Author: ruschein
Date: 2011-01-24 13:03:52 -0800 (Mon, 24 Jan 2011)
New Revision: 23572
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
Modified:
core3/io-impl/trunk/pom.xml
Log:
New task to map network attributes.
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2011-01-24 20:46:03 UTC (rev 23571)
+++ core3/io-impl/trunk/pom.xml 2011-01-24 21:03:52 UTC (rev 23572)
@@ -89,6 +89,16 @@
<version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
<dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>session-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>work-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
<groupId>com.lowagie.text</groupId>
<artifactId>com.springsource.com.lowagie.text</artifactId>
<version>2.0.8</version>
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
2011-01-24 21:03:52 UTC (rev 23572)
@@ -0,0 +1,74 @@
+package org.cytoscape.io.internal.read.attrs;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+
+public final class MapNetworkAttrTask extends AbstractTask {
+ @Tunable(description="Map to current network only")
+ public boolean currentNetworkOnly = true;
+
+ private final CyTableEntry type; // Must be node or edge!
+ private final CyTable newGlobalTable;
+ private final CyNetworkManager networkManager;
+ final private CyApplicationManager applicationManager;
+
+ public MapNetworkAttrTask(final CyTableEntry type, final CyTable
newGlobalTable,
+ final CyNetworkManager networkManager,
+ final CyApplicationManager applicationManager)
+ {
+ this.type = type;
+ this.newGlobalTable = newGlobalTable;
+ this.networkManager = networkManager;
+ this.applicationManager = applicationManager;
+
+ if (!(type instanceof CyNode) && !(type instanceof CyEdge))
+ throw new IllegalArgumentException("\"type\" must be
CyNode.class or CyEdge.class!");
+ }
+
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setTitle("Mapping virtual columns");
+
+ final List<CyTable> targetTables = new ArrayList<CyTable>();
+ if (currentNetworkOnly) {
+ final CyNetwork currentNetwork =
applicationManager.getCurrentNetwork();
+ targetTables.add(type instanceof CyNode ?
currentNetwork.getDefaultNodeTable()
+ :
currentNetwork.getDefaultEdgeTable());
+ } else {
+ final Set<CyNetwork> networks =
networkManager.getNetworkSet();
+ for (final CyNetwork network : networks)
+ targetTables.add(type instanceof CyNode ?
network.getDefaultNodeTable()
+ :
network.getDefaultEdgeTable());
+ }
+
+ mapAll(targetTables);
+ }
+
+ private void mapAll(final List<CyTable> targetTables) {
+ if (targetTables.isEmpty())
+ return;
+
+ if (newGlobalTable.getPrimaryKeyType() != String.class)
+ throw new IllegalStateException("The new table's
primary key is not of type String!");
+ final String sourceTableJoinColumn =
newGlobalTable.getPrimaryKey();
+
+ for (final CyTable targetTable : targetTables) {
+ if (cancelled)
+ return;
+ targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, CyTableEntry.NAME);
+ }
+ }
+}
\ No newline at end of file
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