Author: mes Date: 2012-03-08 14:08:19 -0800 (Thu, 08 Mar 2012) New Revision: 28455
Added: csplugins/trunk/ucsd/mes/edge_bundling_gdeb/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/pom.xml csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/CyActivator.java csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTask.java csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTaskFactory.java Log: initial checkin Added: csplugins/trunk/ucsd/mes/edge_bundling_gdeb/pom.xml =================================================================== --- csplugins/trunk/ucsd/mes/edge_bundling_gdeb/pom.xml (rev 0) +++ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/pom.xml 2012-03-08 22:08:19 UTC (rev 28455) @@ -0,0 +1,94 @@ +<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> + + <properties> + <bundle.symbolicName>edge-bundler</bundle.symbolicName> + <bundle.namespace>org.cytoscape.edge.bundler.internal</bundle.namespace> + <cytoscape.api.version>3.0.0-alpha8-SNAPSHOT</cytoscape.api.version> + + <maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version> + <osgi.api.version>4.2.0</osgi.api.version> + </properties> + + <groupId>org.cytoscape</groupId> + <artifactId>edge-bundler</artifactId> + <packaging>bundle</packaging> + <name>${bundle.symbolicName}</name> + + <version>1.0.0-SNAPSHOT</version> + + <repositories> + <repository> + <id>cytoscape_snapshots</id> + <snapshots> + <enabled>true</enabled> + </snapshots> + <releases> + <enabled>false</enabled> + </releases> + <name>Cytoscape Snapshots</name> + <url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url> + </repository> + <repository> + <id>cytoscape_releases</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Releases</name> + <url>http://code.cytoscape.org/nexus/content/repositories/releases/</url> + </repository> + </repositories> + + <build> + <plugins> + <plugin> + <groupId>org.apache.felix</groupId> + <artifactId>maven-bundle-plugin</artifactId> + <version>${maven-bundle-plugin.version}</version> + <extensions>true</extensions> + <configuration> + <instructions> + <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName> + <Bundle-Version>${project.version}</Bundle-Version> + <Export-Package>!${bundle.namespace}.*</Export-Package> + <Private-Package>${bundle.namespace}.*</Private-Package> + <Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator> + </instructions> + </configuration> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>application-api</artifactId> + <version>${cytoscape.api.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>work-api</artifactId> + <version>${cytoscape.api.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>core-task-api</artifactId> + <version>${cytoscape.api.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>service-api</artifactId> + <version>${cytoscape.api.version}</version> + </dependency> + <dependency> + <groupId>org.osgi</groupId> + <artifactId>org.osgi.core</artifactId> + <version>${osgi.api.version}</version> + </dependency> + + </dependencies> + +</project> Added: csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/CyActivator.java =================================================================== --- csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/CyActivator.java (rev 0) +++ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/CyActivator.java 2012-03-08 22:08:19 UTC (rev 28455) @@ -0,0 +1,25 @@ +package org.cytoscape.edge.bundler.internal; + +import org.cytoscape.task.NetworkViewTaskFactory; +import org.cytoscape.service.util.AbstractCyActivator; +import java.util.Properties; +import org.osgi.framework.BundleContext; + + +public class CyActivator extends AbstractCyActivator { + public CyActivator() { + super(); + } + + public void start(BundleContext bc) { + + EdgeBundlerTaskFactory edgeBundlerTaskFactory = new EdgeBundlerTaskFactory(); + + Properties edgeBundlerTaskFactoryProps = new Properties(); + edgeBundlerTaskFactoryProps.setProperty("preferredMenu","Layout"); + edgeBundlerTaskFactoryProps.setProperty("menuGravity","11.0"); + edgeBundlerTaskFactoryProps.setProperty("title","Bundle Edges"); + registerService(bc,edgeBundlerTaskFactory,NetworkViewTaskFactory.class, edgeBundlerTaskFactoryProps); + } +} + Added: csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTask.java =================================================================== --- csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTask.java (rev 0) +++ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTask.java 2012-03-08 22:08:19 UTC (rev 28455) @@ -0,0 +1,88 @@ +package org.cytoscape.edge.bundler.internal; + +import org.cytoscape.task.AbstractNetworkViewTask; +import org.cytoscape.view.model.CyNetworkView; +import org.cytoscape.work.TaskMonitor; + + +public class EdgeBundlerTask extends AbstractNetworkViewTask { + + @Tunable(description="value of K") + public double K; + + EdgeBundlerTask(CyNetworkView v) { + super(v); + } + + public void run(TaskMonitor tm) { + + } + + private double force(CyEdge p, List<CyEdge> allEdges) { + } + + private double compatibility(View<CyEdge> p, View<CyEdge> q) { + return (angleCompat(p,q) * scaleCompat(p,q) * positionCompat(p,q) * visibilityCompat(p,q)); + } + + private double angleCompat(View<CyEdge> p, View<CyEdge> q) { + View<CyNode> pSource = view.getNodeView(p.getSource()); + View<CyNode> pTarget = view.getNodeView(p.getSource()); + + View<CyNode> qSource = view.getNodeView(q.getSource()); + View<CyNode> qTarget = view.getNodeView(q.getSource()); + + double psx = pSource.getVisualProperty(NODE_X_LOCATION); + double psy = pSource.getVisualProperty(NODE_Y_LOCATION); + double ptx = pTarget.getVisualProperty(NODE_X_LOCATION); + double pty = pTarget.getVisualProperty(NODE_Y_LOCATION); + double a = ptx - psx; + double b = pty - psy; + + double qsx = qSource.getVisualProperty(NODE_X_LOCATION); + double qsy = qSource.getVisualProperty(NODE_Y_LOCATION); + double qtx = qTarget.getVisualProperty(NODE_X_LOCATION); + double qty = qTarget.getVisualProperty(NODE_Y_LOCATION); + double c = qtx - qsx; + double d = qty - qsy; + + double cosAlpha = ((a*c) + (b*d))/(Math.sqrt(a*a + b*b)*Math.sqrt(c*c + d*d)); + + return Math.round(cosAlpha); + } + + private double scaleCompat(View<CyEdge> p, View<CyEdge> q) { + double lavg = (len(p) + len(q))/2.0; + return 2.0/((lavg*Math.min(len(p),len(q))) + (Math.max(len(p),len(q))/lavg)); + } + + private double positionCompat(View<CyEdge> p, View<CyEdge> q) { + double lavg = (len(p) + len(q))/2.0; + + return lavg / (lavg + normMinus( mid(p),mid(q) )); + } + + private Point2D.Double mid(View<CyEdge> p) { + View<CyNode> pSource = view.getNodeView(p.getSource()); + View<CyNode> pTarget = view.getNodeView(p.getSource()); + double psx = pSource.getVisualProperty(NODE_X_LOCATION); + double psy = pSource.getVisualProperty(NODE_Y_LOCATION); + double ptx = pTarget.getVisualProperty(NODE_X_LOCATION); + double pty = pTarget.getVisualProperty(NODE_Y_LOCATION); + return new Point2D.Double((psx-ptx)/2.0,(psy-pty)/2.0); + } + + private double normMinus(Point2D.Double p, Point2D.Double q) { + double x = p.getX() - q.getX() + double y = p.getY() - q.getY() + return Math.sqrt(x*x + y*y); + } + + private double visibilityCompat(View<CyEdge> p, View<CyEdge> q) { + return Math.min(vis(p,q), vis(q,p)); + } + + private double vis(View<CyEdge> p, View<CyEdge> q) { + return Math.max(1.0 - + } +} Added: csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTaskFactory.java =================================================================== --- csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTaskFactory.java (rev 0) +++ csplugins/trunk/ucsd/mes/edge_bundling_gdeb/src/main/java/org/cytoscape/edge/bundler/internal/EdgeBundlerTaskFactory.java 2012-03-08 22:08:19 UTC (rev 28455) @@ -0,0 +1,16 @@ +package org.cytoscape.edge.bundler.internal; + +import org.cytoscape.task.AbstractNetworkViewTaskFactory; +import org.cytoscape.work.TaskIterator; + + +public class EdgeBundlerTaskFactory extends AbstractNetworkViewTaskFactory { + + public EdgeBundlerTaskFactory() { + super(); + } + + public TaskIterator createTaskIterator() { + return new TaskIterator(new EdgeBundlerTask(view)); + } +} -- 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.
