(getRotateAxisX()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisX", rotateAxisX.toString());
}
if (isSetRotateAxisY()) {
- attributes.remove("rotateAxisY");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", String.valueOf(getRotateAxisY()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisY", rotateAxisY.toString());
}
if (isSetRotateAxisZ()) {
- attributes.remove("rotateAxisZ");
- attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", String.valueOf(getRotateAxisZ()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAxisZ", rotateAxisZ.toString());
}
if (isSetRotateAngleInRadians()) {
- attributes.remove("rotateAngleInRadians");
- attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", String.valueOf(getRotateAngleInRadians()));
+ attributes.put(SpatialConstants.shortLabel + ":rotateAngleInRadians", rotateAngleInRadians.toString());
}
return attributes;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -160,7 +160,7 @@
* @param scaleX
*/
public void setScaleX(double scaleX) {
- double oldScaleX = this.scaleX;
+ Double oldScaleX = this.scaleX;
this.scaleX = scaleX;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, this.scaleX);
}
@@ -174,7 +174,7 @@
*/
public boolean unsetScaleX() {
if (isSetScaleX()) {
- double oldScaleX = scaleX;
+ Double oldScaleX = scaleX;
scaleX = null;
firePropertyChange(SpatialConstants.scaleX, oldScaleX, scaleX);
return true;
@@ -212,7 +212,7 @@
* @param scaleY
*/
public void setScaleY(double scaleY) {
- double oldScaleY = this.scaleY;
+ Double oldScaleY = this.scaleY;
this.scaleY = scaleY;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, this.scaleY);
}
@@ -226,7 +226,7 @@
*/
public boolean unsetScaleY() {
if (isSetScaleY()) {
- double oldScaleY = scaleY;
+ Double oldScaleY = scaleY;
scaleY = null;
firePropertyChange(SpatialConstants.scaleY, oldScaleY, scaleY);
return true;
@@ -264,7 +264,7 @@
* @param scaleZ
*/
public void setScaleZ(double scaleZ) {
- double oldScaleZ = this.scaleZ;
+ Double oldScaleZ = this.scaleZ;
this.scaleZ = scaleZ;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, this.scaleZ);
}
@@ -278,7 +278,7 @@
*/
public boolean unsetScaleZ() {
if (isSetScaleZ()) {
- double oldScaleZ = scaleZ;
+ Double oldScaleZ = scaleZ;
scaleZ = null;
firePropertyChange(SpatialConstants.scaleZ, oldScaleZ, scaleZ);
return true;
@@ -308,16 +308,13 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetScaleX()) {
- attributes.remove("scaleX");
- attributes.put(SpatialConstants.shortLabel + ":scaleX", String.valueOf(getScaleX()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleX", scaleX.toString());
}
if (isSetScaleY()) {
- attributes.remove("scaleY");
- attributes.put(SpatialConstants.shortLabel + ":scaleY", String.valueOf(getScaleY()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleY", scaleY.toString());
}
if (isSetScaleZ()) {
- attributes.remove("scaleZ");
- attributes.put(SpatialConstants.shortLabel + ":scaleZ", String.valueOf(getScaleZ()));
+ attributes.put(SpatialConstants.shortLabel + ":scaleZ", scaleZ.toString());
}
return attributes;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -158,7 +158,7 @@
* @param translateX
*/
public void setTranslateX(double translateX) {
- double oldTranslateX = this.translateX;
+ Double oldTranslateX = this.translateX;
this.translateX = translateX;
firePropertyChange(SpatialConstants.translateX, oldTranslateX, this.translateX);
}
@@ -172,7 +172,7 @@
*/
public boolean unsetTranslateX() {
if (isSetTranslateX()) {
- double oldTranslateX = translateX;
+ Double oldTranslateX = translateX;
translateX = null;
firePropertyChange(SpatialConstants.translateX, oldTranslateX, translateX);
return true;
@@ -210,7 +210,7 @@
* @param translateY
*/
public void setTranslateY(double translateY) {
- double oldTranslateY = this.translateY;
+ Double oldTranslateY = this.translateY;
this.translateY = translateY;
firePropertyChange(SpatialConstants.translateY, oldTranslateY, this.translateY);
}
@@ -224,7 +224,7 @@
*/
public boolean unsetTranslateY() {
if (isSetTranslateY()) {
- double oldTranslateY = translateY;
+ Double oldTranslateY = translateY;
translateY = null;
firePropertyChange(SpatialConstants.translateY, oldTranslateY, translateY);
return true;
@@ -262,7 +262,7 @@
* @param translateZ
*/
public void setTranslateZ(double translateZ) {
- double oldTranslateZ = this.translateZ;
+ Double oldTranslateZ = this.translateZ;
this.translateZ = translateZ;
firePropertyChange(SpatialConstants.translateZ, oldTranslateZ, this.translateZ);
}
@@ -276,7 +276,7 @@
*/
public boolean unsetTranslateZ() {
if (isSetTranslateZ()) {
- double oldTranslateZ = translateZ;
+ Double oldTranslateZ = translateZ;
translateZ = null;
firePropertyChange(SpatialConstants.translateZ, oldTranslateZ, translateZ);
return true;
@@ -306,16 +306,13 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetTranslateX()) {
- attributes.remove("translateX");
- attributes.put(SpatialConstants.shortLabel + ":translateX", String.valueOf(getTranslateX()));
+ attributes.put(SpatialConstants.shortLabel + ":translateX", translateX.toString());
}
if (isSetTranslateY()) {
- attributes.remove("translateY");
- attributes.put(SpatialConstants.shortLabel + ":translateY", String.valueOf(getTranslateY()));
+ attributes.put(SpatialConstants.shortLabel + ":translateY", translateY.toString());
}
if (isSetTranslateZ()) {
- attributes.remove("translateZ");
- attributes.put(SpatialConstants.shortLabel + ":translateZ", String.valueOf(getTranslateZ()));
+ attributes.put(SpatialConstants.shortLabel + ":translateZ", translateZ.toString());
}
return attributes;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -23,7 +23,6 @@
import java.util.Map;
-import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -215,7 +214,7 @@
*/
public boolean unsetUnitSize() {
if (isSetUnitSize()) {
- double oldUnitSize = unitSize;
+ Double oldUnitSize = unitSize;
unitSize = null;
firePropertyChange(SpatialConstants.unitSize, oldUnitSize, unitSize);
return true;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -32,7 +32,6 @@
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
-import org.sbml.jsbml.util.TreeNodeChangeEvent;
import org.sbml.jsbml.util.filters.NameFilter;
/**
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -144,7 +144,7 @@
* @param isActive
*/
public void setIsActive(boolean isActive) {
- boolean oldIsActive = this.isActive;
+ Boolean oldIsActive = this.isActive;
this.isActive = isActive;
firePropertyChange(SpatialConstants.isActive, oldIsActive, this.isActive);
}
@@ -157,7 +157,7 @@
*/
public boolean unsetIsActive() {
if (isSetIsActive()) {
- boolean oldIsActive = isActive;
+ Boolean oldIsActive = isActive;
isActive = null;
firePropertyChange(SpatialConstants.isActive, oldIsActive, isActive);
return true;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -31,7 +31,6 @@
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
-import org.sbml.jsbml.util.TreeNodeChangeEvent;
/**
* @author Alex Thomas
@@ -198,12 +197,7 @@
* @param coord1
*/
public void setCoord1(double coord1) {
- Double oldCoord1;
- if (isSetCoord1()) {
- oldCoord1 = this.coord1;
- } else {
- oldCoord1 = null;
- }
+ Double oldCoord1 = this.coord1;
this.coord1 = coord1;
firePropertyChange(SpatialConstants.coord1, oldCoord1, this.coord1);
}
@@ -217,7 +211,7 @@
*/
public boolean unsetCoord1() {
if (isSetCoord1()) {
- double oldCoord1 = coord1;
+ Double oldCoord1 = coord1;
coord1 = null;
firePropertyChange(SpatialConstants.coord1, oldCoord1, coord1);
return true;
@@ -253,12 +247,7 @@
* @param coord2
*/
public void setCoord2(double coord2) {
- Double oldCoord2;
- if (isSetCoord2()) {
- oldCoord2 = this.coord2;
- } else {
- oldCoord2 = null;
- }
+ Double oldCoord2 = this.coord2;
this.coord2 = coord2;
firePropertyChange(SpatialConstants.coord2, oldCoord2, this.coord2);
}
@@ -272,7 +261,7 @@
*/
public boolean unsetCoord2() {
if (isSetCoord2()) {
- double oldCoord2 = coord2;
+ Double oldCoord2 = coord2;
coord2 = null;
firePropertyChange(SpatialConstants.coord2, oldCoord2, coord2);
return true;
@@ -309,12 +298,7 @@
* @param coord3
*/
public void setCoord3(double coord3) {
- Double oldCoord3;
- if (isSetCoord3()) {
- oldCoord3 = coord1;
- } else {
- oldCoord3 = null;
- }
+ Double oldCoord3 = coord1;
this.coord3 = coord3;
firePropertyChange(SpatialConstants.coord3, oldCoord3, this.coord3);
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -153,7 +153,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -167,7 +167,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
@@ -246,11 +246,9 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetOrdinal()) {
- attributes.remove("ordinal");
- attributes.put(SpatialConstants.shortLabel + ":ordinal", String.valueOf(getOrdinal()));
+ attributes.put(SpatialConstants.shortLabel + ":ordinal", ordinal.toString());
}
if (isSetGeometryDefinition()) {
- attributes.remove("geometryDefinition");
attributes.put(SpatialConstants.shortLabel + ":geometryDefinition",
getGeometryDefinition());
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-22 08:36:22 UTC (rev 2205)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-04-22 09:57:59 UTC (rev 2206)
@@ -298,11 +298,9 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
if (isSetSpId()) {
- attributes.remove("spatialRef");
attributes.put(SpatialConstants.shortLabel + ":spatialRef", getSpId());
}
if (isSetSpeciesReference()) {
- attributes.remove("variable");
attributes.put(SpatialConstants.shortLabel + ":variable",
String.valueOf(getSpeciesReference()));
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 13:16:06
|
Revision: 2209
http://sourceforge.net/p/jsbml/code/2209
Author: pdp10
Date: 2015-04-22 13:15:55 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
update spatial package v0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
Added Paths:
-----------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-04-22 11:47:04 UTC (rev 2208)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -31,7 +31,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -40,7 +41,7 @@
/**
*
*/
- ListOf<SpatialPoint> listOfSpatialPoints;
+ ListOf<SpatialPoints> listOfSpatialPoints;
/**
*
*/
@@ -121,6 +122,18 @@
return equal;
}
+ @Override
+ public int hashCode() {
+ final int prime = 1999;
+ int hashCode = super.hashCode();
+ if (isSetListOfParametricObjects()) {
+ hashCode += prime * getListOfParametricObjects().hashCode();
+ }
+ if (isSetListOfSpatialPoints()) {
+ hashCode += prime * getListOfSpatialPoints().hashCode();
+ }
+ return hashCode;
+ }
/**
* Returns {@code true}, if listOfParametricObjects contains at least one element.
@@ -281,9 +294,9 @@
*
* @return the listOfSpatialPoints
*/
- public ListOf<SpatialPoint> getListOfSpatialPoints() {
+ public ListOf<SpatialPoints> getListOfSpatialPoints() {
if (!isSetListOfSpatialPoints()) {
- listOfSpatialPoints = new ListOf<SpatialPoint>(getLevel(),
+ listOfSpatialPoints = new ListOf<SpatialPoints>(getLevel(),
getVersion());
listOfSpatialPoints.setNamespace(SpatialConstants.namespaceURI);
listOfSpatialPoints.setSBaseListType(ListOf.Type.other);
@@ -299,7 +312,7 @@
*
* @param listOfSpatialPoints
*/
- public void setListOfSpatialPoints(ListOf<SpatialPoint> listOfSpatialPoints) {
+ public void setListOfSpatialPoints(ListOf<SpatialPoints> listOfSpatialPoints) {
unsetListOfSpatialPoints();
this.listOfSpatialPoints = listOfSpatialPoints;
registerChild(this.listOfSpatialPoints);
@@ -315,7 +328,7 @@
*/
public boolean unsetListOfSpatialPoints() {
if (isSetListOfSpatialPoints()) {
- ListOf<SpatialPoint> oldSpatialPoints = listOfSpatialPoints;
+ ListOf<SpatialPoints> oldSpatialPoints = listOfSpatialPoints;
listOfSpatialPoints = null;
oldSpatialPoints.fireNodeRemovedEvent();
return true;
@@ -325,27 +338,27 @@
/**
- * Adds a new {@link SpatialPoint} to the listOfSpatialPoints.
+ * Adds a new {@link SpatialPoints} to the listOfSpatialPoints.
* <p>The listOfSpatialPoints is initialized if necessary.
*
- * @param spatialPoint the element to add to the list
+ * @param spatialPoints the element to add to the list
* @return true (as specified by {@link Collection#add})
*/
- public boolean addSpatialPoint(SpatialPoint spatialPoint) {
- return getListOfSpatialPoints().add(spatialPoint);
+ public boolean addSpatialPoints(SpatialPoints spatialPoints) {
+ return getListOfSpatialPoints().add(spatialPoints);
}
/**
* Removes an element from the listOfSpatialPoints.
*
- * @param spatialPoint the element to be removed from the list
+ * @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 removeSpatialPoint(SpatialPoint spatialPoint) {
+ public boolean removeSpatialPoints(SpatialPoints spatialPoints) {
if (isSetListOfSpatialPoints()) {
- return getListOfSpatialPoints().remove(spatialPoint);
+ return getListOfSpatialPoints().remove(spatialPoints);
}
return false;
}
@@ -358,7 +371,7 @@
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size)
*/
- public void removeSpatialPoint(int i) {
+ public void removeSpatialPoints(int i) {
if (!isSetListOfSpatialPoints()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
@@ -370,31 +383,31 @@
/*
- * TODO: if the ID is mandatory for SpatialPoint objects,
+ * TODO: if the ID is mandatory for SpatialPoints objects,
* one should also add this methods
*/
- //public void removeSpatialPoint(String id) {
+ //public void removeSpatialPoints(String id) {
// getListOfSpatialPoints().removeFirst(new NameFilter(id));
//}
/**
- * Creates a new SpatialPoint element and adds it to the ListOfSpatialPoints list
+ * Creates a new SpatialPoints element and adds it to the ListOfSpatialPoints list
* @return
*/
- public SpatialPoint createSpatialPoint() {
- return createSpatialPoint(null);
+ public SpatialPoints createSpatialPoints() {
+ return createSpatialPoints(null);
}
/**
- * Creates a new {@link SpatialPoint} element and adds it to the ListOfSpatialPoints list
+ * Creates a new {@link SpatialPoints} element and adds it to the ListOfSpatialPoints list
* @param id
*
- * @return a new {@link SpatialPoint} element
+ * @return a new {@link SpatialPoints} element
*/
- public SpatialPoint createSpatialPoint(String id) {
- SpatialPoint spatialPoint = new SpatialPoint(id, getLevel(), getVersion());
- addSpatialPoint(spatialPoint);
- return spatialPoint;
+ public SpatialPoints createSpatialPoints(String id) {
+ SpatialPoints spatialPoints = new SpatialPoints(getLevel(), getVersion());
+ addSpatialPoints(spatialPoints);
+ return spatialPoints;
}
/* (non-Javadoc)
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-22 11:47:04 UTC (rev 2208)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -24,14 +24,14 @@
import java.text.MessageFormat;
import java.util.Map;
-import javax.swing.tree.TreeNode;
-
import org.sbml.jsbml.PropertyUndefinedError;
+import org.sbml.jsbml.util.StringTools;
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -55,6 +55,36 @@
QUADRILATERAL;
}
+ public enum CompressionKind {
+ /**
+ *
+ */
+ UNCOMPRESSED,
+ /**
+ *
+ */
+ DEFLATED,
+ /**
+ *
+ */
+ BASE64;
+ }
+
+ public enum DataKind {
+ /**
+ *
+ */
+ UINT8,
+ /**
+ *
+ */
+ UINT16,
+ /**
+ *
+ */
+ UINT32;
+ }
+
/**
*
*/
@@ -66,7 +96,17 @@
/**
*
*/
- private PolygonObject polygonObject;
+ private CompressionKind compression;
+ /**
+ *
+ */
+ private Integer pointIndexLength;
+ /**
+ *
+ */
+ private DataKind dataType;
+
+
/**
* Generated serial version identifier.
*/
@@ -84,19 +124,21 @@
*/
public ParametricObject(ParametricObject po) {
super(po);
-
if (po.isSetDomainType()) {
- domainType = new String(po.getDomainType());
+ setDomainType(po.getDomainType());
}
-
if (po.isSetPolygonType()) {
setPolygonType(po.getPolygonType());
}
-
- if (po.isSetPolygonObject()) {
- setPolygonObject(po.getPolygonObject().clone());
+ if (po.isSetCompression()) {
+ setCompression(po.getCompression());
}
-
+ if (po.isSetPointIndexLength()) {
+ setPointIndexLength(po.getPointIndexLength());
+ }
+ if (po.isSetDataType()) {
+ setDataType(po.getDataType());
+ }
}
@@ -136,16 +178,22 @@
if (equal && isSetDomainType()) {
equal &= po.getDomainType().equals(getDomainType());
}
-
equal &= po.isSetPolygonType() == isSetPolygonType();
if (equal && isSetPolygonType()) {
equal &= po.getPolygonType().equals(getPolygonType());
}
-
- equal &= po.isSetPolygonObject() == isSetPolygonObject();
- if (equal && isSetPolygonObject()) {
- equal &= po.getPolygonObject().equals(getPolygonObject());
+ equal &= po.isSetCompression() == isSetCompression();
+ if (equal && isSetCompression()) {
+ equal &= po.getCompression().equals(getCompression());
}
+ equal &= po.isSetPointIndexLength() == isSetPointIndexLength();
+ if (equal && isSetPointIndexLength()) {
+ equal &= po.getPointIndexLength() == getPointIndexLength();
+ }
+ equal &= po.isSetDataType() == isSetDataType();
+ if (equal && isSetDataType()) {
+ equal &= po.getDataType().equals(getDataType());
+ }
}
return equal;
}
@@ -233,7 +281,7 @@
return domainType != null;
}
-
+
/**
* Sets the value of domain
* @param domain
@@ -261,100 +309,182 @@
return false;
}
+
+
/**
- * Returns the value of polygonObject
+ * Returns the value of compression.
*
- * @return the value of polygonObject
+ * @return the value of compression.
*/
- public PolygonObject getPolygonObject() {
- if (isSetPolygonObject()) {
- return polygonObject;
+ public CompressionKind getCompression() {
+ if (isSetCompression()) {
+ return compression;
}
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.polygonObject, this);
+ // 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.compression, this);
}
/**
- * Returns whether polygonObject is set
+ * Returns whether compression is set.
*
- * @return whether polygonObject is set
+ * @return whether compression is set.
*/
- public boolean isSetPolygonObject() {
- return polygonObject != null;
+ public boolean isSetCompression() {
+ return this.compression != null;
}
+ /**
+ * Sets the value of compression
+ * @param compression
+ */
+ public void setCompression(String compression) {
+ setCompression(CompressionKind.valueOf(compression));
+ }
/**
- * Sets the value of polygonObject
- * @param polygonObject
+ * Sets the value of compression
+ *
+ * @param compression the value of compression to be set.
*/
- public void setPolygonObject(PolygonObject polygonObject) {
- PolygonObject oldPolygonObject = this.polygonObject;
- this.polygonObject = polygonObject;
- firePropertyChange(SpatialConstants.polygonObject, oldPolygonObject, this.polygonObject);
+ public void setCompression(CompressionKind compression) {
+ CompressionKind oldCompression = this.compression;
+ this.compression = compression;
+ firePropertyChange(SpatialConstants.compression, oldCompression, this.compression);
}
/**
- * Unsets the variable polygonObject
+ * Unsets the variable compression.
*
- * @return {@code true}, if polygonObject was set before,
- * otherwise {@code false}
+ * @return {@code true} if compression was set before, otherwise {@code false}.
*/
- public boolean unsetPolygonObject() {
- if (isSetPolygonObject()) {
- PolygonObject oldPolygonObject = polygonObject;
- polygonObject = null;
- firePropertyChange(SpatialConstants.polygonObject, oldPolygonObject, polygonObject);
+ public boolean unsetCompression() {
+ if (isSetCompression()) {
+ CompressionKind oldCompression = this.compression;
+ this.compression = null;
+ firePropertyChange(SpatialConstants.compression, oldCompression, this.compression);
return true;
}
return false;
}
+
+
+ /**
+ * Returns the value of pointIndexLength.
+ *
+ * @return the value of pointIndexLength.
+ */
+ public int getPointIndexLength() {
+ if (isSetPointIndexLength()) {
+ return pointIndexLength.intValue();
+ }
+ // 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.pointIndexLength, this);
+ }
- @Override
- public boolean getAllowsChildren() {
- return true;
+ /**
+ * Returns whether pointIndexLength is set.
+ *
+ * @return whether pointIndexLength is set.
+ */
+ public boolean isSetPointIndexLength() {
+ return this.pointIndexLength != null;
}
- @Override
- public int getChildCount() {
- int count = super.getChildCount();
- if (isSetPolygonObject()) {
- count++;
- }
- return count;
+ /**
+ * Sets the value of pointIndexLength
+ *
+ * @param pointIndexLength the value of pointIndexLength to be set.
+ */
+ public void setPointIndexLength(int pointIndexLength) {
+ Integer oldPointIndexLength = this.pointIndexLength;
+ this.pointIndexLength = pointIndexLength;
+ firePropertyChange(SpatialConstants.pointIndexLength, oldPointIndexLength, this.pointIndexLength);
}
- @Override
- public TreeNode getChildAt(int index) {
- if (index < 0) {
- throw new IndexOutOfBoundsException(index + " < 0");
+ /**
+ * Unsets the variable pointIndexLength.
+ *
+ * @return {@code true} if pointIndexLength was set before, otherwise {@code false}.
+ */
+ public boolean unsetPointIndexLength() {
+ if (isSetPointIndexLength()) {
+ Integer oldPointIndexLength = this.pointIndexLength;
+ this.pointIndexLength = null;
+ firePropertyChange(SpatialConstants.pointIndexLength, oldPointIndexLength, this.pointIndexLength);
+ return true;
}
- int count = super.getChildCount(), pos = 0;
- if (index < count) {
- return super.getChildAt(index);
- } else {
- index -= count;
+ return false;
+ }
+
+
+ /**
+ * Returns the value of dataType.
+ *
+ * @return the value of dataType.
+ */
+ public DataKind getDataType() {
+ if (isSetDataType()) {
+ return dataType;
}
- if (isSetPolygonObject()) {
- if (pos == index) {
- return getPolygonObject();
- }
- pos++;
+ // 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.dataType, this);
+ }
+
+
+ /**
+ * Returns whether dataType is set.
+ *
+ * @return whether dataType is set.
+ */
+ public boolean isSetDataType() {
+ return this.dataType != null;
+ }
+
+ /**
+ * Sets the value of dataType
+ * @param dataType
+ */
+ public void setDataType(String dataType) {
+ setDataType(DataKind.valueOf(dataType));
+ }
+
+ /**
+ * Sets the value of dataType
+ *
+ * @param dataType the value of dataType to be set.
+ */
+ public void setDataType(DataKind dataType) {
+ DataKind oldDataType = this.dataType;
+ this.dataType = dataType;
+ firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
+ }
+
+
+ /**
+ * Unsets the variable dataType.
+ *
+ * @return {@code true} if dataType was set before, otherwise {@code false}.
+ */
+ public boolean unsetDataType() {
+ if (isSetDataType()) {
+ DataKind oldDataType = this.dataType;
+ this.dataType = null;
+ firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
+ return true;
}
- throw new IndexOutOfBoundsException(MessageFormat.format(
- "Index {0,number,integer} >= {1,number,integer}", index,
- +Math.min(pos, 0)));
+ return false;
}
+
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 2003;
int hashCode = super.hashCode();
if (isSetDomainType()) {
hashCode += prime * getDomainType().hashCode();
@@ -362,6 +492,15 @@
if (isSetPolygonType()) {
hashCode += prime * getPolygonType().hashCode();
}
+ if (isSetCompression()) {
+ hashCode += prime * getCompression().hashCode();
+ }
+ if (isSetPointIndexLength()) {
+ hashCode += prime * getPointIndexLength();
+ }
+ if (isSetDataType()) {
+ hashCode += prime * getDataType().hashCode();
+ }
return hashCode;
}
@@ -373,12 +512,26 @@
attributes.remove("domainType");
attributes.put(SpatialConstants.shortLabel + ":domainType", getDomainType());
}
-
if (isSetPolygonType()) {
attributes.remove("polygonType");
attributes.put(SpatialConstants.shortLabel + ":polygonType",
getPolygonType().toString());
}
+ if (isSetCompression()) {
+ attributes.remove("compression");
+ attributes.put(SpatialConstants.shortLabel + ":compression",
+ getCompression().toString());
+ }
+ if (isSetPointIndexLength()) {
+ attributes.remove("pointIndexLength");
+ attributes.put(SpatialConstants.shortLabel + ":pointIndexLength",
+ String.valueOf(getPointIndexLength()));
+ }
+ if (isSetDataType()) {
+ attributes.remove("dataType");
+ attributes.put(SpatialConstants.shortLabel + ":dataType",
+ getDataType().toString());
+ }
return attributes;
}
@@ -398,7 +551,6 @@
SpatialConstants.domainType);
}
}
-
else if (attributeName.equals(SpatialConstants.polygonType)) {
try {
setPolygonType(value);
@@ -406,6 +558,27 @@
MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
}
}
+ else if (attributeName.equals(SpatialConstants.compression)) {
+ try {
+ setCompression(value);
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
+ else if (attributeName.equals(SpatialConstants.pointIndexLength)) {
+ try {
+ setPointIndexLength(StringTools.parseSBMLInt(value));
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
+ else if (attributeName.equals(SpatialConstants.dataType)) {
+ try {
+ setDataType(value);
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
else {
isAttributeRead = false;
}
@@ -424,6 +597,12 @@
builder.append(polygonType);
builder.append(", domain=");
builder.append(domainType);
+ builder.append(", compression=");
+ builder.append(compression);
+ builder.append(", pointIndexLength=");
+ builder.append(pointIndexLength);
+ builder.append(", dataType=");
+ builder.append(dataType);
builder.append("]");
return builder.toString();
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java 2015-04-22 11:47:04 UTC (rev 2208)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -36,6 +36,7 @@
* @version $Rev$
* @since 1.0
* @date Jan 21, 2014
+ * @deprecated
*/
public class PolygonObject extends AbstractSBase {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-22 11:47:04 UTC (rev 2208)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -461,10 +461,14 @@
*/
public static final String listOfParametricObjects = "listOfParametricObjects";
/**
- *
+ * @deprecated
*/
public static final String spatialPoint = "spatialPoint";
/**
+ *
+ */
+ public static final String spatialPoints = "spatialPoints";
+ /**
*
*/
public static final String parametricObject = "parametricObject";
@@ -507,8 +511,17 @@
*
*/
public static final String data = "data";
+ /**
+ *
+ */
+ public static final String pointIndexLength = "pointIndexLength";
/**
+ *
+ */
+ public static final String arrayDataLength = "arrayDataLength";
+
+ /**
* @param level
* @param version
* @return
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-04-22 11:47:04 UTC (rev 2208)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -31,7 +31,8 @@
* @author Alex Thomas
* @author Andreas Dräger
* @since 1.0
- * @version $Rev$
+ * @version $Rev$
+ * @deprecated
*/
public class SpatialPoint extends AbstractSpatialNamedSBase {
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-04-22 13:15:55 UTC (rev 2209)
@@ -0,0 +1,432 @@
+/*
+ * $Id: SpatialPoints.java 0 2015-04-22 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.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;
+
+import java.text.MessageFormat;
+import java.util.Map;
+
+import org.sbml.jsbml.AbstractSBase;
+import org.sbml.jsbml.PropertyUndefinedError;
+import org.sbml.jsbml.util.StringTools;
+
+
+/**
+ * @author Piero Dalle Pezze
+ * @since 1.0
+ * @version $Rev: 0 $
+ */
+public class SpatialPoints extends AbstractSBase {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -3467717442431545263L;
+
+
+ public enum CompressionKind {
+ /**
+ *
+ */
+ UNCOMPRESSED,
+ /**
+ *
+ */
+ DEFLATED,
+ /**
+ *
+ */
+ BASE64;
+ }
+
+ public enum DataKind {
+ /**
+ *
+ */
+ UINT8,
+ /**
+ *
+ */
+ UINT16,
+ /**
+ *
+ */
+ UINT32,
+ /**
+ *
+ */
+ FLOAT,
+ /**
+ *
+ */
+ DOUBLE;
+ }
+
+ /**
+ *
+ */
+ private CompressionKind compression;
+ /**
+ *
+ */
+ private Integer arrayDataLength;
+ /**
+ *
+ */
+ private DataKind dataType;
+
+
+
+
+ /**
+ * Creates an SpatialPoints instance
+ */
+ public SpatialPoints() {
+ super();
+ initDefaults();
+ }
+
+ /**
+ * Creates a SpatialPoints instance with a level and version.
+ *
+ * @param level SBML Level
+ * @param version SBML Version
+ */
+ public SpatialPoints(int level, int version) {
+ super(level, version);
+ }
+
+
+ /**
+ * Clone constructor
+ */
+ public SpatialPoints(SpatialPoints sp) {
+ super(sp);
+ if (sp.isSetCompression()) {
+ setCompression(sp.getCompression());
+ }
+ if (sp.isSetArrayDataLength()) {
+ setArrayDataLength(sp.getArrayDataLength());
+ }
+ if (sp.isSetDataType()) {
+ setDataType(sp.getDataType());
+ }
+ }
+
+
+ /**
+ * clones this class
+ */
+ public SpatialPoints clone() {
+ return new SpatialPoints(this);
+ }
+
+ @Override
+ public boolean equals(Object object) {
+ boolean equal = super.equals(object);
+ if (equal) {
+ SpatialPoints sp = (SpatialPoints) object;
+
+ equal &= sp.isSetCompression() == isSetCompression();
+ if (equal && isSetCompression()) {
+ equal &= sp.getCompression().equals(getCompression());
+ }
+ equal &= sp.isSetArrayDataLength() == isSetArrayDataLength();
+ if (equal && isSetArrayDataLength()) {
+ equal &= sp.getArrayDataLength() == getArrayDataLength();
+ }
+ equal &= sp.isSetDataType() == isSetDataType();
+ if (equal && isSetDataType()) {
+ equal &= sp.getDataType().equals(getDataType());
+ }
+ }
+ return equal;
+ }
+
+ /**
+ * Initializes the default values using the namespace.
+ */
+ public void initDefaults() {
+ setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
+ packageName = SpatialConstants.shortLabel;
+ setPackageVersion(-1);
+ }
+
+ /**
+ * Returns the value of compression.
+ *
+ * @return the value of compression.
+ */
+ public CompressionKind getCompression() {
+ if (isSetCompression()) {
+ return compression;
+ }
+ // 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.compression, this);
+ }
+
+
+ /**
+ * Returns whether compression is set.
+ *
+ * @return whether compression is set.
+ */
+ public boolean isSetCompression() {
+ return this.compression != null;
+ }
+
+ /**
+ * Sets the value of compression
+ * @param compression
+ */
+ public void setCompression(String compression) {
+ setCompression(CompressionKind.valueOf(compression));
+ }
+
+ /**
+ * Sets the value of compression
+ *
+ * @param compression the value of compression to be set.
+ */
+ public void setCompression(CompressionKind compression) {
+ CompressionKind oldCompression = this.compression;
+ this.compression = compression;
+ firePropertyChange(SpatialConstants.compression, oldCompression, this.compression);
+ }
+
+
+ /**
+ * Unsets the variable compression.
+ *
+ * @return {@code true} if compression was set before, otherwise {@code false}.
+ */
+ public boolean unsetCompression() {
+ if (isSetCompression()) {
+ CompressionKind oldCompression = this.compression;
+ this.compression = null;
+ firePropertyChange(SpatialConstants.compression, oldCompression, this.compression);
+ return true;
+ }
+ return false;
+ }
+
+
+ /**
+ * Returns the value of arrayDataLength.
+ *
+ * @return the value of arrayDataLength.
+ */
+ public int getArrayDataLength() {
+ if (isSetArrayDataLength()) {
+ return arrayDataLength.intValue();
+ }
+ // 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.arrayDataLength, this);
+ }
+
+
+ /**
+ * Returns whether arrayDataLength is set.
+ *
+ * @return whether arrayDataLength is set.
+ */
+ public boolean isSetArrayDataLength() {
+ return this.arrayDataLength != null;
+ }
+
+
+ /**
+ * Sets the value of arrayDataLength
+ *
+ * @param arrayDataLength the value of arrayDataLength to be set.
+ */
+ public void setArrayDataLength(int arrayDataLength) {
+ Integer oldArrayDataLength = this.arrayDataLength;
+ this.arrayDataLength = arrayDataLength;
+ firePropertyChange(SpatialConstants.arrayDataLength, oldArrayDataLength, this.arrayDataLength);
+ }
+
+
+ /**
+ * Unsets the variable arrayDataLength.
+ *
+ * @return {@code true} if arrayDataLength was set before, otherwise {@code false}.
+ */
+ public boolean unsetArrayDataLength() {
+ if (isSetArrayDataLength()) {
+ Integer oldArrayDataLength = this.arrayDataLength;
+ this.arrayDataLength = null;
+ firePropertyChange(SpatialConstants.arrayDataLength, oldArrayDataLength, this.arrayDataLength);
+ return true;
+ }
+ return false;
+ }
+
+
+ /**
+ * Returns the value of dataType.
+ *
+ * @return the value of dataType.
+ */
+ public DataKind getDataType() {
+ if (isSetDataType()) {
+ return dataType;
+ }
+ // 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.dataType, this);
+ }
+
+
+ /**
+ * Returns whether dataType is set.
+ *
+ * @return whether dataType is set.
+ */
+ public boolean isSetDataType() {
+ return this.dataType != null;
+ }
+
+ /**
+ * Sets the value of dataType
+ * @param dataType
+ */
+ public void setDataType(String dataType) {
+ setDataType(DataKind.valueOf(dataType));
+ }
+
+ /**
+ * Sets the value of dataType
+ *
+ * @param dataType the value of dataType to be set.
+ */
+ public void setDataType(DataKind dataType) {
+ DataKind oldDataType = this.dataType;
+ this.dataType = dataType;
+ firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
+ }
+
+
+ /**
+ * Unsets the variable dataType.
+ *
+ * @return {@code true} if dataType was set before, otherwise {@code false}.
+ */
+ public boolean unsetDataType() {
+ if (isSetDataType()) {
+ DataKind oldDataType = this.dataType;
+ this.dataType = null;
+ firePropertyChange(SpatialConstants.dataType, oldDataType, this.dataType);
+ return true;
+ }
+ return false;
+ }
+
+
+
+ @Override
+ public int hashCode() {
+ final int prime = 2011;
+ int hashCode = super.hashCode();
+ if (isSetCompression()) {
+ hashCode += prime * getCompression().hashCode();
+ }
+ if (isSetArrayDataLength()) {
+ hashCode += prime * getArrayDataLength();
+ }
+ if (isSetDataType()) {
+ hashCode += prime * getDataType().hashCode();
+ }
+ return hashCode;
+ }
+
+ @Override
+ public Map<String, String> writeXMLAttributes() {
+ Map<String, String> attributes = super.writeXMLAttributes();
+ if (isSetCompression()) {
+ attributes.remove("compression");
+ attributes.put(SpatialConstants.shortLabel + ":compression",
+ getCompression().toString());
+ }
+ if (isSetArrayDataLength()) {
+ attributes.remove("arrayDataLength");
+ attributes.put(SpatialConstants.shortLabel + ":arrayDataLength",
+ String.valueOf(getArrayDataLength()));
+ }
+ if (isSetDataType()) {
+ attributes.remove("dataType");
+ attributes.put(SpatialConstants.shortLabel + ":dataType",
+ getDataType().toString());
+ }
+
+ return attributes;
+ }
+
+
+ @Override
+ public boolean readAttribute(String attributeName, String prefix, String value) {
+ boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
+ && (SpatialConstants.shortLabel == prefix);
+ if (attributeName.equals(SpatialConstants.compression)) {
+ try {
+ setCompression(value);
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
+ else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
+ try {
+ setArrayDataLength(StringTools.parseSBMLInt(value));
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
+ else if (attributeName.equals(SpatialConstants.dataType)) {
+ try {
+ setDataType(value);
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ }
+ }
+ else {
+ isAttributeRead = false;
+ }
+ return isAttributeRead;
+ }
+
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("ParametricObject [compression=");
+ builder.append(compression);
+ builder.append(", arrayDataLength=");
+ builder.append(arrayDataLength);
+ builder.append(", dataType=");
+ builder.append(dataType);
+ builder.append("]");
+ return builder.toString();
+ }
+
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 13:20:47
|
Revision: 2211
http://sourceforge.net/p/jsbml/code/2211
Author: pdp10
Date: 2015-04-22 13:20:39 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
removed class SpatialPoint. This is replaced with SpatialPoints following the update in spatial package v0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
Removed Paths:
-------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-22 13:16:42 UTC (rev 2210)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-22 13:20:39 UTC (rev 2211)
@@ -461,10 +461,6 @@
*/
public static final String listOfParametricObjects = "listOfParametricObjects";
/**
- * @deprecated
- */
- public static final String spatialPoint = "spatialPoint";
- /**
*
*/
public static final String spatialPoints = "spatialPoints";
Deleted: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-04-22 13:16:42 UTC (rev 2210)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoint.java 2015-04-22 13:20:39 UTC (rev 2211)
@@ -1,469 +0,0 @@
-/*
- * $Id$
- * $URL$
- * ----------------------------------------------------------------------------
- * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
- * for the latest version of JSBML and more information about SBML.
- *
- * Copyright (C) 2009-2015 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.ext.spatial;
-
-import java.text.MessageFormat;
-import java.util.Map;
-
-import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.util.StringTools;
-
-/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @since 1.0
- * @version $Rev$
- * @deprecated
- */
-public class SpatialPoint extends AbstractSpatialNamedSBase {
-
- /**
- *
- */
- private String domain;
-
- /**
- *
- */
- private Double coord1;
- /**
- *
- */
- private Double coord2;
- /**
- *
- */
- private Double coord3;
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = -1171421071571874086L;
-
- /**
- *
- */
- public SpatialPoint() {
- super();
- }
-
- /**
- * @param sp
- */
- public SpatialPoint(SpatialPoint sp) {
- super(sp);
-
-
- if (sp.isSetDomain()) {
- domain = new String(sp.getDomain());
- }
-
- if (sp.isSetCoord1()) {
- coord1 = new Double(sp.getCoord1());
- }
-
- if (sp.isSetCoord2()) {
- coord2 = new Double(sp.getCoord2());
- }
-
- if (sp.isSetCoord3()) {
- coord3 = new Double(sp.getCoord3());
- }
- }
-
-
- /**
- * @param level
- * @param version
- */
- public SpatialPoint(int level, int version) {
- super(level, version);
- }
-
-
- /**
- *
- * @param id
- * @param level
- * @param version
- */
- public SpatialPoint(String id, int level, int version) {
- super(id, level, version);
- }
-
-
- @Override
- public SpatialPoint clone() {
- return new SpatialPoint(this);
- }
-
-
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- SpatialPoint sp = (SpatialPoint) object;
-
- equal &= sp.isSetDomain() == isSetDomain();
- if (equal && isSetDomain()) {
- equal &= sp.getDomain().equals(getDomain());
- }
-
- equal &= sp.isSetCoord1() == isSetCoord1();
- if (equal && isSetCoord1()) {
- equal &= sp.getCoord1() == getCoord1();
- }
-
- equal &= sp.isSetCoord2() == isSetCoord2();
- if (equal && isSetCoord2()) {
- equal &= sp.getCoord2() == getCoord2();
- }
-
- equal &= sp.isSetCoord3() == isSetCoord3();
- if (equal && isSetCoord3()) {
- equal &= sp.getCoord3() == getCoord3();
- }
- //TODO: add equal statements for each attribute and class
- }
- return equal;
- }
-
- /**
- * Returns the value of coord1
- *
- * @return the value of coord1
- */
- public double getCoord1() {
- if (isSetCoord1()) {
- return coord1;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord1, this);
- }
-
-
- /**
- * Returns whether coord1 is set
- *
- * @return whether coord1 is set
- */
- public boolean isSetCoord1() {
- return coord1 != null;
- }
-
- /**
- * Sets the value of coord1
- * @param coord1
- */
- public void setCoord1(double coord1) {
- double oldCoord1 = this.coord1;
- this.coord1 = coord1;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, this.coord1);
- }
-
-
- /**
- * Unsets the variable coord1
- *
- * @return {@code true}, if coord1 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord1() {
- if (isSetCoord1()) {
- double oldCoord1 = coord1;
- coord1 = null;
- firePropertyChange(SpatialConstants.coord1, oldCoord1, coord1);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord2
- *
- * @return the value of coord2
- */
- public double getCoord2() {
- if (isSetCoord2()) {
- return coord2;
- }
- //TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord2, this);
- }
-
-
- /**
- * Returns whether coord2 is set
- *
- * @return whether coord2 is set
- */
- public boolean isSetCoord2() {
- return coord2 != null;
- }
-
- /**
- * Sets the value of coord2
- * @param coord2
- */
- public void setCoord2(double coord2) {
- double oldCoord2 = this.coord2;
- this.coord2 = coord2;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, this.coord2);
- }
-
-
- /**
- * Unsets the variable coord2
- *
- * @return {@code true}, if coord2 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord2() {
- if (isSetCoord2()) {
- double oldCoord2 = coord2;
- coord2 = null;
- firePropertyChange(SpatialConstants.coord2, oldCoord2, coord2);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of coord3
- *
- * @return the value of coord3
- */
- public double getCoord3() {
- if (isSetCoord3()) {
- return coord3;
- }
- // TODO:This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.coord3, this);
- }
-
-
- /**
- * Returns whether coord3 is set
- *
- * @return whether coord3 is set
- */
- public boolean isSetCoord3() {
- return coord3 != null;
- }
-
- /**
- * Sets the value of coord3
- * @param coord3
- */
- public void setCoord3(double coord3) {
- double oldCoord3 = this.coord3;
- this.coord3 = coord3;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, this.coord3);
- }
-
-
- /**
- * Unsets the variable coord3
- *
- * @return {@code true}, if coord3 was set before,
- * otherwise {@code false}
- */
- public boolean unsetCoord3() {
- if (isSetCoord3()) {
- double oldCoord3 = coord3;
- coord3 = null;
- firePropertyChange(SpatialConstants.coord3, oldCoord3, coord3);
- return true;
- }
- return false;
- }
-
- /**
- * Returns the value of domain
- *
- * @return the value of domain
- */
- public String getDomain() {
- if (isSetDomain()) {
- return domain;
- }
- // TODO: This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.domain, this);
- }
-
-
- /**
- * Returns whether domain is set
- *
- * @return whether domain is set
- */
- public boolean isSetDomain() {
- return domain != null;
- }
-
- /**
- * Sets the value of domain
- * @param domain
- */
- public void setDomain(String domain) {
- String oldDomain = this.domain;
- this.domain = domain;
- firePropertyChange(SpatialConstants.domain, oldDomain, this.domain);
- }
-
- /**
- * Unsets the variable domain
- *
- * @return {@code true}, if domain was set before,
- * otherwise {@code false}
- */
- public boolean unsetDomain() {
- if (isSetDomain()) {
- String oldDomain = domain;
- domain = null;
- firePropertyChange(SpatialConstants.domain, oldDomain, domain);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetDomain()) {
- hashCode += prime * getDomain().hashCode();
- }
-
- if (isSetCoord1()) {
- hashCode += prime * getCoord1();
- }
-
- if (isSetCoord2()) {
- hashCode += prime * getCoord2();
- }
-
- if (isSetCoord3()) {
- hashCode += prime * getCoord3();
- }
- return hashCode;
- }
-
-
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetDomain()) {
- attributes.remove("domain");
- attributes.put(SpatialConstants.shortLabel + ":domain", getDomain());
- }
-
- if (isSetCoord1()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord1()));
- }
-
- if (isSetCoord2()) {
- attributes.remove("coord1");
- attributes.put(SpatialConstants.shortLabel + ":coord1",
- String.valueOf(getCoord2()));
- }
-
- if (isSetCoord3()) {
- attributes.remove("coord3");
- attributes.put(SpatialConstants.shortLabel + ":coord3",
- String.valueOf(getCoord3()));
- }
- return attributes;
- }
-
-
- @Override
- public boolean readAttribute(String attributeName, String prefix, String value) {
- boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
- && (SpatialConstants.shortLabel == prefix);
- if (!isAttributeRead) {
- isAttributeRead = true;
- if (attributeName.equals(SpatialConstants.domain)) {
- try {
- setDomain(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domain);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord1)) {
- try {
- setCoord1(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord1);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord2)) {
- try {
- setCoord2(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord2);
- }
- }
-
- else if (attributeName.equals(SpatialConstants.coord3)) {
- try {
- setCoord3(StringTools.parseSBMLDouble(value));
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coord3);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("SpatialPoint [domain=");
- builder.append(domain);
- builder.append(", coord1=");
- builder.append(coord1);
- builder.append(", coord2=");
- builder.append(coord2);
- builder.append(", coord3=");
- builder.append(coord3);
- builder.append("]");
- return builder.toString();
- }
-
-
-
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 14:53:50
|
Revision: 2216
http://sourceforge.net/p/jsbml/code/2216
Author: pdp10
Date: 2015-04-22 14:53:42 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
update spatial package v0.90
Modified Paths:
--------------
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
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-04-22 14:36:58 UTC (rev 2215)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-04-22 14:53:42 UTC (rev 2216)
@@ -34,7 +34,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -72,6 +73,7 @@
/**
* @author Alex Thomas
* @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
*/
@@ -83,7 +85,11 @@
/**
*
*/
- DEFLATED;
+ DEFLATED,
+ /**
+ *
+ */
+ BASE64;
}
/**
@@ -111,10 +117,6 @@
/**
*
*/
- private DataKind dataType;
- /**
- *
- */
private Integer numSamples1;
/**
*
@@ -135,6 +137,14 @@
/**
*
*/
+ private Integer samplesLength;
+ /**
+ *
+ */
+ private DataKind dataType;
+ /**
+ *
+ */
private XMLNode data;
/**
@@ -164,6 +174,9 @@
if (sf.isSetCompression()) {
setCompression(sf.getCompression());
}
+ if (sf.isSetSamplesLength()) {
+ setSamplesLength(sf.getSamplesLength());
+ }
if (sf.isSetInterpolation()) {
setInterpolation(sf.getInterpolation());
}
@@ -223,6 +236,10 @@
if (equal && isSetInterpolation()) {
equal &= sf.getInterpolation().equals(getInterpolation());
}
+ equal &= sf.isSetSamplesLength() == isSetSamplesLength();
+ if (equal && isSetSamplesLength()) {
+ equal &= sf.getSamplesLength() == getSamplesLength();
+ }
equal &= sf.isSetDataType() == isSetDataType();
if (equal && isSetDataType()) {
equal &= sf.getDataType().equals(getDataType());
@@ -543,6 +560,67 @@
}
+/**
+ * Returns the value of {@link #samplesLength}.
+ *
+ * @return the value of {@link #samplesLength}.
+ */
+public int getSamplesLength() {
+ if (isSetSamplesLength()) {
+ return samplesLength;
+ }
+ // 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.samplesLength, this);
+}
+
+
+/**
+ * Returns whether {@link #samplesLength} is set.
+ *
+ * @return whether {@link #samplesLength} is set.
+ */
+public boolean isSetSamplesLength() {
+ return this.samplesLength != null;
+}
+
+/**
+ * Sets the value of samplesLength
+ *
+ * @param samplesLength the value of samplesLength to be set.
+ */
+public void setSamplesLength(String samplesLength) {
+ Integer oldSamplesLength = this.samplesLength;
+ this.samplesLength = StringTools.parseSBMLInt(samplesLength);
+ firePropertyChange(SpatialConstants.samplesLength, oldSamplesLength, this.samplesLength);
+}
+
+/**
+ * Sets the value of samplesLength
+ *
+ * @param samplesLength the value of samplesLength to be set.
+ */
+public void setSamplesLength(int samplesLength) {
+ Integer oldSamplesLength = this.samplesLength;
+ this.samplesLength = samplesLength;
+ firePropertyChange(SpatialConstants.samplesLength, oldSamplesLength, this.samplesLength);
+}
+
+
+/**
+ * Unsets the variable samplesLength.
+ *
+ * @return {@code true} if samplesLength was set before, otherwise {@code false}.
+ */
+public boolean unsetSamplesLength() {
+ if (isSetSamplesLength()) {
+ Integer oldSamplesLength = this.samplesLength;
+ this.samplesLength = null;
+ firePropertyChange(SpatialConstants.samplesLength, oldSamplesLength, this.samplesLength);
+ return true;
+ }
+ return false;
+}
+
/**
* Returns the value of data
*
@@ -657,7 +735,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1997;
int hashCode = super.hashCode();
if (isSetNumSamples1()) {
hashCode += prime * getNumSamples1();
@@ -678,6 +756,10 @@
if (isSetCompression()) {
hashCode += prime * getCompression().hashCode();
}
+
+ if (isSetSamplesLength()) {
+ hashCode += prime * getSamplesLength();
+ }
if (isSetInterpolation()) {
hashCode += prime * getInterpolation().hashCode();
@@ -767,6 +849,13 @@
MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
}
}
+ else if (attributeName.equals(SpatialConstants.samplesLength)) {
+ try {
+ setSamplesLength(String.valueOf(value));
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.samplesLength);
+ }
+ }
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(DataKind.valueOf(value));
@@ -800,6 +889,8 @@
builder.append(interpolation);
builder.append(", compression=");
builder.append(compression);
+ builder.append(", samplesLength=");
+ builder.append(samplesLength);
builder.append(", data=");
builder.append(data);
builder.append("]");
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-04-22 14:36:58 UTC (rev 2215)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-04-22 14:53:42 UTC (rev 2216)
@@ -70,7 +70,7 @@
super(sampledFieldGeometry);
if (sampledFieldGeometry.isSetSampledField()) {
- sampledField = new String(sampledFieldGeometry.getSampledField());
+ setSampledField(sampledFieldGeometry.getSampledField());
}
if (isSetListOfSampledVolumes()) {
@@ -372,11 +372,14 @@
*/
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1951;
int hashCode = super.hashCode();
if (isSetSampledField()) {
hashCode += prime * getSampledField().hashCode();
}
+ if (isSetListOfSampledVolumes()) {
+ hashCode += prime * getListOfSampledVolumes().hashCode();
+ }
return hashCode;
}
@@ -416,5 +419,17 @@
}
return isAttributeRead;
}
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("SampledFieldGeometry [sampledField=");
+ builder.append(sampledField);
+ builder.append("]");
+ return builder.toString();
+ }
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-04-22 14:36:58 UTC (rev 2215)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledVolume.java 2015-04-22 14:53:42 UTC (rev 2216)
@@ -31,7 +31,8 @@
/**
* @author Alex Thomas
- * @author Andreas Dräger
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -78,16 +79,16 @@
public SampledVolume(SampledVolume sv) {
super(sv);
if (sv.isSetDomainType()) {
- domainType = new String(sv.getDomainType());
+ setDomainType(sv.getDomainType());
}
if (sv.isSetSampledValue()) {
- sampledValue = new Double(sv.getSampledValue());
+ setSampledValue(sv.getSampledValue());
}
if (sv.isSetMinValue()) {
- minValue = new Double(sv.getMinValue());
+ setMinValue(sv.getMinValue());
}
if (sv.isSetMaxValue()) {
- maxValue = new Double(sv.getMaxValue());
+ setMaxValue(sv.getMaxValue());
}
}
@@ -193,7 +194,7 @@
*/
public double getSampledValue() {
if (isSetSampledValue()) {
- return sampledValue;
+ return sampledValue.doubleValue();
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.sampledValue, this);
@@ -213,7 +214,7 @@
* @param sampledValue
*/
public void setSampledValue(double sampledValue) {
- double oldSampledValue = this.sampledValue;
+ Double oldSampledValue = this.sampledValue;
this.sampledValue = sampledValue;
firePropertyChange(SpatialConstants.sampledValue, oldSampledValue, this.sampledValue);
}
@@ -227,7 +228,7 @@
*/
public boolean unsetSampledValue() {
if (isSetSampledValue()) {
- double oldSampledValue = sampledValue;
+ Double oldSampledValue = sampledValue;
sampledValue = null;
firePropertyChange(SpatialConstants.sampledValue, oldSampledValue, sampledValue);
return true;
@@ -243,7 +244,7 @@
*/
public double getMinValue() {
if (isSetMinValue()) {
- return minValue;
+ return minValue.doubleValue();
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.minValue, this);
@@ -293,7 +294,7 @@
*/
public double getMaxValue() {
if (isSetMaxValue()) {
- return maxValue;
+ return maxValue.doubleValue();
}
throw new PropertyUndefinedError(SpatialConstants.maxValue, this);
}
@@ -339,7 +340,7 @@
@Override
public int hashCode() {
- final int prime = 983;//Change this prime number
+ final int prime = 1949;
int hashCode = super.hashCode();
if (isSetSampledValue()) {
hashCode += prime * getSampledValue();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 15:23:16
|
Revision: 2220
http://sourceforge.net/p/jsbml/code/2220
Author: pdp10
Date: 2015-04-22 15:23:14 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
update spatial package to v0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-04-22 15:16:16 UTC (rev 2219)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialModelPlugin.java 2015-04-22 15:23:14 UTC (rev 2220)
@@ -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: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-04-22 15:16:16 UTC (rev 2219)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialReactionPlugin.java 2015-04-22 15:23:14 UTC (rev 2220)
@@ -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: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-04-22 15:16:16 UTC (rev 2219)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java 2015-04-22 15:23:14 UTC (rev 2220)
@@ -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;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 08:49:28
|
Revision: 2226
http://sourceforge.net/p/jsbml/code/2226
Author: pdp10
Date: 2015-04-23 08:49:20 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package v0.90
Added Paths:
-----------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java 2015-04-23 08:49:20 UTC (rev 2226)
@@ -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
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-04-23 08:49:20 UTC (rev 2226)
@@ -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
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 09:42:48
|
Revision: 2228
http://sourceforge.net/p/jsbml/code/2228
Author: pdp10
Date: 2015-04-23 09:42:41 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package v0.90 - extraction of primitive types
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
Added Paths:
-----------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-23 09:21:12 UTC (rev 2227)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-23 09:42:41 UTC (rev 2228)
@@ -43,25 +43,6 @@
public class AnalyticVolume extends AbstractMathContainer implements SpatialNamedSBase{
/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @version $Rev$
- * @since 1.0
- * @date 10.12.2014
- */
- public static enum FunctionKind {
- /**
- * Math child element contains an inequality
- */
- LAYERED,
- // /**
- // * Shape is represented by a real-valued function whose sign
- // * indicates coverage by the shape
- // */
- // R_FUNCTION;
- }
-
- /**
*
*/
String spatialId;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-04-23 09:21:12 UTC (rev 2227)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-04-23 09:42:41 UTC (rev 2228)
@@ -37,35 +37,6 @@
public class BoundaryCondition extends ParameterType {
/**
- *
- * @author Andreas Dräger
- * @version $Rev$
- * @since 0.8
- */
- public static enum BoundaryKind {
- /**
- * Neumann
- */
- NEUMANN,
- /**
- * Dirichlet
- */
- DIRICHLET,
- /**
- * Robin value coefficient
- */
- ROBIN_VALUECOEFFICIENT,
- /**
- * Robin inward normal gradient coefficient
- */
- ROBIN_INWARDNORMALGRADIENTCOEFFICIENT,
- /**
- * Robin sum
- */
- ROBIN_SUM;
- }
-
- /**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -6986768113234565819L;
@@ -83,7 +54,7 @@
/**
*
*/
- private BoundaryKind type;
+ private BoundaryConditionKind type;
/**
*
@@ -168,7 +139,7 @@
*
* @return the value of type
*/
- public BoundaryKind getType() {
+ public BoundaryConditionKind getType() {
if (isSetType()) {
return type;
}
@@ -191,8 +162,8 @@
* Sets the value of type
* @param type
*/
- public void setType(BoundaryKind type) {
- BoundaryKind oldType = this.type;
+ public void setType(BoundaryConditionKind type) {
+ BoundaryConditionKind oldType = this.type;
this.type = type;
firePropertyChange(SpatialConstants.type, oldType, this.type);
}
@@ -204,7 +175,7 @@
if (!Pattern.matches("[a-z]*", type)) {
throw new SBMLException("The value is not all lower-case.");
}
- setType(BoundaryKind.valueOf(type.toUpperCase()));
+ setType(BoundaryConditionKind.valueOf(type.toUpperCase()));
}
/**
@@ -215,7 +186,7 @@
*/
public boolean unsetType() {
if (isSetType()) {
- BoundaryKind oldType = type;
+ BoundaryConditionKind oldType = type;
type = null;
firePropertyChange(SpatialConstants.type, oldType, type);
return true;
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java 2015-04-23 09:42:41 UTC (rev 2228)
@@ -0,0 +1,52 @@
+/*
+ * $Id: BoundaryConditionKind.java 2109 2015-01-05 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.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 BoundaryConditionKind {
+ /**
+ * Neumann
+ */
+ NEUMANN,
+ /**
+ * Dirichlet
+ */
+ DIRICHLET,
+ /**
+ * Robin value coefficient
+ */
+ ROBIN_VALUECOEFFICIENT,
+ /**
+ * Robin inward normal gradient coefficient
+ */
+ ROBIN_INWARDNORMALGRADIENTCOEFFICIENT,
+ /**
+ * Robin sum
+ */
+ ROBIN_SUM;
+}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-23 09:21:12 UTC (rev 2227)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-04-23 09:42:41 UTC (rev 2228)
@@ -37,44 +37,6 @@
public class CSGPrimitive extends CSGNode{
/**
- * @author Alex Thomas
- * @version $Rev$
- * @since 1.0
- * @date 10.12.2014
- */
- public enum PrimitiveKind {
- /**
- * sphere
- */
- SPHERE,
- /**
- * cube
- */
- CUBE,
- /**
- * cylinder
- */
- CYLINDER,
- /**
- * cone
- */
- CONE,
- /**
- * circle
- */
- CIRCLE,
- /**
- * square
- */
- SQUARE,
- /**
- * rightTriangle
- */
- RIGHTTRIANGLE;
-
- }
-
- /**
*
*/
private static final long serialVersionUID = -6783804853380306509L;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 09:43:44
|
Revision: 2229
http://sourceforge.net/p/jsbml/code/2229
Author: pdp10
Date: 2015-04-23 09:43:42 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package v0.90 - extraction of primitive types
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
Added Paths:
-----------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-23 09:42:41 UTC (rev 2228)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-23 09:43:42 UTC (rev 2229)
@@ -38,54 +38,6 @@
public class ParametricObject extends AbstractSpatialNamedSBase {
/**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @version $Rev$
- * @since 1.0
- */
- public enum PolygonKind {
- /**
- *
- */
- TRIANGLE,
-
- /**
- *
- */
- QUADRILATERAL;
- }
-
- public enum CompressionKind {
- /**
- *
- */
- UNCOMPRESSED,
- /**
- *
- */
- DEFLATED,
- /**
- *
- */
- BASE64;
- }
-
- public enum DataKind {
- /**
- *
- */
- UINT8,
- /**
- *
- */
- UINT16,
- /**
- *
- */
- UINT32;
- }
-
- /**
*
*/
private PolygonKind polygonType;
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java 2015-04-23 09:43:42 UTC (rev 2229)
@@ -0,0 +1,42 @@
+/*
+ * $Id: PolygonKind.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/PolygonKind.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 Alex Thomas
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
+ * @version $Rev: 2209 $
+ * @since 1.0
+ */
+public enum PolygonKind {
+ /**
+ *
+ */
+ TRIANGLE,
+
+ /**
+ *
+ */
+ QUADRILATERAL;
+}
\ No newline at end of file
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.java 2015-04-23 09:43:42 UTC (rev 2229)
@@ -0,0 +1,62 @@
+/*
+ * $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 Alex Thomas
+ * @author Piero Dalle Pezze
+ * @version $Rev: 2203 $
+ * @since 1.0
+ * @date 10.12.2014
+ */
+public enum PrimitiveKind {
+ /**
+ * sphere
+ */
+ SPHERE,
+ /**
+ * cube
+ */
+ CUBE,
+ /**
+ * cylinder
+ */
+ CYLINDER,
+ /**
+ * cone
+ */
+ CONE,
+ /**
+ * circle
+ */
+ CIRCLE,
+ /**
+ * square
+ */
+ SQUARE,
+ /**
+ * rightTriangle
+ */
+ RIGHTTRIANGLE;
+
+}
\ No newline at end of file
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SetOperation.java 2015-04-23 09:43:42 UTC (rev 2229)
@@ -0,0 +1,45 @@
+/*
+ * $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 Alex Thomas
+ * @author Piero Dalle Pezze
+ * @version $Rev: 2203 $
+ * @since 1.0
+ * @date 10.12.2014
+ */
+public enum SetOperation {
+ /**
+ *
+ */
+ UNION,
+ /**
+ *
+ */
+ INTERSECTION,
+ /**
+ *
+ */
+ RELATIVECOMPONENT;
+}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-04-23 09:42:41 UTC (rev 2228)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-04-23 09:43:42 UTC (rev 2229)
@@ -42,44 +42,6 @@
private static final long serialVersionUID = -3467717442431545263L;
- public enum CompressionKind {
- /**
- *
- */
- UNCOMPRESSED,
- /**
- *
- */
- DEFLATED,
- /**
- *
- */
- BASE64;
- }
-
- public enum DataKind {
- /**
- *
- */
- UINT8,
- /**
- *
- */
- UINT16,
- /**
- *
- */
- UINT32,
- /**
- *
- */
- FLOAT,
- /**
- *
- */
- DOUBLE;
- }
-
/**
*
*/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 09:44:33
|
Revision: 2230
http://sourceforge.net/p/jsbml/code/2230
Author: pdp10
Date: 2015-04-23 09:44:25 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package v0.90 - extraction of primitive types
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
Added Paths:
-----------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-04-23 09:43:42 UTC (rev 2229)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-04-23 09:44:25 UTC (rev 2230)
@@ -37,28 +37,7 @@
/**
*
- * @author
- * @version
- * @since
*/
- public static enum DiffusionKind {
- /**
- * Isotropic
- */
- ISOTROPIC,
- /**
- * Tensor
- */
- TENSOR,
- /**
- * Anisotropic
- */
- ANISOTROPIC;
- }
-
- /**
- *
- */
private DiffusionKind diffusionKind;
/**
*
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java 2015-04-23 09:44:25 UTC (rev 2230)
@@ -0,0 +1,44 @@
+/*
+ * $Id: DiffusionKind.java 2109 2015-01-05 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.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 DiffusionKind {
+ /**
+ * Isotropic
+ */
+ ISOTROPIC,
+ /**
+ * Tensor
+ */
+ TENSOR,
+ /**
+ * Anisotropic
+ */
+ ANISOTROPIC;
+}
\ No newline at end of file
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java 2015-04-23 09:44:25 UTC (rev 2230)
@@ -0,0 +1,42 @@
+/*
+ * $Id: BoundaryConditionKind.java 2109 2015-01-05 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.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 Alex Thomas
+ * @author Andreas Dräger
+ * @version $Rev: 2205 $
+ * @since 1.0
+ * @date 10.12.2014
+ */
+public enum FunctionKind {
+ /**
+ * Math child element contains an inequality
+ */
+ LAYERED,
+ // /**
+ // * Shape is represented by a real-valued function whose sign
+ // * indicates coverage by the shape
+ // */
+ // R_FUNCTION;
+}
\ No newline at end of file
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java 2015-04-23 09:44:25 UTC (rev 2230)
@@ -0,0 +1,36 @@
+/*
+ * $Id: GeometryKind.java 2109 2015-01-05 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.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 Alex Thomas
+ * @author Piero Dalle Pezze
+ * @version $Rev: 2206 $
+ * @since 0.8
+ */
+public enum GeometryKind {
+ /**
+ * cartesian
+ */
+ CARTESIAN;
+}
\ No newline at end of file
Added: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java (rev 0)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java 2015-04-23 09:44:25 UTC (rev 2230)
@@ -0,0 +1,41 @@
+/*
+ * $Id: InterpolationKind.java 2109 2015-01-05 04:50:45Z pdp10 $
+ * $URL: svn+ssh://pd...@sv.../p/jsbml/code/trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.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 Alex Thomas
+ * @author Andreas Dräger
+ * @author Piero Dalle Pezze
+ * @version $Rev: 2216 $
+ * @since 1.0
+ */
+public enum InterpolationKind {
+ /**
+ *
+ */
+ NEARESTNEIGHBOR,
+ /**
+ *
+ */
+ LINEAR;
+}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 09:47:05
|
Revision: 2231
http://sourceforge.net/p/jsbml/code/2231
Author: pdp10
Date: 2015-04-23 09:46:58 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package v0.90 - extraction of primitive types
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-23 09:44:25 UTC (rev 2230)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-04-23 09:46:58 UTC (rev 2231)
@@ -44,27 +44,6 @@
public class CSGSetOperator extends CSGNode {
/**
- * @author Alex Thomas
- * @version $Rev$
- * @since 1.0
- * @date 10.12.2014
- */
- public static enum SetOperation {
- /**
- *
- */
- UNION,
- /**
- *
- */
- INTERSECTION,
- /**
- *
- */
- RELATIVECOMPONENT;
- }
-
- /**
*
*/
private static final long serialVersionUID = 3448308755493169761L;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-23 09:44:25 UTC (rev 2230)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-04-23 09:46:58 UTC (rev 2231)
@@ -43,19 +43,6 @@
*/
public class Geometry extends AbstractSpatialNamedSBase {
- /**
- *
- * @author Alex Thomas
- * @version $Rev$
- * @since 0.8
- */
- public static enum GeometryKind {
- /**
- * cartesian
- */
- CARTESIAN;
- }
-
/**
* Generated serial version identifier.
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-04-23 09:44:25 UTC (rev 2230)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-04-23 09:46:58 UTC (rev 2231)
@@ -41,74 +41,6 @@
*/
public class SampledField extends AbstractSpatialNamedSBase {
- /**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @version $Rev$
- * @since 1.0
- */
- public enum DataKind {
- /**
- *
- */
- DOUBLE,
- /**
- *
- */
- FLOAT,
- /**
- *
- */
- UINT8,
- /**
- *
- */
- UINT16,
- /**
- *
- */
- UINT32;
- }
-
- /**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @author Piero Dalle Pezze
- * @version $Rev$
- * @since 1.0
- */
- public enum CompressionKind {
- /**
- *
- */
- UNCOMPRESSED,
- /**
- *
- */
- DEFLATED,
- /**
- *
- */
- BASE64;
- }
-
- /**
- * @author Alex Thomas
- * @author Andreas Dräger
- * @version $Rev$
- * @since 1.0
- */
- public enum InterpolationKind {
- /**
- *
- */
- NEARESTNEIGHBOR,
- /**
- *
- */
- LINEAR;
- }
-
/**
* Generated serial version identifier.
*/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-23 12:52:44
|
Revision: 2235
http://sourceforge.net/p/jsbml/code/2235
Author: pdp10
Date: 2015-04-23 12:52:36 +0000 (Thu, 23 Apr 2015)
Log Message:
-----------
update spatial package to v0.90 - added arrayData to SpatialPoints.
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-23 12:13:02 UTC (rev 2234)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-04-23 12:52:36 UTC (rev 2235)
@@ -514,21 +514,21 @@
try {
setCompression(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
}
}
else if (attributeName.equals(SpatialConstants.pointIndexLength)) {
try {
setPointIndexLength(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.pointIndexLength);
}
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-23 12:13:02 UTC (rev 2234)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-23 12:52:36 UTC (rev 2235)
@@ -515,6 +515,11 @@
/**
*
*/
+ public static final String arrayData = "arrayData";
+
+ /**
+ *
+ */
public static final String arrayDataLength = "arrayDataLength";
/**
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-04-23 12:13:02 UTC (rev 2234)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-04-23 12:52:36 UTC (rev 2235)
@@ -54,7 +54,10 @@
*
*/
private DataKind dataType;
-
+ /**
+ *
+ */
+ private String arrayData;
@@ -91,6 +94,9 @@
if (sp.isSetDataType()) {
setDataType(sp.getDataType());
}
+ if (sp.isSetArrayData()) {
+ setArrayData(sp.getArrayData());
+ }
}
@@ -111,6 +117,10 @@
if (equal && isSetCompression()) {
equal &= sp.getCompression().equals(getCompression());
}
+ equal &= sp.isSetArrayData() == isSetArrayData();
+ if (equal && isSetArrayData()) {
+ equal &= sp.getArrayData() == getArrayData();
+ }
equal &= sp.isSetArrayDataLength() == isSetArrayDataLength();
if (equal && isSetArrayDataLength()) {
equal &= sp.getArrayDataLength() == getArrayDataLength();
@@ -192,6 +202,78 @@
/**
+ * Returns the value of {@link #arrayData}.
+ *
+ * @return the value of {@link #arrayData}.
+ */
+ public String getArrayData() {
+ if (isSetArrayData()) {
+ return arrayData;
+ }
+ // 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.arrayData, this);
+ }
+
+
+ /**
+ * Returns whether {@link #arrayData} is set.
+ *
+ * @return whether {@link #arrayData} is set.
+ */
+ public boolean isSetArrayData() {
+ return this.arrayData != null;
+ }
+
+
+ /**
+ * Sets the value of arrayData
+ *
+ * @param arrayData the value of arrayData to be set.
+ */
+ public void setArrayData(String arrayData) {
+ String oldArrayData = this.arrayData;
+ this.arrayData = arrayData;
+ arrayDataLength = 1;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ }
+
+
+ /**
+ * Unsets the variable arrayData.
+ *
+ * @return {@code true} if arrayData was set before, otherwise {@code false}.
+ */
+ public boolean unsetArrayData() {
+ if (isSetArrayData()) {
+ String oldArrayData = this.arrayData;
+ this.arrayData = null;
+ arrayDataLength = null;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Appends the variable data to arrayData.
+ * @return {@code true} if data was appended to arrayData, otherwise {@code false}.
+ */
+ public boolean append(String data) {
+ if (isSetArrayData()) {
+ String oldArrayData = this.arrayData;
+ if(compression == CompressionKind.UNCOMPRESSED) {
+ this.arrayData = this.arrayData + "; " + data;
+ } else { // data is compressed
+ this.arrayData = this.arrayData + " " + data;
+ }
+ arrayDataLength++;
+ firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+ return true;
+ }
+ return false;
+ }
+
+ /**
* Returns the value of arrayDataLength.
*
* @return the value of arrayDataLength.
@@ -313,6 +395,9 @@
if (isSetArrayDataLength()) {
hashCode += prime * getArrayDataLength();
}
+ if (isSetArrayData()) {
+ hashCode += prime * getArrayData().hashCode();
+ }
if (isSetDataType()) {
hashCode += prime * getDataType().hashCode();
}
@@ -332,6 +417,11 @@
attributes.put(SpatialConstants.shortLabel + ":arrayDataLength",
String.valueOf(getArrayDataLength()));
}
+ if (isSetArrayData()) {
+ attributes.remove("arrayData");
+ attributes.put(SpatialConstants.shortLabel + ":arrayData",
+ getArrayData());
+ }
if (isSetDataType()) {
attributes.remove("dataType");
attributes.put(SpatialConstants.shortLabel + ":dataType",
@@ -350,21 +440,28 @@
try {
setCompression(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
}
}
else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
try {
setArrayDataLength(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.arrayDataLength);
}
}
+ else if (attributeName.equals(SpatialConstants.arrayData)) {
+ try {
+ setArrayData(value);
+ } catch (Exception e) {
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.arrayData);
+ }
+ }
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
}
}
else {
@@ -382,6 +479,8 @@
StringBuilder builder = new StringBuilder();
builder.append("ParametricObject [compression=");
builder.append(compression);
+ builder.append(", arrayData=");
+ builder.append(arrayData);
builder.append(", arrayDataLength=");
builder.append(arrayDataLength);
builder.append(", dataType=");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-05-13 15:26:17
|
Revision: 2296
http://sourceforge.net/p/jsbml/code/2296
Author: pdp10
Date: 2015-05-13 15:26:14 +0000 (Wed, 13 May 2015)
Log Message:
-----------
tested on files analytic_3d.xml, sampled_fields.xml .
Added logger to classes
Modified Paths:
--------------
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/BoundaryConditionKind.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/CompressionKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.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/FunctionKind.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/GeometryKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.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/PolygonKind.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PrimitiveKind.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/SetOperation.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.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/SpatialSpeciesPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -27,6 +27,7 @@
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;
@@ -39,7 +40,12 @@
* @version $Rev$
*/
public abstract class AbstractSpatialNamedSBase extends AbstractSBase implements SpatialNamedSBase {
-
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(AbstractSpatialNamedSBase.class);
+
/**
* Generated serial version identifier.
*/
@@ -238,8 +244,8 @@
try {
setSpatialId(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.spatialId);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.spatialId, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.ResourceBundle;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
@@ -35,8 +36,14 @@
* @version $Rev$
*/
public class AdjacentDomains extends AbstractSpatialNamedSBase {
-
+
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(AdjacentDomains.class);
+
+ /**
*
*/
private String domain1;
@@ -271,16 +278,16 @@
try {
setDomain1(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domain1);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domain1, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.domain2)) {
try {
setDomain2(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domain2);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domain2, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdvectionCoefficient.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
@@ -35,7 +36,12 @@
*/
public class AdvectionCoefficient extends ParameterType {
-
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(AdvectionCoefficient.class);
+
/**
* Generated serial version identifier.
*/
@@ -178,9 +184,8 @@
try {
setCoordinate(CoordinateKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coordinate);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinate, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -26,6 +26,7 @@
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;
@@ -42,7 +43,13 @@
*/
public class AnalyticVolume extends AbstractMathContainer implements SpatialNamedSBase{
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(AnalyticVolume.class);
+
+ /**
*
*/
String spatialId;
@@ -413,31 +420,33 @@
try {
setSpatialId(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.spatialId);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.spatialId, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.ordinal)) {
try {
setOrdinal(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.ordinal);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.ordinal, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.domainType)) {
try {
setDomainType(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domainType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.functionType)) {
- if (!Pattern.matches("[a-z]*", value)) {
- throw new SBMLException("The value is not all lower-case.");
+ try {
+ setFunctionType(FunctionKind.valueOf(value));
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.functionType, getElementName()));
}
- setFunctionType(FunctionKind.valueOf(value.toUpperCase()));
}
else {
isAttributeRead = false;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Boundary.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
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;
@@ -36,7 +37,13 @@
* @version $Rev$
*/
public class Boundary extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(Boundary.class);
+
/**
* Generated serial version identifier.
*/
@@ -198,9 +205,8 @@
try{
setValue(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.value);
-
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.value, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.regex.Pattern;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBMLException;
@@ -35,7 +36,13 @@
* @version $Rev$
*/
public class BoundaryCondition extends ParameterType {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(BoundaryCondition.class);
+
/**
* Generated serial version identifier.
*/
@@ -172,10 +179,7 @@
* @param type
*/
public void setType(String type) {
- if (!Pattern.matches("[a-z]*", type)) {
- throw new SBMLException("The value is not all lower-case.");
- }
- setType(BoundaryConditionKind.valueOf(type.toUpperCase()));
+ setType(BoundaryConditionKind.valueOf(type));
}
/**
@@ -329,21 +333,19 @@
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.type)) {
- // TODO: In the specs v0.90, the type name begins with capital letter.
- if (!Pattern.matches("[a-z]*", value)) {
- throw new SBMLException("The value is not all lower-case.");
- }
try {
setType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.type);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.type, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.coordinateBoundary)) {
try {
setCoordinateBoundary(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coordinateBoundary);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinateBoundary, getElementName()));
}
}
@@ -351,7 +353,8 @@
try {
setBoundaryDomainType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.boundaryDomainType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.boundaryDomainType, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryConditionKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -32,21 +32,21 @@
/**
* Neumann
*/
- NEUMANN,
+ Neumann,
/**
* Dirichlet
*/
- DIRICHLET,
+ Dirichlet,
/**
* Robin value coefficient
*/
- ROBIN_VALUECOEFFICIENT,
+ Robin_valueCoefficient,
/**
* Robin inward normal gradient coefficient
*/
- ROBIN_INWARDNORMALGRADIENTCOEFFICIENT,
+ Robin_inwardNormalGradientCoefficient,
/**
* Robin sum
*/
- ROBIN_SUM;
+ Robin_sum;
}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGObject.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -27,6 +27,7 @@
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;
@@ -39,7 +40,13 @@
* @version $Rev$
*/
public class CSGObject extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGObject.class);
+
/**
* Generated serial version identifier.
*/
@@ -342,8 +349,8 @@
try {
setDomainType(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domainType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
@@ -351,7 +358,8 @@
try {
setOrdinal(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value, SpatialConstants.ordinal);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.ordinal, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPrimitive.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.ResourceBundle;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
@@ -36,7 +37,13 @@
*/
public class CSGPrimitive extends CSGNode{
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGPrimitive.class);
+
+ /**
*
*/
private static final long serialVersionUID = -6783804853380306509L;
@@ -202,8 +209,8 @@
try {
setPrimitiveType(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.primitiveType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.primitiveType, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGPseudoPrimitive.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.ResourceBundle;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
@@ -36,7 +37,13 @@
*/
public class CSGPseudoPrimitive extends CSGNode{
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGPseudoPrimitive.class);
+
+ /**
*
*/
private static final long serialVersionUID = 303742063326104808L;
@@ -194,8 +201,8 @@
try {
setCsgObjectRef(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.primitiveType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.primitiveType, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGRotation.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -36,7 +37,13 @@
*/
public class CSGRotation extends CSGTransformation {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGRotation.class);
+
+ /**
*
*/
private static final long serialVersionUID = -4799604235135248586L;
@@ -395,31 +402,32 @@
try {
setRotateAxisX(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.rotateAxisX);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.rotateAxisX, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.rotateAxisY)) {
try {
setRotateAxisY(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.rotateAxisY);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.rotateAxisY, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.rotateAxisZ)) {
try {
setRotateAxisZ(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.rotateAxisZ);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.rotateAxisZ, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.rotateAngleInRadians)) {
try {
setRotateAngleInRadians(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.rotateAngleInRadians);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.rotateAngleInRadians, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGScale.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -37,7 +38,13 @@
*/
public class CSGScale extends CSGTransformation {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGScale.class);
+
+ /**
*
*/
private static final long serialVersionUID = 7021488698800177528L;
@@ -330,24 +337,24 @@
try {
setScaleX(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.scaleX);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.scaleX, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.scaleY)) {
try {
setScaleY(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.scaleY);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.scaleY, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.scaleZ)) {
try {
setScaleZ(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.scaleZ);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.scaleZ, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -29,6 +29,7 @@
import javax.swing.tree.TreeNode;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBMLException;
@@ -43,7 +44,13 @@
*/
public class CSGSetOperator extends CSGNode {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGSetOperator.class);
+
+ /**
*
*/
private static final long serialVersionUID = 3448308755493169761L;
@@ -661,17 +668,20 @@
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.operationType)) {
- if (!Pattern.matches("[a-z]*", value)) {
- throw new SBMLException("The value is not all lower-case.");
+ try {
+ setOperationType(SetOperation.valueOf(value));
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.operationType, getElementName()));
}
- setOperationType(SetOperation.valueOf(value.toUpperCase()));
}
else if (attributeName.equals(SpatialConstants.complementA)) {
try {
setComplementA(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.complementA);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.complementA, getElementName()));
}
}
@@ -679,7 +689,8 @@
try {
setComplementB(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.complementB);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.complementB, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGTranslation.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -36,7 +37,13 @@
*/
public class CSGTranslation extends CSGTransformation {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CSGTranslation.class);
+
+ /**
*
*/
private static final long serialVersionUID = 7030963917812170311L;
@@ -328,24 +335,24 @@
try {
setTranslateX(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.translateX);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.translateX, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.translateY)) {
try {
setTranslateY(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.translateY);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.translateY, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.translateZ)) {
try {
setTranslateZ(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.translateZ);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.translateZ, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -21,8 +21,10 @@
*/
package org.sbml.jsbml.ext.spatial;
+import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -35,7 +37,13 @@
* @version $Rev$
*/
public class CompartmentMapping extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CompartmentMapping.class);
+
/**
* Generated serial version identifier.
*/
@@ -273,10 +281,20 @@
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(SpatialConstants.domainType)) {
- setDomainType(value);
+ try {
+ setDomainType(value);
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
+ }
}
else if (attributeName.equals(SpatialConstants.unitSize)) {
- setUnitSize(StringTools.parseSBMLDouble(value));
+ try {
+ setUnitSize(StringTools.parseSBMLDouble(value));
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.unitSize, getElementName()));
+ }
}
else {
isAttributeRead = false;
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompressionKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -32,13 +32,13 @@
/**
* If no compression is used
*/
- UNCOMPRESSED,
+ uncompressed,
/**
* If the deflation algorithm was used to compress the text version of the data
*/
- DEFLATED,
+ deflated,
/**
* If the base 64 algorithm was used to transform the binary form of the actual members into text
*/
- BASE64;
+ base64;
}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -23,17 +23,16 @@
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.Model;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBaseWithUnit;
import org.sbml.jsbml.Unit;
import org.sbml.jsbml.Unit.Kind;
import org.sbml.jsbml.UnitDefinition;
-import org.sbml.jsbml.util.ResourceManager;
/**
* @author Alex Thomas
@@ -43,7 +42,13 @@
* @version $Rev$
*/
public class CoordinateComponent extends AbstractSpatialNamedSBase implements
-SBaseWithUnit {
+SBaseWithUnit {
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CoordinateComponent.class);
/**
* Generated serial version identifier.
@@ -71,11 +76,6 @@
*/
private String unit;
- /**
- *
- */
- private static final ResourceBundle bundle = ResourceManager.getBundle("org.sbml.jsbml.ext.spatial.Messages");
-
/**
*
*/
@@ -159,6 +159,7 @@
public void setBoundaryMinimum(Boundary boundaryMinimum) {
Boundary oldMinimum = this.boundaryMinimum;
this.boundaryMinimum = boundaryMinimum;
+ registerChild(boundaryMinimum);
firePropertyChange(SpatialConstants.boundaryMinimum, oldMinimum, this.boundaryMinimum);
}
@@ -210,6 +211,7 @@
public void setBoundaryMaximum(Boundary boundaryMaximum) {
Boundary oldMaximum = boundaryMaximum;
this.boundaryMaximum = boundaryMaximum;
+ registerChild(boundaryMaximum);
firePropertyChange(SpatialConstants.boundaryMaximum, oldMaximum, boundaryMaximum);
}
@@ -521,22 +523,22 @@
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
-
+
if (attributeName.equals(SpatialConstants.type)) {
try {
setType(CoordinateKind.valueOf(value));
}
catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.type);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.type, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.unit)) {
try {
setUnits(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.unit);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.unit, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -32,14 +32,14 @@
/**
* cartesianX
*/
- CARTESIANX,
+ cartesianX,
/**
* cartesianY
*/
- CARTESIANY,
+ cartesianY,
/**
* cartesianZ
*/
- CARTESIANZ;
+ cartesianZ;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.regex.Pattern;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.SBMLException;
@@ -38,10 +39,16 @@
* @version $Rev$
* @since 1.0
* @date 09.09.2011
+ * @deprecated Not present in spec 0.90, as be moved into DiffusionCoefficient.
*/
public abstract class CoordinateReference extends AbstractSBase {
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(CoordinateReference.class);
+
+ /**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -7651871640808157489L;
@@ -117,10 +124,7 @@
* @param coordinate
*/
public void setCoordinate(String coordinate) {
- if (!Pattern.matches("[a-z]*", coordinate)) {
- throw new SBMLException("The value is not all lower-case.");
- }
- setCoordinate(CoordinateKind.valueOf(coordinate.toUpperCase()));
+ setCoordinate(CoordinateKind.valueOf(coordinate));
}
/**
@@ -160,13 +164,13 @@
&& (SpatialConstants.shortLabel == prefix);
if (!isAttributeRead) {
isAttributeRead = true;
+ System.out.println(attributeName);
if (attributeName.equals(SpatialConstants.coordinate)) {
try {
setCoordinate(value);
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coordinate);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinate, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -33,15 +33,15 @@
/**
* To indicate 8-bit unsigned integer
*/
- UINT8,
+ uint8,
/**
* To indicate 16-bit unsigned integer
*/
- UINT16,
+ uint16,
/**
* To indicate 32-bit unsigned integer
*/
- UINT32,
+ uint32,
/**
* To indicate single-precision (32-bit) floating point values
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionCoefficient.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,7 +24,9 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
+import org.sbml.jsbml.xml.parsers.SpatialParser;
/**
@@ -47,6 +49,11 @@
*
*/
private CoordinateKind coordinateReference2;
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(DiffusionCoefficient.class);
/**
@@ -317,12 +324,11 @@
public Map<String, String> writeXMLAttributes() {
Map<String, String> attributes = super.writeXMLAttributes();
-
if (isSetDiffusionKind()) {
attributes.remove("type");
attributes.put(SpatialConstants.shortLabel + ":type",
- String.valueOf(getDiffusionKind()));
- }
+ String.valueOf(getDiffusionKind()).toLowerCase());
+ }
if (isSetCoordinateReference1()) {
attributes.remove("coordinateReference1");
@@ -330,7 +336,6 @@
String.valueOf(getCoordinateReference1()));
}
-
if (isSetCoordinateReference2()) {
attributes.remove("coordinateReference2");
attributes.put(SpatialConstants.shortLabel + ":coordinateReference2",
@@ -347,13 +352,13 @@
&& (SpatialConstants.shortLabel == prefix);
if (!isAttributeRead) {
isAttributeRead = true;
+
if (attributeName.equals(SpatialConstants.type)) {
try {
setDiffusionKind(DiffusionKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.type);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.type, getElementName()));
}
}
@@ -361,7 +366,7 @@
try {
setCoordinateReference1(CoordinateKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coordinateReference1);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinateReference1, getElementName()));
}
}
@@ -369,7 +374,7 @@
try {
setCoordinateReference2(CoordinateKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.coordinateReference2);
+ logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinateReference2, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DiffusionKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -32,13 +32,13 @@
/**
* Isotropic
*/
- ISOTROPIC,
+ isotropic,
/**
* Tensor
*/
- TENSOR,
+ tensor,
/**
* Anisotropic
*/
- ANISOTROPIC;
+ anisotropic;
}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -29,6 +29,7 @@
import javax.swing.tree.TreeNode;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBMLException;
@@ -42,7 +43,13 @@
* @version $Rev$
*/
public class Domain extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(Domain.class);
+
/**
* Generated serial version identifier.
*/
@@ -398,8 +405,8 @@
try {
setDomainType(value);
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domainType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DomainType.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.util.StringTools;
@@ -36,7 +37,13 @@
* @version $Rev$
*/
public class DomainType extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(DomainType.class);
+
/**
* Generated serial version identifier.
*/
@@ -202,8 +209,8 @@
try {
setSpatialDimensions(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.spatialDimensions);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.spatialDimensions, getElementName()));
isAttributeRead = false;
}
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/FunctionKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -33,7 +33,7 @@
/**
* Math child element contains an inequality
*/
- LAYERED,
+ layered,
// /**
// * Shape is represented by a real-valued function whose sign
// * indicates coverage by the shape
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -29,6 +29,7 @@
import javax.swing.tree.TreeNode;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
@@ -43,6 +44,12 @@
*/
public class Geometry extends AbstractSpatialNamedSBase {
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(Geometry.class);
+
/**
* Generated serial version identifier.
*/
@@ -1205,8 +1212,8 @@
try {
setCoordinateSystem(GeometryKind.valueOf(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coordinateSystem);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coordinateSystem, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryDefinition.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -34,7 +35,13 @@
* @version $Rev$
*/
public abstract class GeometryDefinition extends AbstractSpatialNamedSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(GeometryDefinition.class);
+
/**
* Generated serial version identifier.
*/
@@ -204,9 +211,8 @@
try {
setIsActive(StringTools.parseSBMLBoolean(value));
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.isActive);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.isActive, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/GeometryKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -30,7 +30,8 @@
*/
public enum GeometryKind {
/**
- * cartesian
+ *
*/
- CARTESIAN;
+ cartesian;
+
}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -27,6 +27,7 @@
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;
@@ -40,7 +41,13 @@
* @version $Rev$
*/
public class InteriorPoint extends AbstractSBase {
-
+
+
+ /**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(InteriorPoint.class);
+
/**
* Generated serial version identifier.
*/
@@ -367,24 +374,24 @@
try {
setCoord1(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coord1);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coord1, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.coord2)) {
try {
setCoord2(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coord2);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coord2, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.coord3)) {
try {
setCoord3(StringTools.parseSBMLDouble(value));
} catch (Exception e) {
- MessageFormat.format(bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.coord3);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.coord3, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InterpolationKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -33,9 +33,9 @@
/**
*
*/
- NEARESTNEIGHBOR,
+ nearestneighbor,
/**
*
*/
- LINEAR;
+ linear;
}
\ No newline at end of file
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -26,6 +26,7 @@
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.StringTools;
@@ -38,7 +39,13 @@
*/
public class OrdinalMapping extends AbstractSBase {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(OrdinalMapping.class);
+
+ /**
*
*/
private static final long serialVersionUID = -7174553771288567408L;
@@ -268,16 +275,16 @@
try {
setOrdinal(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.ordinal);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.ordinal, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.geometryDefinition)) {
try {
setGeometryDefinition(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.geometryDefinition);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.geometryDefinition, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -26,6 +26,7 @@
import javax.swing.tree.TreeNode;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLException;
@@ -40,7 +41,13 @@
*/
public class ParameterType extends AbstractSBase {
+
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(ParameterType.class);
+
+ /**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 1359841900912406174L;
@@ -320,16 +327,16 @@
try {
setSpId(value);
} catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.spatialId);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.spatialId, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.variable)) {
try {
setSpeciesReference(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.variable);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.variable, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -24,6 +24,7 @@
import java.text.MessageFormat;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
@@ -38,6 +39,11 @@
public class ParametricObject extends AbstractSpatialNamedSBase {
/**
+ * A {@link Logger} for this class.
+ */
+ private Logger logger = Logger.getLogger(ParametricObject.class);
+
+ /**
*
*/
private PolygonKind polygonType;
@@ -581,36 +587,40 @@
try {
setDomainType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.domainType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.polygonType)) {
try {
setPolygonType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.polygonType, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.compression)) {
try {
setCompression(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.compression, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.pointIndexLength)) {
try {
setPointIndexLength(StringTools.parseSBMLInt(value));
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.pointIndexLength);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.pointIndexLength, getElementName()));
}
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
setDataType(value);
} catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
}
}
else {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java 2015-05-12 16:08:17 UTC (rev 2295)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonKind.java 2015-05-13 15:26:14 UTC (rev 2296)
@@ -33,10 +33,10 @@
/**
*
*/
- TRIANGLE,
+ triangle,
/**
*
*/
- QUADRILATERAL;
+ quadrilateral;
}
\ No newlin...
[truncated message content] |
|
From: <pd...@us...> - 2015-05-13 15:48:43
|
Revision: 2297
http://sourceforge.net/p/jsbml/code/2297
Author: pdp10
Date: 2015-05-13 15:48:41 +0000 (Wed, 13 May 2015)
Log Message:
-----------
Set DataKind fields to upper case to avoid conflicts with Java primitive types float / double
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.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/SpatialPoints.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-13 15:26:14 UTC (rev 2296)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/DataKind.java 2015-05-13 15:48:41 UTC (rev 2297)
@@ -23,7 +23,12 @@
/**
- * This enum type was created following the specifications defined in Spatial Package v0.90.
+ * This enum type was created following the specifications defined in Spatial Package v0.90.
+ *
+ * The fields here are intentionally left upper case (in contrast to the spec where they are lower case)
+ * because float and double are in conflict with the Java primitive types float and double.
+ * Classes using DataKind need to use the methods toLowerCase() and toUpperCase() to deal with these values
+ * in the methods writeXMLAttributes() and readAttribute().
* @author Piero Dalle Pezze
* @version $Rev$
* @since 1.0
@@ -33,15 +38,15 @@
/**
* To indicate 8-bit unsigned integer
*/
- uint8,
+ UINT8,
/**
* To indicate 16-bit unsigned integer
*/
- uint16,
+ UINT16,
/**
* To indicate 32-bit unsigned integer
*/
- uint32,
+ UINT32,
/**
* To indicate single-precision (32-bit) floating point values
*/
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-13 15:26:14 UTC (rev 2296)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java 2015-05-13 15:48:41 UTC (rev 2297)
@@ -569,8 +569,9 @@
}
if (isSetDataType()) {
attributes.remove("dataType");
+ // see DataKind.java
attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType().toString());
+ getDataType().toString().toLowerCase());
}
return attributes;
@@ -617,7 +618,8 @@
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
- setDataType(value);
+ // see DataKind.java
+ setDataType(value.toUpperCase());
} catch (Exception e) {
logger.warn(MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-13 15:26:14 UTC (rev 2296)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-13 15:48:41 UTC (rev 2297)
@@ -804,8 +804,9 @@
String.valueOf(getNumSamples3()));
}
if (isSetDataType()) {
+ // see DataKind.java
attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType().toString());
+ getDataType().toString().toLowerCase());
}
if (isSetCompression()) {
attributes.put(SpatialConstants.shortLabel + ":compression",
@@ -873,7 +874,8 @@
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
- setDataType(DataKind.valueOf(value));
+ // see DataKind.java
+ setDataType(DataKind.valueOf(value.toUpperCase()));
} catch (Exception e) {
logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-13 15:26:14 UTC (rev 2296)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-13 15:48:41 UTC (rev 2297)
@@ -421,8 +421,9 @@
}
if (isSetDataType()) {
attributes.remove("dataType");
+ // see DataKind.java
attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType().toString());
+ getDataType().toString().toLowerCase());
}
return attributes;
@@ -451,7 +452,8 @@
}
else if (attributeName.equals(SpatialConstants.dataType)) {
try {
- setDataType(value);
+ // see DataKind.java
+ setDataType(value.toUpperCase());
} catch (Exception e) {
logger.warn(MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-05-14 10:14:30
|
Revision: 2301
http://sourceforge.net/p/jsbml/code/2301
Author: pdp10
Date: 2015-05-14 10:14:27 +0000 (Thu, 14 May 2015)
Log Message:
-----------
updated to specs 0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-13 16:10:56 UTC (rev 2300)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java 2015-05-14 10:14:27 UTC (rev 2301)
@@ -850,8 +850,8 @@
logger.warn(MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.numSamples3, getElementName()));
}
}
-
- else if (attributeName.equals(SpatialConstants.interpolation)) {
+ // TODO: update the following IF, after Lucian has decided whether it is called interpolation or interpolationType
+ else if (attributeName.equals(SpatialConstants.interpolation) || attributeName.equals("interpolationType")) {
try {
setInterpolation(InterpolationKind.valueOf(value));
} catch (Exception e) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-13 16:10:56 UTC (rev 2300)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java 2015-05-14 10:14:27 UTC (rev 2301)
@@ -434,33 +434,40 @@
public boolean readAttribute(String attributeName, String prefix, String value) {
boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
&& (SpatialConstants.shortLabel == prefix);
- if (attributeName.equals(SpatialConstants.compression)) {
- try {
- setCompression(value);
- } catch (Exception e) {
- logger.warn(MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.compression, getElementName()));
+ if(!isAttributeRead) {
+ isAttributeRead = true;
+
+ if (attributeName.equals(SpatialConstants.compression)) {
+ try {
+ setCompression(value);
+
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.compression, getElementName()));
+ }
}
- }
- else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
- try {
- setArrayDataLength(StringTools.parseSBMLInt(value));
- } catch (Exception e) {
- logger.warn(MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.arrayDataLength, getElementName()));
+ else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
+ try {
+ setArrayDataLength(StringTools.parseSBMLInt(value));
+
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.arrayDataLength, getElementName()));
+ }
}
- }
- else if (attributeName.equals(SpatialConstants.dataType)) {
- try {
- // see DataKind.java
- setDataType(value.toUpperCase());
- } catch (Exception e) {
- logger.warn(MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
+ else if (attributeName.equals(SpatialConstants.dataType)) {
+ try {
+ // see DataKind.java
+ setDataType(value.toUpperCase());
+
+ } catch (Exception e) {
+ logger.warn(MessageFormat.format(
+ SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.dataType, getElementName()));
+ }
+ }
+ else {
+ isAttributeRead = false;
}
- }
- else {
- isAttributeRead = false;
}
return isAttributeRead;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X