Author: mes
Date: 2012-04-06 14:19:10 -0700 (Fri, 06 Apr 2012)
New Revision: 28756
Added:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBFilter.java
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java
Removed:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java
Modified:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml
Log:
began rename to CDB
Modified: csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml
===================================================================
--- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml 2012-04-06
21:14:41 UTC (rev 28755)
+++ csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml 2012-04-06
21:19:10 UTC (rev 28756)
@@ -11,7 +11,7 @@
<groupId>cytoscape</groupId>
<artifactId>gxp-reader</artifactId>
<packaging>jar</packaging>
- <name>GXP Reader Plugin</name>
+ <name>CDB Reader Plugin</name>
<build>
<plugins>
@@ -33,7 +33,7 @@
<configuration>
<archive>
<manifestEntries>
-
<Cytoscape-Plugin>cytoscape.gxp.GXPReaderPlugin</Cytoscape-Plugin>
+
<Cytoscape-Plugin>cytoscape.gxp.CDBReaderPlugin</Cytoscape-Plugin>
</manifestEntries>
</archive>
<descriptors>
Copied:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBFilter.java
(from rev 28754,
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java)
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBFilter.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBFilter.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -0,0 +1,81 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ 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; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.gxp;
+
+import cytoscape.data.ImportHandler;
+
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.util.CyFileFilter;
+
+import java.io.File;
+import java.io.IOException;
+
+
+public class CDBFilter extends CyFileFilter {
+ /**
+ * CDB Files are Graphs.
+ */
+ private static String fileNature = ImportHandler.GRAPH_NATURE;
+
+ /**
+ * File Extensions.
+ */
+ private static String[] fileExtensions = { "cdb" };
+
+ /**
+ * Filter Description.
+ */
+ private static String description = "CDB files";
+
+ /**
+ * Constructor.
+ */
+ public CDBFilter() {
+ super(fileExtensions, description, fileNature);
+ }
+
+ /**
+ * Gets the appropirate GraphReader object.
+ *
+ * @param fileName File Name.
+ * @return GraphReader Object.
+ */
+ public GraphReader getReader(String fileName) {
+ return new CDBGraphReader(fileName);
+ }
+}
Copied:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java
(from rev 28754,
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java)
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -0,0 +1,211 @@
+
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ 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; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+
+package cytoscape.gxp;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+
+import org.jdom.input.SAXBuilder;
+
+
+import cytoscape.data.readers.AbstractGraphReader;
+import cytoscape.data.readers.GraphReader;
+
+import cytoscape.view.CyNetworkView;
+import cytoscape.view.CytoscapeDesktop;
+
+import cytoscape.visual.*;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.net.URL;
+
+import java.util.*;
+
+
+/**
+ * @author Mike Smoot
+ */
+public class CDBGraphReader extends AbstractGraphReader implements GraphReader
{
+ // node id from file -> node
+ private Map<String,CyNode> geneIdMap;
+
+ private List<Integer> nodeIds;
+ private List<Integer> edgeIds;
+ private URL fileURL;
+
+ /**
+ * Creates a new SBMLGraphReader object.
+ *
+ * @param filename DOCUMENT ME!
+ */
+ public CDBGraphReader(String filename) {
+ super(filename);
+ fileURL = null;
+ }
+
+ /**
+ * Creates a new SBMLGraphReader object.
+ *
+ * @param url DOCUMENT ME!
+ */
+ public CDBGraphReader(URL url) {
+ super(null);
+ fileURL = url;
+ fileName = null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void read() throws IOException {
+ InputStream instream;
+
+ if ((fileURL == null) && (fileName != null))
+ instream = new FileInputStream(fileName);
+ else if ((fileURL != null) && (fileName == null))
+ instream = fileURL.openStream();
+ else
+ throw new IOException("No file to open!");
+
+ nodeIds = new ArrayList<Integer>();
+ edgeIds = new ArrayList<Integer>();
+
+ geneIdMap = new HashMap<String,CyNode>();
+
+ try {
+
+ // Actual work
+ SAXBuilder builder = new SAXBuilder(false);
+ Document doc = builder.build(instream);
+
+ createGeneNodes( getTable(doc,"Genes") );
+ createRegulatorsRegulatorsEdges(
getTable(doc,"Regulators_Regulators") );
+
+ } catch (JDOMException je) {
+ throw new IOException("JDOM failure parsing file.",je);
+ }
+ }
+
+ private void createRegulatorsRegulatorsEdges(Element
regulatorsRegulators) {
+ for ( Object o :
regulatorsRegulators.getChildren("Regulator_Gene") ) {
+ Element regulatorGene = (Element)o;
+ String regulatorId =
regulatorGene.getAttributeValue("Regulator_Id");
+ String geneId =
regulatorGene.getAttributeValue("Gene_Id");
+ if ( regulatorId == null ||
+ geneId == null ||
+ !geneIdMap.containsKey(regulatorId) ||
+ !geneIdMap.containsKey(geneId) )
+ continue;
+
+ CyNode na = geneIdMap.get(regulatorId);
+ CyNode nb = geneIdMap.get(geneId);
+ CyEdge e =
Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true);
+ edgeIds.add( e.getRootGraphIndex() );
+ }
+ }
+
+
+ private void createGeneNodes(Element genes) {
+ for ( Object o : genes.getChildren("Gene") ) {
+ Element gene = (Element) o;
+ CyNode node =
Cytoscape.getCyNode(gene.getAttributeValue("ORF"),true);
+ String id = gene.getAttributeValue("Id");
+ geneIdMap.put(id,node);
+ nodeIds.add( node.getRootGraphIndex() );
+ }
+ }
+
+ private Element getTable(Document doc, String tableName) {
+ for ( Object e : doc.getRootElement().getChildren("Table") )
+ if (
tableName.equals(((Element)e).getAttributeValue("Type")) )
+ return (Element)e;
+
+ return null;
+ }
+
+ public void doPostProcessing(CyNetwork network) {
+ /*
+ // Set SBML specific visual style
+ VisualMappingManager manager =
Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = manager.getCalculatorCatalog();
+
+ VisualStyle vs =
catalog.getVisualStyle(SBMLVisualStyleFactory.SBMLReader_VS);
+
+ if (vs == null) {
+ vs = SBMLVisualStyleFactory.createVisualStyle(network);
+ catalog.addVisualStyle(vs);
+ }
+
+ manager.setVisualStyle(vs);
+ Cytoscape.getCurrentNetworkView().setVisualStyle(vs.getName());
+ Cytoscape.getCurrentNetworkView().applyVizmapper(vs);
+ */
+ }
+
+ public int[] getNodeIndicesArray() {
+ int[] nodes = new int[nodeIds.size()];
+
+ for (int i = 0; i < nodes.length; i++)
+ nodes[i] = nodeIds.get(i).intValue();
+
+ return nodes;
+ }
+
+ public int[] getEdgeIndicesArray() {
+ int[] edges = new int[edgeIds.size()];
+
+ for (int i = 0; i < edges.length; i++)
+ edges[i] = edgeIds.get(i).intValue();
+
+ return edges;
+ }
+}
Copied:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java
(from rev 28754,
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java)
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -0,0 +1,23 @@
+package cytoscape.gxp;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.ImportHandler;
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ * This class is used to instantiate your plugin. Put whatever initialization
code
+ * you need into the no argument constructor (the only one that will be
called).
+ * The actual functionality of your plugin can be in this class, but should
+ * probably be separated into separted classes that get instantiated here.
+ */
+public class CDBReaderPlugin extends CytoscapePlugin {
+
+ public CDBReaderPlugin() {
+ super();
+ ImportHandler ih = Cytoscape.getImportHandler();
+ ih.addFilter(new CDBFilter());
+ }
+}
+
+
Deleted:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java
2012-04-06 21:14:41 UTC (rev 28755)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -1,81 +0,0 @@
-
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- 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; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-
-package cytoscape.gxp;
-
-import cytoscape.data.ImportHandler;
-
-import cytoscape.data.readers.GraphReader;
-
-import cytoscape.util.CyFileFilter;
-
-import java.io.File;
-import java.io.IOException;
-
-
-public class GXPFilter extends CyFileFilter {
- /**
- * GXP Files are Graphs.
- */
- private static String fileNature = ImportHandler.GRAPH_NATURE;
-
- /**
- * File Extensions.
- */
- private static String[] fileExtensions = { "gxp" };
-
- /**
- * Filter Description.
- */
- private static String description = "GXP files";
-
- /**
- * Constructor.
- */
- public GXPFilter() {
- super(fileExtensions, description, fileNature);
- }
-
- /**
- * Gets the appropirate GraphReader object.
- *
- * @param fileName File Name.
- * @return GraphReader Object.
- */
- public GraphReader getReader(String fileName) {
- return new GXPGraphReader(fileName);
- }
-}
Deleted:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
2012-04-06 21:14:41 UTC (rev 28755)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -1,211 +0,0 @@
-
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- 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; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-
-package cytoscape.gxp;
-
-import cytoscape.CyEdge;
-import cytoscape.CyNetwork;
-import cytoscape.CyNode;
-import cytoscape.Cytoscape;
-
-import cytoscape.data.CyAttributes;
-import cytoscape.data.Semantics;
-
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-
-import org.jdom.input.SAXBuilder;
-
-
-import cytoscape.data.readers.AbstractGraphReader;
-import cytoscape.data.readers.GraphReader;
-
-import cytoscape.view.CyNetworkView;
-import cytoscape.view.CytoscapeDesktop;
-
-import cytoscape.visual.*;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import java.net.URL;
-
-import java.util.*;
-
-
-/**
- * @author Mike Smoot
- */
-public class GXPGraphReader extends AbstractGraphReader implements GraphReader
{
- // node id from file -> node
- private Map<String,CyNode> geneIdMap;
-
- private List<Integer> nodeIds;
- private List<Integer> edgeIds;
- private URL fileURL;
-
- /**
- * Creates a new SBMLGraphReader object.
- *
- * @param filename DOCUMENT ME!
- */
- public GXPGraphReader(String filename) {
- super(filename);
- fileURL = null;
- }
-
- /**
- * Creates a new SBMLGraphReader object.
- *
- * @param url DOCUMENT ME!
- */
- public GXPGraphReader(URL url) {
- super(null);
- fileURL = url;
- fileName = null;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
- */
- public void read() throws IOException {
- InputStream instream;
-
- if ((fileURL == null) && (fileName != null))
- instream = new FileInputStream(fileName);
- else if ((fileURL != null) && (fileName == null))
- instream = fileURL.openStream();
- else
- throw new IOException("No file to open!");
-
- nodeIds = new ArrayList<Integer>();
- edgeIds = new ArrayList<Integer>();
-
- geneIdMap = new HashMap<String,CyNode>();
-
- try {
-
- // Actual work
- SAXBuilder builder = new SAXBuilder(false);
- Document doc = builder.build(instream);
-
- createGeneNodes( getTable(doc,"Genes") );
- createRegulatorsRegulatorsEdges(
getTable(doc,"Regulators_Regulators") );
-
- } catch (JDOMException je) {
- throw new IOException("JDOM failure parsing file.",je);
- }
- }
-
- private void createRegulatorsRegulatorsEdges(Element
regulatorsRegulators) {
- for ( Object o :
regulatorsRegulators.getChildren("Regulator_Gene") ) {
- Element regulatorGene = (Element)o;
- String regulatorId =
regulatorGene.getAttributeValue("Regulator_Id");
- String geneId =
regulatorGene.getAttributeValue("Gene_Id");
- if ( regulatorId == null ||
- geneId == null ||
- !geneIdMap.containsKey(regulatorId) ||
- !geneIdMap.containsKey(geneId) )
- continue;
-
- CyNode na = geneIdMap.get(regulatorId);
- CyNode nb = geneIdMap.get(geneId);
- CyEdge e =
Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true);
- edgeIds.add( e.getRootGraphIndex() );
- }
- }
-
-
- private void createGeneNodes(Element genes) {
- for ( Object o : genes.getChildren("Gene") ) {
- Element gene = (Element) o;
- CyNode node =
Cytoscape.getCyNode(gene.getAttributeValue("ORF"),true);
- String id = gene.getAttributeValue("Id");
- geneIdMap.put(id,node);
- nodeIds.add( node.getRootGraphIndex() );
- }
- }
-
- private Element getTable(Document doc, String tableName) {
- for ( Object e : doc.getRootElement().getChildren("Table") )
- if (
tableName.equals(((Element)e).getAttributeValue("Type")) )
- return (Element)e;
-
- return null;
- }
-
- public void doPostProcessing(CyNetwork network) {
- /*
- // Set SBML specific visual style
- VisualMappingManager manager =
Cytoscape.getVisualMappingManager();
- CalculatorCatalog catalog = manager.getCalculatorCatalog();
-
- VisualStyle vs =
catalog.getVisualStyle(SBMLVisualStyleFactory.SBMLReader_VS);
-
- if (vs == null) {
- vs = SBMLVisualStyleFactory.createVisualStyle(network);
- catalog.addVisualStyle(vs);
- }
-
- manager.setVisualStyle(vs);
- Cytoscape.getCurrentNetworkView().setVisualStyle(vs.getName());
- Cytoscape.getCurrentNetworkView().applyVizmapper(vs);
- */
- }
-
- public int[] getNodeIndicesArray() {
- int[] nodes = new int[nodeIds.size()];
-
- for (int i = 0; i < nodes.length; i++)
- nodes[i] = nodeIds.get(i).intValue();
-
- return nodes;
- }
-
- public int[] getEdgeIndicesArray() {
- int[] edges = new int[edgeIds.size()];
-
- for (int i = 0; i < edges.length; i++)
- edges[i] = edgeIds.get(i).intValue();
-
- return edges;
- }
-}
Deleted:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java
2012-04-06 21:14:41 UTC (rev 28755)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java
2012-04-06 21:19:10 UTC (rev 28756)
@@ -1,23 +0,0 @@
-package cytoscape.gxp;
-
-import cytoscape.Cytoscape;
-import cytoscape.data.ImportHandler;
-import cytoscape.plugin.CytoscapePlugin;
-
-
-/**
- * This class is used to instantiate your plugin. Put whatever initialization
code
- * you need into the no argument constructor (the only one that will be
called).
- * The actual functionality of your plugin can be in this class, but should
- * probably be separated into separted classes that get instantiated here.
- */
-public class GXPReaderPlugin extends CytoscapePlugin {
-
- public GXPReaderPlugin() {
- super();
- ImportHandler ih = Cytoscape.getImportHandler();
- ih.addFilter(new GXPFilter());
- }
-}
-
-
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