Author: kono
Date: 2011-05-09 18:20:07 -0700 (Mon, 09 May 2011)
New Revision: 24990
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
Log:
Fixed to make this bundle compatible with new network IO API. Infinite loop
problem still remains and cannot apply layout. Why...?
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-10 01:09:27 UTC (rev 24989)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-05-10 01:20:07 UTC (rev 24990)
@@ -40,6 +40,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -84,8 +85,11 @@
taskMonitor.setProgress(0.0);
taskMonitor.setStatusMessage("Creating Cytoscape Network...");
+
insertTasksAfterCurrentTask(viewReader, new
GenerateNetworkViewsTask(name, viewReader, networkManager,
networkViewManager, namingUtil, viewThreshold));
+
+ taskMonitor.setProgress(1.0);
}
private int getViewThreshold() {
@@ -126,22 +130,23 @@
taskMonitor.setProgress(0.0);
final CyNetwork[] networks = viewReader.getCyNetworks();
-
+
for (CyNetwork network : networks) {
network.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(name));
networkManager.addNetwork(network);
final int numGraphObjects = network.getNodeCount() +
network.getEdgeCount();
-// if (numGraphObjects < viewThreshold) {
-//
networkViewManager.addNetworkView(viewReader.buildCyNetworkView(network));
-// //view.fitContent();
-// }
+ if (numGraphObjects < viewThreshold) {
+ final CyNetworkView view =
viewReader.buildCyNetworkView(network);
+ networkViewManager.addNetworkView(view);
+ view.fitContent();
+ }
informUserOfGraphStats(network, numGraphObjects,
taskMonitor);
+
}
- taskMonitor.setProgress(1.0);
}
/**
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-05-10 01:09:27 UTC (rev 24989)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-05-10 01:20:07 UTC (rev 24990)
@@ -142,6 +142,8 @@
this.cyNetworks = new CyNetwork[] {network};
tm.setProgress(1.0);
+
+ logger.debug("SIF file loaded: ID = " + network.getSUID());
}
private void createEdge(final Interaction itr, final CyNetwork network,
final Map<String, CyNode> nMap) {
@@ -170,12 +172,11 @@
public CyNetworkView buildCyNetworkView(CyNetwork network) {
final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
- if (view.isEmptyView())
- return view;
-
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(view);
- insertTasksAfterCurrentTask(layout.getTaskIterator());
+
+ // FIXME: this causes infinite loop...Why?
+ //insertTasksAfterCurrentTask(layout.getTaskIterator());
return view;
}
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-10 01:09:27 UTC (rev 24989)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReaderTest.java
2011-05-10 01:20:07 UTC (rev 24990)
@@ -29,11 +29,6 @@
findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
- // Test low threshold
- setViewThreshold(5);
- CyNetworkView[] nullViews = getViews("sample.sif");
- assertNotNull(nullViews);
- assertTrue(nullViews[0].isEmptyView());
}
/**
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