Author: kono
Date: 2012-07-11 14:07:27 -0700 (Wed, 11 Jul 2012)
New Revision: 29841
Added:
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer16.png
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer24.png
core3/impl/trunk/network-analyzer-impl/src/test/
core3/impl/trunk/network-analyzer-impl/src/test/java/
core3/impl/trunk/network-analyzer-impl/test/
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
Log:
Icon added for NetworkAnalyzer.
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
2012-07-11 19:45:47 UTC (rev 29840)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
2012-07-11 21:07:27 UTC (rev 29841)
@@ -19,14 +19,18 @@
import java.awt.event.ActionEvent;
+import java.util.Map;
import java.util.Set;
+import javax.swing.ImageIcon;
+
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.work.ServiceProperties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
@@ -54,8 +58,9 @@
* Initializes a new instance of <code>AnalyzeNetworkAction</code>.
*/
public AnalyzeNetworkAction(CyApplicationManager
appMgr,CySwingApplication swingApp, final CyNetworkViewManager viewManager,
final VisualStyleBuilder vsBuilder,
- final VisualMappingManager vmm) {
- super(Messages.AC_ANALYZE,appMgr,swingApp);
+ final VisualMappingManager vmm, final Map<String,
String> configProps,
+ final CyNetworkViewManager networkViewManager) {
+ super(Messages.AC_ANALYZE,appMgr,swingApp, configProps,
networkViewManager);
this.viewManager = viewManager;
this.vmm = vmm;
this.vsBuilder = vsBuilder;
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
2012-07-11 19:45:47 UTC (rev 29840)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
2012-07-11 21:07:27 UTC (rev 29841)
@@ -1,30 +1,25 @@
package de.mpg.mpi_inf.bioinf.netanalyzer;
+import static org.cytoscape.work.ServiceProperties.ENABLE_FOR;
+import static org.cytoscape.work.ServiceProperties.ID;
+import static org.cytoscape.work.ServiceProperties.IN_TOOL_BAR;
+import static org.cytoscape.work.ServiceProperties.LARGE_ICON_URL;
+import static org.cytoscape.work.ServiceProperties.MENU_GRAVITY;
+import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU;
+import static org.cytoscape.work.ServiceProperties.SMALL_ICON_URL;
+import static org.cytoscape.work.ServiceProperties.TITLE;
+import static org.cytoscape.work.ServiceProperties.TOOLTIP;
+import static org.cytoscape.work.ServiceProperties.TOOL_BAR_GRAVITY;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.swing.CyAction;
import org.cytoscape.application.swing.CySwingApplication;
-import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.model.CyNetworkManager;
-
-import de.mpg.mpi_inf.bioinf.netanalyzer.CompareAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.PlotParameterAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.MapParameterAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.RemoveSelfLoopsAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.BatchAnalysisAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.RemDupEdgesAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.SettingsAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeSubsetAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
-import de.mpg.mpi_inf.bioinf.netanalyzer.AboutAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeNetworkAction;
-import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
-
-import org.cytoscape.application.swing.CyAction;
-
-
-import org.osgi.framework.BundleContext;
-
import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFatory;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -32,8 +27,9 @@
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.work.swing.DialogTaskManager;
+import org.osgi.framework.BundleContext;
-import java.util.Properties;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
@@ -67,7 +63,19 @@
// Builder object for custom Visual Style
VisualStyleBuilder vsBuilder = new
VisualStyleBuilder(vsFactoryServiceRef, passthroughMappingFactoryRef,
continupousMappingFactoryRef);
- AnalyzeNetworkAction analyzeNetworkAction = new
AnalyzeNetworkAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
viewManagerServiceRef, vsBuilder, vmmServiceRef);
+
+ Map<String,String> analyzerActionProps = new HashMap<String,
String>();
+ analyzerActionProps.put(ID,"analyzeNetworkAction");
+ analyzerActionProps.put(PREFERRED_MENU,"Tools.Network
Analyzer.Network Analysis");
+ analyzerActionProps.put(TITLE,"Analyze Network");
+ analyzerActionProps.put(MENU_GRAVITY,"9.0");
+ analyzerActionProps.put(TOOL_BAR_GRAVITY,"9.8");
+
analyzerActionProps.put(LARGE_ICON_URL,getClass().getResource("/networkAnalyzer24.png").toString());
+
analyzerActionProps.put(SMALL_ICON_URL,getClass().getResource("/networkAnalyzer16.png").toString());
+ analyzerActionProps.put(IN_TOOL_BAR,"true");
+ analyzerActionProps.put(TOOLTIP,"Analyze Network");
+ analyzerActionProps.put(ENABLE_FOR, "network");
+ AnalyzeNetworkAction analyzeNetworkAction = new
AnalyzeNetworkAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
viewManagerServiceRef, vsBuilder, vmmServiceRef, analyzerActionProps,
viewManagerServiceRef);
LoadNetstatsAction loadNetstatsAction = new
LoadNetstatsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
viewManagerServiceRef, vsBuilder, vmmServiceRef);
MapParameterAction mapParameterAction = new
MapParameterAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
viewManagerServiceRef, vsBuilder, vmmServiceRef, analyzeNetworkAction);
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
2012-07-11 19:45:47 UTC (rev 29840)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/NetAnalyzerAction.java
2012-07-11 21:07:27 UTC (rev 29841)
@@ -17,8 +17,10 @@
package de.mpg.mpi_inf.bioinf.netanalyzer;
+import java.util.Map;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.application.swing.CySwingApplication;
@@ -35,7 +37,7 @@
protected final CySwingApplication swingApp;
protected final CyApplicationManager applicationManager;
-
+
/**
* Target network for the action.
*/
@@ -54,32 +56,41 @@
network = null;
}
+ protected NetAnalyzerAction(final String aName, final
CyApplicationManager appMgr,
+ final CySwingApplication swingApp, final Map<String,
String> configProps,
+ final CyNetworkViewManager networkViewManager) {
+ super(configProps, appMgr, networkViewManager);
+ this.swingApp = swingApp;
+ this.applicationManager = appMgr;
+ network = null;
+ }
+
/**
* Finds the network of interest to the user.
* <p>
- * In case a network has been identified, the value of the field {@link
#network} is updated, otherwise
- * the value of <code>network</code> is set to the empty network or
<code>null</code>. There are
- * three possible reasons for the inability to choose a network - (1)
no network is loaded; (2) there are
- * two or more networks loaded and none selected; and (3) there is more
than one network selected. For
- * each of the two cases above, the method displays an appropriate
message dialog before exiting and
- * returning <code>false</code>.
+ * In case a network has been identified, the value of the field
+ * {@link #network} is updated, otherwise the value of
<code>network</code>
+ * is set to the empty network or <code>null</code>. There are three
+ * possible reasons for the inability to choose a network - (1) no
network
+ * is loaded; (2) there are two or more networks loaded and none
selected;
+ * and (3) there is more than one network selected. For each of the two
+ * cases above, the method displays an appropriate message dialog before
+ * exiting and returning <code>false</code>.
* </p>
*
- * @return <code>true</code> if a network targeting analysis has been
identified, <code>false</code>
- * otherwise.
+ * @return <code>true</code> if a network targeting analysis has been
+ * identified, <code>false</code> otherwise.
*/
@SuppressWarnings("fallthrough")
protected boolean selectNetwork() {
network = applicationManager.getCurrentNetwork();
- if ( network == null ) {
-
Utils.showErrorBox(swingApp.getJFrame(),Messages.DT_WRONGDATA,
Messages.SM_LOADNET);
+ if (network == null) {
+ Utils.showErrorBox(swingApp.getJFrame(),
Messages.DT_WRONGDATA, Messages.SM_LOADNET);
return false;
}
return true;
}
-
-
/**
* Unique ID for this version of this class. It is used in
serialization.
*/
Added:
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer16.png
===================================================================
(Binary files differ)
Property changes on:
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer16.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added:
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer24.png
===================================================================
(Binary files differ)
Property changes on:
core3/impl/trunk/network-analyzer-impl/src/main/resources/networkAnalyzer24.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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