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From: <pd...@us...> - 2015-04-22 14:15:33
|
Revision: 2210
http://sourceforge.net/p/jsbml/code/2210
Author: pdp10
Date: 2015-04-22 13:16:42 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
update spatial package v0.90
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-04-22 13:15:55 UTC (rev 2209)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java 2015-04-22 13:16:42 UTC (rev 2210)
@@ -68,7 +68,7 @@
import org.sbml.jsbml.ext.spatial.SpatialConstants;
import org.sbml.jsbml.ext.spatial.SpatialModelPlugin;
import org.sbml.jsbml.ext.spatial.SpatialParameterPlugin;
-import org.sbml.jsbml.ext.spatial.SpatialPoint;
+import org.sbml.jsbml.ext.spatial.SpatialPoints;
import org.sbml.jsbml.ext.spatial.SpatialReactionPlugin;
import org.sbml.jsbml.ext.spatial.SpatialSpeciesPlugin;
import org.sbml.jsbml.ext.spatial.SpatialSymbolReference;
@@ -77,6 +77,7 @@
/**
* @author Andreas Dräger
+ * @author Piero Dalle Pezze
* @since 1.0
* @version $Rev$
*/
@@ -378,7 +379,7 @@
} else if (contextObject instanceof ParametricGeometry) {
ParametricGeometry pg = (ParametricGeometry) contextObject;
if (elementName.equals(SpatialConstants.listOfSpatialPoints)){
- ListOf<SpatialPoint> listOfSpatialPoints = pg.getListOfSpatialPoints();
+ ListOf<SpatialPoints> listOfSpatialPoints = pg.getListOfSpatialPoints();
return listOfSpatialPoints;
} else if (elementName.equals(SpatialConstants.listOfParametricObjects)){
ListOf<ParametricObject> listOfParametricObjects = pg.getListOfParametricObjects();
@@ -387,9 +388,11 @@
} else if (contextObject instanceof ParametricObject) {
ParametricObject po = (ParametricObject) contextObject;
if (elementName.equals(SpatialConstants.imageData)){
- PolygonObject polygonObject = new PolygonObject();
- po.setPolygonObject(polygonObject);
- return polygonObject;
+ // TODO: THIS NEEDS to be updated with the details provided in the spatial package v0.90,
+ // See ArrayData text child and PointIndex text child
+ //PolygonObject polygonObject = new PolygonObject();
+ //po.setPolygonObject(polygonObject);
+ //return polygonObject;
}
}
@@ -491,10 +494,10 @@
CSGHomogeneousTransformation elem = new CSGHomogeneousTransformation();
csgso.addCSGNode(elem);
return elem;
- } else if (elementName.equals(SpatialConstants.spatialPoint)) {
+ } else if (elementName.equals(SpatialConstants.spatialPoints)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
- SpatialPoint elem = new SpatialPoint();
- pg.addSpatialPoint(elem);
+ SpatialPoints elem = new SpatialPoints();
+ pg.addSpatialPoints(elem);
return elem;
} else if (elementName.equals(SpatialConstants.parametricObject)) {
ParametricGeometry pg = (ParametricGeometry) listOf.getParentSBMLObject();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2015-04-22 14:12:16
|
Revision: 2213
http://sourceforge.net/p/jsbml/code/2213
Author: andreas-draeger
Date: 2015-04-22 13:50:09 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Updated FBC package according to latest specification draft.
Modified Paths:
--------------
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java 2015-04-22 13:22:24 UTC (rev 2212)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCConstants.java 2015-04-22 13:50:09 UTC (rev 2213)
@@ -178,6 +178,36 @@
*/
public static final String or = "or";
+ /**
+ * Introduced to FBC in version 2.
+ */
+ public static final String associatedSpecies = "associatedSpecies";
+
+ /**
+ *
+ */
+ public static final String fluxObjective = "fluxObjective";
+
+ /**
+ *
+ */
+ public static final String objective = "objective";
+
+ /**
+ *
+ */
+ public static final String fluxBound = "fluxBound";
+
+ /**
+ *
+ */
+ public static final String listOfFluxObjectives = "listOfFluxObjectives";
+
+ /**
+ *
+ */
+ public static final String listOfFluxes = "listOfFluxes";
+
static {
namespaces = new ArrayList<String>();
namespaces.add(namespaceURI_L3V1V1);
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-04-22 13:22:24 UTC (rev 2212)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-04-22 13:50:09 UTC (rev 2213)
@@ -23,6 +23,7 @@
import java.util.Map;
import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.UniqueNamedSBase;
/**
@@ -48,6 +49,65 @@
/**
*
*/
+ private String associatedSpecies;
+
+
+ /**
+ * Returns the value of {@link #associatedSpecies}.
+ *
+ * @return the value of {@link #associatedSpecies}.
+ */
+ public String getAssociatedSpecies() {
+ //TODO: if variable is boolean, create an additional "isVar"
+ //TODO: return primitive data type if possible (e.g., int instead of Integer)
+ if (isSetAssociatedSpecies()) {
+ return associatedSpecies;
+ }
+ // 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(FBCConstants.associatedSpecies, this);
+ }
+
+
+ /**
+ * Returns whether {@link #associatedSpecies} is set.
+ *
+ * @return whether {@link #associatedSpecies} is set.
+ */
+ public boolean isSetAssociatedSpecies() {
+ return associatedSpecies != null;
+ }
+
+
+ /**
+ * Sets the value of associatedSpecies
+ *
+ * @param associatedSpecies the value of associatedSpecies to be set.
+ */
+ public void setAssociatedSpecies(String associatedSpecies) {
+ String oldAssociatedSpecies = this.associatedSpecies;
+ this.associatedSpecies = associatedSpecies;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, this.associatedSpecies);
+ }
+
+
+ /**
+ * Unsets the variable associatedSpecies.
+ *
+ * @return {@code true} if associatedSpecies was set before, otherwise {@code false}.
+ */
+ public boolean unsetAssociatedSpecies() {
+ if (isSetAssociatedSpecies()) {
+ String oldAssociatedSpecies = associatedSpecies;
+ associatedSpecies = null;
+ firePropertyChange(FBCConstants.associatedSpecies, oldAssociatedSpecies, associatedSpecies);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ *
+ */
public GeneProduct() {
super();
initDefaults();
@@ -186,6 +246,8 @@
if (attributeName.equals(FBCConstants.geneProductIdentifier) || attributeName.equals(FBCConstants.label)) {
setLabel(value);
+ } else if (attributeName.equals(FBCConstants.associatedSpecies)) {
+ setAssociatedSpecies(value);
} else {
isAttributeRead = false;
}
@@ -260,6 +322,9 @@
if (isSetLabel()) {
attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.label, getLabel());
}
+ if (isSetAssociatedSpecies()) {
+ attributes.put(FBCConstants.shortLabel + ":" + FBCConstants.associatedSpecies, getAssociatedSpecies());
+ }
return attributes;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-04-22 13:22:24 UTC (rev 2212)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-04-22 13:50:09 UTC (rev 2213)
@@ -313,7 +313,7 @@
}
throw new IndexOutOfBoundsException(MessageFormat.format(
"Index {0,number,integer} >= {1,number,integer}",
- index, +Math.min(pos, 0)));
+ index, Math.min(pos, 0)));
}
/* (non-Javadoc)
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-04-22 13:22:24 UTC (rev 2212)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/xml/parsers/FBCParser.java 2015-04-22 13:50:09 UTC (rev 2213)
@@ -69,6 +69,7 @@
* @since 1.0
* @version $Rev$
*/
+@SuppressWarnings("deprecation")
@ProviderFor(ReadingParser.class)
public class FBCParser extends AbstractReaderWriter implements PackageParser {
@@ -191,7 +192,7 @@
*/
// Create the proper object and link it to his parent.
@Override
- @SuppressWarnings({"unchecked", "deprecation"})
+ @SuppressWarnings({"unchecked"})
public Object processStartElement(String elementName, String uri, String prefix,
boolean hasAttributes, boolean hasNamespaces, Object contextObject)
{
@@ -226,7 +227,7 @@
} else if (contextObject instanceof Objective) {
Objective objective = (Objective) contextObject;
- if (elementName.equals("listOfFluxObjectives") || elementName.equals("listOfFluxes")) {
+ if (elementName.equals(FBCConstants.listOfFluxObjectives) || elementName.equals(FBCConstants.listOfFluxes)) {
// listOfFluxes was the first name of listOfFluxObjectives in the preliminary specifications
ListOf<FluxObjective> listOfFluxObjectives = objective.getListOfFluxObjectives();
groupList = FBCList.listOfFluxObjectives;
@@ -285,7 +286,7 @@
else if (contextObject instanceof ListOf<?>) {
ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
- if (elementName.equals("fluxBound")
+ if (elementName.equals(FBCConstants.fluxBound)
&& groupList.equals(FBCList.listOfFluxBounds)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -294,7 +295,7 @@
extendeModel.addFluxBound(fluxBound);
return fluxBound;
- } else if (elementName.equals("objective")
+ } else if (elementName.equals(FBCConstants.objective)
&& groupList.equals(FBCList.listOfObjectives)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -303,7 +304,7 @@
extendeModel.addObjective(objective);
return objective;
- } else if (elementName.equals("fluxObjective")
+ } else if (elementName.equals(FBCConstants.fluxObjective)
&& groupList.equals(FBCList.listOfFluxObjectives)) {
Objective objective = (Objective) listOf.getParentSBMLObject();
@@ -311,7 +312,7 @@
objective.addFluxObjective(fluxObjective);
return fluxObjective;
- } else if (elementName.equals("geneProduct")
+ } else if (elementName.equals(FBCConstants.geneProduct)
&& groupList.equals(FBCList.listOfGeneProducts)) {
Model model = (Model) listOf.getParentSBMLObject();
FBCModelPlugin extendeModel = (FBCModelPlugin) model.getExtension(FBCConstants.shortLabel);
@@ -329,12 +330,13 @@
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.WritingParser#writeElement(org.sbml.jsbml.xml.stax.SBMLObjectForXML, java.lang.Object)
*/
- @SuppressWarnings("deprecation")
@Override
public void writeElement(SBMLObjectForXML xmlObject,
Object sbmlElementToWrite) {
- logger.debug("FBCParser: writeElement");
+ if (logger.isDebugEnabled()) {
+ logger.debug("FBCParser: writeElement");
+ }
if (sbmlElementToWrite instanceof SBase) {
SBase sbase = (SBase) sbmlElementToWrite;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-22 13:22:35
|
Revision: 2212
http://sourceforge.net/p/jsbml/code/2212
Author: pdp10
Date: 2015-04-22 13:22:24 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Removed class ImageData following specs spatial package v0.90
Removed Paths:
-------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
Deleted: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-04-22 13:20:39 UTC (rev 2211)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ImageData.java 2015-04-22 13:22:24 UTC (rev 2212)
@@ -1,359 +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.Arrays;
-import java.util.Map;
-import java.util.StringTokenizer;
-
-import org.sbml.jsbml.AbstractSBase;
-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 ImageData extends AbstractSBase {
-
- /**
- * Generated serial version identifier.
- */
- private static final long serialVersionUID = 1872012239027099782L;
-
- /**
- *
- */
- private Integer samplesLength; // TODO: is this field really required??
- /**
- *
- */
- private Integer[] samples;
-
- /**
- *
- */
- private String dataType;
-
- /**
- *
- */
- public ImageData() {
- super();
- initDefaults();
- }
-
- /**
- * @param im
- */
- public ImageData(ImageData im) {
- super(im);
- if (im.isSetSamples()) {
- setSamples(im.getSamples().clone());
- samplesLength = samples.length;
- }
- if (im.isSetDataType()) {
- setDataType(im.getDataType());
- }
- }
-
- /**
- * @param level
- * @param version
- */
- public ImageData(int level, int version) {
- super(level, version);
- initDefaults();
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#clone()
- */
- @Override
- public ImageData clone() {
- return new ImageData(this);
- }
-
- /**
- * 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
- setPackageVersion(-1);
- packageName = SpatialConstants.shortLabel;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#equals(java.lang.Object)
- */
- @Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- ImageData im = (ImageData) object;
-
- equal &= im.isSetSamples() == isSetSamples();
- if (equal && isSetSamples()) {
- equal &= im.getSamples().equals(getSamples());
- }
-
- equal &= im.isSetDataType() == isSetDataType();
- if (equal && isSetDataType()) {
- equal &= im.getDataType().equals(getDataType());
- }
-
- }
- return equal;
- }
-
-
- /**
- * Returns the value of samples
- *
- * @return the value of samples
- */
- public Integer[] getSamples() {
- if (isSetSamples()) {
- return samples;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samples, this);
- }
-
-
- /**
- * Returns whether samples is set
- *
- * @return whether samples is set
- */
- public boolean isSetSamples() {
- return samples != null;
- }
-
- /**
- * Sets the value of samples
- * @param samples
- */
- public void setSamples(Integer... samples) {
- Integer[] oldSamples = this.samples;
- this.samples = samples;
- samplesLength = samples.length;
- firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
- firePropertyChange(SpatialConstants.samples, oldSamples.length, samplesLength);
- }
-
- /**
- * Unsets the variable samples
- *
- * @return {@code true}, if samples was set before,
- * otherwise {@code false}
- */
- public boolean unsetSamples() {
- if (isSetSamples()) {
- Integer[] oldSamples = samples;
- samples = null;
- samplesLength = null;
- firePropertyChange(SpatialConstants.samples, oldSamples, samples);
- firePropertyChange(SpatialConstants.samplesLength, oldSamples.length, samplesLength);
- return true;
- }
- return false;
- }
-
-
- /**
- * Returns the value of samplesLength
- *
- * @return the value of samplesLength
- */
- public int getSamplesLength() {
- if (isSetSamplesLength()) {
- return samplesLength;
- }
- // This is necessary if we cannot return null here.
- throw new PropertyUndefinedError(SpatialConstants.samplesLength, this);
- }
-
-
- /**
- * Returns whether samplesLength is set
- *
- * @return whether samplesLength is set
- */
- public boolean isSetSamplesLength() {
- return samplesLength != null;
- }
-
-
- /**
- * Returns the value of dataType
- *
- * @return the value of dataType
- */
- public String getDataType() {
- if (isSetDataType()) {
- return dataType;
- }
- return null;
- }
-
-
- /**
- * Returns whether dataType is set
- *
- * @return whether dataType is set
- */
- public boolean isSetDataType() {
- return dataType != null;
- }
-
- /**
- * Sets the value of dataType
- * @param dataType
- */
- public void setDataType(String dataType) {
- String 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()) {
- String oldDataType = dataType;
- dataType = null;
- firePropertyChange(SpatialConstants.dataType, oldDataType, dataType);
- return true;
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#hashCode()
- */
- @Override
- public int hashCode() {
- final int prime = 983;//Change this prime number
- int hashCode = super.hashCode();
- if (isSetSamples()) {
- hashCode += prime * getSamples().hashCode();
- }
- if (isSetDataType()) {
- hashCode += prime * getDataType().hashCode();
- }
-
- return hashCode;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#writeXMLAttributes()
- */
- @Override
- public Map<String, String> writeXMLAttributes() {
- Map<String, String> attributes = super.writeXMLAttributes();
- if (isSetSamples()) {
- attributes.remove("samples");
- attributes.put(SpatialConstants.shortLabel + ":samples", Arrays.toString(getSamples()));
- }
-
- if (isSetSamplesLength()) {
- attributes.remove("samplesLength");
- attributes.put(SpatialConstants.shortLabel + ":samplesLength",
- String.valueOf(getSamplesLength()));
- }
-
- if (isSetDataType()) {
- attributes.remove("dataType");
- attributes.put(SpatialConstants.shortLabel + ":dataType",
- getDataType());
- }
- return attributes;
- }
-
- /* (non-Javadoc)
- * @see org.sbml.jsbml.AbstractSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
- */
- @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.samples)) {
- StringTokenizer test = new StringTokenizer(value);
- Integer[] samplesTemp = new Integer[test.countTokens()];
- int i = 0;
- while(test.hasMoreTokens()) {
- try {
- samplesTemp[i] = StringTools.parseSBMLInt(test.nextToken());
- i++;
- } catch (Exception e) {
- MessageFormat.format(
- SpatialConstants.bundle.getString("COULD_NOT_READ"), value,
- SpatialConstants.pointIndex);
- }
- }
- if (samplesTemp.length > 0) {
- unsetSamples();
- setSamples(samplesTemp);
- }
- }
- else if (attributeName.equals(SpatialConstants.dataType)) {
- try {
- setDataType(value);
- } catch (Exception e) {
- MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
- }
- }
- else {
- isAttributeRead = false;
- }
- }
- return isAttributeRead;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- @Override
- public String toString() {
- StringBuilder builder = new StringBuilder();
- builder.append("ImageData [samplesLength=");
- builder.append(samplesLength);
- builder.append(", dataType=");
- builder.append(dataType);
- builder.append(", samples=");
- builder.append(Arrays.toString(samples)); // TODO - Should we really print the whole content of the array here?
- 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 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: <nik...@us...> - 2015-04-22 13:15:45
|
Revision: 2207
http://sourceforge.net/p/jsbml/code/2207
Author: niko-rodrigue
Date: 2015-04-22 11:35:00 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
corrected one error in FormulaParserLL3.jj that was not adding the first argument of a function in most cases, some problems remain there, I think.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java 2015-04-22 09:57:59 UTC (rev 2206)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java 2015-04-22 11:35:00 UTC (rev 2207)
@@ -548,67 +548,84 @@
}
final public Token string() throws ParseException {
+ trace_call("string");
+ try {
Token t;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LOG:
- t = jj_consume_token(LOG);
- break;
- case STRING:
- t = jj_consume_token(STRING);
- break;
- default:
- jj_la1[0] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LOG:
+ t = jj_consume_token(LOG);
+ break;
+ case STRING:
+ t = jj_consume_token(STRING);
+ break;
+ default:
+ jj_la1[0] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
{if (true) return t;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("string");
+ }
}
final public ASTNode parse() throws ParseException {
+ trace_call("parse");
+ try {
ASTNode node = null;
- node = expression();
+ node = expression();
{if (true) return node;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("parse");
+ }
}
final private ASTNode expression() throws ParseException {
+ trace_call("expression");
+ try {
ASTNode value = null;
- value = termLevel2();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case 0:
- jj_consume_token(0);
- break;
- case EOL:
- jj_consume_token(EOL);
- break;
- default:
- jj_la1[1] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ value = termLevel2();
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case 0:
+ jj_consume_token(0);
+ break;
+ case EOL:
+ jj_consume_token(EOL);
+ break;
+ default:
+ jj_la1[1] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
{if (true) return value;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("expression");
+ }
}
final private ASTNode termLevel2() throws ParseException {
+ trace_call("termLevel2");
+ try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
Token t;
- leftChild = termLevel3();
- label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = termLevel3();
+ leftChild = termLevel3();
+ label_1:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case BOOLEAN_LOGIC:
+ ;
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ break label_1;
+ }
+ t = jj_consume_token(BOOLEAN_LOGIC);
+ rightChild = termLevel3();
// TODO - do we want to ignore the case for those cases ?
String s = t.image;
Type type = null; // ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
@@ -630,29 +647,34 @@
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel2");
+ }
}
final private ASTNode termLevel3() throws ParseException {
+ trace_call("termLevel3");
+ try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
Token t;
- leftChild = termLevel4();
- label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[3] = jj_gen;
- break label_2;
- }
- t = jj_consume_token(COMPARISON);
- rightChild = termLevel4();
+ leftChild = termLevel4();
+ label_2:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case COMPARISON:
+ ;
+ break;
+ default:
+ jj_la1[3] = jj_gen;
+ break label_2;
+ }
+ t = jj_consume_token(COMPARISON);
+ rightChild = termLevel4();
String s = t.image;
Type type = null;
@@ -684,83 +706,93 @@
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel3");
+ }
}
final private ASTNode termLevel4() throws ParseException {
+ trace_call("termLevel4");
+ try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel5();
- label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_3;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = termLevel5();
+ leftChild = termLevel5();
+ label_3:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ case MINUS:
+ ;
+ break;
+ default:
+ jj_la1[4] = jj_gen;
+ break label_3;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ jj_consume_token(PLUS);
+ rightChild = termLevel5();
node = new ASTNode('+');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = termLevel5();
+ break;
+ case MINUS:
+ jj_consume_token(MINUS);
+ rightChild = termLevel5();
node = new ASTNode('-');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
+ break;
+ default:
+ jj_la1[5] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel4");
+ }
}
final private ASTNode termLevel5() throws ParseException {
+ trace_call("termLevel5");
+ try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel6();
- label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_4;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = termLevel6();
+ leftChild = termLevel6();
+ label_4:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ case DIVIDE:
+ case MODULO:
+ ;
+ break;
+ default:
+ jj_la1[6] = jj_gen;
+ break label_4;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ jj_consume_token(TIMES);
+ rightChild = termLevel6();
node = new ASTNode('*');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = termLevel6();
+ break;
+ case DIVIDE:
+ jj_consume_token(DIVIDE);
+ rightChild = termLevel6();
Integer left, right;
left = getInteger(leftChild);
right = getInteger(rightChild);
@@ -778,85 +810,100 @@
node.addChild(rightChild);
leftChild = node;
}
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = termLevel6();
+ break;
+ case MODULO:
+ jj_consume_token(MODULO);
+ rightChild = termLevel6();
node = createModulo(leftChild, rightChild);
leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
+ break;
+ default:
+ jj_la1[7] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel5");
+ }
}
final private ASTNode termLevel6() throws ParseException {
+ trace_call("termLevel6");
+ try {
ASTNode node = null;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case MINUS:
- jj_consume_token(MINUS);
- node = termLevel7();
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case MINUS:
+ jj_consume_token(MINUS);
+ node = termLevel7();
ASTNode uiMinus = new ASTNode('-');
uiMinus.addChild(node);
{if (true) return uiMinus;}
- break;
- case NOT:
- jj_consume_token(NOT);
- node = termLevel7();
+ break;
+ case NOT:
+ jj_consume_token(NOT);
+ node = termLevel7();
ASTNode not = new ASTNode(Type.LOGICAL_NOT);
not.addChild(node);
{if (true) return not;}
- break;
- case INTEGER:
- case NUMBER:
- case EXPNUMBER:
- case OPEN_PAR:
- case LEFT_BRACES:
- case LOG:
- case STRING:
- node = termLevel7();
+ break;
+ case INTEGER:
+ case NUMBER:
+ case EXPNUMBER:
+ case OPEN_PAR:
+ case LEFT_BRACES:
+ case LOG:
+ case STRING:
+ node = termLevel7();
{if (true) return node;}
- break;
- default:
- jj_la1[8] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
+ break;
+ default:
+ jj_la1[8] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
+ throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel6");
}
- throw new Error("Missing return statement in function");
}
final private ASTNode termLevel7() throws ParseException {
+ trace_call("termLevel7");
+ try {
ASTNode rightChild;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel8();
- label_5:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
- }
- jj_consume_token(POWER);
- rightChild = termLevel8();
+ leftChild = termLevel8();
+ label_5:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case POWER:
+ ;
+ break;
+ default:
+ jj_la1[9] = jj_gen;
+ break label_5;
+ }
+ jj_consume_token(POWER);
+ rightChild = termLevel8();
node = new ASTNode(Type.POWER);
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel7");
+ }
}
final private ASTNode termLevel8() throws ParseException, NumberFormatException {
+ trace_call("termLevel8");
+ try {
Token t;
double d;
int i;
@@ -866,21 +913,21 @@
String s;
String vals [ ];
ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case INTEGER:
- t = jj_consume_token(INTEGER);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case INTEGER:
+ t = jj_consume_token(INTEGER);
i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
node.setValue(i);
{if (true) return node;}
- break;
- case NUMBER:
- t = jj_consume_token(NUMBER);
+ break;
+ case NUMBER:
+ t = jj_consume_token(NUMBER);
d = Double.parseDouble(t.image);
node.setValue(d);
{if (true) return node;}
- break;
- case EXPNUMBER:
- t = jj_consume_token(EXPNUMBER);
+ break;
+ case EXPNUMBER:
+ t = jj_consume_token(EXPNUMBER);
s = t.image;
vals = s.toLowerCase().split("e");
if (vals [ 1 ].startsWith("+"))
@@ -893,28 +940,28 @@
}
node.setValue(Double.parseDouble(vals [ 0 ]), i);
{if (true) return node;}
- break;
- default:
- jj_la1[14] = jj_gen;
- if (jj_2_1(2)) {
- t = string();
- jj_consume_token(OPEN_PAR);
- child = termLevel2();
- label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
+ break;
+ default:
+ jj_la1[14] = jj_gen;
+ if (jj_2_1(2)) {
+ t = string();
+ jj_consume_token(OPEN_PAR);
+ child = termLevel2();
+ label_6:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[10] = jj_gen;
+ break label_6;
+ }
+ jj_consume_token(SPLITTER);
+ furtherChild = termLevel2();
+ arguments.add(furtherChild);
}
- jj_consume_token(SPLITTER);
- furtherChild = termLevel2();
- arguments.add(furtherChild);
- }
- jj_consume_token(CLOSE_PAR);
+ jj_consume_token(CLOSE_PAR);
s = t.image;
Type type = null;
if (ignoreCase)
@@ -925,10 +972,11 @@
{
type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
node.setType(type);
+ node.addChild(child);
}
else if (s.equals("ln"))
{
- checkSize(arguments, 0);
+ checkSize(arguments, 0); // TODO - we need to set the type for all those if-then-else cases
node.addChild(child);
}
else if (s.equals("lambda"))
@@ -983,95 +1031,96 @@
{
node.setName(s);
}
+
for (ASTNode argument : arguments)
{
node.addChild(argument);
}
{if (true) return node;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case OPEN_PAR:
- jj_consume_token(OPEN_PAR);
- node = termLevel2();
- jj_consume_token(CLOSE_PAR);
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case OPEN_PAR:
+ jj_consume_token(OPEN_PAR);
+ node = termLevel2();
+ jj_consume_token(CLOSE_PAR);
{if (true) return node;}
- break;
- default:
- jj_la1[15] = jj_gen;
- if (jj_2_2(4)) {
- t = jj_consume_token(STRING);
+ break;
+ default:
+ jj_la1[15] = jj_gen;
+ if (jj_2_2(4)) {
+ t = jj_consume_token(STRING);
ASTNode selector = new ASTNode();
selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
selector.addChild(new ASTNode(t.image));
- label_7:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
+ label_7:
+ while (true) {
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
+ jj_consume_token(RIGHT_BRACKET);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[11] = jj_gen;
+ break label_7;
+ }
}
- }
{if (true) return selector;}
- } else if (jj_2_3(2)) {
- jj_consume_token(LEFT_BRACES);
- node = termLevel2();
+ } else if (jj_2_3(2)) {
+ jj_consume_token(LEFT_BRACES);
+ node = termLevel2();
ASTNode selector = new ASTNode();
vector = new ASTNode();
boolean isSelector = false;
selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
vector.setType(ASTNode.Type.VECTOR);
vector.addChild(node);
- label_8:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[12] = jj_gen;
- break label_8;
+ label_8:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[12] = jj_gen;
+ break label_8;
+ }
+ jj_consume_token(SPLITTER);
+ node = termLevel2();
+ vector.addChild(node);
}
- jj_consume_token(SPLITTER);
- node = termLevel2();
- vector.addChild(node);
- }
- jj_consume_token(RIGHT_BRACES);
+ jj_consume_token(RIGHT_BRACES);
selector.addChild(vector);
- label_9:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[13] = jj_gen;
- break label_9;
- }
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
+ label_9:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[13] = jj_gen;
+ break label_9;
+ }
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
isSelector = true;
selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
+ jj_consume_token(RIGHT_BRACKET);
+ }
{if (true) return isSelector ? selector : vector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACES:
- jj_consume_token(LEFT_BRACES);
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACES:
+ jj_consume_token(LEFT_BRACES);
vector = new ASTNode();
vector.setType(ASTNode.Type.VECTOR);
- jj_consume_token(RIGHT_BRACES);
+ jj_consume_token(RIGHT_BRACES);
{if (true) return vector;}
- break;
- case STRING:
- t = jj_consume_token(STRING);
+ break;
+ case STRING:
+ t = jj_consume_token(STRING);
s = t.image;
if (ignoreCase)
{
@@ -1119,17 +1168,20 @@
node = new ASTNode(s);
}
{if (true) return node;}
- break;
- default:
- jj_la1[16] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
+ break;
+ default:
+ jj_la1[16] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
}
}
}
+ throw new Error("Missing return statement in function");
+ } finally {
+ trace_return("termLevel8");
}
- throw new Error("Missing return statement in function");
}
private boolean jj_2_1(int xla) {
@@ -1232,17 +1284,17 @@
return false;
}
- private boolean jj_3R_14() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
- return false;
- }
-
private boolean jj_3R_35() {
if (jj_scan_token(OPEN_PAR)) return true;
if (jj_3R_12()) return true;
return false;
}
+ private boolean jj_3R_14() {
+ if (jj_scan_token(BOOLEAN_LOGIC)) return true;
+ return false;
+ }
+
private boolean jj_3R_29() {
if (jj_3R_30()) return true;
Token xsp;
@@ -1369,6 +1421,12 @@
return false;
}
+ private boolean jj_3_3() {
+ if (jj_scan_token(LEFT_BRACES)) return true;
+ if (jj_3R_12()) return true;
+ return false;
+ }
+
private boolean jj_3R_26() {
if (jj_scan_token(TIMES)) return true;
return false;
@@ -1393,12 +1451,6 @@
return false;
}
- private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_12()) return true;
- return false;
- }
-
/** Generated Token Manager. */
public FormulaParserLL3TokenManager token_source;
SimpleCharStream jj_input_stream;
@@ -1511,6 +1563,7 @@
}
}
}
+ trace_token(token, "");
return token;
}
token = oldToken;
@@ -1548,6 +1601,7 @@
else token = token.next = token_source.getNextToken();
jj_ntk = -1;
jj_gen++;
+ trace_token(token, " (in getNextToken)");
return token;
}
@@ -1633,14 +1687,57 @@
return new ParseException(token, exptokseq, tokenImage);
}
- /** Enable tracing. */
+ private int trace_indent = 0;
+ private boolean trace_enabled = true;
+
+/** Enable tracing. */
final public void enable_tracing() {
+ trace_enabled = true;
}
- /** Disable tracing. */
+/** Disable tracing. */
final public void disable_tracing() {
+ trace_enabled = false;
}
+ private void trace_call(String s) {
+ if (trace_enabled) {
+ for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
+ System.out.println("Call: " + s);
+ }
+ trace_indent = trace_indent + 2;
+ }
+
+ private void trace_return(String s) {
+ trace_indent = trace_indent - 2;
+ if (trace_enabled) {
+ for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
+ System.out.println("Return: " + s);
+ }
+ }
+
+ private void trace_token(Token t, String where) {
+ if (trace_enabled) {
+ for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
+ System.out.print("Consumed token: <" + tokenImage[t.kind]);
+ if (t.kind != 0 && !tokenImage[t.kind].equals("\"" + t.image + "\"")) {
+ System.out.print(": \"" + t.image + "\"");
+ }
+ System.out.println(" at line " + t.beginLine + " column " + t.beginColumn + ">" + where);
+ }
+ }
+
+ private void trace_scan(Token t1, int t2) {
+ if (trace_enabled) {
+ for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
+ System.out.print("Visited token: <" + tokenImage[t1.kind]);
+ if (t1.kind != 0 && !tokenImage[t1.kind].equals("\"" + t1.image + "\"")) {
+ System.out.print(": \"" + t1.image + "\"");
+ }
+ System.out.println(" at line " + t1.beginLine + " column " + t1.beginColumn + ">; Expected token: <" + tokenImage[t2] + ">");
+ }
+ }
+
private void jj_rescan_token() {
jj_rescan = true;
for (int i = 0; i < 3; i++) {
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj 2015-04-22 09:57:59 UTC (rev 2206)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj 2015-04-22 11:35:00 UTC (rev 2207)
@@ -4,7 +4,7 @@
options
{
JDK_VERSION = "1.5";
-
+ DEBUG_PARSER = false;
static = false;
}
@@ -1078,10 +1078,11 @@
{
type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
node.setType(type);
+ node.addChild(child);
}
else if (s.equals("ln"))
{
- checkSize(arguments, 0);
+ checkSize(arguments, 0); // TODO - we need to set the type for all those if-then-else cases
node.addChild(child);
}
else if (s.equals("lambda"))
@@ -1136,6 +1137,7 @@
{
node.setName(s);
}
+
for (ASTNode argument : arguments)
{
node.addChild(argument);
Modified: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-04-22 09:57:59 UTC (rev 2206)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/ASTNodeInfixParsingTest.java 2015-04-22 11:35:00 UTC (rev 2207)
@@ -126,6 +126,7 @@
assertTrue(n.getType() == ASTNode.Type.FUNCTION_COS);
assertTrue(n.isFunction() == true);
assertTrue(n.isName() == false);
+ assertTrue(n.getChildCount() == 1);
assertTrue(n.getName() == null); // TODO - should the original String be conserved and accessible through getName()
assertTrue(n.toFormula().equals("cos(x)"));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-22 12:19:34
|
Revision: 2208
http://sourceforge.net/p/jsbml/code/2208
Author: niko-rodrigue
Date: 2015-04-22 11:47:04 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
recompiled FormulaParserLL3.jj whithout debugging information + corrected the last failing test for core.
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/TestInfixOperatorPrecedence.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java 2015-04-22 11:35:00 UTC (rev 2207)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java 2015-04-22 11:47:04 UTC (rev 2208)
@@ -548,84 +548,67 @@
}
final public Token string() throws ParseException {
- trace_call("string");
- try {
Token t;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LOG:
- t = jj_consume_token(LOG);
- break;
- case STRING:
- t = jj_consume_token(STRING);
- break;
- default:
- jj_la1[0] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LOG:
+ t = jj_consume_token(LOG);
+ break;
+ case STRING:
+ t = jj_consume_token(STRING);
+ break;
+ default:
+ jj_la1[0] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
{if (true) return t;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("string");
- }
}
final public ASTNode parse() throws ParseException {
- trace_call("parse");
- try {
ASTNode node = null;
- node = expression();
+ node = expression();
{if (true) return node;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("parse");
- }
}
final private ASTNode expression() throws ParseException {
- trace_call("expression");
- try {
ASTNode value = null;
- value = termLevel2();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case 0:
- jj_consume_token(0);
- break;
- case EOL:
- jj_consume_token(EOL);
- break;
- default:
- jj_la1[1] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ value = termLevel2();
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case 0:
+ jj_consume_token(0);
+ break;
+ case EOL:
+ jj_consume_token(EOL);
+ break;
+ default:
+ jj_la1[1] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
{if (true) return value;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("expression");
- }
}
final private ASTNode termLevel2() throws ParseException {
- trace_call("termLevel2");
- try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
Token t;
- leftChild = termLevel3();
- label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = termLevel3();
+ leftChild = termLevel3();
+ label_1:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case BOOLEAN_LOGIC:
+ ;
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ break label_1;
+ }
+ t = jj_consume_token(BOOLEAN_LOGIC);
+ rightChild = termLevel3();
// TODO - do we want to ignore the case for those cases ?
String s = t.image;
Type type = null; // ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
@@ -647,34 +630,29 @@
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel2");
- }
}
final private ASTNode termLevel3() throws ParseException {
- trace_call("termLevel3");
- try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
Token t;
- leftChild = termLevel4();
- label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[3] = jj_gen;
- break label_2;
- }
- t = jj_consume_token(COMPARISON);
- rightChild = termLevel4();
+ leftChild = termLevel4();
+ label_2:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case COMPARISON:
+ ;
+ break;
+ default:
+ jj_la1[3] = jj_gen;
+ break label_2;
+ }
+ t = jj_consume_token(COMPARISON);
+ rightChild = termLevel4();
String s = t.image;
Type type = null;
@@ -706,93 +684,83 @@
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel3");
- }
}
final private ASTNode termLevel4() throws ParseException {
- trace_call("termLevel4");
- try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel5();
- label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_3;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = termLevel5();
+ leftChild = termLevel5();
+ label_3:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ case MINUS:
+ ;
+ break;
+ default:
+ jj_la1[4] = jj_gen;
+ break label_3;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ jj_consume_token(PLUS);
+ rightChild = termLevel5();
node = new ASTNode('+');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = termLevel5();
+ break;
+ case MINUS:
+ jj_consume_token(MINUS);
+ rightChild = termLevel5();
node = new ASTNode('-');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ break;
+ default:
+ jj_la1[5] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
}
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel4");
- }
}
final private ASTNode termLevel5() throws ParseException {
- trace_call("termLevel5");
- try {
ASTNode rightChild = null;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel6();
- label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_4;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = termLevel6();
+ leftChild = termLevel6();
+ label_4:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ case DIVIDE:
+ case MODULO:
+ ;
+ break;
+ default:
+ jj_la1[6] = jj_gen;
+ break label_4;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ jj_consume_token(TIMES);
+ rightChild = termLevel6();
node = new ASTNode('*');
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = termLevel6();
+ break;
+ case DIVIDE:
+ jj_consume_token(DIVIDE);
+ rightChild = termLevel6();
Integer left, right;
left = getInteger(leftChild);
right = getInteger(rightChild);
@@ -810,100 +778,85 @@
node.addChild(rightChild);
leftChild = node;
}
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = termLevel6();
+ break;
+ case MODULO:
+ jj_consume_token(MODULO);
+ rightChild = termLevel6();
node = createModulo(leftChild, rightChild);
leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ break;
+ default:
+ jj_la1[7] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
}
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel5");
- }
}
final private ASTNode termLevel6() throws ParseException {
- trace_call("termLevel6");
- try {
ASTNode node = null;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case MINUS:
- jj_consume_token(MINUS);
- node = termLevel7();
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case MINUS:
+ jj_consume_token(MINUS);
+ node = termLevel7();
ASTNode uiMinus = new ASTNode('-');
uiMinus.addChild(node);
{if (true) return uiMinus;}
- break;
- case NOT:
- jj_consume_token(NOT);
- node = termLevel7();
+ break;
+ case NOT:
+ jj_consume_token(NOT);
+ node = termLevel7();
ASTNode not = new ASTNode(Type.LOGICAL_NOT);
not.addChild(node);
{if (true) return not;}
- break;
- case INTEGER:
- case NUMBER:
- case EXPNUMBER:
- case OPEN_PAR:
- case LEFT_BRACES:
- case LOG:
- case STRING:
- node = termLevel7();
+ break;
+ case INTEGER:
+ case NUMBER:
+ case EXPNUMBER:
+ case OPEN_PAR:
+ case LEFT_BRACES:
+ case LOG:
+ case STRING:
+ node = termLevel7();
{if (true) return node;}
- break;
- default:
- jj_la1[8] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ break;
+ default:
+ jj_la1[8] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel6");
- }
}
final private ASTNode termLevel7() throws ParseException {
- trace_call("termLevel7");
- try {
ASTNode rightChild;
ASTNode leftChild;
ASTNode node = null;
- leftChild = termLevel8();
- label_5:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
- }
- jj_consume_token(POWER);
- rightChild = termLevel8();
+ leftChild = termLevel8();
+ label_5:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case POWER:
+ ;
+ break;
+ default:
+ jj_la1[9] = jj_gen;
+ break label_5;
+ }
+ jj_consume_token(POWER);
+ rightChild = termLevel8();
node = new ASTNode(Type.POWER);
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
- }
+ }
{if (true) return leftChild;}
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel7");
- }
}
final private ASTNode termLevel8() throws ParseException, NumberFormatException {
- trace_call("termLevel8");
- try {
Token t;
double d;
int i;
@@ -913,21 +866,21 @@
String s;
String vals [ ];
ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case INTEGER:
- t = jj_consume_token(INTEGER);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case INTEGER:
+ t = jj_consume_token(INTEGER);
i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
node.setValue(i);
{if (true) return node;}
- break;
- case NUMBER:
- t = jj_consume_token(NUMBER);
+ break;
+ case NUMBER:
+ t = jj_consume_token(NUMBER);
d = Double.parseDouble(t.image);
node.setValue(d);
{if (true) return node;}
- break;
- case EXPNUMBER:
- t = jj_consume_token(EXPNUMBER);
+ break;
+ case EXPNUMBER:
+ t = jj_consume_token(EXPNUMBER);
s = t.image;
vals = s.toLowerCase().split("e");
if (vals [ 1 ].startsWith("+"))
@@ -940,28 +893,28 @@
}
node.setValue(Double.parseDouble(vals [ 0 ]), i);
{if (true) return node;}
- break;
- default:
- jj_la1[14] = jj_gen;
- if (jj_2_1(2)) {
- t = string();
- jj_consume_token(OPEN_PAR);
- child = termLevel2();
- label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
- }
- jj_consume_token(SPLITTER);
- furtherChild = termLevel2();
+ break;
+ default:
+ jj_la1[14] = jj_gen;
+ if (jj_2_1(2)) {
+ t = string();
+ jj_consume_token(OPEN_PAR);
+ child = termLevel2();
+ label_6:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[10] = jj_gen;
+ break label_6;
+ }
+ jj_consume_token(SPLITTER);
+ furtherChild = termLevel2();
arguments.add(furtherChild);
- }
- jj_consume_token(CLOSE_PAR);
+ }
+ jj_consume_token(CLOSE_PAR);
s = t.image;
Type type = null;
if (ignoreCase)
@@ -1037,90 +990,90 @@
node.addChild(argument);
}
{if (true) return node;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case OPEN_PAR:
- jj_consume_token(OPEN_PAR);
- node = termLevel2();
- jj_consume_token(CLOSE_PAR);
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case OPEN_PAR:
+ jj_consume_token(OPEN_PAR);
+ node = termLevel2();
+ jj_consume_token(CLOSE_PAR);
{if (true) return node;}
- break;
- default:
- jj_la1[15] = jj_gen;
- if (jj_2_2(4)) {
- t = jj_consume_token(STRING);
+ break;
+ default:
+ jj_la1[15] = jj_gen;
+ if (jj_2_2(4)) {
+ t = jj_consume_token(STRING);
ASTNode selector = new ASTNode();
selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
selector.addChild(new ASTNode(t.image));
- label_7:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
+ label_7:
+ while (true) {
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
- }
+ jj_consume_token(RIGHT_BRACKET);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[11] = jj_gen;
+ break label_7;
}
+ }
{if (true) return selector;}
- } else if (jj_2_3(2)) {
- jj_consume_token(LEFT_BRACES);
- node = termLevel2();
+ } else if (jj_2_3(2)) {
+ jj_consume_token(LEFT_BRACES);
+ node = termLevel2();
ASTNode selector = new ASTNode();
vector = new ASTNode();
boolean isSelector = false;
selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
vector.setType(ASTNode.Type.VECTOR);
vector.addChild(node);
- label_8:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[12] = jj_gen;
- break label_8;
- }
- jj_consume_token(SPLITTER);
- node = termLevel2();
+ label_8:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[12] = jj_gen;
+ break label_8;
+ }
+ jj_consume_token(SPLITTER);
+ node = termLevel2();
vector.addChild(node);
+ }
+ jj_consume_token(RIGHT_BRACES);
+ selector.addChild(vector);
+ label_9:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[13] = jj_gen;
+ break label_9;
}
- jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
- label_9:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[13] = jj_gen;
- break label_9;
- }
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
isSelector = true;
selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
+ jj_consume_token(RIGHT_BRACKET);
+ }
{if (true) return isSelector ? selector : vector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACES:
- jj_consume_token(LEFT_BRACES);
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACES:
+ jj_consume_token(LEFT_BRACES);
vector = new ASTNode();
vector.setType(ASTNode.Type.VECTOR);
- jj_consume_token(RIGHT_BRACES);
+ jj_consume_token(RIGHT_BRACES);
{if (true) return vector;}
- break;
- case STRING:
- t = jj_consume_token(STRING);
+ break;
+ case STRING:
+ t = jj_consume_token(STRING);
s = t.image;
if (ignoreCase)
{
@@ -1168,20 +1121,17 @@
node = new ASTNode(s);
}
{if (true) return node;}
- break;
- default:
- jj_la1[16] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ break;
+ default:
+ jj_la1[16] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
}
}
}
}
+ }
throw new Error("Missing return statement in function");
- } finally {
- trace_return("termLevel8");
- }
}
private boolean jj_2_1(int xla) {
@@ -1563,7 +1513,6 @@
}
}
}
- trace_token(token, "");
return token;
}
token = oldToken;
@@ -1601,7 +1550,6 @@
else token = token.next = token_source.getNextToken();
jj_ntk = -1;
jj_gen++;
- trace_token(token, " (in getNextToken)");
return token;
}
@@ -1687,57 +1635,14 @@
return new ParseException(token, exptokseq, tokenImage);
}
- private int trace_indent = 0;
- private boolean trace_enabled = true;
-
-/** Enable tracing. */
+ /** Enable tracing. */
final public void enable_tracing() {
- trace_enabled = true;
}
-/** Disable tracing. */
+ /** Disable tracing. */
final public void disable_tracing() {
- trace_enabled = false;
}
- private void trace_call(String s) {
- if (trace_enabled) {
- for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
- System.out.println("Call: " + s);
- }
- trace_indent = trace_indent + 2;
- }
-
- private void trace_return(String s) {
- trace_indent = trace_indent - 2;
- if (trace_enabled) {
- for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
- System.out.println("Return: " + s);
- }
- }
-
- private void trace_token(Token t, String where) {
- if (trace_enabled) {
- for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
- System.out.print("Consumed token: <" + tokenImage[t.kind]);
- if (t.kind != 0 && !tokenImage[t.kind].equals("\"" + t.image + "\"")) {
- System.out.print(": \"" + t.image + "\"");
- }
- System.out.println(" at line " + t.beginLine + " column " + t.beginColumn + ">" + where);
- }
- }
-
- private void trace_scan(Token t1, int t2) {
- if (trace_enabled) {
- for (int i = 0; i < trace_indent; i++) { System.out.print(" "); }
- System.out.print("Visited token: <" + tokenImage[t1.kind]);
- if (t1.kind != 0 && !tokenImage[t1.kind].equals("\"" + t1.image + "\"")) {
- System.out.print(": \"" + t1.image + "\"");
- }
- System.out.println(" at line " + t1.beginLine + " column " + t1.beginColumn + ">; Expected token: <" + tokenImage[t2] + ">");
- }
- }
-
private void jj_rescan_token() {
jj_rescan = true;
for (int i = 0; i < 3; i++) {
Modified: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/TestInfixOperatorPrecedence.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/TestInfixOperatorPrecedence.java 2015-04-22 11:35:00 UTC (rev 2207)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/TestInfixOperatorPrecedence.java 2015-04-22 11:47:04 UTC (rev 2208)
@@ -107,7 +107,7 @@
// TODO: Test by comparing nodes in the tree
System.out.println(n.toMathML());
System.out.println(n.toFormula());
- assertTrue(n.toFormula().equals("5+2*4+4*8"));
+ assertTrue(n.toFormula().equals("5+(2*4)+(4*8)"));
}
/**
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()));
}
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|
|
From: <nik...@us...> - 2015-04-22 08:36:29
|
Revision: 2205
http://sourceforge.net/p/jsbml/code/2205
Author: niko-rodrigue
Date: 2015-04-22 08:36:22 +0000 (Wed, 22 Apr 2015)
Log Message:
-----------
Corrected SBMLError so that the message from Exceptions extending it is displayed + fixed AnalyticVolume to prevent NullPointerException when the ordinal is not defined
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/src/org/sbml/jsbml/SBMLError.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-22 08:09:38 UTC (rev 2204)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-04-22 08:36:22 UTC (rev 2205)
@@ -1743,6 +1743,8 @@
"Cannot register {0}.", sbase.getElementName()));
}
+ // TODO - set package version and namespace if needed
+
/*
* Now, we can add all previous listeners. The next change will
* be fired after registering all ids.
@@ -1772,6 +1774,8 @@
private void registerChild(SBasePlugin sbasePlugin) {
// Could/Should be used by the method #firePropertyChange
+ // TODO - set package version and namespace if needed
+
int childCount = sbasePlugin.getChildCount();
if (childCount > 0) {
Modified: trunk/core/src/org/sbml/jsbml/SBMLError.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLError.java 2015-04-22 08:09:38 UTC (rev 2204)
+++ trunk/core/src/org/sbml/jsbml/SBMLError.java 2015-04-22 08:36:22 UTC (rev 2205)
@@ -131,6 +131,8 @@
*/
public SBMLError(String message) {
super(message);
+ this.message = new Message();
+ this.message.setMessage(message);
}
/**
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-22 08:09:38 UTC (rev 2204)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-22 08:36:22 UTC (rev 2205)
@@ -306,7 +306,7 @@
* @param ordinal
*/
public void setOrdinal(int ordinal) {
- int oldOrdinal = this.ordinal;
+ Integer oldOrdinal = this.ordinal;
this.ordinal = ordinal;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, this.ordinal);
}
@@ -319,7 +319,7 @@
*/
public boolean unsetOrdinal() {
if (isSetOrdinal()) {
- int oldOrdinal = ordinal;
+ Integer oldOrdinal = ordinal;
ordinal = null;
firePropertyChange(SpatialConstants.ordinal, oldOrdinal, ordinal);
return true;
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: <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: <and...@us...> - 2015-04-21 15:04:28
|
Revision: 2202
http://sourceforge.net/p/jsbml/code/2202
Author: andreas-draeger
Date: 2015-04-21 15:04:20 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Added a createTrigger method that can be used for SBML with Level < 3.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/Event.java
Modified: trunk/core/src/org/sbml/jsbml/Event.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/Event.java 2015-04-21 14:49:22 UTC (rev 2201)
+++ trunk/core/src/org/sbml/jsbml/Event.java 2015-04-21 15:04:20 UTC (rev 2202)
@@ -332,6 +332,18 @@
return t;
}
+ /**
+ * Creates a new {@link Trigger} instance and sets it to this {@link Event}.
+ *
+ * @param math math the math expression for the new {@link Trigger}
+ * @return the new {@link Trigger} instance.
+ */
+ public Trigger createTrigger(ASTNode math) {
+ Trigger t = createTrigger();
+ t.setMath(math);
+ return t;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBaseWithUnit#equals(java.lang.Object)
*/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-21 14:49:24
|
Revision: 2201
http://sourceforge.net/p/jsbml/code/2201
Author: niko-rodrigue
Date: 2015-04-21 14:49:22 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected compilation error on FormulaParser.jj
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj
Removed Paths:
-------------
branches/astnode2-merging-alternate/jsbml.log
Property Changed:
----------------
branches/astnode2-merging-alternate/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-04-21 14:25:17 UTC (rev 2200)
+++ branches/astnode2-merging-alternate 2015-04-21 14:49:22 UTC (rev 2201)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:ignore
## -3,3 +3,4 ##
dist
build
bin
+jsbml.log
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java 2015-04-21 14:25:17 UTC (rev 2200)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java 2015-04-21 14:49:22 UTC (rev 2201)
@@ -286,6 +286,7 @@
ASTNode node = null;
Token t;
Type type = null;
+ String s;
leftChild = TermLvl2();
label_3:
while (true) {
@@ -320,7 +321,7 @@
case BOOLEAN_LOGIC:
t = jj_consume_token(BOOLEAN_LOGIC);
rightChild = TermLvl2();
- type = Type.getTypeFor(t.image);
+ s = t.image;
if (s.equalsIgnoreCase("or") || s.equals("||"))
{
@@ -724,11 +725,6 @@
finally { jj_save(2, xla); }
}
- private boolean jj_3R_26() {
- if (jj_scan_token(EXPNUMBER)) return true;
- return false;
- }
-
private boolean jj_3R_12() {
Token xsp;
xsp = jj_scanpos;
@@ -872,13 +868,13 @@
return false;
}
- private boolean jj_3R_34() {
- if (jj_scan_token(FACTORIAL)) return true;
+ private boolean jj_3R_32() {
+ if (jj_scan_token(STRING)) return true;
return false;
}
- private boolean jj_3R_32() {
- if (jj_scan_token(STRING)) return true;
+ private boolean jj_3R_34() {
+ if (jj_scan_token(FACTORIAL)) return true;
return false;
}
@@ -894,17 +890,17 @@
return false;
}
- private boolean jj_3R_33() {
- if (jj_scan_token(POWER)) return true;
- return false;
- }
-
private boolean jj_3_3() {
if (jj_scan_token(LEFT_BRACES)) return true;
if (jj_3R_10()) return true;
return false;
}
+ private boolean jj_3R_33() {
+ if (jj_scan_token(POWER)) return true;
+ return false;
+ }
+
private boolean jj_3R_20() {
Token xsp;
xsp = jj_scanpos;
@@ -920,6 +916,12 @@
return false;
}
+ private boolean jj_3R_30() {
+ if (jj_scan_token(NOT)) return true;
+ if (jj_3R_10()) return true;
+ return false;
+ }
+
private boolean jj_3R_13() {
if (jj_3R_19()) return true;
Token xsp;
@@ -930,12 +932,6 @@
return false;
}
- private boolean jj_3R_30() {
- if (jj_scan_token(NOT)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
private boolean jj_3R_27() {
if (jj_scan_token(OPEN_PAR)) return true;
if (jj_3R_10()) return true;
@@ -957,14 +953,19 @@
return false;
}
+ private boolean jj_3R_29() {
+ if (jj_scan_token(MINUS)) return true;
+ if (jj_3R_19()) return true;
+ return false;
+ }
+
private boolean jj_3R_22() {
if (jj_scan_token(DIVIDE)) return true;
return false;
}
- private boolean jj_3R_29() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_19()) return true;
+ private boolean jj_3R_26() {
+ if (jj_scan_token(EXPNUMBER)) return true;
return false;
}
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj 2015-04-21 14:25:17 UTC (rev 2200)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj 2015-04-21 14:49:22 UTC (rev 2201)
@@ -453,6 +453,7 @@
ASTNode node = null;
Token t;
Type type = null;
+ String s;
}
{
leftChild = TermLvl2()
@@ -473,7 +474,7 @@
}
| t = < BOOLEAN_LOGIC > rightChild = TermLvl2()
{
- type = Type.getTypeFor(t.image);
+ s = t.image;
if (s.equalsIgnoreCase("or") || s.equals("||"))
{
Deleted: branches/astnode2-merging-alternate/jsbml.log
===================================================================
--- branches/astnode2-merging-alternate/jsbml.log 2015-04-21 14:25:17 UTC (rev 2200)
+++ branches/astnode2-merging-alternate/jsbml.log 2015-04-21 14:49:22 UTC (rev 2201)
@@ -1,6337 +0,0 @@
-[19:13:05,391 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:13:05,399 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:13:05,400 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:13:05,400 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:13:05,400 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:13:05,401 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:13:05,401 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:13:05,411 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:13:05,416 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:13:05,426 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:13:05,431 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:13:05,437 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:13:05,437 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:13:05,473 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:13:05,484 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:13:05,484 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:13:05,490 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:13:05,495 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:13:05,688 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:13:05,689 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:13:05,689 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:13:05,690 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:13:05,800 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:13:06,027 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:13:06,100 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:13:06,106 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:13:06,123 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:13:06,130 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:13:06,270 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:13:06,984 ERROR Model:3950] - An element of type objective with the id "O1" is already present in this model "model". The new element will not be added to the model.
-[19:13:06,984 ERROR SBMLDocument:444] - An element with the metaid "FB1" is already present in the SBML document. The new element will not get added to it.
-[19:13:06,984 ERROR SBMLDocument:444] - An element with the metaid "S2" is already present in the SBML document. The new element will not get added to it.
-[19:13:07,016 ERROR Model:648] - A Port with the id "S3" is already present in this model model. The new element will not be added to the model.
-[19:13:07,020 ERROR Model:648] - A Port with the id "S3" is already present in this model modelDef2. The new element will not be added to the model.
-[19:13:07,021 ERROR Model:3950] - An element of type species with the id "S3" is already present in this model "modelDef2". The new element will not be added to the model.
-[19:13:07,032 ERROR IdentifierException:75] - An element with the metaid "S1" is already present in the SBML document. The element replacedBy will not be annotated with it.
-[19:13:07,052 WARN AbstractSBase:1639] - SBaseRef 'SBaseRef [portRef=S1, idRef=null, unitRef=null, metaIdRef=null]' is associated to the different parent 'c'. Please remove it there before adding it to this 'port' or add a clone of it to this element.
-[19:13:07,058 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD1" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:13:07,058 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD2" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:13:07,058 ERROR IdentifierException:62] - An element with the id "AD2" is already present in the SBML model. The identifier of dimension will not be set to this value.
-[19:13:07,058 WARN ArraysSBasePlugin:769] - A Dimension with the id "AD1" is not present in this model identified by id[model]. Nothing to be done.
-[19:13:07,069 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:13:07,070 ERROR IdentifierException:62] - An element with the id "G1" is already present in the SBML model. The identifier of group will not be set to this value.
-[19:13:07,070 ERROR Model:3950] - An element of type member with the id "GM1" is already present in this model "model". The new element will not be added to the model.
-[19:13:07,070 ERROR Model:3950] - An element of type memberConstraint with the id "GMC1" is already present in this model "model". The new element will not be added to the model.
-[19:13:07,071 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:13:07,071 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:13:07,177 ERROR ArraysSBasePlugin:702] - A Dimension with the id "dim" is already present in this species identified by id[]. The new element will not be added to the model.
-[19:27:18,304 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:27:18,334 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:27:18,334 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:27:18,348 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:27:18,348 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:27:18,348 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:27:18,348 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:27:18,358 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:27:18,364 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:27:18,375 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:27:18,380 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:27:18,393 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:27:18,394 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:27:18,420 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:27:18,430 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:27:18,430 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:27:18,436 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:27:18,441 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:27:18,680 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:27:18,681 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:27:18,681 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:27:18,682 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:27:18,794 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:27:19,041 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:27:19,109 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:27:19,115 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:27:19,126 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:27:19,132 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:27:19,528 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:27:24,129 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:27:24,131 WARN XMLNodeReader:262] - The type of String '' on the element model (Model) is unknown! Some data might be lost.
-[19:27:24,131 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:27:24,156 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:27:24,156 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:27:24,157 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:27:24,157 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:27:24,180 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:27:24,181 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:27:24,181 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:27:24,182 WARN XMLNodeReader:262] - The type of String 'annotation' on the element reaction (Reaction) is unknown! Some data might be lost.
-[19:27:24,182 WARN XMLNodeReader:262] - The type of String 'annotation' on the element speciesReference (SpeciesReference) is unknown! Some data might be lost.
-[19:27:24,182 WARN SBMLCoreParser:650] - The element listOfProducts is not recognized
-[19:27:24,183 WARN SBMLCoreParser:653] - The element speciesReference is not recognized
-[19:27:24,183 WARN SBMLCoreParser:209] - Could not recognize the attribute "constant" on the element speciesReference. Please check the specification for SBML.
-[19:27:24,242 WARN SBMLCoreParser:209] - Could not recognize the attribute "species" on the element speciesReference. Please check the specification for SBML.
-[19:27:24,242 WARN SBMLCoreParser:209] - Could not recognize the attribute "stoichiometry" on the element speciesReference. Please check the specification for SBML.
-[19:27:24,243 WARN XMLNodeReader:262] - The type of String 'annotation' on the element model (Model) is unknown! Some data might be lost.
-[19:27:24,318 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:27:24,318 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:27:24,319 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:27:24,319 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:27:24,475 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:27:24,478 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:27:24,504 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:27:24,506 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:29:53,772 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:29:53,810 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:29:53,811 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:29:53,811 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:29:53,811 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:29:53,811 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:29:53,812 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:29:53,821 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:29:53,826 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:29:53,836 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:29:53,841 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:29:53,846 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:29:53,846 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:29:53,883 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:29:53,893 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:29:53,893 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:29:53,899 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:29:53,906 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:29:54,376 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:29:54,376 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:29:54,377 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:29:54,377 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:29:54,511 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:29:54,763 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:29:54,834 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:29:54,840 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:29:54,851 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:29:54,856 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:29:55,516 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:29:58,428 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:29:58,430 WARN XMLNodeReader:262] - The type of String '' on the element model (Model) is unknown! Some data might be lost.
-[19:29:58,431 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:29:58,462 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:29:58,463 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:29:58,463 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:29:58,464 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:29:58,488 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:29:58,488 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:29:58,488 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:29:58,489 WARN XMLNodeReader:262] - The type of String 'annotation' on the element reaction (Reaction) is unknown! Some data might be lost.
-[19:29:58,489 WARN XMLNodeReader:262] - The type of String 'annotation' on the element speciesReference (SpeciesReference) is unknown! Some data might be lost.
-[19:29:58,490 WARN SBMLCoreParser:650] - The element listOfProducts is not recognized
-[19:29:58,490 WARN SBMLCoreParser:653] - The element speciesReference is not recognized
-[19:29:58,490 WARN SBMLCoreParser:209] - Could not recognize the attribute "constant" on the element speciesReference. Please check the specification for SBML.
-[19:29:58,530 WARN SBMLCoreParser:209] - Could not recognize the attribute "species" on the element speciesReference. Please check the specification for SBML.
-[19:29:58,531 WARN SBMLCoreParser:209] - Could not recognize the attribute "stoichiometry" on the element speciesReference. Please check the specification for SBML.
-[19:29:58,531 WARN XMLNodeReader:262] - The type of String 'annotation' on the element model (Model) is unknown! Some data might be lost.
-[19:29:58,630 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:29:58,630 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:29:58,630 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:29:58,631 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:29:58,831 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:29:58,833 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:29:58,854 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:29:58,856 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:32:25,321 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:32:25,354 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:32:25,354 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:32:25,355 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:32:25,355 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:32:25,355 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:32:25,355 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:32:25,365 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:32:25,371 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:32:25,382 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:32:25,387 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:32:25,400 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:32:25,400 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:32:25,432 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:32:25,443 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:32:25,443 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:32:25,449 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:32:25,455 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:32:25,708 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:32:25,709 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:32:25,709 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:32:25,709 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:32:25,821 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:32:26,061 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:32:26,129 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:32:26,134 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:32:26,145 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:32:26,151 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:32:26,985 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:32:29,887 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:32:29,888 WARN XMLNodeReader:262] - The type of String '' on the element model (Model) is unknown! Some data might be lost.
-[19:32:29,889 WARN XMLNodeReader:262] - The type of String '' on the element sbml (SBMLDocument) is unknown! Some data might be lost.
-[19:32:29,912 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:32:29,913 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:32:29,914 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:32:29,914 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:32:29,937 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:32:29,938 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:32:29,938 WARN XMLNodeReader:262] - The type of String 'annotation' on the element species (Species) is unknown! Some data might be lost.
-[19:32:29,939 WARN XMLNodeReader:262] - The type of String 'annotation' on the element reaction (Reaction) is unknown! Some data might be lost.
-[19:32:29,939 WARN XMLNodeReader:262] - The type of String 'annotation' on the element speciesReference (SpeciesReference) is unknown! Some data might be lost.
-[19:32:29,940 WARN SBMLCoreParser:650] - The element listOfProducts is not recognized
-[19:32:29,940 WARN SBMLCoreParser:653] - The element speciesReference is not recognized
-[19:32:29,940 WARN SBMLCoreParser:209] - Could not recognize the attribute "constant" on the element speciesReference. Please check the specification for SBML.
-[19:32:29,988 WARN SBMLCoreParser:209] - Could not recognize the attribute "species" on the element speciesReference. Please check the specification for SBML.
-[19:32:29,988 WARN SBMLCoreParser:209] - Could not recognize the attribute "stoichiometry" on the element speciesReference. Please check the specification for SBML.
-[19:32:29,988 WARN XMLNodeReader:262] - The type of String 'annotation' on the element model (Model) is unknown! Some data might be lost.
-[19:32:30,106 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:32:30,107 WARN XMLNodeReader:262] - The type of String '' on the element parameter (Parameter) is unknown! Some data might be lost.
-[19:32:30,107 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:32:30,108 WARN XMLNodeReader:262] - The type of String '' on the element assignmentRule (AssignmentRule) is unknown! Some data might be lost.
-[19:32:30,365 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:32:30,369 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:32:30,390 WARN XMLNodeReader:262] - The type of String '' on the element compartment (Compartment) is unknown! Some data might be lost.
-[19:32:30,392 WARN XMLNodeReader:262] - The type of String '' on the element event (Event) is unknown! Some data might be lost.
-[19:34:39,977 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:34:40,050 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:34:40,050 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:34:40,050 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:34:40,051 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:34:40,082 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:34:40,082 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:34:40,093 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:34:40,098 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:34:40,110 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:34:40,116 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:34:40,122 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:34:40,122 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:34:40,243 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:34:40,253 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:34:40,253 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:34:40,259 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:34:40,264 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:34:40,760 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:34:40,761 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:34:40,761 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:34:40,761 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:34:40,863 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:34:41,114 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:34:41,182 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:34:41,188 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:34:41,213 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:34:41,218 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:34:41,576 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:34:47,963 ERROR Model:3950] - An element of type objective with the id "O1" is already present in this model "model". The new element will not be added to the model.
-[19:34:47,963 ERROR SBMLDocument:444] - An element with the metaid "FB1" is already present in the SBML document. The new element will not get added to it.
-[19:34:47,964 ERROR SBMLDocument:444] - An element with the metaid "S2" is already present in the SBML document. The new element will not get added to it.
-[19:34:48,395 ERROR Model:648] - A Port with the id "S3" is already present in this model model. The new element will not be added to the model.
-[19:34:48,483 ERROR Model:648] - A Port with the id "S3" is already present in this model modelDef2. The new element will not be added to the model.
-[19:34:48,483 ERROR Model:3950] - An element of type species with the id "S3" is already present in this model "modelDef2". The new element will not be added to the model.
-[19:34:48,541 ERROR IdentifierException:75] - An element with the metaid "S1" is already present in the SBML document. The element replacedBy will not be annotated with it.
-[19:34:48,661 WARN AbstractSBase:1639] - SBaseRef 'SBaseRef [portRef=S1, idRef=null, unitRef=null, metaIdRef=null]' is associated to the different parent 'c'. Please remove it there before adding it to this 'port' or add a clone of it to this element.
-[19:34:48,666 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD1" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:34:48,666 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD2" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:34:48,666 ERROR IdentifierException:62] - An element with the id "AD2" is already present in the SBML model. The identifier of dimension will not be set to this value.
-[19:34:48,667 WARN ArraysSBasePlugin:769] - A Dimension with the id "AD1" is not present in this model identified by id[model]. Nothing to be done.
-[19:34:48,962 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:34:48,962 ERROR IdentifierException:62] - An element with the id "G1" is already present in the SBML model. The identifier of group will not be set to this value.
-[19:34:48,962 ERROR Model:3950] - An element of type member with the id "GM1" is already present in this model "model". The new element will not be added to the model.
-[19:34:48,962 ERROR Model:3950] - An element of type memberConstraint with the id "GMC1" is already present in this model "model". The new element will not be added to the model.
-[19:34:48,963 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:34:48,963 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:34:49,732 ERROR ArraysSBasePlugin:702] - A Dimension with the id "dim" is already present in this species identified by id[]. The new element will not be added to the model.
-[19:37:45,822 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[19:37:45,840 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[19:37:45,840 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[19:37:45,841 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[19:37:45,841 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:37:45,841 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[19:37:45,841 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:37:45,851 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[19:37:45,856 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:37:45,867 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[19:37:45,873 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:37:45,878 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:37:45,878 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[19:37:45,913 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:37:45,922 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[19:37:45,923 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[19:37:45,929 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:37:45,934 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:37:46,117 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[19:37:46,118 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[19:37:46,119 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[19:37:46,119 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[19:37:46,235 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[19:37:46,468 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:37:46,543 WARN Model:1120] - Could not create Product because no reactions have been defined yet.
-[19:37:46,549 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[19:37:46,568 WARN Model:1012] - Could not create LocalParameter for KineticLaw because no reactions have been defined yet.
-[19:37:46,574 WARN Model:1176] - Could not create Reactant because no reactions have been defined yet.
-[19:37:46,775 WARN AbstractSBase:1635] - Trying to register curve 'curve', which is already registered under speciesReferenceGlyph 'speciesReferenceGlyph [id=glyph, reference=null]'.
-[19:37:49,031 ERROR Model:3950] - An element of type objective with the id "O1" is already present in this model "model". The new element will not be added to the model.
-[19:37:49,032 ERROR SBMLDocument:444] - An element with the metaid "FB1" is already present in the SBML document. The new element will not get added to it.
-[19:37:49,032 ERROR SBMLDocument:444] - An element with the metaid "S2" is already present in the SBML document. The new element will not get added to it.
-[19:37:49,198 ERROR Model:648] - A Port with the id "S3" is already present in this model model. The new element will not be added to the model.
-[19:37:49,256 ERROR Model:648] - A Port with the id "S3" is already present in this model modelDef2. The new element will not be added to the model.
-[19:37:49,257 ERROR Model:3950] - An element of type species with the id "S3" is already present in this model "modelDef2". The new element will not be added to the model.
-[19:37:49,314 ERROR IdentifierException:75] - An element with the metaid "S1" is already present in the SBML document. The element replacedBy will not be annotated with it.
-[19:37:49,385 WARN AbstractSBase:1639] - SBaseRef 'SBaseRef [portRef=S1, idRef=null, unitRef=null, metaIdRef=null]' is associated to the different parent 'c'. Please remove it there before adding it to this 'port' or add a clone of it to this element.
-[19:37:49,389 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD1" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:37:49,389 ERROR ArraysSBasePlugin:702] - A Dimension with the id "AD2" is already present in this species identified by id[S1]. The new element will not be added to the model.
-[19:37:49,390 ERROR IdentifierException:62] - An element with the id "AD2" is already present in the SBML model. The identifier of dimension will not be set to this value.
-[19:37:49,390 WARN ArraysSBasePlugin:769] - A Dimension with the id "AD1" is not present in this model identified by id[model]. Nothing to be done.
-[19:37:49,510 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:37:49,511 ERROR IdentifierException:62] - An element with the id "G1" is already present in the SBML model. The identifier of group will not be set to this value.
-[19:37:49,511 ERROR Model:3950] - An element of type member with the id "GM1" is already present in this model "model". The new element will not be added to the model.
-[19:37:49,511 ERROR Model:3950] - An element of type memberConstraint with the id "GMC1" is already present in this model "model". The new element will not be added to the model.
-[19:37:49,512 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[19:37:49,512 ERROR Model:3950] - An element of type group with the id "G1" is already present in this model "model". The new element will not be added to the model.
-[19:37:50,018 ERROR ArraysSBasePlugin:702] - A Dimension with the id "dim" is already present in this species identified by id[]. The new element will not be added to the model.
-[13:34:45,465 WARN ASTNode:4210] - Could not compile ASTNode to formula: cannot write unknown syntax tree nodes to a formula String
-[13:34:45,720 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:45,727 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:45,844 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:45,861 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:47,213 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:49,671 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:49,678 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:49,741 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:49,744 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:51,906 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:51,908 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:51,969 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:51,988 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:52,885 ERROR SBMLDocument:444] - An element with the metaid "c0" is already present in the SBML document. The new element will not get added to it.
-[13:34:52,893 ERROR Model:3950] - An element of type model with the id "model" is already present in this model "model". The new element will not be added to the model.
-[13:34:52,899 ERROR Model:3950] - An element of type reaction with the id "R1" is already present in this model "model". The new element will not be added to the model.
-[13:34:52,900 ERROR Model:3950] - An element of type speciesReference with the id "SP1" is already present in this model "model". The new element will not be added to the model.
-[13:34:52,901 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[13:34:52,902 ERROR SBMLDocument:444] - An element with the metaid "SP1" is already present in the SBML document. The new element will not get added to it.
-[13:34:52,902 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[13:34:52,916 ERROR SBMLDocument:444] - An element with the metaid "LP1" is already present in the SBML document. The new element will not get added to it.
-[13:34:52,921 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[13:34:52,947 WARN AbstractSBase:1639] - Species 'S3' is associated to the different parent 'listOfSpecies'. Please remove it there before adding it to this 'model' or add a clone of it to this element.
-[13:34:52,953 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[13:34:52,964 ERROR KineticLaw:753] - A local parameter with the id 'LP1' is already present in the listOfParameters. The new element will not be added to the list.
-[13:34:52,966 ERROR KineticLaw:884] - The list of local parameters will not be set as some ids are duplicated.
-[13:34:52,988 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[13:34:53,003 WARN Model:1647] - Some of the reactions containing the local parameter LP1 have no id defined!
-[13:34:53,005 WARN Model:1647] - Some of the reactions containing the local parameter LP1_2 have no id defined!
-[13:34:53,015 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[13:34:53,028 ERROR Model:3950] - An element of type species with the id "S1" is already present in this model "model". The new element will not be added to the model.
-[13:34:53,512 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,513 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,535 WARN ASTNode:4210] - Could not compile ASTNode to formula: cannot write unknown syntax tree nodes to a formula String
-[13:34:53,540 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,541 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,542 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,543 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,543 WARN MathMLXMLStreamCompiler:319] - !!!!! I don't know what to do with the node of type UNKNOWN ASTUnknown []
-[13:34:53,558 WARN ASTNode:4210] - Could not compile ASTNode to formula: cannot write unknown syntax tree nodes to a formula String
-[13:34:53,563 WARN ASTNode:4210] - Could not compile ASTNode to formula: cannot write unknown syntax tree nodes to a formula String
-[13:34:53,622 ERROR KineticLaw:753] - A local parameter with the id 'lp1' is already present in the listOfParameters. The new element will not be added to the list.
-[13:34:53,652 ERROR Model:3950] - An element of type compartment with the id "c1" is already present in this model "myModel". The new element will not be added to the model.
-[13:34:53,654 ERROR IdentifierException:62] - An element with the id "c1" is already present in the SBML model. The identifier of compartment will not be set to this value.
-[13:34:53,656 WARN AbstractSBase:1635] - Trying to register compartment 'c1', which is already registered under listOfCompartments 'listOfCompartments'.
-[13:34:53,741 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:53,749 WARN MathMLStaxParser:221] - processCharactersOf : !!!!!!!!! I don't know what to do with that : csymbol !!!!!!!!!!
-[13:34:54,629 WARN Model:966] - Could not create KineticLaw because no reactions have been defined yet.
-[13:34:55,239 WARN AbstractSBase:1639] - Trigger 'trigger' is associated to the different parent 'event'. Please remove it there before adding it to this 'event' or add a clone of it to this element.
-[13:34:55,344 WARN ASTNode:4210] - Could not compile ASTNode to formula: cannot write unknown syntax tree nodes to a formula String
-[13:34:55,349 WARN AbstractMathContainer:237] - Could not create infix formula from syntax tree.
-org.sbml.jsbml.SBMLException: cannot write unknown syntax tree nodes to a formula String
- at org.sbml.jsbml.util.compilers.FormulaCompiler.unknownValue(FormulaCompiler.java:1080)
- at org.sbml.jsbml.ASTNode.compile(ASTNode.java:1970)
- at org.sbml.jsbml.util.compilers.FormulaCompiler.checkBrackets(FormulaCompiler.java:445)
- at org.sbml.jsbml.util.compilers.FormulaCompiler.plus(FormulaCompiler.java:930)
- at org.sbml.jsbml.ASTNode.compile(ASTNode.java:1680)
- at org.sbml.jsbml.ASTNode.toFormula(ASTNode.java:4140)
- at org.sbml.jsb...
[truncated message content] |
|
From: <nik...@us...> - 2015-04-21 14:25:19
|
Revision: 2200
http://sourceforge.net/p/jsbml/code/2200
Author: niko-rodrigue
Date: 2015-04-21 14:25:17 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected AnalyticVolume writeXMLAttributes. No need to write metaid and SBOTerm as they are in the sbml core namespace and written in AbstractSBase
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 14:21:45 UTC (rev 2199)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 14:25:17 UTC (rev 2200)
@@ -415,14 +415,7 @@
attributes.remove("functionType");
attributes.put(SpatialConstants.shortLabel + ":functionType", getFunctionType().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());
- }
+
return attributes;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-21 14:21:47
|
Revision: 2199
http://sourceforge.net/p/jsbml/code/2199
Author: niko-rodrigue
Date: 2015-04-21 14:21:45 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected AnalyticVolume copy constructor to use setter
Modified Paths:
--------------
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 13:54:32 UTC (rev 2198)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-04-21 14:21:45 UTC (rev 2199)
@@ -103,16 +103,16 @@
public AnalyticVolume(AnalyticVolume node) {
super(node);
if (node.isSetSpatialId()) {
- spatialId = new String(node.getSpatialId());
+ setSpatialId(node.getSpatialId());
}
if (node.isSetOrdinal()) {
- ordinal = new Integer(node.getOrdinal());
+ setOrdinal(node.getOrdinal());
}
if (node.isSetFunctionType()) {
- functionType = node.getFunctionType();
+ setFunctionType(node.getFunctionType());
}
if (node.isSetDomainType()) {
- domainType = node.getDomainType();
+ setDomainType(node.getDomainType());
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <pd...@us...> - 2015-04-21 13:54:40
|
Revision: 2198
http://sourceforge.net/p/jsbml/code/2198
Author: pdp10
Date: 2015-04-21 13:54:32 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Corrected compilation errors
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/AnalyticGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
trunk/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java
Added Paths:
-----------
trunk/src/
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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -105,9 +105,7 @@
}
@Override
- public AbstractSpatialNamedSBase clone() {
- return new AbstractSpatialNamedSBase(this);
- }
+ public abstract AbstractSpatialNamedSBase clone();
/**
* 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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -67,9 +67,7 @@
}
@Override
- public AbstractSpatialSBasePlugin clone() {
- return new AbstractSpatialSBasePlugin(this);
- }
+ public abstract AbstractSpatialSBasePlugin clone();
/**
* Initializes the default values using the namespace.
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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -295,39 +295,6 @@
}
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/CSGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-04-21 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -90,17 +90,29 @@
}
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
@Override
- public boolean equals(Object object) {
- boolean equal = super.equals(object);
- if (equal) {
- CSGeometry csg = (CSGeometry) object;
- equal &= csg.isSetListOfCSGObjects() == isSetListOfCSGObjects();
- if (equal && isSetListOfCSGObjects()) {
- equal &= csg.getListOfCSGObjects().equals(getListOfCSGObjects());
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+ if (!super.equals(obj)) {
+ return false;
+ }
+ if (getClass() != obj.getClass()) {
+ return false;
+ }
+ CSGeometry other = (CSGeometry) obj;
+ if (listOfCSGObjects == null) {
+ if (other.listOfCSGObjects != null) {
+ return false;
}
+ } else if (!listOfCSGObjects.equals(other.listOfCSGObjects)) {
+ return false;
}
- return equal;
+ return true;
}
@@ -258,17 +270,29 @@
return csgo;
}
- /**
- * TODO: optionally, create additional create methods with more
- * variables, for instance "bar" variable
+ /* (non-Javadoc)
+ * @see java.lang.Object#hashCode()
*/
- // public CSGObject createCSGObject(String id, int bar) {
- // CSGObject csgo = createCSGObject(id);
- // csgo.setBar(bar);
- // return csgo;
- // }
- /**
- *
+ @Override
+ public int hashCode() {
+ final int prime = 1301;
+ int result = super.hashCode();
+ result = prime * result
+ + ((listOfCSGObjects == null) ? 0 : listOfCSGObjects.hashCode());
+ return result;
+ }
+
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
*/
-
+ @Override
+ public String toString() {
+ StringBuilder builder = new StringBuilder();
+ builder.append("CS [spatialId=");
+ builder.append(spatialId);
+ builder.append("]");
+ return builder.toString();
+ }
+
}
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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -225,21 +225,12 @@
/**
*
- * @return get compartment instance of {@link Compartment} class
- */
- public Compartment getCompartmentInstance() {
- Model m = getModel();
- return m != null ? m.getCompartment(getCompartment()) : null;
- }
-
- /**
- *
* @return the domainType instance of the {@link DomainType} class
*/
public DomainType getDomainTypeInstance() {
Model m = getModel();
if (m!=null) {
- SpatialModelPlugin sm = (SpatialModelPlugin) m.getExtension(getCompartmentInstance().getElementName());
+ SpatialModelPlugin sm = (SpatialModelPlugin) m.getExtension(packageName);
sm.getGeometry().getListOfDomainTypes().get(getDomainType());
}
return null;
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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateComponent.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -454,10 +454,10 @@
hashCode += prime * getUnits().hashCode();
}
if (isSetBoundaryMaximum()) {
- hashCode += prime * getBoundaryMaximum()().hashCode();
+ hashCode += prime * getBoundaryMaximum().hashCode();
}
if (isSetBoundaryMinimum()) {
- hashCode += prime * getBoundaryMinimum()().hashCode();
+ hashCode += prime * getBoundaryMinimum().hashCode();
}
return hashCode;
}
@@ -509,14 +509,6 @@
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;
}
@@ -547,22 +539,6 @@
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/SpatialCompartmentPlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java 2015-04-21 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialCompartmentPlugin.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -22,7 +22,6 @@
package org.sbml.jsbml.ext.spatial;
import java.text.MessageFormat;
-import java.util.Map;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.ListOf;
@@ -202,33 +201,6 @@
}
@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();
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 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -355,10 +355,6 @@
/**
*
*/
- public static final String listOfAnalyticVolumes = "listOfAnalyticVolumes";
- /**
- *
- */
public static final String coordinateComponent = "coordinateComponent";
/**
*
Modified: trunk/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java
===================================================================
--- trunk/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java 2015-04-21 13:25:49 UTC (rev 2197)
+++ trunk/extensions/spatial/test/org/sbml/jsbml/ext/spatial/SpatialTest.java 2015-04-21 13:54:32 UTC (rev 2198)
@@ -84,7 +84,6 @@
CompartmentMapping spatialCompMap = new CompartmentMapping();
spatialComp.setCompartmentMapping(spatialCompMap);
- spatialCompMap.setCompartment("comp1");
spatialCompMap.setDomainType("DomainType1");
SBMLWriter.write(doc, System.out, ' ', (short) 2);
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: <nik...@us...> - 2015-04-21 13:15:22
|
Revision: 2196
http://sourceforge.net/p/jsbml/code/2196
Author: niko-rodrigue
Date: 2015-04-21 13:15:20 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected FormulaParserLL3.jj so that we have the same behavior as before + removed the files related to merging problems
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserLL3.jj
Removed Paths:
-------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.mine
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.r2129
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.r2142
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj.mine
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj.r2129
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj.r2142
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java.mine
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java.r2129
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java.r2142
Deleted: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.mine
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.mine 2015-04-21 13:07:56 UTC (rev 2195)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.mine 2015-04-21 13:15:20 UTC (rev 2196)
@@ -1,1213 +0,0 @@
-/* Generated By:JavaCC: Do not edit this line. FormulaParser.java */
-/*
- * $Id: FormulaParser.java 2142 2015-03-16 15:34:34Z niko-rodrigue $
- * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/src/org/sbml/jsbml/text/parser/FormulaParser.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.text.parser;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.InvalidPropertiesFormatException;
-import java.util.Properties;
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.ASTNode.Type;
-import org.sbml.jsbml.resources.Resource;
-
-/**
- * Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- * <p>
- * Support almost the same syntax as defined in <a href="http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/libsbml.html#parseFormula(java.lang.String)">
- * the LibSBML C-inspired infix notation taken from SBML Level 1 parser</a>.
- *
- * @author Alexander Dörr
- * @author Nicolas Rodriguez
- * @since 0.8
- * @version $Rev: 2142 $
- */
-public class FormulaParser implements IFormulaParser, FormulaParserConstants {
- public static Properties stringToType = new Properties();
-
- static
- {
- String path = "cfg/ASTNodeTokens.xml";
- try
- {
- stringToType.loadFromXML(Resource.class.getResourceAsStream(path));
- }
- catch (InvalidPropertiesFormatException e)
- {
- throw new RuntimeException("Invalid configuration file entries in file " + Resource.class.getResource(path), e);
- }
- catch (IOException e)
- {
- throw new RuntimeException("Could not read configuration file " + Resource.class.getResource(path), e);
- }
- }
-
- private void checkSize(ArrayList < ASTNode > arguments, int i) throws ParseException
- {
- if (arguments.size() > i)
- {
- throw new ParseException();
- }
- }
-
- private Integer getInteger(ASTNode node)
- {
- if (node.isUMinus())
- {
- if (node.getChild(0).isInteger())
- {
- return - node.getChild(0).getInteger();
- }
- else
- {
- return null;
- }
- }
- else
- {
- if (node.isInteger())
- {
- return node.getInteger();
- }
- else
- {
- return null;
- }
- }
- }
-
- /**
- * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- *
- * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
- *
- * @param leftChild
- * @param rightChild
- * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- * @see http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F
- */
- private ASTNode createModulo(ASTNode leftChild, ASTNode rightChild)
- {
- ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
-
- ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
- ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
- aDividedByB.addChild(leftChild);
- aDividedByB.addChild(rightChild);
-
- floorNode.addChild(aDividedByB);
- node.addChild(floorNode);
-
- ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
- greaterThan.addChild(aDividedByB.clone());
- greaterThan.addChild(new ASTNode(0));
-
- node.addChild(greaterThan);
-
- ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
- ceilNode.addChild(aDividedByB.clone());
-
- node.addChild(ceilNode);
-
- return node;
- }
-
- final public Token string() throws ParseException {
- Token t;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LOG:
- t = jj_consume_token(LOG);
- break;
- case STRING:
- t = jj_consume_token(STRING);
- break;
- default:
- jj_la1[0] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- {if (true) return t;}
- throw new Error("Missing return statement in function");
- }
-
- final public ASTNode parse() throws ParseException {
- ASTNode node = null;
- node = Expression();
- {if (true) return node;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode Expression() throws ParseException {
- ASTNode value = null;
- value = TermLvl1();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case 0:
- jj_consume_token(0);
- break;
- case EOL:
- jj_consume_token(EOL);
- break;
- default:
- jj_la1[1] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- {if (true) return value;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl3() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
- leftChild = Primary();
- label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- case FACTORIAL:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- jj_consume_token(POWER);
- rightChild = Primary();
- node = new ASTNode(Type.POWER);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case FACTORIAL:
- jj_consume_token(FACTORIAL);
- node = new ASTNode(Type.FUNCTION_FACTORIAL);
- node.addChild(leftChild);
- leftChild = node;
- break;
- default:
- jj_la1[3] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl2() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
- Type type = null;
- leftChild = TermLvl3();
- label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_2;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = TermLvl3();
- node = new ASTNode('*');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = TermLvl3();
- Integer left, right;
- left = getInteger(leftChild);
- right = getInteger(rightChild);
- if (left != null && right != null)
- {
- node = new ASTNode(Type.RATIONAL);
- node.setValue(left, right);
- leftChild = node;
- }
- else
- {
- node = new ASTNode('/');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = TermLvl3();
- node = createModulo(leftChild, rightChild);
- leftChild = node;
- break;
- case COMPARISON:
- t = jj_consume_token(COMPARISON);
- rightChild = TermLvl3();
- type = Type.getTypeFor(t.image);
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl1() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
- Type type = null;
- leftChild = TermLvl2();
- label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_3;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = TermLvl2();
- node = new ASTNode('+');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = TermLvl2();
- node = new ASTNode('-');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case BOOLEAN_LOGIC:
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = TermLvl2();
- type = Type.getTypeFor(t.image);
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode Primary() throws ParseException, NumberFormatException {
- Token t;
- double d;
- int i;
- ASTNode node = null;
- ASTNode vector = new ASTNode();
- ASTNode child, furtherChild;
- String s;
- String vals [ ];
- ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case INTEGER:
- t = jj_consume_token(INTEGER);
- i = Integer.parseInt(t.image);
- node = new ASTNode(Type.INTEGER);
- node.setValue(i);
- {if (true) return node;}
- break;
- case NUMBER:
- t = jj_consume_token(NUMBER);
- d = Double.parseDouble(t.image);
- node = new ASTNode(Type.REAL);
- node.setValue(d);
- {if (true) return node;}
- break;
- case EXPNUMBER:
- t = jj_consume_token(EXPNUMBER);
- s = t.image;
- vals = s.toLowerCase().split("e");
- if (vals [ 1 ].startsWith("+"))
- {
- i = Integer.parseInt(vals [ 1 ].substring(1));
- }
- else
- {
- i = Integer.parseInt(vals [ 1 ]);
- }
- node = new ASTNode(Type.REAL_E);
- node.setValue(Double.parseDouble(vals [ 0 ]), i);
- {if (true) return node;}
- break;
- default:
- jj_la1[12] = jj_gen;
- if (jj_2_1(2)) {
- t = string();
- jj_consume_token(OPEN_PAR);
- child = TermLvl1();
- label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SLPITTER:
- ;
- break;
- default:
- jj_la1[8] = jj_gen;
- break label_4;
- }
- jj_consume_token(SLPITTER);
- furtherChild = TermLvl1();
- arguments.add(furtherChild);
- }
- jj_consume_token(CLOSE_PAR);
- s = t.image;
- Type type = null;
-
- if (stringToType.containsKey(s.toLowerCase()))
- {
- type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
- }
- if (s.equalsIgnoreCase("abs"))
- {
- type = Type.FUNCTION_ABS;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("factorial"))
- {
- checkSize(arguments, 1);
- type = Type.FUNCTION_FACTORIAL;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("eq"))
- {
- checkSize(arguments, 1);
- type = Type.VECTOR;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("pow"))
- {
- checkSize(arguments, 1);
- type = Type.FUNCTION_POWER;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("sqr"))
- {
- checkSize(arguments, 0);
- type = Type.FUNCTION_EXP;
- node = new ASTNode(type);
- node.addChild(child);
- node.addChild(new ASTNode(2));
- }
- else if (s.equalsIgnoreCase("sqrt"))
- {
- checkSize(arguments, 0);
- type = Type.FUNCTION_ROOT;
- node = new ASTNode(type);
- node.addChild(new ASTNode(2));
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("not"))
- {
- checkSize(arguments, 0);
- type = Type.LOGICAL_NOT;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("ln"))
- {
- checkSize(arguments, 0);
- type = Type.FUNCTION_LN;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("lt"))
- {
- checkSize(arguments, 0);
- type = Type.RELATIONAL_LT;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("lambda"))
- {
- type = Type.LAMBDA;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("piecewise"))
- {
- type = Type.FUNCTION_PIECEWISE;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("selector"))
- {
- type = Type.FUNCTION_SELECTOR;
- node = new ASTNode(type);
- node.addChild(child);
- }
- else
- {
- node = new ASTNode(Type.FUNCTION);
- node.addChild(child);
- }
-
- if (type == null)
- {
- node = new ASTNode();
- node.setName(s);
- }
- for (ASTNode argument : arguments)
- {
- node.addChild(argument);
- }
- {if (true) return node;}
- } else if (jj_2_2(4)) {
- t = jj_consume_token(STRING);
- ASTNode selector = new ASTNode();
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- selector.addChild(new ASTNode(t.image));
- label_5:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = TermLvl1();
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
- }
- }
- {if (true) return selector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case OPEN_PAR:
- jj_consume_token(OPEN_PAR);
- node = TermLvl1();
- jj_consume_token(CLOSE_PAR);
- {if (true) return node;}
- break;
- default:
- jj_la1[13] = jj_gen;
- if (jj_2_3(2)) {
- jj_consume_token(LEFT_BRACES);
- node = TermLvl1();
- ASTNode selector = new ASTNode();
- boolean isSelector = false;
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- vector.setType(ASTNode.Type.VECTOR);
- vector.addChild(node);
- label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SLPITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
- }
- jj_consume_token(SLPITTER);
- node = TermLvl1();
- vector.addChild(node);
- }
- jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
- label_7:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
- }
- jj_consume_token(LEFT_BRACKET);
- node = TermLvl1();
- isSelector = true;
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
- {if (true) return isSelector ? selector : vector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACES:
- jj_consume_token(LEFT_BRACES);
- vector.setType(ASTNode.Type.VECTOR);
- jj_consume_token(RIGHT_BRACES);
- {if (true) return vector;}
- break;
- case MINUS:
- jj_consume_token(MINUS);
- node = Primary();
- ASTNode uiMinus = new ASTNode('-');
- uiMinus.addChild(node);
- {if (true) return uiMinus;}
- break;
- case NOT:
- jj_consume_token(NOT);
- node = TermLvl1();
- ASTNode not = new ASTNode(Type.LOGICAL_NOT);
- not.addChild(node);
- {if (true) return not;}
- break;
- case LOG:
- jj_consume_token(LOG);
- child = Primary();
- node = new ASTNode(Type.FUNCTION_LN);
- node.addChild(child);
- {if (true) return node;}
- break;
- case STRING:
- t = jj_consume_token(STRING);
- s = t.image;
- if (s.equalsIgnoreCase("true"))
- {
- node = new ASTNode(Type.CONSTANT_TRUE);
- }
- else if (s.equalsIgnoreCase("false"))
- {
- node = new ASTNode(Type.CONSTANT_FALSE);
- }
- else if (s.equalsIgnoreCase("pi"))
- {
- node = new ASTNode(Type.CONSTANT_PI);
- }
- else if (s.equalsIgnoreCase("avogadro"))
- {
- node = new ASTNode(Type.NAME_AVOGADRO);
- }
- else if (s.equalsIgnoreCase("time"))
- {
- node = new ASTNode(Type.NAME_TIME);
- }
- else if (s.equalsIgnoreCase("exponentiale"))
- {
- node = new ASTNode(Type.CONSTANT_E);
- }
- else if (s.equalsIgnoreCase("-infinity"))
- {
- node = new ASTNode(Double.NEGATIVE_INFINITY);
- }
- else if (s.equalsIgnoreCase("infinity"))
- {
- node = new ASTNode(Double.POSITIVE_INFINITY);
- }
- else
- {
- node = new ASTNode(s);
- }
- {if (true) return node;}
- break;
- default:
- jj_la1[14] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- }
- }
- }
- throw new Error("Missing return statement in function");
- }
-
- private boolean jj_2_1(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_1(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(0, xla); }
- }
-
- private boolean jj_2_2(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_2(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(1, xla); }
- }
-
- private boolean jj_2_3(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_3(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(2, xla); }
- }
-
- private boolean jj_3R_13() {
- if (jj_3R_18()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_19()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_8() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_scan_token(27)) {
- jj_scanpos = xsp;
- if (jj_scan_token(28)) return true;
- }
- return false;
- }
-
- private boolean jj_3R_12() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_15()) {
- jj_scanpos = xsp;
- if (jj_3R_16()) {
- jj_scanpos = xsp;
- if (jj_3R_17()) return true;
- }
- }
- return false;
- }
-
- private boolean jj_3R_15() {
- if (jj_scan_token(PLUS)) return true;
- return false;
- }
-
- private boolean jj_3R_25() {
- if (jj_scan_token(NUMBER)) return true;
- return false;
- }
-
- private boolean jj_3R_28() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_scan_token(RIGHT_BRACES)) return true;
- return false;
- }
-
- private boolean jj_3R_21() {
- if (jj_scan_token(DIVIDE)) return true;
- return false;
- }
-
- private boolean jj_3_2() {
- if (jj_scan_token(STRING)) return true;
- Token xsp;
- if (jj_3R_9()) return true;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_9()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_10() {
- if (jj_3R_11()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_12()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_24() {
- if (jj_scan_token(INTEGER)) return true;
- return false;
- }
-
- private boolean jj_3R_18() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_24()) {
- jj_scanpos = xsp;
- if (jj_3R_25()) {
- jj_scanpos = xsp;
- if (jj_3R_26()) {
- jj_scanpos = xsp;
- if (jj_3_1()) {
- jj_scanpos = xsp;
- if (jj_3_2()) {
- jj_scanpos = xsp;
- if (jj_3R_27()) {
- jj_scanpos = xsp;
- if (jj_3_3()) {
- jj_scanpos = xsp;
- if (jj_3R_28()) {
- jj_scanpos = xsp;
- if (jj_3R_29()) {
- jj_scanpos = xsp;
- if (jj_3R_30()) {
- jj_scanpos = xsp;
- if (jj_3R_31()) {
- jj_scanpos = xsp;
- if (jj_3R_32()) return true;
- }
- }
- }
- }
- }
- }
- }
- }
- }
- }
- }
- return false;
- }
-
- private boolean jj_3R_9() {
- if (jj_scan_token(LEFT_BRACKET)) return true;
- if (jj_3R_10()) return true;
- if (jj_scan_token(RIGHT_BRACKET)) return true;
- return false;
- }
-
- private boolean jj_3R_14() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_20()) {
- jj_scanpos = xsp;
- if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) {
- jj_scanpos = xsp;
- if (jj_3R_23()) return true;
- }
- }
- }
- return false;
- }
-
- private boolean jj_3R_20() {
- if (jj_scan_token(TIMES)) return true;
- return false;
- }
-
- private boolean jj_3R_11() {
- if (jj_3R_13()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_14()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_32() {
- if (jj_scan_token(STRING)) return true;
- return false;
- }
-
- private boolean jj_3R_23() {
- if (jj_scan_token(COMPARISON)) return true;
- return false;
- }
-
- private boolean jj_3_1() {
- if (jj_3R_8()) return true;
- if (jj_scan_token(OPEN_PAR)) return true;
- return false;
- }
-
- private boolean jj_3R_31() {
- if (jj_scan_token(LOG)) return true;
- if (jj_3R_18()) return true;
- return false;
- }
-
- private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_22() {
- if (jj_scan_token(MODULO)) return true;
- return false;
- }
-
- private boolean jj_3R_34() {
- if (jj_scan_token(FACTORIAL)) return true;
- return false;
- }
-
- private boolean jj_3R_17() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
- return false;
- }
-
- private boolean jj_3R_30() {
- if (jj_scan_token(NOT)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_27() {
- if (jj_scan_token(OPEN_PAR)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_33() {
- if (jj_scan_token(POWER)) return true;
- return false;
- }
-
- private boolean jj_3R_19() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_33()) {
- jj_scanpos = xsp;
- if (jj_3R_34()) return true;
- }
- return false;
- }
-
- private boolean jj_3R_29() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_18()) return true;
- return false;
- }
-
- private boolean jj_3R_16() {
- if (jj_scan_token(MINUS)) return true;
- return false;
- }
-
- private boolean jj_3R_26() {
- if (jj_scan_token(EXPNUMBER)) return true;
- return false;
- }
-
- /** Generated Token Manager. */
- public FormulaParserTokenManager token_source;
- SimpleCharStream jj_input_stream;
- /** Current token. */
- public Token token;
- /** Next token. */
- public Token jj_nt;
- private int jj_ntk;
- private Token jj_scanpos, jj_lastpos;
- private int jj_la;
- private int jj_gen;
- final private int[] jj_la1 = new int[15];
- static private int[] jj_la1_0;
- static {
- jj_la1_init_0();
- }
- private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0x18000000,0x80000001,0x4200,0x4200,0x203800,0x203800,0x400500,0x400500,0x80,0x80000,0x80,0x80000,0x68,0x8000,0x1c020400,};
- }
- final private JJCalls[] jj_2_rtns = new JJCalls[3];
- private boolean jj_rescan = false;
- private int jj_gc = 0;
-
- /** Constructor with InputStream. */
- public FormulaParser(java.io.InputStream stream) {
- this(stream, null);
- }
- /** Constructor with InputStream and supplied encoding */
- public FormulaParser(java.io.InputStream stream, String encoding) {
- try { jj_input_stream = new SimpleCharStream(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
- token_source = new FormulaParserTokenManager(jj_input_stream);
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Reinitialise. */
- public void ReInit(java.io.InputStream stream) {
- ReInit(stream, null);
- }
- /** Reinitialise. */
- public void ReInit(java.io.InputStream stream, String encoding) {
- try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
- token_source.ReInit(jj_input_stream);
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Constructor. */
- public FormulaParser(java.io.Reader stream) {
- jj_input_stream = new SimpleCharStream(stream, 1, 1);
- token_source = new FormulaParserTokenManager(jj_input_stream);
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Reinitialise. */
- public void ReInit(java.io.Reader stream) {
- jj_input_stream.ReInit(stream, 1, 1);
- token_source.ReInit(jj_input_stream);
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Constructor with generated Token Manager. */
- public FormulaParser(FormulaParserTokenManager tm) {
- token_source = tm;
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Reinitialise. */
- public void ReInit(FormulaParserTokenManager tm) {
- token_source = tm;
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- private Token jj_consume_token(int kind) throws ParseException {
- Token oldToken;
- if ((oldToken = token).next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
- jj_ntk = -1;
- if (token.kind == kind) {
- jj_gen++;
- if (++jj_gc > 100) {
- jj_gc = 0;
- for (int i = 0; i < jj_2_rtns.length; i++) {
- JJCalls c = jj_2_rtns[i];
- while (c != null) {
- if (c.gen < jj_gen) c.first = null;
- c = c.next;
- }
- }
- }
- return token;
- }
- token = oldToken;
- jj_kind = kind;
- throw generateParseException();
- }
-
- static private final class LookaheadSuccess extends java.lang.Error { }
- final private LookaheadSuccess jj_ls = new LookaheadSuccess();
- private boolean jj_scan_token(int kind) {
- if (jj_scanpos == jj_lastpos) {
- jj_la--;
- if (jj_scanpos.next == null) {
- jj_lastpos = jj_scanpos = jj_scanpos.next = token_source.getNextToken();
- } else {
- jj_lastpos = jj_scanpos = jj_scanpos.next;
- }
- } else {
- jj_scanpos = jj_scanpos.next;
- }
- if (jj_rescan) {
- int i = 0; Token tok = token;
- while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
- if (tok != null) jj_add_error_token(kind, i);
- }
- if (jj_scanpos.kind != kind) return true;
- if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
- return false;
- }
-
-
-/** Get the next Token. */
- final public Token getNextToken() {
- if (token.next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
- jj_ntk = -1;
- jj_gen++;
- return token;
- }
-
-/** Get the specific Token. */
- final public Token getToken(int index) {
- Token t = token;
- for (int i = 0; i < index; i++) {
- if (t.next != null) t = t.next;
- else t = t.next = token_source.getNextToken();
- }
- return t;
- }
-
- private int jj_ntk() {
- if ((jj_nt=token.next) == null)
- return (jj_ntk = (token.next=token_source.getNextToken()).kind);
- else
- return (jj_ntk = jj_nt.kind);
- }
-
- private java.util.List<int[]> jj_expentries = new java.util.ArrayList<int[]>();
- private int[] jj_expentry;
- private int jj_kind = -1;
- private int[] jj_lasttokens = new int[100];
- private int jj_endpos;
-
- private void jj_add_error_token(int kind, int pos) {
- if (pos >= 100) return;
- if (pos == jj_endpos + 1) {
- jj_lasttokens[jj_endpos++] = kind;
- } else if (jj_endpos != 0) {
- jj_expentry = new int[jj_endpos];
- for (int i = 0; i < jj_endpos; i++) {
- jj_expentry[i] = jj_lasttokens[i];
- }
- jj_entries_loop: for (java.util.Iterator<?> it = jj_expentries.iterator(); it.hasNext();) {
- int[] oldentry = (int[])(it.next());
- if (oldentry.length == jj_expentry.length) {
- for (int i = 0; i < jj_expentry.length; i++) {
- if (oldentry[i] != jj_expentry[i]) {
- continue jj_entries_loop;
- }
- }
- jj_expentries.add(jj_expentry);
- break jj_entries_loop;
- }
- }
- if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
- }
- }
-
- /** Generate ParseException. */
- public ParseException generateParseException() {
- jj_expentries.clear();
- boolean[] la1tokens = new boolean[32];
- if (jj_kind >= 0) {
- la1tokens[jj_kind] = true;
- jj_kind = -1;
- }
- for (int i = 0; i < 15; i++) {
- if (jj_la1[i] == jj_gen) {
- for (int j = 0; j < 32; j++) {
- if ((jj_la1_0[i] & (1<<j)) != 0) {
- la1tokens[j] = true;
- }
- }
- }
- }
- for (int i = 0; i < 32; i++) {
- if (la1tokens[i]) {
- jj_expentry = new int[1];
- jj_expentry[0] = i;
- jj_expentries.add(jj_expentry);
- }
- }
- jj_endpos = 0;
- jj_rescan_token();
- jj_add_error_token(0, 0);
- int[][] exptokseq = new int[jj_expentries.size()][];
- for (int i = 0; i < jj_expentries.size(); i++) {
- exptokseq[i] = jj_expentries.get(i);
- }
- return new ParseException(token, exptokseq, tokenImage);
- }
-
- /** Enable tracing. */
- final public void enable_tracing() {
- }
-
- /** Disable tracing. */
- final public void disable_tracing() {
- }
-
- private void jj_rescan_token() {
- jj_rescan = true;
- for (int i = 0; i < 3; i++) {
- try {
- JJCalls p = jj_2_rtns[i];
- do {
- if (p.gen > jj_gen) {
- jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
- switch (i) {
- case 0: jj_3_1(); break;
- case 1: jj_3_2(); break;
- case 2: jj_3_3(); break;
- }
- }
- p = p.next;
- } while (p != null);
- } catch(LookaheadSuccess ls) { }
- }
- jj_rescan = false;
- }
-
- private void jj_save(int index, int xla) {
- JJCalls p = jj_2_rtns[index];
- while (p.gen > jj_gen) {
- if (p.next == null) { p = p.next = new JJCalls(); break; }
- p = p.next;
- }
- p.gen = jj_gen + xla - jj_la; p.first = token; p.arg = xla;
- }
-
- static final class JJCalls {
- int gen;
- Token first;
- int arg;
- JJCalls next;
- }
-
-}
Deleted: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.r2129
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.r2129 2015-04-21 13:07:56 UTC (rev 2195)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java.r2129 2015-04-21 13:15:20 UTC (rev 2196)
@@ -1,1154 +0,0 @@
-/* Generated By:JavaCC: Do not edit this line. FormulaParser.java */
-/*
- * $Id: FormulaParser.java 2142 2015-03-16 15:34:34Z niko-rodrigue $
- * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/src/org/sbml/jsbml/text/parser/FormulaParser.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.text.parser;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.InvalidPropertiesFormatException;
-import java.util.Properties;
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.ASTNode.Type;
-import org.sbml.jsbml.resources.Resource;
-
-/**
- * Class used to parse infix mathematical formula and returns a representation of it as an Abstract Syntax Tree (AST).
- * <p>
- * Support almost the same syntax as defined in <a href="http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/libsbml.html#parseFormula(java.lang.String)">
- * the LibSBML C-inspired infix notation taken from SBML Level 1 parser</a>.
- *
- * @author Alexander Dörr
- * @author Nicolas Rodriguez
- * @since 0.8
- * @version $Rev: 2142 $
- */
-public class FormulaParser implements IFormulaParser, FormulaParserConstants {
- public static Properties stringToType = new Properties();
-
- static
- {
- String path = "cfg/ASTNodeTokens.xml";
- try
- {
- stringToType.loadFromXML(Resource.class.getResourceAsStream(path));
- }
- catch (InvalidPropertiesFormatException e)
- {
- throw new RuntimeException("Invalid configuration file entries in file " + Resource.class.getResource(path), e);
- }
- catch (IOException e)
- {
- throw new RuntimeException("Could not read configuration file " + Resource.class.getResource(path), e);
- }
- }
-
- private void checkSize(ArrayList < ASTNode > arguments, int i) throws ParseException
- {
- if (arguments.size() > i)
- {
- throw new ParseException();
- }
- }
-
- private Integer getInteger(ASTNode node)
- {
- if (node.isUMinus())
- {
- if (node.getChild(0).isInteger())
- {
- return - node.getChild(0).getInteger();
- }
- else
- {
- return null;
- }
- }
- else
- {
- if (node.isInteger())
- {
- return node.getInteger();
- }
- else
- {
- return null;
- }
- }
- }
-
- final public Token string() throws ParseException {
- Token t;
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LOG:
- t = jj_consume_token(LOG);
- break;
- case STRING:
- t = jj_consume_token(STRING);
- break;
- default:
- jj_la1[0] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- {if (true) return t;}
- throw new Error("Missing return statement in function");
- }
-
- final public ASTNode parse() throws ParseException {
- ASTNode node = null;
- node = Expression();
- {if (true) return node;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode Expression() throws ParseException {
- ASTNode value = null;
- value = TermLvl1();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case 0:
- jj_consume_token(0);
- break;
- case EOL:
- jj_consume_token(EOL);
- break;
- default:
- jj_la1[1] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- {if (true) return value;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl3() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
- leftChild = Primary();
- label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- case FACTORIAL:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- jj_consume_token(POWER);
- rightChild = Primary();
- node = new ASTNode(Type.POWER);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case FACTORIAL:
- jj_consume_token(FACTORIAL);
- node = new ASTNode(Type.FUNCTION_FACTORIAL);
- node.addChild(leftChild);
- leftChild = node;
- break;
- default:
- jj_la1[3] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl2() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
- leftChild = TermLvl3();
- label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_2;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = TermLvl3();
- node = new ASTNode('*');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = TermLvl3();
- Integer left, right;
- left = getInteger(leftChild);
- right = getInteger(rightChild);
- if (left != null && right != null)
- {
- node = new ASTNode();
- node.setValue(left, right);
- leftChild = node;
- }
- else
- {
- node = new ASTNode('/');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode TermLvl1() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
- String s;
- Type type = null;
- leftChild = TermLvl2();
- label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- case COMPARISON:
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_3;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = TermLvl2();
- node = new ASTNode('+');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = TermLvl2();
- node = new ASTNode('-');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case BOOLEAN_LOGIC:
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = TermLvl2();
- s = t.image;
- if (s.equalsIgnoreCase("or"))
- {
- type = ASTNode.Type.LOGICAL_OR;
- }
- else if (s.equalsIgnoreCase("and"))
- {
- type = ASTNode.Type.LOGICAL_AND;
- }
- else if (s.equalsIgnoreCase("xor"))
- {
- type = ASTNode.Type.LOGICAL_XOR;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case COMPARISON:
- t = jj_consume_token(COMPARISON);
- rightChild = TermLvl2();
- s = t.image;
- if (s.equalsIgnoreCase("<"))
- {
- type = ASTNode.Type.RELATIONAL_LT;
- }
- else if (s.equalsIgnoreCase(">"))
- {
- type = ASTNode.Type.RELATIONAL_GT;
- }
- else if (s.equalsIgnoreCase("=="))
- {
- type = ASTNode.Type.RELATIONAL_EQ;
- }
- else if (s.equalsIgnoreCase("!="))
- {
- type = ASTNode.Type.RELATIONAL_NEQ;
- }
- else if (s.equalsIgnoreCase(">="))
- {
- type = ASTNode.Type.RELATIONAL_GEQ;
- }
- else if (s.equalsIgnoreCase("<="))
- {
- type = ASTNode.Type.RELATIONAL_LEQ;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode Primary() throws ParseException, NumberFormatException {
- Token t;
- double d;
- int i;
- ASTNode node = new ASTNode();
- ASTNode vector = new ASTNode();
- ASTNode child, furtherChild;
- String s;
- String vals [ ];
- ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case INTEGER:
- t = jj_consume_token(INTEGER);
- i = Integer.parseInt(t.image);
- node.setValue(i);
- {if (true) return node;}
- break;
- case NUMBER:
- t = jj_consume_token(NUMBER);
- d = Double.parseDouble(t.image);
- node.setValue(d);
- {if (true) return node;}
- break;
- case EXPNUMBER:
- t = jj_consume_token(EXPNUMBER);
- s = t.image;
- vals = s.toLowerCase().split("e");
- if (vals [ 1 ].startsWith("+"))
- {
- i = Integer.parseInt(vals [ 1 ].substring(1));
- }
- else
- {
- i = Integer.parseInt(vals [ 1 ]);
- }
- node.setValue(Double.parseDouble(vals [ 0 ]), i);
- {if (true) return node;}
- break;
- default:
- jj_la1[12] = jj_gen;
- if (jj_2_1(2)) {
- t = string();
- jj_consume_token(OPEN_PAR);
- child = TermLvl1();
- label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SLPITTER:
- ;
- break;
- default:
- jj_la1[8] = jj_gen;
- break label_4;
- }
- jj_consume_token(SLPITTER);
- furtherChild = TermLvl1();
- arguments.add(furtherChild);
- }
- jj_consume_token(CLOSE_PAR);
- s = t.image;
- Type type = null;
-
- if (stringToType.containsKey(s.toLowerCase()))
- {
- type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
- }
-
- if (s.equalsIgnoreCase("pow"))
- {
- checkSize(arguments, 1);
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("sqr"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- node.addChild(new ASTNode(2));
- }
- else if (s.equalsIgnoreCase("sqrt"))
- {
- checkSize(arguments, 0);
- node.addChild(new ASTNode(2));
- node.addChild(child);
- }
- else if (s.equalsIgnoreCase("not"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.LOGICAL_NOT;
- }
- else if (s.equalsIgnoreCase("ln"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.FUNCTION_LN;
- }
- else if (s.equalsIgnoreCase("lambda"))
- {
- node.addChild(child);
- type = Type.LAMBDA;
- }
- else if (s.equalsIgnoreCase("piecewise"))
- {
- node.addChild(child);
- type = Type.FUNCTION_PIECEWISE;
- }
- else
- {
- node.addChild(child);
- }
-
- if (type != null)
- {
- node.setType(type);
- }
- else
- {
- node.setName(s);
- }
- for (ASTNode argument : arguments)
- {
- node.addChild(argument);
- }
- {if (true) return node;}
- } else if (jj_2_2(4)) {
- t = jj_consume_token(STRING);
- ASTNode selector = new ASTNode();
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- selector.addChild(new ASTNode(t.image));
- label_5:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = TermLvl1();
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
- }
- }
- {if (true) return selector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case OPEN_PAR:
- jj_consume_token(OPEN_PAR);
- node = TermLvl1();
- jj_consume_token(CLOSE_PAR);
- {if (true) return node;}
- break;
- default:
- jj_la1[13] = jj_gen;
- if (jj_2_3(2)) {
- jj_consume_token(LEFT_BRACES);
- node = TermLvl1();
- ASTNode selector = new ASTNode();
- boolean isSelector = false;
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- vector.setType(ASTNode.Type.VECTOR);
- vector.addChild(node);
- label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SLPITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
- }
- jj_consume_token(SLPITTER);
- node = TermLvl1();
- vector.addChild(node);
- }
- jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
- label_7:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
- }
- jj_consume_token(LEFT_BRACKET);
- node = TermLvl1();
- isSelector = true;
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
- {if (true) return isSelector ? selector : vector;}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACES:
- jj_consume_token(LEFT_BRACES);
- vector.setType(ASTNode.Type.VECTOR);
- jj_consume_token(RIGHT_BRACES);
- {if (true) return vector;}
- break;
- case MINUS:
- jj_consume_token(MINUS);
- node = Primary();
- ASTNode uiMinus = new ASTNode('-');
- uiMinus.addChild(node);
- {if (true) return uiMinus;}
- break;
- case NOT:
- jj_consume_token(NOT);
- node = TermLvl1();
- ASTNode not = new ASTNode(Type.LOGICAL_NOT);
- not.addChild(node);
- {if (true) return not;}
- break;
- case LOG:
- jj_consume_token(LOG);
- child = Primary();
- node = new ASTNode(Type.FUNCTION_LN);
- node.addChild(child);
- {if (true) return node;}
- break;
- case STRING:
- t = jj_consume_token(STRING);
- s = t.image;
- if (s.equalsIgnoreCase("true"))
- {
- node = new ASTNode(Type.CONSTANT_TRUE);
- }
- else if (s.equalsIgnoreCase("false"))
- {
- node = new ASTNode(Type.CONSTANT_FALSE);
- }
- else if (s.equalsIgnoreCase("pi"))
- {
- node = new ASTNode(Type.CONSTANT_PI);
- }
- else if (s.equalsIgnoreCase("avogadro"))
- {
- node = new ASTNode(Type.NAME_AVOGADRO);
- }
- else if (s.equalsIgnoreCase("time"))
- {
- node = new ASTNode(Type.NAME_TIME);
- }
- else if (s.equalsIgnoreCase("exponentiale"))
- {
- node = new ASTNode(Type.CONSTANT_E);
- }
- else if (s.equalsIgnoreCase("-infinity"))
- {
- node = new ASTNode(Double.NEGATIVE_INFINITY);
- }
- else if (s.equalsIgnoreCase("infinity"))
- {
- node = new ASTNode(Double.POSITIVE_INFINITY);
- }
- else
- {
- node = new ASTNode(s);
- }
- {if (true) return node;}
- break;
- default:
- jj_la1[14] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- }
- }
- }
- throw new Error("Missing return statement in function");
- }
-
- private boolean jj_2_1(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_1(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(0, xla); }
- }
-
- private boolean jj_2_2(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_2(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(1, xla); }
- }
-
- private boolean jj_2_3(int xla) {
- jj_la = xla; jj_lastpos = jj_scanpos = token;
- try { return !jj_3_3(); }
- catch(LookaheadSuccess ls) { return true; }
- finally { jj_save(2, xla); }
- }
-
- private boolean jj_3R_29() {
- if (jj_scan_token(NOT)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_17() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
- return false;
- }
-
- private boolean jj_3R_26() {
- if (jj_scan_token(OPEN_PAR)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_22() {
- if (jj_scan_token(DIVIDE)) return true;
- return false;
- }
-
- private boolean jj_3R_28() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_19()) return true;
- return false;
- }
-
- private boolean jj_3R_16() {
- if (jj_scan_token(MINUS)) return true;
- return false;
- }
-
- private boolean jj_3R_14() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) return true;
- }
- return false;
- }
-
- private boolean jj_3R_21() {
- if (jj_scan_token(TIMES)) return true;
- return false;
- }
-
- private boolean jj_3R_25() {
- if (jj_scan_token(EXPNUMBER)) return true;
- return false;
- }
-
- private boolean jj_3R_12() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_15()) {
- jj_scanpos = xsp;
- if (jj_3R_16()) {
- jj_scanpos = xsp;
- if (jj_3R_17()) {
- jj_scanpos = xsp;
- if (jj_3R_18()) return true;
- }
- }
- }
- return false;
- }
-
- private boolean jj_3R_15() {
- if (jj_scan_token(PLUS)) return true;
- return false;
- }
-
- private boolean jj_3R_27() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_scan_token(RIGHT_BRACES)) return true;
- return false;
- }
-
- private boolean jj_3R_11() {
- if (jj_3R_13()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_14()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3_2() {
- if (jj_scan_token(STRING)) return true;
- Token xsp;
- if (jj_3R_9()) return true;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_9()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_10() {
- if (jj_3R_11()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_12()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_24() {
- if (jj_scan_token(NUMBER)) return true;
- return false;
- }
-
- private boolean jj_3R_9() {
- if (jj_scan_token(LEFT_BRACKET)) return true;
- if (jj_3R_10()) return true;
- if (jj_scan_token(RIGHT_BRACKET)) return true;
- return false;
- }
-
- private boolean jj_3R_23() {
- if (jj_scan_token(INTEGER)) return true;
- return false;
- }
-
- private boolean jj_3R_19() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_23()) {
- jj_scanpos = xsp;
- if (jj_3R_24()) {
- jj_scanpos = xsp;
- if (jj_3R_25()) {
- jj_scanpos = xsp;
- if (jj_3_1()) {
- jj_scanpos = xsp;
- if (jj_3_2()) {
- jj_scanpos = xsp;
- if (jj_3R_26()) {
- jj_scanpos = xsp;
- if (jj_3_3()) {
- jj_scanpos = xsp;
- if (jj_3R_27()) {
- jj_scanpos = xsp;
- if (jj_3R_28()) {
- jj_scanpos = xsp;
- if (jj_3R_29()) {
- jj_scanpos = xsp;
- if (jj_3R_30()) {
- jj_scanpos = xsp;
- if (jj_3R_31()) return true;
- }
- }
- }
- }
- }
- }
- }
- }
- }
- }
- }
- return false;
- }
-
- private boolean jj_3R_18() {
- if (jj_scan_token(COMPARISON)) return true;
- return false;
- }
-
- private boolean jj_3R_33() {
- if (jj_scan_token(FACTORIAL)) return true;
- return false;
- }
-
- private boolean jj_3R_31() {
- if (jj_scan_token(STRING)) return true;
- return false;
- }
-
- private boolean jj_3R_32() {
- if (jj_scan_token(POWER)) return true;
- return false;
- }
-
- private boolean jj_3R_20() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_32()) {
- jj_scanpos = xsp;
- if (jj_3R_33()) return true;
- }
- return false;
- }
-
- private boolean jj_3R_30() {
- if (jj_scan_token(LOG)) return true;
- if (jj_3R_19()) return true;
- return false;
- }
-
- private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_13() {
- if (jj_3R_19()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_20()) { jj_scanpos = xsp; break; }
- }
- return false;
- }
-
- private boolean jj_3R_8() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_scan_token(26)) {
- jj_scanpos = xsp;
- if (jj_scan_token(27)) return true;
- }
- return false;
- }
-
- private boolean jj_3_1() {
- if (jj_3R_8()) return true;
- if (jj_scan_token(OPEN_PAR)) return true;
- return false;
- }
-
- /** Generated Token Manager. */
- public FormulaParserTokenManager token_source;
- SimpleCharStream jj_input_stream;
- /** Current token. */
- public Token token;
- /** Next token. */
- public Token jj_nt;
- private int jj_ntk;
- private Token jj_scanpos, jj_lastpos;
- private int jj_la;
- private int jj_gen;
- final private int[] jj_la1 = new int[15];
- static private int[] jj_la1_0;
- static {
- jj_la1_init_0();
- }
- private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0xc000000,0x40000001,0x2200,0x2200,0x1800,0x1800,0x300500,0x300500,0x80,0x40000,0x80,0x40000,0x68,0x4000,0xe010400,};
- }
- final private JJCalls[] jj_2_rtns = new JJCalls[3];
- private boolean jj_rescan = false;
- private int jj_gc = 0;
-
- /** Constructor with InputStream. */
- public FormulaParser(java.io.InputStream stream) {
- this(stream, null);
- }
- /** Constructor with InputStream and supplied encoding */
- public FormulaParser(java.io.InputStream stream, String encoding) {
- try { jj_input_stream = new SimpleCharStream(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
- token_source = new FormulaParserTokenManager(jj_input_stream);
- token = new Token();
- jj_ntk = -1;
- jj_gen = 0;
- for (int i = 0; i < 15; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
- }
-
- /** Reinitialise. */
- public void ReInit(java.io.InputStream stream) {
- ReInit(stream, null);
- }
- /** Reinitialise. ...
[truncated message content] |
|
From: <and...@us...> - 2015-04-21 13:07:58
|
Revision: 2195
http://sourceforge.net/p/jsbml/code/2195
Author: andreas-draeger
Date: 2015-04-21 13:07:56 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
Implemented a new method to filter validation errors by severity.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/SBMLErrorLog.java
Modified: trunk/core/src/org/sbml/jsbml/SBMLErrorLog.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLErrorLog.java 2015-04-21 13:00:30 UTC (rev 2194)
+++ trunk/core/src/org/sbml/jsbml/SBMLErrorLog.java 2015-04-21 13:07:56 UTC (rev 2195)
@@ -23,6 +23,7 @@
import java.io.File;
import java.util.ArrayList;
+import java.util.LinkedList;
import java.util.List;
import org.sbml.jsbml.util.Option;
@@ -170,39 +171,45 @@
* @see #getNumErrors()
*/
public int getNumFailsWithSeverity(SBMLError.SEVERITY severity) {
+ return getErrorsBySeverity(severity).size();
+ }
- int nbWithSeverity = 0;
-
+ /**
+ *
+ * @param severity
+ * @return
+ */
+ public List<SBMLError> getErrorsBySeverity(SBMLError.SEVERITY severity) {
+ List<SBMLError> listOfErrors = new LinkedList<SBMLError>();
for (SBMLError error : validationErrors) {
switch(severity) {
case INFO: {
if (error.isInfo()) {
- nbWithSeverity++;
+ listOfErrors.add(error);
}
break;
}
case WARNING: {
if (error.isWarning()) {
- nbWithSeverity++;
+ listOfErrors.add(error);
}
break;
}
case ERROR: {
if (error.isError()) {
- nbWithSeverity++;
+ listOfErrors.add(error);
}
break;
}
case FATAL: {
if (error.isFatal()) {
- nbWithSeverity++;
+ listOfErrors.add(error);
}
break;
}
}
}
-
- return nbWithSeverity;
+ return listOfErrors;
}
/**
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: <nik...@us...> - 2015-04-21 12:59:33
|
Revision: 2193
http://sourceforge.net/p/jsbml/code/2193
Author: niko-rodrigue
Date: 2015-04-21 12:59:30 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected FormulaParser.jj so that we have the same behavior as before
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java 2015-04-21 12:25:38 UTC (rev 2192)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.java 2015-04-21 12:59:30 UTC (rev 2193)
@@ -229,7 +229,6 @@
case TIMES:
case DIVIDE:
case MODULO:
- case COMPARISON:
;
break;
default:
@@ -271,15 +270,6 @@
node = createModulo(leftChild, rightChild);
leftChild = node;
break;
- case COMPARISON:
- t = jj_consume_token(COMPARISON);
- rightChild = TermLvl3();
- type = Type.getTypeFor(t.image);
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
default:
jj_la1[5] = jj_gen;
jj_consume_token(-1);
@@ -302,6 +292,7 @@
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case PLUS:
case MINUS:
+ case COMPARISON:
case BOOLEAN_LOGIC:
;
break;
@@ -330,11 +321,57 @@
t = jj_consume_token(BOOLEAN_LOGIC);
rightChild = TermLvl2();
type = Type.getTypeFor(t.image);
+
+ if (s.equalsIgnoreCase("or") || s.equals("||"))
+ {
+ type = ASTNode.Type.LOGICAL_OR;
+ }
+ else if (s.equalsIgnoreCase("and") || s.equals("&&"))
+ {
+ type = ASTNode.Type.LOGICAL_AND;
+ }
+ else if (s.equalsIgnoreCase("xor"))
+ {
+ type = ASTNode.Type.LOGICAL_XOR;
+ }
node = new ASTNode(type);
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
break;
+ case COMPARISON:
+ t = jj_consume_token(COMPARISON);
+ rightChild = TermLvl2();
+ s = t.image;
+ if (s.equalsIgnoreCase("<"))
+ {
+ type = ASTNode.Type.RELATIONAL_LT;
+ }
+ else if (s.equalsIgnoreCase(">"))
+ {
+ type = ASTNode.Type.RELATIONAL_GT;
+ }
+ else if (s.equalsIgnoreCase("=="))
+ {
+ type = ASTNode.Type.RELATIONAL_EQ;
+ }
+ else if (s.equalsIgnoreCase("!="))
+ {
+ type = ASTNode.Type.RELATIONAL_NEQ;
+ }
+ else if (s.equalsIgnoreCase(">="))
+ {
+ type = ASTNode.Type.RELATIONAL_GEQ;
+ }
+ else if (s.equalsIgnoreCase("<="))
+ {
+ type = ASTNode.Type.RELATIONAL_LEQ;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
default:
jj_la1[7] = jj_gen;
jj_consume_token(-1);
@@ -687,14 +724,68 @@
finally { jj_save(2, xla); }
}
+ private boolean jj_3R_26() {
+ if (jj_scan_token(EXPNUMBER)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_12() {
+ Token xsp;
+ xsp = jj_scanpos;
+ if (jj_3R_15()) {
+ jj_scanpos = xsp;
+ if (jj_3R_16()) {
+ jj_scanpos = xsp;
+ if (jj_3R_17()) {
+ jj_scanpos = xsp;
+ if (jj_3R_18()) return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ private boolean jj_3R_15() {
+ if (jj_scan_token(PLUS)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_14() {
+ Token xsp;
+ xsp = jj_scanpos;
+ if (jj_3R_21()) {
+ jj_scanpos = xsp;
+ if (jj_3R_22()) {
+ jj_scanpos = xsp;
+ if (jj_3R_23()) return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean jj_3R_21() {
+ if (jj_scan_token(TIMES)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_25() {
+ if (jj_scan_token(NUMBER)) return true;
+ return false;
+ }
+
private boolean jj_3R_28() {
if (jj_scan_token(LEFT_BRACES)) return true;
if (jj_scan_token(RIGHT_BRACES)) return true;
return false;
}
- private boolean jj_3R_21() {
- if (jj_scan_token(DIVIDE)) return true;
+ private boolean jj_3R_10() {
+ if (jj_3R_11()) return true;
+ Token xsp;
+ while (true) {
+ xsp = jj_scanpos;
+ if (jj_3R_12()) { jj_scanpos = xsp; break; }
+ }
return false;
}
@@ -709,12 +800,12 @@
return false;
}
- private boolean jj_3R_10() {
- if (jj_3R_11()) return true;
+ private boolean jj_3R_11() {
+ if (jj_3R_13()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
- if (jj_3R_12()) { jj_scanpos = xsp; break; }
+ if (jj_3R_14()) { jj_scanpos = xsp; break; }
}
return false;
}
@@ -724,7 +815,7 @@
return false;
}
- private boolean jj_3R_18() {
+ private boolean jj_3R_19() {
Token xsp;
xsp = jj_scanpos;
if (jj_3R_24()) {
@@ -764,41 +855,25 @@
return false;
}
- private boolean jj_3R_14() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_20()) {
- jj_scanpos = xsp;
- if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) {
- jj_scanpos = xsp;
- if (jj_3R_23()) return true;
- }
- }
- }
+ private boolean jj_3R_9() {
+ if (jj_scan_token(LEFT_BRACKET)) return true;
+ if (jj_3R_10()) return true;
+ if (jj_scan_token(RIGHT_BRACKET)) return true;
return false;
}
- private boolean jj_3R_20() {
- if (jj_scan_token(TIMES)) return true;
+ private boolean jj_3R_18() {
+ if (jj_scan_token(COMPARISON)) return true;
return false;
}
- private boolean jj_3R_9() {
- if (jj_scan_token(LEFT_BRACKET)) return true;
- if (jj_3R_10()) return true;
- if (jj_scan_token(RIGHT_BRACKET)) return true;
+ private boolean jj_3R_23() {
+ if (jj_scan_token(MODULO)) return true;
return false;
}
- private boolean jj_3R_11() {
- if (jj_3R_13()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_14()) { jj_scanpos = xsp; break; }
- }
+ private boolean jj_3R_34() {
+ if (jj_scan_token(FACTORIAL)) return true;
return false;
}
@@ -807,11 +882,6 @@
return false;
}
- private boolean jj_3R_23() {
- if (jj_scan_token(COMPARISON)) return true;
- return false;
- }
-
private boolean jj_3_1() {
if (jj_3R_8()) return true;
if (jj_scan_token(OPEN_PAR)) return true;
@@ -820,49 +890,22 @@
private boolean jj_3R_31() {
if (jj_scan_token(LOG)) return true;
- if (jj_3R_18()) return true;
+ if (jj_3R_19()) return true;
return false;
}
- private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_10()) return true;
+ private boolean jj_3R_33() {
+ if (jj_scan_token(POWER)) return true;
return false;
}
- private boolean jj_3R_22() {
- if (jj_scan_token(MODULO)) return true;
- return false;
- }
-
- private boolean jj_3R_34() {
- if (jj_scan_token(FACTORIAL)) return true;
- return false;
- }
-
- private boolean jj_3R_17() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
- return false;
- }
-
- private boolean jj_3R_30() {
- if (jj_scan_token(NOT)) return true;
+ private boolean jj_3_3() {
+ if (jj_scan_token(LEFT_BRACES)) return true;
if (jj_3R_10()) return true;
return false;
}
- private boolean jj_3R_27() {
- if (jj_scan_token(OPEN_PAR)) return true;
- if (jj_3R_10()) return true;
- return false;
- }
-
- private boolean jj_3R_33() {
- if (jj_scan_token(POWER)) return true;
- return false;
- }
-
- private boolean jj_3R_19() {
+ private boolean jj_3R_20() {
Token xsp;
xsp = jj_scanpos;
if (jj_3R_33()) {
@@ -872,29 +915,30 @@
return false;
}
- private boolean jj_3R_29() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_18()) return true;
+ private boolean jj_3R_17() {
+ if (jj_scan_token(BOOLEAN_LOGIC)) return true;
return false;
}
- private boolean jj_3R_16() {
- if (jj_scan_token(MINUS)) return true;
+ private boolean jj_3R_13() {
+ if (jj_3R_19()) return true;
+ Token xsp;
+ while (true) {
+ xsp = jj_scanpos;
+ if (jj_3R_20()) { jj_scanpos = xsp; break; }
+ }
return false;
}
- private boolean jj_3R_26() {
- if (jj_scan_token(EXPNUMBER)) return true;
+ private boolean jj_3R_30() {
+ if (jj_scan_token(NOT)) return true;
+ if (jj_3R_10()) return true;
return false;
}
- private boolean jj_3R_13() {
- if (jj_3R_18()) return true;
- Token xsp;
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_19()) { jj_scanpos = xsp; break; }
- }
+ private boolean jj_3R_27() {
+ if (jj_scan_token(OPEN_PAR)) return true;
+ if (jj_3R_10()) return true;
return false;
}
@@ -908,26 +952,19 @@
return false;
}
- private boolean jj_3R_12() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_15()) {
- jj_scanpos = xsp;
- if (jj_3R_16()) {
- jj_scanpos = xsp;
- if (jj_3R_17()) return true;
- }
- }
+ private boolean jj_3R_16() {
+ if (jj_scan_token(MINUS)) return true;
return false;
}
- private boolean jj_3R_15() {
- if (jj_scan_token(PLUS)) return true;
+ private boolean jj_3R_22() {
+ if (jj_scan_token(DIVIDE)) return true;
return false;
}
- private boolean jj_3R_25() {
- if (jj_scan_token(NUMBER)) return true;
+ private boolean jj_3R_29() {
+ if (jj_scan_token(MINUS)) return true;
+ if (jj_3R_19()) return true;
return false;
}
@@ -948,7 +985,7 @@
jj_la1_init_0();
}
private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0x18000000,0x80000001,0x4200,0x4200,0x203800,0x203800,0x400500,0x400500,0x80,0x80000,0x80,0x80000,0x68,0x8000,0x1c020400,};
+ jj_la1_0 = new int[] {0x18000000,0x80000001,0x4200,0x4200,0x3800,0x3800,0x600500,0x600500,0x80,0x80000,0x80,0x80000,0x68,0x8000,0x1c020400,};
}
final private JJCalls[] jj_2_rtns = new JJCalls[3];
private boolean jj_rescan = false;
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj 2015-04-21 12:25:38 UTC (rev 2192)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParser.jj 2015-04-21 12:59:30 UTC (rev 2193)
@@ -274,6 +274,7 @@
< AND :
"And"
| "AND"
+ | "and"
| "&&" >
}
@@ -282,6 +283,7 @@
< OR :
"OR"
| "Or"
+ | "or"
| "||" >
}
@@ -438,14 +440,6 @@
node = createModulo(leftChild, rightChild);
leftChild = node;
}
- | t = < COMPARISON > rightChild = TermLvl3()
- {
- type = Type.getTypeFor(t.image);
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
)*
{
return leftChild;
@@ -480,11 +474,56 @@
| t = < BOOLEAN_LOGIC > rightChild = TermLvl2()
{
type = Type.getTypeFor(t.image);
+
+ if (s.equalsIgnoreCase("or") || s.equals("||"))
+ {
+ type = ASTNode.Type.LOGICAL_OR;
+ }
+ else if (s.equalsIgnoreCase("and") || s.equals("&&"))
+ {
+ type = ASTNode.Type.LOGICAL_AND;
+ }
+ else if (s.equalsIgnoreCase("xor"))
+ {
+ type = ASTNode.Type.LOGICAL_XOR;
+ }
node = new ASTNode(type);
node.addChild(leftChild);
node.addChild(rightChild);
leftChild = node;
}
+ | t = < COMPARISON > rightChild = TermLvl2()
+ {
+ s = t.image;
+ if (s.equalsIgnoreCase("<"))
+ {
+ type = ASTNode.Type.RELATIONAL_LT;
+ }
+ else if (s.equalsIgnoreCase(">"))
+ {
+ type = ASTNode.Type.RELATIONAL_GT;
+ }
+ else if (s.equalsIgnoreCase("=="))
+ {
+ type = ASTNode.Type.RELATIONAL_EQ;
+ }
+ else if (s.equalsIgnoreCase("!="))
+ {
+ type = ASTNode.Type.RELATIONAL_NEQ;
+ }
+ else if (s.equalsIgnoreCase(">="))
+ {
+ type = ASTNode.Type.RELATIONAL_GEQ;
+ }
+ else if (s.equalsIgnoreCase("<="))
+ {
+ type = ASTNode.Type.RELATIONAL_LEQ;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
)*
{
return leftChild;
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java 2015-04-21 12:25:38 UTC (rev 2192)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/text/parser/FormulaParserTokenManager.java 2015-04-21 12:59:30 UTC (rev 2193)
@@ -45,7 +45,7 @@
if ((active0 & 0x8000000L) != 0L)
{
jjmatchedKind = 28;
- return 65;
+ return 69;
}
if ((active0 & 0x4000L) != 0L)
return 11;
@@ -57,7 +57,7 @@
{
jjmatchedKind = 28;
jjmatchedPos = 1;
- return 65;
+ return 69;
}
return -1;
default :
@@ -139,7 +139,7 @@
{
case 103:
if ((active0 & 0x8000000L) != 0L)
- return jjStartNfaWithStates_0(2, 27, 65);
+ return jjStartNfaWithStates_0(2, 27, 69);
break;
default :
break;
@@ -157,7 +157,7 @@
private int jjMoveNfa_0(int startState, int curPos)
{
int startsAt = 0;
- jjnewStateCnt = 65;
+ jjnewStateCnt = 69;
int i = 1;
jjstateSet[0] = startState;
int kind = 0x7fffffff;
@@ -172,18 +172,12 @@
{
switch(jjstateSet[--i])
{
- case 7:
- if ((0x3ff000000000000L & l) != 0L)
- jjCheckNAddStates(0, 2);
- else if (curChar == 46)
- jjCheckNAdd(8);
- break;
case 0:
if ((0x3ff000000000000L & l) != 0L)
{
if (kind > 3)
kind = 3;
- jjCheckNAddStates(3, 8);
+ jjCheckNAddStates(0, 5);
}
else if ((0x2400L & l) != 0L)
{
@@ -196,7 +190,7 @@
kind = 21;
}
else if (curChar == 38)
- jjAddStates(9, 10);
+ jjAddStates(6, 7);
else if (curChar == 46)
jjCheckNAddTwoStates(34, 8);
else if (curChar == 33)
@@ -220,7 +214,13 @@
else if (curChar == 60)
jjCheckNAdd(11);
break;
- case 65:
+ case 7:
+ if ((0x3ff000000000000L & l) != 0L)
+ jjCheckNAddStates(8, 10);
+ else if (curChar == 46)
+ jjCheckNAdd(8);
+ break;
+ case 69:
case 20:
if ((0x3ff000000000000L & l) == 0L)
break;
@@ -230,7 +230,7 @@
break;
case 1:
if ((0x3ff000000000000L & l) != 0L)
- jjCheckNAddStates(0, 2);
+ jjCheckNAddStates(8, 10);
break;
case 2:
if (curChar == 46)
@@ -296,7 +296,7 @@
break;
if (kind > 3)
kind = 3;
- jjCheckNAddStates(3, 8);
+ jjCheckNAddStates(0, 5);
break;
case 29:
if ((0x3ff000000000000L & l) == 0L)
@@ -336,7 +336,7 @@
break;
case 35:
if (curChar == 38)
- jjAddStates(9, 10);
+ jjAddStates(6, 7);
break;
case 36:
if (curChar == 38 && kind > 22)
@@ -384,12 +384,16 @@
jjAddStates(21, 24);
else if (curChar == 120)
jjAddStates(25, 26);
+ else if (curChar == 111)
+ jjCheckNAddTwoStates(47, 48);
+ else if (curChar == 97)
+ jjAddStates(27, 28);
else if (curChar == 78)
- jjAddStates(27, 28);
+ jjAddStates(29, 30);
else if (curChar == 110)
jjstateSet[jjnewStateCnt++] = 17;
break;
- case 65:
+ case 69:
if ((0x7fffffe87fffffeL & l) != 0L)
{
if (kind > 28)
@@ -405,7 +409,7 @@
break;
case 4:
if ((0x2000000020L & l) != 0L)
- jjAddStates(29, 30);
+ jjAddStates(31, 32);
break;
case 16:
if (curChar == 116 && kind > 26)
@@ -444,7 +448,7 @@
break;
case 24:
if (curChar == 78)
- jjAddStates(27, 28);
+ jjAddStates(29, 30);
break;
case 25:
if (curChar == 84 && kind > 26)
@@ -455,106 +459,116 @@
jjstateSet[jjnewStateCnt++] = 25;
break;
case 38:
+ if (curChar == 97)
+ jjAddStates(27, 28);
+ break;
+ case 39:
+ if (curChar == 100 && kind > 22)
+ kind = 22;
+ break;
+ case 40:
+ case 65:
+ if (curChar == 110)
+ jjCheckNAdd(39);
+ break;
+ case 41:
+ if (curChar == 100 && kind > 23)
+ kind = 23;
+ break;
+ case 42:
+ case 66:
+ if (curChar == 110)
+ jjCheckNAdd(41);
+ break;
+ case 43:
if (curChar == 124)
jjAddStates(11, 12);
break;
- case 39:
+ case 44:
if (curChar == 124 && kind > 22)
kind = 22;
break;
- case 40:
+ case 45:
if (curChar == 124 && kind > 24)
kind = 24;
break;
- case 41:
- if (curChar == 120)
- jjAddStates(25, 26);
+ case 46:
+ if (curChar == 111)
+ jjCheckNAddTwoStates(47, 48);
break;
- case 42:
+ case 47:
if (curChar == 114 && kind > 22)
kind = 22;
break;
- case 43:
- case 47:
+ case 48:
+ if (curChar == 114 && kind > 24)
+ kind = 24;
+ break;
+ case 49:
+ if (curChar == 120)
+ jjAddStates(25, 26);
+ break;
+ case 50:
+ case 54:
if (curChar == 111)
- jjCheckNAdd(42);
+ jjCheckNAdd(47);
break;
- case 44:
+ case 51:
if (curChar == 114 && kind > 25)
kind = 25;
break;
- case 45:
case 52:
+ case 59:
if (curChar == 111)
- jjCheckNAdd(44);
+ jjCheckNAdd(51);
break;
- case 46:
+ case 53:
if (curChar == 88)
jjAddStates(21, 24);
break;
- case 48:
+ case 55:
if (curChar == 82 && kind > 22)
kind = 22;
break;
- case 49:
+ case 56:
if (curChar == 79)
- jjCheckNAdd(48);
+ jjCheckNAdd(55);
break;
- case 50:
+ case 57:
if (curChar == 82 && kind > 25)
kind = 25;
break;
- case 51:
+ case 58:
if (curChar == 79)
- jjstateSet[jjnewStateCnt++] = 50;
+ jjstateSet[jjnewStateCnt++] = 57;
break;
- case 53:
+ case 60:
if (curChar == 79)
jjCheckNAddStates(17, 20);
break;
- case 54:
+ case 61:
if (curChar == 82 && kind > 24)
kind = 24;
break;
- case 55:
- if (curChar == 114 && kind > 24)
- kind = 24;
- break;
- case 56:
+ case 62:
if (curChar == 65)
jjAddStates(13, 16);
break;
- case 57:
+ case 63:
if (curChar == 68 && kind > 22)
kind = 22;
break;
- case 58:
+ case 64:
if (curChar == 78)
- jjstateSet[jjnewStateCnt++] = 57;
+ jjstateSet[jjnewStateCnt++] = 63;
break;
- case 59:
- if (curChar == 100 && kind > 22)
- kind = 22;
- break;
- case 60:
- if (curChar == 110)
- jjstateSet[jjnewStateCnt++] = 59;
- break;
- case 61:
- if (curChar == 100 && kind > 23)
- kind = 23;
- break;
- case 62:
- if (curChar == 110)
- jjstateSet[jjnewStateCnt++] = 61;
- break;
- case 63:
+ case 67:
if (curChar == 68 && kind > 23)
kind = 23;
break;
- case 64:
+ case 68:
if (curChar == 78)
- jjstateSet[jjnewStateCnt++] = 63;
+ jjstateSet[jjnewStateCnt++] = 67;
break;
default : break;
}
@@ -579,15 +593,16 @@
kind = 0x7fffffff;
}
++curPos;
- if ((i = jjnewStateCnt) == (startsAt = 65 - (jjnewStateCnt = startsAt)))
+ if ((i = jjnewStateCnt) == (startsAt = 69 - (jjnewStateCnt = startsAt)))
return curPos;
try { curChar = input_stream.readChar(); }
catch(java.io.IOException e) { return curPos; }
}
}
static final int[] jjnextStates = {
- 1, 2, 4, 29, 30, 31, 1, 2, 4, 36, 37, 39, 40, 58, 60, 62,
- 64, 42, 48, 54, 55, 47, 49, 51, 52, 43, 45, 26, 27, 5, 6,
+ 29, 30, 31, 1, 2, 4, 36, 37, 1, 2, 4, 44, 45, 64, 65, 66,
+ 68, 47, 55, 61, 48, 54, 56, 58, 59, 50, 52, 40, 42, 26, 27, 5,
+ 6,
};
/** Token literal values. */
@@ -607,8 +622,8 @@
0x6L,
};
protected SimpleCharStream input_stream;
-private final int[] jjrounds = new int[65];
-private final int[] jjstateSet = new int[130];
+private final int[] jjrounds = new int[69];
+private final int[] jjstateSet = new int[138];
protected char curChar;
/** Constructor. */
public FormulaParserTokenManager(SimpleCharStream stream){
@@ -635,7 +650,7 @@
{
int i;
jjround = 0x80000001;
- for (i = 65; i-- > 0;)
+ for (i = 69; i-- > 0;)
jjrounds[i] = 0x80000000;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-21 12:25:50
|
Revision: 2192
http://sourceforge.net/p/jsbml/code/2192
Author: niko-rodrigue
Date: 2015-04-21 12:25:38 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
corrected the ASTNode.getReal and ASTNode.isReal method to return correct values for Exponetial and Rational numbers as well, should work with any numbers, I think
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-04-21 12:21:07 UTC (rev 2191)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/ASTNode.java 2015-04-21 12:25:38 UTC (rev 2192)
@@ -1548,9 +1548,8 @@
* @param exponent
*/
public ASTNode(double mantissa, int exponent) {
- astnode2 = new ASTCnExponentialNode();
- ((ASTCnExponentialNode) astnode2).setMantissa(mantissa);
- ((ASTCnExponentialNode) astnode2).setExponent(exponent);
+ this(ASTNode.Type.REAL_E);
+ setValue(mantissa, exponent);
}
/**
@@ -2800,7 +2799,22 @@
* if this node is not of type real.
*/
public double getReal() {
- return isReal() ? ((ASTCnRealNode) astnode2).getReal() : Double.NaN;
+ if (isReal()) { // TODO - return the value for any AStNumber ?
+ // TODO - modify ASTCnNumberNode to return double for the getNumber() method
+ if (astnode2 instanceof ASTCnRealNode) {
+ return ((ASTCnRealNode) astnode2).getNumber();
+ }
+ else if (astnode2 instanceof ASTCnExponentialNode) {
+ ASTCnExponentialNode ast = (ASTCnExponentialNode) astnode2;
+ return Double.valueOf(ast.getMantissa() + "e" + ast.getExponent());
+ }
+ else if (astnode2 instanceof ASTCnRationalNode) {
+ ASTCnRationalNode ast = (ASTCnRationalNode) astnode2;
+ return Double.valueOf(ast.getNumerator() + "/" + ast.getDenominator());
+ }
+ }
+
+ return Double.NaN;
}
/**
@@ -3164,7 +3178,8 @@
*/
public boolean isReal() {
return astnode2 instanceof ASTCnRealNode
- || astnode2 instanceof ASTCnRationalNode;
+ || astnode2 instanceof ASTCnRationalNode
+ || astnode2 instanceof ASTCnExponentialNode;
}
/**
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2015-04-21 12:21:14
|
Revision: 2191
http://sourceforge.net/p/jsbml/code/2191
Author: andreas-draeger
Date: 2015-04-21 12:21:07 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
There is now a new (deprecated) method to create a StoichiometryMath object on SpeciesReference.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/SpeciesReference.java
Modified: trunk/core/src/org/sbml/jsbml/SpeciesReference.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SpeciesReference.java 2015-04-21 11:55:22 UTC (rev 2190)
+++ trunk/core/src/org/sbml/jsbml/SpeciesReference.java 2015-04-21 12:21:07 UTC (rev 2191)
@@ -198,6 +198,20 @@
return isSetStoichiometry() ? false : true;
}
+ /**
+ *
+ * @param math
+ * @return
+ * @deprecated since SBML Level 3 this should not be used anymore.
+ */
+ @Deprecated
+ public StoichiometryMath createStoichiometryMath(ASTNode math) {
+ StoichiometryMath sm = new StoichiometryMath(getLevel(), getVersion());
+ sm.setMath(math);
+ setStoichiometryMath(sm);
+ return sm;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SimpleSpeciesReference#equals(java.lang.Object)
*/
@@ -345,8 +359,8 @@
/**
*
- * @return the stoichiometryMath of this SpeciesReference. Can be null if
- * the stoichiometryMath is not set.
+ * @return the stoichiometryMath of this SpeciesReference. Can be {@code null}
+ * if the stoichiometryMath is not set.
* @deprecated since SBML Level 3 this should not be used anymore.
*/
@Deprecated
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <nik...@us...> - 2015-04-21 11:55:25
|
Revision: 2190
http://sourceforge.net/p/jsbml/code/2190
Author: niko-rodrigue
Date: 2015-04-21 11:55:22 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
added some svn:ignore properties to avoid some common files that we don't want in the repository
Property Changed:
----------------
branches/astnode2-merging-alternate/
branches/astnode2-merging-alternate/core/
branches/astnode2-merging-alternate/core/dist/
Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate 2015-04-21 11:48:11 UTC (rev 2189)
+++ branches/astnode2-merging-alternate 2015-04-21 11:55:22 UTC (rev 2190)
Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,5 ##
+.classpath
+.project
+dist
+build
+bin
Index: branches/astnode2-merging-alternate/core
===================================================================
--- branches/astnode2-merging-alternate/core 2015-04-21 11:48:11 UTC (rev 2189)
+++ branches/astnode2-merging-alternate/core 2015-04-21 11:55:22 UTC (rev 2190)
Property changes on: branches/astnode2-merging-alternate/core
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+build
Index: branches/astnode2-merging-alternate/core/dist
===================================================================
--- branches/astnode2-merging-alternate/core/dist 2015-04-21 11:48:11 UTC (rev 2189)
+++ branches/astnode2-merging-alternate/core/dist 2015-04-21 11:55:22 UTC (rev 2190)
Property changes on: branches/astnode2-merging-alternate/core/dist
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-04-21 11:48:14
|
Revision: 2189
http://sourceforge.net/p/jsbml/code/2189
Author: niko-rodrigue
Date: 2015-04-21 11:48:11 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
cleaned a bit by removing the bin folder + added some cast to be able to compile the code + moved one test file from core to the base dir as it was using the arrays package
Modified Paths:
--------------
branches/astnode2-merging-alternate/core/build.xml
branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
Added Paths:
-----------
branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/
branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/
branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java
Removed Paths:
-------------
branches/astnode2-merging-alternate/bin/
branches/astnode2-merging-alternate/core/dist/jsbml-1.1-a1/
branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java
Modified: branches/astnode2-merging-alternate/core/build.xml
===================================================================
--- branches/astnode2-merging-alternate/core/build.xml 2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/build.xml 2015-04-21 11:48:11 UTC (rev 2189)
@@ -167,8 +167,7 @@
<copy todir="${build.src}" overwrite="yes">
<fileset
dir="${src.dir}"
- excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip org/sbml/jsbml/math/**">
- <!-- TODO remove org/sbml/jsbml/math from the filters when the package is ready -->
+ excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip">
</fileset>
</copy>
Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java 2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java 2015-04-21 11:48:11 UTC (rev 2189)
@@ -122,7 +122,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> and(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> value = dimensionless();
+ ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
boolean val = true;
for (ASTNode2 v : values) {
val &= v.compile(this).toBoolean();
@@ -647,7 +647,7 @@
*/
@Override
public <T> ASTNode2Value<Double> getConstantE() {
- ASTNode2Value<Double> v = dimensionless();
+ ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
v.setValue(Math.E);
return v;
}
@@ -657,7 +657,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> getConstantFalse() {
- ASTNode2Value<Boolean> v = dimensionless();
+ ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
v.setValue(false);
return v;
}
@@ -667,7 +667,7 @@
*/
@Override
public <T> ASTNode2Value<Double> getConstantPi() {
- ASTNode2Value<Double> v = dimensionless();
+ ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
v.setValue(Math.PI);
return v;
}
@@ -677,7 +677,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> getConstantTrue() {
- ASTNode2Value<Boolean> v = dimensionless();
+ ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
v.setValue(true);
return v;
}
@@ -796,7 +796,7 @@
@Override
// TODO: Specify generic type T i.e. ASTNode2Value<?>
public <T> ASTNode2Value<?> lt(ASTNode2 left, ASTNode2 right) throws SBMLException {
- ASTNode2Value<?> v = dimensionless(), leftvalue, rightvalue;
+ ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -851,7 +851,7 @@
@Override
// TODO: Specify type T i.e. ASTNode2Value<Boolean>
public ASTNode2Value<?> neq(ASTNode2 left, ASTNode2 right) throws SBMLException {
- ASTNode2Value<?> v = dimensionless(), leftvalue, rightvalue;
+ ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -864,7 +864,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> not(ASTNode2 value) throws SBMLException {
- ASTNode2Value<Boolean> v = dimensionless();
+ ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
v.setValue(!value.compile(this).toBoolean());
return v;
}
@@ -874,7 +874,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> or(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> v = dimensionless();
+ ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
v.setValue(false);
for (ASTNode2 value : values) {
if (value.compile(this).toBoolean()) {
@@ -1326,7 +1326,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> xor(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> value = dimensionless();
+ ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
boolean v = false;
for (int i = 0; i < values.size(); i++) {
if (values.get(i).compile(this).toBoolean()) {
Deleted: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java 2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java 2015-04-21 11:48:11 UTC (rev 2189)
@@ -1,119 +0,0 @@
-/*
- * $Id: RecursionTest.java 2088 2014-11-16 06:56:46Z kofiav $
- * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/test/org/sbml/jsbml/math/test/RecursionTest.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) 2009-2014 jointly by the following organizations:
- * 1. The University of Tuebingen, Germany
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- * 3. The California Institute of Technology, Pasadena, CA, USA
- * 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is provided
- * in the file named "LICENSE.txt" included with this software distribution
- * and also available online as <http://sbml.org/Software/JSBML/License>.
- * ----------------------------------------------------------------------------
- */
-package org.sbml.jsbml.math.test;
-
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.AssignmentRule;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.Parameter;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.ext.arrays.ArraysConstants;
-import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
-import org.sbml.jsbml.ext.arrays.Dimension;
-import org.sbml.jsbml.ext.arrays.Index;
-import org.sbml.jsbml.text.parser.ParseException;
-
-/**
- *
- * @author Andreas Dräger
- * @version $Rev: 2088 $
- * @since 1.0
- * @date 16.10.2014
- */
-public class RecursionTest {
-
- /**
- * @param args
- * @throws ParseException
- */
- public static void main(String[] args) throws ParseException {
-// ASTNode ast = ASTNode.parseFormula("3 * 1/1");
-// System.out.println(ast.getType());
-// JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(ast)));
-// System.out.println(ast.toFormula());
-
- SBMLDocument doc = new SBMLDocument(3,1);
- Model model = doc.createModel();
-
- Parameter n = new Parameter("n");
- n.setValue(10);
- model.addParameter(n);
-
- Parameter X = new Parameter("X");
-
- model.addParameter(X);
- ArraysSBasePlugin arraysSBasePluginX = new ArraysSBasePlugin(X);
-
- X.addExtension(ArraysConstants.shortLabel, arraysSBasePluginX);
-
- Dimension dimX = new Dimension("i");
- dimX.setSize(n.getId());
- dimX.setArrayDimension(0);
-
- arraysSBasePluginX.addDimension(dimX);
-
- Parameter Y = new Parameter("Y");
-
- model.addParameter(Y);
- ArraysSBasePlugin arraysSBasePluginY = new ArraysSBasePlugin(Y);
-
- Y.addExtension(ArraysConstants.shortLabel, arraysSBasePluginY);
- Dimension dimY = new Dimension("i");
- dimY.setSize(n.getId());
- dimY.setArrayDimension(0);
-
- arraysSBasePluginY.addDimension(dimY);
-
- AssignmentRule rule = new AssignmentRule();
- model.addRule(rule);
- rule.setMetaId("rule");
-
- ArraysSBasePlugin arraysSBasePluginRule = new ArraysSBasePlugin(rule);
- rule.addExtension(ArraysConstants.shortLabel, arraysSBasePluginRule);
-
- Dimension dimRule = new Dimension("i");
- dimRule.setSize(n.getId());
- dimRule.setArrayDimension(0);
- arraysSBasePluginRule.addDimension(dimRule);
-
- Index indexRule = new Index();
- indexRule.setArrayDimension(0);
- indexRule.setReferencedAttribute("variable");
- ASTNode indexMath = new ASTNode();
-
- indexMath = ASTNode.diff(new ASTNode(9), new ASTNode("i"));
- indexRule.setMath(indexMath);
- arraysSBasePluginRule.addIndex(indexRule);
-
- rule.setVariable("Y");
- ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
-
- rule.setMath(ruleMath);
-
- JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(indexMath)));
-
- }
-
-}
Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java 2015-04-21 11:48:11 UTC (rev 2189)
@@ -25,6 +25,7 @@
import java.util.Map;
import java.util.ResourceBundle;
+import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.ResourceManager;
@@ -303,5 +304,5 @@
builder.append("]");
return builder.toString();
}
-
+
}
Added: branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java
===================================================================
--- branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java (rev 0)
+++ branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java 2015-04-21 11:48:11 UTC (rev 2189)
@@ -0,0 +1,119 @@
+/*
+ * $Id: RecursionTest.java 2088 2014-11-16 06:56:46Z kofiav $
+ * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/test/org/sbml/jsbml/math/test/RecursionTest.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) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.math.test;
+
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTree;
+
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.AssignmentRule;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Parameter;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.arrays.ArraysConstants;
+import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
+import org.sbml.jsbml.ext.arrays.Dimension;
+import org.sbml.jsbml.ext.arrays.Index;
+import org.sbml.jsbml.text.parser.ParseException;
+
+/**
+ *
+ * @author Andreas Dräger
+ * @version $Rev: 2088 $
+ * @since 1.0
+ * @date 16.10.2014
+ */
+public class RecursionTest {
+
+ /**
+ * @param args
+ * @throws ParseException
+ */
+ public static void main(String[] args) throws ParseException {
+// ASTNode ast = ASTNode.parseFormula("3 * 1/1");
+// System.out.println(ast.getType());
+// JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(ast)));
+// System.out.println(ast.toFormula());
+
+ SBMLDocument doc = new SBMLDocument(3,1);
+ Model model = doc.createModel();
+
+ Parameter n = new Parameter("n");
+ n.setValue(10);
+ model.addParameter(n);
+
+ Parameter X = new Parameter("X");
+
+ model.addParameter(X);
+ ArraysSBasePlugin arraysSBasePluginX = new ArraysSBasePlugin(X);
+
+ X.addExtension(ArraysConstants.shortLabel, arraysSBasePluginX);
+
+ Dimension dimX = new Dimension("i");
+ dimX.setSize(n.getId());
+ dimX.setArrayDimension(0);
+
+ arraysSBasePluginX.addDimension(dimX);
+
+ Parameter Y = new Parameter("Y");
+
+ model.addParameter(Y);
+ ArraysSBasePlugin arraysSBasePluginY = new ArraysSBasePlugin(Y);
+
+ Y.addExtension(ArraysConstants.shortLabel, arraysSBasePluginY);
+ Dimension dimY = new Dimension("i");
+ dimY.setSize(n.getId());
+ dimY.setArrayDimension(0);
+
+ arraysSBasePluginY.addDimension(dimY);
+
+ AssignmentRule rule = new AssignmentRule();
+ model.addRule(rule);
+ rule.setMetaId("rule");
+
+ ArraysSBasePlugin arraysSBasePluginRule = new ArraysSBasePlugin(rule);
+ rule.addExtension(ArraysConstants.shortLabel, arraysSBasePluginRule);
+
+ Dimension dimRule = new Dimension("i");
+ dimRule.setSize(n.getId());
+ dimRule.setArrayDimension(0);
+ arraysSBasePluginRule.addDimension(dimRule);
+
+ Index indexRule = new Index();
+ indexRule.setArrayDimension(0);
+ indexRule.setReferencedAttribute("variable");
+ ASTNode indexMath = new ASTNode();
+
+ indexMath = ASTNode.diff(new ASTNode(9), new ASTNode("i"));
+ indexRule.setMath(indexMath);
+ arraysSBasePluginRule.addIndex(indexRule);
+
+ rule.setVariable("Y");
+ ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
+
+ rule.setMath(ruleMath);
+
+ JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(indexMath)));
+
+ }
+
+}
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