Author: pwang
Date: 2011-01-19 15:45:13 -0800 (Wed, 19 Jan 2011)
New Revision: 23517
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
Log:
Clean up
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
2011-01-19 23:44:23 UTC (rev 23516)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
2011-01-19 23:45:13 UTC (rev 23517)
@@ -53,6 +53,8 @@
import org.cytoscape.work.TaskMonitor;
import java.io.IOException;
import java.net.URL;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
import java.util.HashMap;
import java.util.Map;
@@ -60,7 +62,7 @@
/**
*
*/
-public class ImportNetworkTask extends AbstractTask implements
CyNetworkViewReader {
+public class ImportNetworkTask extends AbstractTask { //implements
CyNetworkViewReader {
protected CyNetworkView[] cyNetworkViews;
protected VisualStyle[] visualstyles;
@@ -77,150 +79,76 @@
* @param source DOCUMENT ME!
*/
public ImportNetworkTask(String networkName, final GraphReader reader,
final URL source) {
-
this.reader = reader;
this.source = source;
-
}
@Override
public void run(TaskMonitor tm) throws IOException {
+
try {
tm.setProgress(0.10);
this.reader.setNetwork(network);
+
+ if (this.cancelled){
+ return;
+ }
+
this.reader.read();
+
tm.setProgress(0.80);
- //readInput(tm);
- //createNetwork(tm);
- } finally {
- //if (inputStream != null) {
- // inputStream.close();
- // inputStream = null;
- //}
- }
- }
-
- private void readInput(TaskMonitor tm) throws IOException {
- //tm.setProgress(0.00);
-
- /*
- String delimiter = DEF_DELIMITER;
-
- final String rawText = readUtil.getInputString(inputStream);
-
- tm.setProgress(0.10);
- if (rawText.indexOf("\t") >= 0)
- delimiter = "\t";
-
- final String[] lines = rawText.split(LINE_SEP);
-
- tm.setProgress(0.15);
- final int size = lines.length;
- for (int i = 0; i < size; i++) {
- if (lines[i].length() <= 0)
- continue;
- interactions.add(new Interaction(lines[i], delimiter));
- }
- */
- //tm.setProgress(0.20);
- }
-
-
- private void createNetwork(TaskMonitor tm) {
-
- // Create network model. At this point, there are no
nodes/edges.
- final CyNetwork network =
CytoscapeServices.cyNetworkFactoryServiceRef.getInstance();
-
- Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
-
- // put all node names in the Set
- //for (Interaction interaction : interactions) {
- // nodeMap.put(interaction.getSource(), null);
- // for (String target : interaction.getTargets())
- // nodeMap.put(target, null);
- //}
-
- tm.setProgress(0.25);
-
- for (String nodeName : nodeMap.keySet()) {
- if (cancelled)
+ if (this.cancelled){
return;
+ }
+
+ final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactoryServiceRef.getNetworkView(network);
+
+ CytoscapeServices.netMgr.addNetwork(network);
+
CytoscapeServices.networkViewManager.addNetworkView(view);
- //tm.setProgress(progress);
+ tm.setProgress(0.95);
- final CyNode node = network.addNode();
- //node.getCyRow().set(NODE_NAME_ATTR_LABEL, nodeName);
- nodeMap.put(nodeName, node);
+ view.fitContent();
+
+ } finally {
+ //
}
-
- tm.setProgress(0.65);
- // Now loop over the interactions again, this time creating
edges
- // between
- // all sources and each of their respective targets.
- String srcName;
- String interactionType;
- CyEdge edge;
+ tm.setProgress(1.0);
- /*
- for (Interaction interaction : interactions) {
- if (cancelled)
- return;
+ informUserOfGraphStats(network, tm);
+ }
- srcName = interaction.getSource();
- interactionType = interaction.getType();
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(final CyNetwork newNetwork, final
TaskMonitor taskMonitor) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
- for (String tgtName : interaction.getTargets()) {
- edge = network.addEdge(nodeMap.get(srcName),
nodeMap
- .get(tgtName), true);
- edge.getCyRow().set(NODE_NAME_ATTR_LABEL,
- srcName + " (" +
interactionType + ") " + tgtName);
- edge.getCyRow().set(INTERACTION,
interactionType);
- }
- }
- */
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(newNetwork.getCyRow().get("title", String.class));
+ sb.append("\n\nNetwork contains "
+ + formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
- tm.setProgress(0.90);
-
- final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactoryServiceRef.getNetworkView(network);
-
+ String thresh = "100";
//CytoscapeServices.cytoscapePropertiesServiceRef.getProperties().getProperty("viewThreshold");
- TaskFactory tf =
CytoscapeServices.cyLayoutsServiceRef.getDefaultLayout(view);
- TaskIterator ti = tf.getTaskIterator();
- Task task = ti.next();
- insertTasksAfterCurrentTask(task);
+ if (newNetwork.getNodeCount() < Integer.parseInt(thresh)) {
+ sb.append("Network is under " + thresh
+ + " nodes. A view will be
automatically created.");
+ } else {
+ sb.append("Network is over " + thresh
+ + " nodes. A view has not been
created."
+ + " If you wish to view this network,
use "
+ + "\"Create View\" from the \"Edit\"
menu.");
+ }
- // SIF always creates only one network.
- this.cyNetworkViews = new CyNetworkView[] { view };
-
- nodeMap.clear();
- nodeMap = null;
-
- tm.setProgress(1.0);
- }
+ taskMonitor.setStatusMessage(sb.toString());
+ }
-
- @Override
- public void cancel(){
- }
-
-
- /**
- * Gets the Task Title.
- *
- * @return Task Title.
- */
- public String getTitle() {
- return new String("Loading Network and Edge Attributes");
- }
-
- public CyNetworkView[] getNetworkViews() {
- return cyNetworkViews;
- }
-
- public VisualStyle[] getVisualStyles() {
- return visualstyles;
- }
}
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