Author: pwang
Date: 2012-09-12 16:26:21 -0700 (Wed, 12 Sep 2012)
New Revision: 30359
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReader.java
Log:
Add a new method
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReader.java
2012-09-12 22:40:43 UTC (rev 30358)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkReader.java
2012-09-12 23:26:21 UTC (rev 30359)
@@ -5,12 +5,14 @@
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import org.cytoscape.io.internal.util.ReadUtils;
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyNode;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -18,6 +20,7 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.util.ListSingleSelection;
+import org.cytoscape.model.subnetwork.CySubNetwork;
public abstract class AbstractNetworkReader extends AbstractTask implements
CyNetworkReader {
@@ -36,6 +39,7 @@
public ListSingleSelection<Object> networkCollection;
protected HashMap<String, CyRootNetwork> name2RootMap;
+ protected Map<String, CyNode> nMap = new HashMap<String, CyNode>(10000);
public AbstractNetworkReader(InputStream inputStream, final
CyNetworkViewFactory cyNetworkViewFactory,
final CyNetworkFactory cyNetworkFactory, final
CyNetworkManager cyNetworkManager, final CyRootNetworkManager
cyRootNetworkManager) {
@@ -69,4 +73,19 @@
public CyNetwork[] getNetworks() {
return cyNetworks;
}
+
+ protected void initNodeMap(CyNetwork rootNetwork){
+ Iterator<CySubNetwork> subnetworkIt =
cyRootNetworkManager.getRootNetwork(rootNetwork).getSubNetworkList().iterator();
+
+ while(subnetworkIt.hasNext()){
+ CySubNetwork subnetwork = subnetworkIt.next();
+
+ Iterator<CyNode> nodeIt =
subnetwork.getNodeList().iterator();
+ while(nodeIt.hasNext()){
+ CyNode node = nodeIt.next();
+ String name =
subnetwork.getDefaultNodeTable().getRow(node).get(CyNetwork.NAME, String.class);
+ this.nMap.put(name, node);
+ }
+ }
+ }
}
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