Author: mes Date: 2011-10-07 13:32:33 -0700 (Fri, 07 Oct 2011) New Revision: 27084
Added: csplugins/trunk/ucsd/mes/gxp-reader/ csplugins/trunk/ucsd/mes/gxp-reader/pom.xml csplugins/trunk/ucsd/mes/gxp-reader/src/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/assembly/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/assembly/src.xml csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/gxp/ csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/gxp/plugin.props csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/mime.types Log: initial shot at a GXP reader Added: csplugins/trunk/ucsd/mes/gxp-reader/pom.xml =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/pom.xml (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/pom.xml 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,108 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> + <modelVersion>4.0.0</modelVersion> + + <groupId>cytoscape</groupId> + <artifactId>gxp-reader</artifactId> + <version>1.0-SNAPSHOT</version> + <packaging>jar</packaging> + <name>GXP Reader Plugin</name> + + <build> + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-compiler-plugin</artifactId> + <version>2.3.2</version> + <configuration> + <source>1.6</source> + <target>1.6</target> + <optimize>true</optimize> + <showWarnings>true</showWarnings> + <showDeprecation>true</showDeprecation> + </configuration> + </plugin> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>2.2-beta-5</version> + <configuration> + <archive> + <manifestEntries> + <Cytoscape-Plugin>cytoscape.gxp.GXPReaderPlugin</Cytoscape-Plugin> + </manifestEntries> + </archive> + <descriptors> + <descriptor>src/main/assembly/src.xml</descriptor> + </descriptors> + </configuration> + <executions> + <execution> + <id>make-assembly</id> + <phase>package</phase> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>cytoscape</groupId> + <artifactId>application</artifactId> + <version>2.8.3-SNAPSHOT</version> + <scope>provided</scope> + </dependency> + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>3.8.1</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.jdom</groupId> + <artifactId>jdom</artifactId> + <version>1.1</version> + <scope>provided</scope> + </dependency> + </dependencies> + + <repositories> + <repository> + <id>cytoscape_snapshots</id> + <snapshots> + <enabled>true</enabled> + </snapshots> + <releases> + <enabled>false</enabled> + </releases> + <name>Cytoscape Snapshots</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> + </repository> + <repository> + <id>cytoscape_releases</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Releases</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> + </repository> + <repository> + <id>cytoscape_thirdparty</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Third Party</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> + </repository> + </repositories> + +</project> Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/assembly/src.xml =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/assembly/src.xml (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/assembly/src.xml 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,18 @@ +<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"; + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd";> + <id>jar-with-dependencies</id> + <formats> + <format>jar</format> + </formats> + <includeBaseDirectory>false</includeBaseDirectory> + <dependencySets> + <dependencySet> + <outputDirectory>/</outputDirectory> + <useProjectArtifact>true</useProjectArtifact> + <unpack>true</unpack> + <scope>runtime</scope> + <useTransitiveDependencies>false</useTransitiveDependencies> + </dependencySet> + </dependencySets> +</assembly> Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java 2011-10-07 20:32:33 UTC (rev 27084) @@ -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 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); + } +} Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,268 @@ + +/* + 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> nodeIdMap; + + // module id from file -> list of nodes in module + private Map<String,List<CyNode>> moduleMap; + + // regulator id from file -> list of nodes in regulator + private Map<String,List<CyNode>> regulatorMap; + + + 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>(); + + nodeIdMap = new HashMap<String,CyNode>(); + // module -> list of nodes in module + moduleMap = new HashMap<String,List<CyNode>>(); + // regulator -> list of nodes in regulator + regulatorMap = new HashMap<String,List<CyNode>>(); + + try { + + // Actual work + SAXBuilder builder = new SAXBuilder(false); + Document doc = builder.build(instream); + + createNodes( getTable(doc,"Genes") ); + createModules( getTable(doc,"Genes_Modules") ); + createRegulators( getTable(doc,"Regulators_Regulators") ); + createEdges( getTable(doc, "Modules_Regulator") ); + + } catch (JDOMException je) { + throw new IOException("JDOM failure parsing file.",je); + } + } + + private void createEdges(Element moduleRegulators) { + for ( Object o : moduleRegulators.getChildren("Module_Regulator") ) { + Element moduleRegulator = (Element)o; + String moduleId = moduleRegulator.getAttributeValue("Module_Id"); + String regId = moduleRegulator.getAttributeValue("Regulator_Id"); + if ( moduleId == null || regId == null || !moduleMap.containsKey(moduleId) || !regulatorMap.containsKey(regId) ) + continue; + + for ( CyNode na : regulatorMap.get(regId) ) { + for (CyNode nb : moduleMap.get(moduleId) ) { + CyEdge e = Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true); + edgeIds.add( e.getRootGraphIndex() ); + } + } + } + } + + private void createRegulators(Element regulators) { + for ( Object o : regulators.getChildren("Regulator_Gene") ) { + Element regulator = (Element) o; + String regId = regulator.getAttributeValue("Regulator_Id"); + if ( !regulatorMap.containsKey(regId) ) + regulatorMap.put(regId,new ArrayList<CyNode>()); + CyNode node = nodeIdMap.get( regulator.getAttributeValue("Gene_Id") ); + if ( node == null ) { + System.out.println("unable to createRegulator for gene_id " + regulator.getAttributeValue("Gene_Id")); + continue; + } + regulatorMap.get(regId).add( node ); + Cytoscape.getNodeAttributes().setAttribute(node.getIdentifier(),"GXP_Regulator_Id",regId); + } + } + + private void createModules(Element geneModules) { + for ( Object o : geneModules.getChildren("Gene_Module") ) { + Element geneModule = (Element) o; + CyNode node = nodeIdMap.get( geneModule.getAttributeValue("Gene_Id") ); + if ( node != null ) { + String moduleId = geneModule.getAttributeValue("Module_Id"); + Cytoscape.getNodeAttributes().setAttribute(node.getIdentifier(),"GXP_Module_Id",moduleId); + if ( !moduleMap.containsKey(moduleId) ) + moduleMap.put(moduleId,new ArrayList<CyNode>()); + moduleMap.get(moduleId).add(node); + } + } + } + + private void createNodes(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"); + System.out.println("creating node: " + id + " " + node.getIdentifier()); + nodeIdMap.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; + } + + /** + * DOCUMENT ME! + * + * @param network DOCUMENT ME! + */ + 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); + */ + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + 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; + } +} Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java 2011-10-07 20:32:33 UTC (rev 27084) @@ -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 GXPReaderPlugin extends CytoscapePlugin { + + public GXPReaderPlugin() { + super(); + ImportHandler ih = Cytoscape.getImportHandler(); + ih.addFilter(new GXPFilter()); + } +} + + Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,165 @@ + +/* + 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 sbmlreader; + +import cytoscape.*; + +import cytoscape.data.Semantics; + +import cytoscape.view.CytoscapeDesktop; + +import cytoscape.visual.*; + +import cytoscape.visual.calculators.*; + +import cytoscape.visual.mappings.*; + +import cytoscape.visual.ui.*; + +import giny.view.EdgeView; + +import java.awt.Color; + + +/** + * VisualStyleFactory.java + * This class defines the visualstyle in Cytoscape for the SBMLReader plugin. + * + * @author W.P.A. Ligtenberg, Eindhoven University of Technology + */ +public class SBMLVisualStyleFactory { + /** + * + */ + public static final String SBMLReader_VS = "SBMLReader Style"; + + /** + * + */ + public static final String NODE_TYPE_ATT = "sbml type"; + + /** + * + */ + public static final String EDGE_TYPE_ATT = "interaction"; + + /** + * DOCUMENT ME! + * + * @param network DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static VisualStyle createVisualStyle(CyNetwork network) { + VisualMappingManager vmManager = Cytoscape.getVisualMappingManager(); + NodeAppearanceCalculator nodeAppCalc = new NodeAppearanceCalculator(); + EdgeAppearanceCalculator edgeAppCalc = new EdgeAppearanceCalculator(); + CalculatorCatalog calculatorCatalog = vmManager.getCalculatorCatalog(); + + // ------------------------------ Set node shapes ---------------------------// + DiscreteMapping disMapping = new DiscreteMapping(NodeShape.RECT, + ObjectMapping.NODE_MAPPING); + disMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false); + disMapping.putMapValue("species", NodeShape.DIAMOND); + disMapping.putMapValue("reaction", NodeShape.ELLIPSE); + + Calculator shapeCalculator = new BasicCalculator("SBMLReader Shape Calculator", + disMapping, + VisualPropertyType.NODE_SHAPE); + nodeAppCalc.setCalculator(shapeCalculator); + + // ------------------------------ Set the label ------------------------------// + // Display the value for geneName as a label + String cName = "sbml name"; + Calculator nlc = calculatorCatalog.getCalculator(VisualPropertyType.NODE_LABEL, cName); + + if (nlc == null) { + PassThroughMapping m = new PassThroughMapping(new String(), cName); + nlc = new BasicCalculator(cName, m, VisualPropertyType.NODE_LABEL); + } + + nodeAppCalc.setCalculator(nlc); + + //--------------------- Set the size of the nodes --------------------------// + //Discrete mapping on nodeType + Double speciesNodeSize = new Double(30); + Double reactionNodeSize = new Double(30); + DiscreteMapping sizeMapping = new DiscreteMapping(reactionNodeSize, + ObjectMapping.NODE_MAPPING); + sizeMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false); + sizeMapping.putMapValue("species", speciesNodeSize); + sizeMapping.putMapValue("reaction", reactionNodeSize); + + Calculator sizeCalculator = new BasicCalculator("SBMLReader Size Calculator", + sizeMapping, + VisualPropertyType.NODE_SIZE); + nodeAppCalc.setCalculator(sizeCalculator); + nodeAppCalc.setNodeSizeLocked(true); + + // ------------------------------ Set edge arrow shape ---------------------------// + DiscreteMapping arrowMapping = new DiscreteMapping(ArrowShape.DELTA, + ObjectMapping.NODE_MAPPING); + arrowMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false); + arrowMapping.putMapValue("reaction-product", ArrowShape.ARROW); + arrowMapping.putMapValue("reaction-reactant", ArrowShape.NONE); + arrowMapping.putMapValue("reaction-modifier", ArrowShape.CIRCLE); + + Calculator edgeArrowCalculator = new BasicCalculator("SBMLReader Edge Arrow Calculator", + arrowMapping, + VisualPropertyType.EDGE_SRCARROW_SHAPE); + edgeAppCalc.setCalculator(edgeArrowCalculator); + + // ------------------------------ Set edge colour ---------------------------// + DiscreteMapping edgeColorMapping = new DiscreteMapping(Color.BLACK, + ObjectMapping.NODE_MAPPING); + edgeColorMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false); + edgeColorMapping.putMapValue("reaction-product", Color.GREEN); + edgeColorMapping.putMapValue("reaction-reactant", Color.RED); + edgeColorMapping.putMapValue("reaction-modifier", Color.BLACK); + + Calculator edgeColorCalculator = new BasicCalculator("SBMLReader Edge Color Calculator", + edgeColorMapping, + VisualPropertyType.EDGE_COLOR); + edgeAppCalc.setCalculator(edgeColorCalculator); + + //------------------------- Create a visual style -------------------------------// + GlobalAppearanceCalculator gac = vmManager.getVisualStyle().getGlobalAppearanceCalculator(); + VisualStyle visualStyle = new VisualStyle(SBMLReader_VS, nodeAppCalc, edgeAppCalc, gac); + + return visualStyle; + } +} Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/gxp/plugin.props =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/gxp/plugin.props (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/cytoscape/gxp/plugin.props 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,26 @@ +# This props file would be filled out and included in the plugin jar file. +# This props file will be used to put information into the Plugin Manager +# about the plugin + +# -- The following properties are REQUIRED -- # + +# The plugin name that will be displayed to users +pluginName=GXPReaderPlugin + +# Description used to give users information about the plugin such as what it does. +# Html tags are encouraged for formatting purposes. +pluginDescription=GXP Reader Plugin + +# Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03 +pluginVersion=0.1 + +# Compatible Cytoscape version +cytoscapeVersion=2.8 + +# Category, use one of the categories listed on the website or create your own +pluginCategory=Network and Attribute I/O + +# List of authors. Note each author and institution pair are separated by a : (colon) +# each additional author institution pair must be separated from other pairs bye a ; (semicolon) +pluginAuthorsIntsitutions=Mike Smoot:UCSD + Added: csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/mime.types =================================================================== --- csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/mime.types (rev 0) +++ csplugins/trunk/ucsd/mes/gxp-reader/src/main/resources/mime.types 2011-10-07 20:32:33 UTC (rev 27084) @@ -0,0 +1,26 @@ +# +# A simple, old format, mime.types file +# +text/html html htm HTML HTM +text/plain txt text TXT TEXT +image/gif gif GIF +image/ief ief +image/jpeg jpeg jpg jpe JPG +image/tiff tiff tif +image/png png PNG +image/x-xwindowdump xwd +application/postscript ai eps ps +application/rtf rtf +application/x-tex tex +application/x-texinfo texinfo texi +application/x-troff t tr roff +audio/basic au +audio/midi midi mid +audio/x-aifc aifc +audio/x-aiff aif aiff +audio/x-mpeg mpeg mpg +audio/x-wav wav +video/mpeg mpeg mpg mpe +video/quicktime qt mov +video/x-msvideo avi +application/json json -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
