Author: pwang
Date: 2010-08-17 17:20:51 -0700 (Tue, 17 Aug 2010)
New Revision: 21436
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/LoadInputStreamTaskFactoryImpl.java
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/LoadNetworkFileTaskFactoryImpl.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskFactoryImpl.java
Log:
Refactored
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 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -45,8 +45,8 @@
import java.awt.Event;
import java.io.IOException;
-import org.cytoscape.io.read.CyReader;
-import org.cytoscape.io.read.CyReaderManager;
+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.view.model.CyNetworkView;
@@ -63,13 +63,13 @@
*/
abstract class AbstractLoadNetworkTask extends AbstractTask {
- protected CyReader reader;
+ protected CyNetworkViewProducer reader;
protected URI uri;
protected TaskMonitor taskMonitor;
protected String name;
protected Thread myThread = null;
protected boolean interrupted = false;
- protected CyReaderManager mgr;
+ protected CyNetworkViewProducerManager mgr;
protected CyNetworkViewFactory gvf;
protected CyLayouts cyl;
protected CyNetworkManager netmgr;
@@ -77,7 +77,7 @@
protected CyNetworkNaming namingUtil;
- public AbstractLoadNetworkTask(CyReaderManager mgr,
CyNetworkViewFactory gvf,
+ public AbstractLoadNetworkTask(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf,
CyLayouts cyl, CyNetworkManager netmgr, Properties
props,
CyNetworkNaming namingUtil) {
this.mgr = mgr;
@@ -88,7 +88,7 @@
this.namingUtil = namingUtil;
}
- protected void loadNetwork(CyReader reader) throws Exception {
+ protected void loadNetwork(CyNetworkViewProducer reader) throws
Exception {
if (reader == null)
throw new Exception("Could not read file: file reader
was null");
@@ -102,12 +102,14 @@
taskMonitor.setStatusMessage("Creating Cytoscape
Network...");
- final Map<Class<?>, Object> readData = reader.read();
+ //final Map<Class<?>, Object> readData = reader.read();
- CyNetwork cyNetwork = (CyNetwork)
readData.get(CyNetwork.class);
+ CyNetworkView[] cyNetworkViews =
reader.getNetworkViews();
+
+ CyNetwork cyNetwork = cyNetworkViews[0].getModel();
cyNetwork.attrs().set("name",
namingUtil.getSuggestedNetworkTitle(name));
- CyNetworkView view = (CyNetworkView)
readData.get(CyNetworkView.class);
+ CyNetworkView view = cyNetworkViews[0];
if (view == null)
view = gvf.getNetworkView(cyNetwork);
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 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTask.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -40,7 +40,7 @@
import java.io.InputStream;
import java.util.Properties;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskMonitor;
@@ -56,7 +56,7 @@
@Tunable(description = "InputStream to load")
public InputStream inputstream;
- public LoadInputStreamTask(CyReaderManager mgr, CyNetworkViewFactory
gvf,
+ public LoadInputStreamTask(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf,
CyLayouts cyl, CyNetworkManager netmgr, Properties
props, CyNetworkNaming namingUtil) {
super(mgr, gvf, cyl, netmgr, props, namingUtil);
}
@@ -71,7 +71,7 @@
}
this.taskMonitor = taskMonitor;
- reader = mgr.getReader(inputstream, NETWORK);
+ reader = mgr.getProducer(inputstream);
name = inputstream.toString();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTaskFactoryImpl.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTaskFactoryImpl.java
2010-08-18 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadInputStreamTaskFactoryImpl.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -39,7 +39,7 @@
import java.util.Properties;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -54,7 +54,7 @@
*/
public class LoadInputStreamTaskFactoryImpl implements TaskFactory {
- private CyReaderManager mgr;
+ private CyNetworkViewProducerManager mgr;
private CyNetworkViewFactory gvf;
private CyLayouts cyl;
private CyNetworkManager netmgr;
@@ -62,7 +62,7 @@
private CyNetworkNaming cyNetworkNaming;
- public LoadInputStreamTaskFactoryImpl(CyReaderManager mgr,
+ public LoadInputStreamTaskFactoryImpl(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf, CyLayouts cyl,
CyNetworkManager netmgr,
CyProperty<Properties> cyProp, CyNetworkNaming
cyNetworkNaming) {
this.mgr = mgr;
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 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -42,7 +42,7 @@
import java.io.File;
import java.util.Properties;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.TaskMonitor;
@@ -60,7 +60,7 @@
@Tunable(description = "Network file to load",flags = {Param.network})
public File file;
- public LoadNetworkFileTask(CyReaderManager mgr, CyNetworkViewFactory
gvf,
+ public LoadNetworkFileTask(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf,
CyLayouts cyl, CyNetworkManager netmgr, Properties
props, CyNetworkNaming namingUtil) {
super(mgr, gvf, cyl, netmgr, props, namingUtil);
}
@@ -71,7 +71,7 @@
public void run(TaskMonitor taskMonitor) throws Exception {
this.taskMonitor = taskMonitor;
- reader = mgr.getReader(file.toURI(), NETWORK);
+ reader = mgr.getProducer((file.toURI()));
uri = file.toURI();
name = file.getName();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskFactoryImpl.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskFactoryImpl.java
2010-08-18 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskFactoryImpl.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -39,7 +39,7 @@
import java.util.Properties;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -54,7 +54,7 @@
*/
public class LoadNetworkFileTaskFactoryImpl implements TaskFactory {
- private CyReaderManager mgr;
+ private CyNetworkViewProducerManager mgr;
private CyNetworkViewFactory gvf;
private CyLayouts cyl;
private CyNetworkManager netmgr;
@@ -62,7 +62,7 @@
private CyNetworkNaming cyNetworkNaming;
- public LoadNetworkFileTaskFactoryImpl(CyReaderManager mgr,
+ public LoadNetworkFileTaskFactoryImpl(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf, CyLayouts cyl,
CyNetworkManager netmgr,
CyProperty<Properties> cyProp, CyNetworkNaming
cyNetworkNaming) {
this.mgr = mgr;
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
2010-08-18 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTask.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -45,7 +45,7 @@
import java.util.Properties;
import org.cytoscape.io.DataCategory;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -67,7 +67,7 @@
static String BAD_INTERNET_SETTINGS_MSG = "<html><p>Cytoscape has
failed to connect to the URL. Please ensure that:</p><p><ol><li>the URL is
correct,</li><li>your computer is able to connect to the Internet,
and</li><li>your proxy settings are correct.</li></ol></p><p>The reason for the
failure is: %s</html>";
- public LoadNetworkURLTask(CyReaderManager mgr, CyNetworkViewFactory gvf,
+ public LoadNetworkURLTask(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf,
CyLayouts cyl, CyNetworkManager netmgr, Properties
props,
CyNetworkNaming namingUtil, StreamUtil streamUtil) {
super(mgr, gvf, cyl, netmgr, props, namingUtil);
@@ -98,7 +98,7 @@
}
taskMonitor.setStatusMessage("Reading network...");
- reader = mgr.getReader(url.toURI(),DataCategory.NETWORK);
+ reader = mgr.getProducer(url.toURI());
taskMonitor.setStatusMessage("Loading network...");
loadNetwork(reader);
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskFactoryImpl.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskFactoryImpl.java
2010-08-18 00:20:04 UTC (rev 21435)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskFactoryImpl.java
2010-08-18 00:20:51 UTC (rev 21436)
@@ -40,7 +40,7 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.layout.CyLayouts;
-import org.cytoscape.io.read.CyReaderManager;
+import org.cytoscape.io.read.CyNetworkViewProducerManager;
import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -56,7 +56,7 @@
*/
public class LoadNetworkURLTaskFactoryImpl implements TaskFactory {
- private CyReaderManager mgr;
+ private CyNetworkViewProducerManager mgr;
private CyNetworkViewFactory gvf;
private CyLayouts cyl;
private CyNetworkManager netmgr;
@@ -65,7 +65,7 @@
private CyNetworkNaming cyNetworkNaming;
- public LoadNetworkURLTaskFactoryImpl(CyReaderManager mgr,
+ public LoadNetworkURLTaskFactoryImpl(CyNetworkViewProducerManager mgr,
CyNetworkViewFactory gvf, CyLayouts cyl,
CyNetworkManager netmgr,
CyProperty<Properties> cyProps, CyNetworkNaming
cyNetworkNaming,
StreamUtil streamUtil) {
@@ -83,6 +83,8 @@
}
public Task getTask() {
- return new LoadNetworkURLTask(mgr, gvf, cyl, netmgr, props,
cyNetworkNaming, streamUtil);
+ //return new LoadNetworkURLTask(mgr, gvf, cyl, netmgr, props,
cyNetworkNaming, streamUtil);
+
+ return null;
}
}
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