Author: kono
Date: 2010-08-18 16:49:14 -0700 (Wed, 18 Aug 2010)
New Revision: 21464
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/LoadInputStreamTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
Log:
SIF reader fixed and it loads network.
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
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -37,27 +37,23 @@
package org.cytoscape.task.internal.loadnetwork;
+import java.io.IOException;
import java.net.URI;
import java.text.DecimalFormat;
import java.text.NumberFormat;
-import java.util.Map;
import java.util.Properties;
-import java.awt.Event;
-import java.io.IOException;
import org.cytoscape.io.read.CyNetworkViewProducer;
import org.cytoscape.io.read.CyNetworkViewProducerManager;
-import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.session.CyNetworkManager;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.task.AbstractTask;
+import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.task.AbstractTask;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.session.CyNetworkNaming;
-
/**
* Task to load a new network.
*/
@@ -77,9 +73,9 @@
protected CyNetworkNaming namingUtil;
- public AbstractLoadNetworkTask(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf,
- CyLayouts cyl, CyNetworkManager netmgr, Properties
props,
- CyNetworkNaming namingUtil) {
+ public AbstractLoadNetworkTask(CyNetworkViewProducerManager mgr,
+ CyNetworkViewFactory gvf, CyLayouts cyl,
CyNetworkManager netmgr,
+ Properties props, CyNetworkNaming namingUtil) {
this.mgr = mgr;
this.gvf = gvf;
this.cyl = cyl;
@@ -88,53 +84,40 @@
this.namingUtil = namingUtil;
}
- protected void loadNetwork(CyNetworkViewProducer reader) throws
Exception {
- if (reader == null)
- throw new Exception("Could not read file: file reader
was null");
+ protected void loadNetwork(final CyNetworkViewProducer viewProducer)
throws Exception {
+
+ if (viewProducer == null)
+ throw new IllegalArgumentException("Could not read
file: Network View Producer is null.");
- try {
- myThread = Thread.currentThread();
+ myThread = Thread.currentThread();
- taskMonitor.setStatusMessage("Reading in Network
Data...");
+ taskMonitor.setStatusMessage("Reading in Network Data...");
+ taskMonitor.setProgress(-1.0);
+ taskMonitor.setStatusMessage("Creating Cytoscape Network...");
+
+ viewProducer.run(taskMonitor);
+
+ final CyNetworkView[] cyNetworkViews =
viewProducer.getNetworkViews();
- taskMonitor.setProgress(-1.0);
+ if (cyNetworkViews == null || cyNetworkViews.length < 0)
+ throw new IOException("Could not create view model for
the producer.");
- taskMonitor.setStatusMessage("Creating Cytoscape
Network...");
+ // Model should not be null. It will be tested in ViewImpl.
+ final CyNetwork cyNetwork = cyNetworkViews[0].getModel();
+ cyNetwork.attrs()
+ .set("name",
namingUtil.getSuggestedNetworkTitle(name));
+ CyNetworkView view = cyNetworkViews[0];
-
- //final Map<Class<?>, Object> readData = reader.read();
+ if (view == null)
+ view = gvf.getNetworkView(cyNetwork);
- CyNetworkView[] cyNetworkViews =
reader.getNetworkViews();
-
- CyNetwork cyNetwork = cyNetworkViews[0].getModel();
- cyNetwork.attrs().set("name",
-
namingUtil.getSuggestedNetworkTitle(name));
- CyNetworkView view = cyNetworkViews[0];
+ view.fitContent();
- if (view == null)
- view = gvf.getNetworkView(cyNetwork);
+ netmgr.addNetwork(cyNetwork);
+ netmgr.addNetworkView(view);
- view.fitContent();
-
- netmgr.addNetwork(cyNetwork);
- netmgr.addNetworkView(view);
-
-
- if (cyNetwork != null) {
- informUserOfGraphStats(cyNetwork);
- } else {
- StringBuffer sb = new StringBuffer();
- sb.append("Could not read network from: ");
- sb.append(name);
- sb.append("\nThis file may not be a valid file
format.");
- throw new IOException(sb.toString());
- }
-
- taskMonitor.setProgress(1.0);
-
- } finally {
- reader = null;
- }
+ informUserOfGraphStats(cyNetwork);
+ taskMonitor.setProgress(1.0);
}
abstract public void run(TaskMonitor taskMonitor) throws Exception;
@@ -171,8 +154,7 @@
public void cancel() {
super.cancel();
- if (reader != null)
- {
+ if (reader != null) {
reader.cancel();
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTask.java
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTask.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -75,7 +75,6 @@
name = inputstream.toString();
-
if (reader == null) {
uri = null;
System.out.println("The reader is null");
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -37,21 +37,18 @@
package org.cytoscape.task.internal.loadnetwork;
-import static org.cytoscape.io.DataCategory.NETWORK;
-
import java.io.File;
import java.util.Properties;
import org.cytoscape.io.read.CyNetworkViewProducerManager;
+import org.cytoscape.session.CyNetworkManager;
+import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.Tunable.Param;
-import org.cytoscape.session.CyNetworkManager;
-import org.cytoscape.session.CyNetworkNaming;
-
/**
* Specific instance of AbstractLoadNetworkTask that loads a File.
*/
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -23,7 +23,7 @@
protected CyLayouts layouts;
- public CyNetworkView[] getNetworkViews(){
+ public CyNetworkView[] getNetworkViews() {
return cyNetworkViews;
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -133,9 +133,9 @@
if (networkViewProducer == null) {
throw new IllegalArgumentException("File type is not
supported.");
}
-
+
+ System.out.println("### Producer found: " +
networkViewProducer);
return networkViewProducer;
-
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
2010-08-18 23:38:54 UTC (rev 21463)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
2010-08-18 23:49:14 UTC (rev 21464)
@@ -94,7 +94,6 @@
}
createNetwork(tm);
-
}
@@ -120,9 +119,7 @@
}
tm.setProgress(0.05);
-
- int nodeCount = nodeMap.size();
-
+
CyNode node;
for (String nodeName : nodeMap.keySet()) {
if (this.cancel){
@@ -145,8 +142,6 @@
String srcName;
String interactionType;
CyEdge edge;
-
- int edgeCount = interactions.size();
for (Interaction interaction : interactions) {
@@ -173,6 +168,8 @@
final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
layouts.getDefaultLayout().doLayout(view);
+ // SIF always creates only one network.
+ this.cyNetworkViews = new CyNetworkView[1];
this.cyNetworkViews[0] = view;
tm.setProgress(0.99);
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