Author: clopes Date: 2011-09-16 11:54:21 -0700 (Fri, 16 Sep 2011) New Revision: 26840
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAnalyzeAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
Log:
Fixed incorrect file filter name and changed the analyze action to be enabled
when there is a network, not a network view.
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAnalyzeAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAnalyzeAction.java
2011-09-16 05:03:14 UTC (rev 26839)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAnalyzeAction.java
2011-09-16 18:54:21 UTC (rev 26840)
@@ -23,12 +23,12 @@
import org.cytoscape.mcode.internal.view.MCODEResultsPanel;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.events.NetworkAddedEvent;
+import org.cytoscape.model.events.NetworkAddedListener;
+import org.cytoscape.model.events.NetworkDestroyedEvent;
+import org.cytoscape.model.events.NetworkDestroyedListener;
import org.cytoscape.service.util.CyServiceRegistrar;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.events.NetworkViewAddedEvent;
-import org.cytoscape.view.model.events.NetworkViewAddedListener;
-import org.cytoscape.view.model.events.NetworkViewDestroyedEvent;
-import org.cytoscape.view.model.events.NetworkViewDestroyedListener;
import org.cytoscape.work.TaskManager;
/**
@@ -70,8 +70,8 @@
/**
* Simple score and find action for MCODE. This should be the default for
general users.
*/
-public class MCODEAnalyzeAction extends AbstractMCODEAction implements
NetworkViewAddedListener,
- NetworkViewDestroyedListener {
+public class MCODEAnalyzeAction extends AbstractMCODEAction implements
NetworkAddedListener,
+ NetworkDestroyedListener {
private static final long serialVersionUID = 87924889404093104L;
@@ -96,8 +96,9 @@
this.registrar = registrar;
this.taskManager = taskManager;
this.mcodeUtil = mcodeUtil;
-
- enableFor = "networkAndView";
+
+ // The analysis should be disabled when there is no network
+ enableFor = "network";
}
/**
@@ -216,58 +217,49 @@
@Override
public void handleEvent(final
AnalysisCompletedEvent e) {
- SwingUtilities.invokeLater(new
Runnable() {
+ MCODEResultsPanel resultsPanel = null;
+ boolean resultFound = false;
- @Override
- public void run() {
- MCODEResultsPanel
resultsPanel = null;
- boolean resultFound =
false;
+ // Display clusters in a new modal
dialog box
+ if (e.isSuccessful()) {
+ if (e.getClusters() != null &&
e.getClusters().length > 0) {
+ resultFound = true;
+
mcodeUtil.addNetworkResult(network.getSUID());
- // Display clusters in
a new modal dialog box
- if (e.isSuccessful()) {
- if
(e.getClusters() != null && e.getClusters().length > 0) {
-
resultFound = true;
-
mcodeUtil.addNetworkResult(network.getSUID());
+
MCODEDiscardResultAction discardResultAction = new MCODEDiscardResultAction(
+
"Discard Result",
+
resultId,
+
applicationManager,
+
swingApplication,
+
registrar,
+
mcodeUtil);
-
MCODEDiscardResultAction discardResultAction = new MCODEDiscardResultAction(
-
"Discard
Result",
-
resultId,
-
applicationManager,
-
swingApplication,
-
registrar,
-
mcodeUtil);
+ resultsPanel = new
MCODEResultsPanel(e.getClusters(), alg, mcodeUtil, network, networkView,
+
e.getImageList(), resultId,
swingApplication,
+
discardResultAction);
-
resultsPanel = new MCODEResultsPanel(e.getClusters(), alg, mcodeUtil, network,
-
networkView,
e.getImageList(), resultId,
-
swingApplication, discardResultAction);
+
registrar.registerService(resultsPanel, CytoPanelComponent.class, new
Properties());
+ } else {
+
JOptionPane.showMessageDialog(swingApplication.getJFrame(),
+
"No clusters were found.\n"
+
+ "You can try changing the
MCODE parameters or\n"
+
+ "modifying your node
selection if you are using\n"
+
+ "a selection-specific
scope.",
+
"No Results",
+
JOptionPane.WARNING_MESSAGE);
+ }
+ }
-
registrar.registerService(resultsPanel, CytoPanelComponent.class, new
Properties());
- } else {
-
JOptionPane
-
.showMessageDialog(swingApplication.getJFrame(),
-
"No clusters were found.\n"
-
+ "You can try
changing the MCODE parameters or\n"
-
+ "modifying your
node selection if you are using\n"
-
+ "a
selection-specific scope.",
-
"No Results",
-
JOptionPane.WARNING_MESSAGE);
- }
- }
+ CytoPanel cytoPanel =
swingApplication.getCytoPanel(CytoPanelName.EAST);
- CytoPanel cytoPanel =
swingApplication.getCytoPanel(CytoPanelName.EAST);
+ // This if statement ensures that the
east cytopanel is not loaded if there are no results in it
+ if (resultFound || (analyze ==
INTERRUPTION && cytoPanel.indexOfComponent(resultsPanel) >= 0)) {
+ // Focus the result panel
+ int index =
cytoPanel.indexOfComponent(resultsPanel);
+
cytoPanel.setSelectedIndex(index);
- // This if statement
ensures that the east cytopanel is not loaded if there are no results in it
- if (resultFound ||
- (analyze ==
INTERRUPTION && cytoPanel.indexOfComponent(resultsPanel) >= 0)) {
- // Focus the
result panel
- int index =
cytoPanel.indexOfComponent(resultsPanel);
-
cytoPanel.setSelectedIndex(index);
-
- if
(cytoPanel.getState() == CytoPanelState.HIDE)
-
cytoPanel.setState(CytoPanelState.DOCK);
- }
- }
- });
+ if (cytoPanel.getState() ==
CytoPanelState.HIDE) cytoPanel.setState(CytoPanelState.DOCK);
+ }
}
};
@@ -279,12 +271,12 @@
}
@Override
- public void handleEvent(NetworkViewAddedEvent e) {
+ public void handleEvent(NetworkAddedEvent e) {
updateEnableState();
}
@Override
- public void handleEvent(NetworkViewDestroyedEvent e) {
+ public void handleEvent(NetworkDestroyedEvent e) {
updateEnableState();
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2011-09-16 05:03:14 UTC (rev 26839)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2011-09-16 18:54:21 UTC (rev 26840)
@@ -690,7 +690,7 @@
try {
// Call save method in MCODE get the file name
Collection<FileChooserFilter> filters = new
ArrayList<FileChooserFilter>();
- filters.add(new FileChooserFilter("BioPAX format",
"txt"));
+ filters.add(new FileChooserFilter("Text format",
"txt"));
File file =
fileUtil.getFile(swingApplication.getJFrame(),
"Export Graph as Interactions",
FileUtil.SAVE,
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-16 05:03:14 UTC (rev 26839)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-16 18:54:21 UTC (rev 26840)
@@ -89,8 +89,8 @@
<osgi:service id="analyzeActionService" ref="analyzeAction">
<osgi:interfaces>
-
<value>org.cytoscape.view.model.events.NetworkViewAddedListener</value>
-
<value>org.cytoscape.view.model.events.NetworkViewDestroyedListener</value>
+ <value>org.cytoscape.model.events.NetworkAddedListener</value>
+ <value>org.cytoscape.model.events.NetworkDestroyedListener</value>
</osgi:interfaces>
</osgi:service>
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