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[Jsbml-svn] SF.net SVN: jsbml:[1879] trunk/modules/celldesigner/src/org/sbml/jsbml/ celldesigner
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From: <yva...@us...> - 2014-07-16 08:26:44
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Revision: 1879
http://sourceforge.net/p/jsbml/code/1879
Author: yvazirabad
Date: 2014-07-16 08:26:36 +0000 (Wed, 16 Jul 2014)
Log Message:
-----------
CD/JSBML Synchronization additions in AbstractCellDesignerPlugin
few methods changed in PluginSBMLReader to protected visibility from private
SwingWork renamed to CellDesignerModelConverter
Modified Paths:
--------------
trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/AbstractCellDesignerPlugin.java
trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/PluginSBMLReader.java
Added Paths:
-----------
trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/CellDesignerModelConverter.java
Modified: trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/AbstractCellDesignerPlugin.java
===================================================================
--- trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/AbstractCellDesignerPlugin.java 2014-07-15 22:31:25 UTC (rev 1878)
+++ trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/AbstractCellDesignerPlugin.java 2014-07-16 08:26:36 UTC (rev 1879)
@@ -23,18 +23,34 @@
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import javax.swing.SwingWorker;
import javax.xml.stream.XMLStreamException;
import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
+import jp.sbi.celldesigner.plugin.PluginCompartment;
import jp.sbi.celldesigner.plugin.PluginModel;
+import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.util.TreeNodeChangeListener;
/**
* A basic implementation of a CellDesigner plug-in that takes care of
@@ -65,7 +81,7 @@
/**
* Map of CellDesigner PluginModels and JSBML Models
*/
- protected Map<PluginModel, Model> modelMap= new HashMap<PluginModel, Model>();
+ protected final Map<PluginModel, Model> modelMap = Collections.synchronizedMap(new HashMap<PluginModel, Model>());
/**
*
@@ -78,11 +94,7 @@
reader = new PluginSBMLReader();
writer = new PluginSBMLWriter(this);
} catch (Throwable t) {
- t.printStackTrace();
- Throwable cause = t.getCause();
- if (cause != null) {
- cause.printStackTrace();
- }
+ new GUIErrorConsole(t);
}
}
@@ -107,15 +119,16 @@
public void startPlugin() throws XMLStreamException {
setStarted(true);
// Synchronize changes from this plug-in to CellDesigner:
- if (!modelMap.containsKey(getSelectedModel())) {
- SwingWorker<SBMLDocument, Throwable> worker = new SwingWork(getReader(), getSelectedModel());
+ if (!compareModels(getSelectedModel())) {
+ SwingWorker<SBMLDocument, Throwable> worker = new CellDesignerModelConverter(getReader(), getSelectedModel());
final AbstractCellDesignerPlugin plugin = this;
worker.addPropertyChangeListener(new PropertyChangeListener() {
@Override
public void propertyChange(PropertyChangeEvent evt) {
if (evt.getPropertyName().equals("state") && evt.getNewValue().equals(SwingWorker.StateValue.DONE)) {
try {
- SwingWork swing = (SwingWork)evt.getSource();
+ CellDesignerModelConverter swing = (CellDesignerModelConverter)evt.getSource();
+ //JOptionPane.showMessageDialog(null, new JScrollPane(new JTextArea("Called inside startPlugin")));
document = swing.get();
document.addTreeNodeChangeListener(new PluginChangeListener(plugin));
modelMap.put(swing.getPluginModel(), document.getModel());
@@ -138,6 +151,43 @@
return document;
}
+ public boolean compareModels(PluginModel sbase)
+ {
+ for (PluginModel key : modelMap.keySet()) {
+ PluginModel pModel = key;
+ // JOptionPane.showMessageDialog(null, new JScrollPane(new JTextArea("checkSize of the mapInside: "+modelMap.size()+"\t"+sbase.getId().trim()+"\t"+pModel.getId().trim()+
+ // "\t"+pModel.getId().trim().equals(sbase.getId().trim()))));
+ if (pModel.getId().trim().equals(sbase.getId().trim()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public Model getAssociatedModel(PluginModel pModel)
+ {
+ for (Map.Entry<PluginModel, Model> entry : modelMap.entrySet()) {
+ PluginModel pluginModel = entry.getKey();
+ Model model = entry.getValue();
+ if (pluginModel.getId().equals(pModel.getId())) {
+ return model;
+ }
+ }
+ return null;
+ }
+
+ public void printMap()
+ {
+ String output = "";
+ for (Map.Entry<PluginModel, Model> entry : modelMap.entrySet()) {
+ PluginModel pModel = entry.getKey();
+ Model model = entry.getValue();
+ output += pModel.getId() + "\tmodel Id: " + model.getId() + "\tSize of the map: "+modelMap.size()+"\n";
+ }
+ JOptionPane.showMessageDialog(null, new JScrollPane(new JTextArea(output)));
+ }
+
/* (non-Javadoc)
* @see jp.sbi.celldesigner.plugin.CellDesignerPlug#modelClosed(jp.sbi.celldesigner.plugin.PluginSBase)
*/
@@ -154,8 +204,18 @@
*/
@Override
public void modelOpened(PluginSBase sbase) {
- // TODO Auto-generated method stub
- System.out.println("modelOpened " + sbase);
+ if (sbase instanceof PluginModel)
+ {
+ PluginModel pModel = (PluginModel) sbase;
+ SwingWorker<SBMLDocument, Throwable> worker = new CellDesignerModelConverter(getReader(), pModel);
+ if (!compareModels(pModel)) {
+ try {
+ modelMap.put(pModel, reader.convertModel(pModel).getModel());
+ } catch (XMLStreamException e) {
+ new GUIErrorConsole(e);
+ }
+ }
+ }
}
/* (non-Javadoc)
@@ -163,8 +223,10 @@
*/
@Override
public void modelSelectChanged(PluginSBase sbase) {
- // TODO Auto-generated method stub
- System.out.println("modelSelectChanged " + sbase);
+ if (sbase instanceof PluginModel)
+ {
+ PluginModel pModel = (PluginModel)sbase;
+ }
}
/* (non-Javadoc)
@@ -181,8 +243,68 @@
*/
@Override
public void SBaseChanged(PluginSBase sbase) {
- // TODO Auto-generated method stub
- System.out.println("SBaseChanged " + sbase);
+ PluginModel currentModel = getSelectedModel();
+ Model associatedJSBMLModel = getAssociatedModel(currentModel);
+ Layout layout = ((LayoutModelPlugin)associatedJSBMLModel.getExtension("layout")).getLayout(0);
+ List<TreeNodeChangeListener> treeNodeList = new ArrayList<TreeNodeChangeListener>();
+ document = new SBMLDocument(associatedJSBMLModel.getLevel(), associatedJSBMLModel.getVersion());
+ document.setModel(associatedJSBMLModel);
+
+ treeNodeList.addAll(document.getListOfTreeNodeChangeListeners());
+ document.removeAllTreeNodeChangeListeners();
+
+ if (sbase instanceof PluginCompartment)
+ {
+ PluginCompartment pCompartment = (PluginCompartment)sbase;
+ Compartment newCompartment = null;
+ try {
+ newCompartment = reader.readCompartment(pCompartment);
+ } catch (XMLStreamException e) {
+ new GUIErrorConsole(e);
+ }
+
+ layout.removeCompartmentGlyph("cGlyph_" + pCompartment.getId());
+ layout.removeTextGlyph("tGlyph_" + pCompartment.getId());
+ LayoutConverter.extractLayout((PluginCompartment)sbase, layout);
+ associatedJSBMLModel.removeCompartment(newCompartment.getId());
+ associatedJSBMLModel.addCompartment(newCompartment);
+ }
+ else if (sbase instanceof PluginSpecies)
+ {
+ PluginSpecies pSpecies = (PluginSpecies) sbase;
+ Species newSpecies = null;
+ try {
+ newSpecies = reader.readSpecies(pSpecies);
+ } catch (XMLStreamException e) {
+ new GUIErrorConsole(e);
+ }
+ associatedJSBMLModel.removeSpecies(pSpecies.getId());
+ associatedJSBMLModel.addSpecies(newSpecies);
+ }
+ else if (sbase instanceof PluginSpeciesAlias)
+ {
+ PluginSpeciesAlias pSpeciesAlias = (PluginSpeciesAlias) sbase;
+ layout.removeSpeciesGlyph("sGlyph_" + pSpeciesAlias.getSpecies().getId());
+ layout.removeTextGlyph("tGlyph_" + pSpeciesAlias.getSpecies().getId());
+ LayoutConverter.extractLayout(pSpeciesAlias, layout);
+ }
+ else if (sbase instanceof PluginReaction)
+ {
+ PluginReaction pReaction = (PluginReaction) sbase;
+ Reaction newReaction = null;
+ try {
+ newReaction = reader.readReaction(pReaction);
+ } catch (XMLStreamException e) {
+ new GUIErrorConsole(e);
+ }
+ layout.removeReactionGlyph("rGlyph_" + pReaction.getId());
+ layout.removeTextGlyph("tGlyph_" + pReaction.getId());
+ LayoutConverter.extractLayout(pReaction, layout);
+ associatedJSBMLModel.removeReaction(newReaction.getId());
+ associatedJSBMLModel.addReaction(newReaction);
+ }
+ document.setModel(associatedJSBMLModel);
+ document.addAllChangeListeners(treeNodeList);
}
/* (non-Javadoc)
Copied: trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/CellDesignerModelConverter.java (from rev 1868, trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/SwingWork.java)
===================================================================
--- trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/CellDesignerModelConverter.java (rev 0)
+++ trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/CellDesignerModelConverter.java 2014-07-16 08:26:36 UTC (rev 1879)
@@ -0,0 +1,81 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 6. Marquette University, Milwaukee, WI, USA
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.celldesigner;
+
+import javax.swing.SwingWorker;
+
+import jp.sbi.celldesigner.plugin.PluginModel;
+
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.layout.LayoutConstants;
+import org.sbml.jsbml.ext.render.RenderConstants;
+
+
+/**
+ * @author Ibrahim Vazirabad
+ * @version $Rev$
+ * @since 1.0
+ * @date Jun 10, 2014
+ */
+public class CellDesignerModelConverter extends SwingWorker<SBMLDocument, Throwable> {
+
+ private PluginSBMLReader sbmlReader;
+ private PluginModel pluginModel;
+
+
+ /**
+ * @return the pluginModel
+ */
+ public PluginModel getPluginModel() {
+ return pluginModel;
+ }
+
+ /**
+ * @param reader
+ * @param selectedModel
+ */
+ public CellDesignerModelConverter(PluginSBMLReader reader, PluginModel selectedModel) {
+ sbmlReader=reader;
+ pluginModel=selectedModel;
+ }
+
+ @Override
+ protected SBMLDocument doInBackground() throws Exception {
+ try{
+ Model model = sbmlReader.convertModel(pluginModel);
+ SBMLDocument doc = new SBMLDocument(model.getLevel(), model.getVersion());
+ doc.addNamespace(LayoutConstants.shortLabel, "xmlns", LayoutConstants.getNamespaceURI(doc.getLevel(), doc.getVersion()));
+ doc.addNamespace(RenderConstants.shortLabel, "xmlns", RenderConstants.getNamespaceURI(doc.getLevel(), doc.getVersion()));
+ doc.getSBMLDocumentAttributes().put(LayoutConstants.shortLabel + ":required", "false");
+ doc.getSBMLDocumentAttributes().put(RenderConstants.shortLabel + ":required", "false");
+ doc.setModel(model);
+ return doc;
+ }
+ catch (Throwable e)
+ {
+ publish(e);
+ }
+ return null;
+ }
+};
Modified: trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/PluginSBMLReader.java
===================================================================
--- trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/PluginSBMLReader.java 2014-07-15 22:31:25 UTC (rev 1878)
+++ trunk/modules/celldesigner/src/org/sbml/jsbml/celldesigner/PluginSBMLReader.java 2014-07-16 08:26:36 UTC (rev 1879)
@@ -233,7 +233,7 @@
* @return
* @throws XMLStreamException
*/
- private Compartment readCompartment(PluginCompartment compartment) throws XMLStreamException {
+ protected Compartment readCompartment(PluginCompartment compartment) throws XMLStreamException {
Compartment c = new Compartment(compartment.getId(), level, version);
PluginUtils.transferNamedSBaseProperties(compartment, c);
if ((compartment.getOutside() != null) && (compartment.getOutside().length() > 0) && (c.getLevel() < 3)) {
@@ -480,7 +480,7 @@
PluginCompartment pCompartment = originalModel.getCompartment(i);
model.addCompartment(readCompartment(pCompartment));
LayoutConverter.extractLayout(pCompartment, layout);
- RenderConverter.extractRenderInformation(pCompartment, renderPlugin);
+ //RenderConverter.extractRenderInformation(pCompartment, renderPlugin, layout);
//gets the compartment size
layout.createDimensions("Layout_Size", originalModel.getCompartment(i).getWidth(),
originalModel.getCompartment(i).getHeight(), 1d);
@@ -609,7 +609,7 @@
* @return
* @throws XMLStreamException
*/
- private Reaction readReaction(PluginReaction reac) throws XMLStreamException {
+ protected Reaction readReaction(PluginReaction reac) throws XMLStreamException {
logger.debug("Translating reaction " + reac.getId());
Reaction reaction = new Reaction(reac.getId(), level, version);
PluginUtils.transferNamedSBaseProperties(reac, reaction);
@@ -675,7 +675,7 @@
* @return
* @throws XMLStreamException
*/
- private Species readSpecies(PluginSpecies species) throws XMLStreamException {
+ protected Species readSpecies(PluginSpecies species) throws XMLStreamException {
Species s = new Species(level, version);
PluginUtils.transferNamedSBaseProperties(species, s);
int sbo = SBO.convertAlias2SBO(species.getSpeciesAlias(0).getType());
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