Author: clopes
Date: 2011-08-25 13:24:28 -0700 (Thu, 25 Aug 2011)
New Revision: 26636
Modified:
csplugins/trunk/toronto/clopes/mcode/pom.xml
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/AbstractMCODEAction.java
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/MCODECloseAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEOpenAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECurrentParameters.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
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/view/MCODEMainPanel.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Closing the plugin now removes the related CytoPanels correctly.
Fixed most of the issues with node selection (had to remove workaround used for
creating cluster images).
Modified: csplugins/trunk/toronto/clopes/mcode/pom.xml
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/pom.xml 2011-08-24 23:35:48 UTC
(rev 26635)
+++ csplugins/trunk/toronto/clopes/mcode/pom.xml 2011-08-25 20:24:28 UTC
(rev 26636)
@@ -141,12 +141,6 @@
<version>4.8.2</version>
<scope>test</scope>
</dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>test-support</artifactId>
- <version>3.0.0-alpha2</version>
- <scope>test</scope>
- </dependency>
</dependencies>
</project>
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/AbstractMCODEAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/AbstractMCODEAction.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/AbstractMCODEAction.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -1,5 +1,8 @@
package org.cytoscape.mcode.internal;
+import java.util.ArrayList;
+import java.util.Collection;
+
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.application.swing.CySwingApplication;
@@ -30,7 +33,7 @@
* @return Cytoscape's results panel
*/
protected CytoPanel getResultsCytoPanel() {
- return swingApplication.getCytoPanel(CytoPanelName.WEST);
+ return swingApplication.getCytoPanel(CytoPanelName.EAST);
}
/**
@@ -49,18 +52,19 @@
}
/**
- * @return The results panel of the plugin if it is opened, and null
otherwise
+ * @return The result panels of the plugin if it is opened, or an empty
collection otherwise
*/
- protected MCODEResultsPanel getResultsPanel() {
+ protected Collection<MCODEResultsPanel> getResultPanels() {
+ Collection<MCODEResultsPanel> panels = new
ArrayList<MCODEResultsPanel>();
CytoPanel cytoPanel = getResultsCytoPanel();
int count = cytoPanel.getCytoPanelComponentCount();
for (int i = 0; i < count; i++) {
if (cytoPanel.getComponentAt(i) instanceof
MCODEResultsPanel)
- return (MCODEResultsPanel)
cytoPanel.getComponentAt(i);
+ panels.add((MCODEResultsPanel)
cytoPanel.getComponentAt(i));
}
- return null;
+ return panels;
}
/**
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
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAnalyzeAction.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -2,9 +2,7 @@
import java.awt.event.ActionEvent;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
import java.util.Properties;
import javax.swing.JOptionPane;
@@ -19,7 +17,6 @@
import org.cytoscape.mcode.internal.event.AnalysisCompletedEvent;
import org.cytoscape.mcode.internal.event.AnalysisCompletedListener;
import org.cytoscape.mcode.internal.model.MCODEAlgorithm;
-import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
import org.cytoscape.mcode.internal.model.MCODEParameterSet;
import org.cytoscape.mcode.internal.task.MCODEAnalyzeTaskFactory;
import org.cytoscape.mcode.internal.util.MCODEUtil;
@@ -87,9 +84,6 @@
private final TaskManager taskManager;
private final MCODEUtil mcodeUtil;
- //Keeps track of networks (id is key) and their respective algorithms
- private Map<Long, MCODEAlgorithm> networkManager;
-
private MCODEResultsPanel resultPanel;
int analyze = FIRST_TIME;
@@ -107,7 +101,6 @@
this.mcodeUtil = mcodeUtil;
enableFor = "networkAndView";
- networkManager = new HashMap<Long, MCODEAlgorithm>();
}
/**
@@ -160,14 +153,14 @@
// of that network (so as to determine if rescoring/refinding
is required for
// this network without interference by parameters of other
networks)
// otherwise we construct a new alg class
- if (networkManager.containsKey(network.getSUID())) {
- alg = networkManager.get(network.getSUID());
+ if (mcodeUtil.containsNetworkAlgorithm(network.getSUID())) {
+ alg = mcodeUtil.getNetworkAlgorithm(network.getSUID());
// Get a copy of the last saved parameters for
comparison with the current ones
- savedParamsCopy =
MCODECurrentParameters.getInstance().getParamsCopy(network.getSUID());
+ savedParamsCopy =
mcodeUtil.getCurrentParameters().getParamsCopy(network.getSUID());
} else {
alg = new MCODEAlgorithm(null, mcodeUtil);
- savedParamsCopy =
MCODECurrentParameters.getInstance().getParamsCopy(null);
- networkManager.put(network.getSUID(), alg);
+ savedParamsCopy =
mcodeUtil.getCurrentParameters().getParamsCopy(null);
+ mcodeUtil.addNetworkAlgorithm(network.getSUID(), alg);
analyze = FIRST_TIME;
}
@@ -180,7 +173,7 @@
currentParamsCopy.getDegreeCutoff() !=
savedParamsCopy.getDegreeCutoff() || analyze == FIRST_TIME) {
analyze = RESCORE;
System.err.println("Analysis: score network, find
clusters");
-
MCODECurrentParameters.getInstance().setParams(currentParamsCopy, resultId,
network.getSUID());
+
mcodeUtil.getCurrentParameters().setParams(currentParamsCopy, resultId,
network.getSUID());
} else if
(!currentParamsCopy.getScope().equals(savedParamsCopy.getScope()) ||
(!currentParamsCopy.getScope().equals(MCODEParameterSet.NETWORK) &&
currentParamsCopy
.getSelectedNodes() !=
savedParamsCopy.getSelectedNodes()) ||
@@ -196,11 +189,11 @@
.getFluffNodeDensityCutoff())))) {
analyze = REFIND;
System.err.println("Analysis: find clusters");
-
MCODECurrentParameters.getInstance().setParams(currentParamsCopy, resultId,
network.getSUID());
+
mcodeUtil.getCurrentParameters().setParams(currentParamsCopy, resultId,
network.getSUID());
} else {
analyze = INTERRUPTION;
interruptedMessage = "The parameters you
specified\nhave not changed.";
-
MCODECurrentParameters.getInstance().setParams(currentParamsCopy, resultId,
network.getSUID());
+
mcodeUtil.getCurrentParameters().setParams(currentParamsCopy, resultId,
network.getSUID());
}
// Finally we save the current parameters
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODECloseAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODECloseAction.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODECloseAction.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -1,6 +1,7 @@
package org.cytoscape.mcode.internal;
import java.awt.event.ActionEvent;
+import java.util.Collection;
import javax.swing.JOptionPane;
@@ -10,7 +11,7 @@
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
import org.cytoscape.application.swing.CytoPanelState;
-import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
+import org.cytoscape.mcode.internal.util.MCODEUtil;
import org.cytoscape.mcode.internal.view.MCODEMainPanel;
import org.cytoscape.mcode.internal.view.MCODEResultsPanel;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -23,13 +24,16 @@
private static final long serialVersionUID = -8309835257402089360L;
private final CyServiceRegistrar registrar;
+ private final MCODEUtil mcodeUtil;
public MCODECloseAction(final String name,
final
CyApplicationManager applicationManager,
final
CySwingApplication swingApplication,
- final
CyServiceRegistrar registrar) {
+ final
CyServiceRegistrar registrar,
+ final MCODEUtil
mcodeUtil) {
super(name, applicationManager, swingApplication);
this.registrar = registrar;
+ this.mcodeUtil = mcodeUtil;
setPreferredMenu("Plugins.MCODE");
}
@@ -43,9 +47,9 @@
//First we must make sure that the plugin is opened
if (isOpened()) {
- MCODEResultsPanel resultsPanel = getResultsPanel();
+ Collection<MCODEResultsPanel> resultPanels =
getResultPanels();
- if (resultsPanel != null) {
+ if (resultPanels.size() > 0) {
String message = "You are about to close the
MCODE plugin.\nDo you wish to continue?";
int result =
JOptionPane.showOptionDialog(swingApplication.getJFrame(),
new Object[] { message },
@@ -56,11 +60,12 @@
null,
null);
if (result == JOptionPane.YES_OPTION) {
- int resultId =
resultsPanel.getResultId();
-
MCODECurrentParameters.removeResultParams(resultId);
+ for (MCODEResultsPanel p :
resultPanels) {
+ int resultId = p.getResultId();
+
mcodeUtil.getCurrentParameters().removeResultParams(resultId);
+ registrar.unregisterService(p,
CytoPanelComponent.class);
+ }
-
registrar.unregisterService(resultsPanel, CytoPanelComponent.class);
-
if
(cytoPanel.getCytoPanelComponentCount() == 0) {
cytoPanel.setState(CytoPanelState.HIDE);
}
@@ -72,6 +77,8 @@
if (mainPanel != null) {
registrar.unregisterService(mainPanel,
CytoPanelComponent.class);
}
+
+ mcodeUtil.reset();
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEOpenAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEOpenAction.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEOpenAction.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -7,6 +7,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
+import org.cytoscape.mcode.internal.util.MCODEUtil;
import org.cytoscape.mcode.internal.view.MCODEMainPanel;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -19,15 +20,18 @@
private final CyServiceRegistrar registrar;
private final MCODEAnalyzeAction analyzeAction;
+ private final MCODEUtil mcodeUtil;
public MCODEOpenAction(final String name,
final CyApplicationManager
applicationManager,
final CySwingApplication
swingApplication,
final CyServiceRegistrar
registrar,
- final MCODEAnalyzeAction
analyzeAction) {
+ final MCODEAnalyzeAction
analyzeAction,
+ final MCODEUtil mcodeUtil) {
super(name, applicationManager, swingApplication);
this.registrar = registrar;
this.analyzeAction = analyzeAction;
+ this.mcodeUtil = mcodeUtil;
setPreferredMenu("Plugins.MCODE");
}
@@ -43,11 +47,10 @@
// First we must make sure that the plugin is not
already open
if (!isOpened()) {
- mainPanel = new
MCODEMainPanel(swingApplication);
+ mainPanel = new
MCODEMainPanel(swingApplication, mcodeUtil);
mainPanel.addAction(analyzeAction);
registrar.registerService(mainPanel,
CytoPanelComponent.class, new Properties());
-
analyzeAction.updateEnableState();
} else {
mainPanel = getMainPanel();
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -113,7 +113,7 @@
public MCODEAlgorithm(final Long networkID, final MCODEUtil mcodeUtil) {
this.mcodeUtil = mcodeUtil;
//get current parameters
- params =
MCODECurrentParameters.getInstance().getParamsCopy(networkID);
+ params =
mcodeUtil.getCurrentParameters().getParamsCopy(networkID);
}
public MCODEAlgorithm(final TaskMonitor taskMonitor, final Long
networkID, final MCODEUtil mcodeUtil) {
@@ -122,7 +122,7 @@
}
public void setTaskMonitor(TaskMonitor taskMonitor, Long networkID) {
- params =
MCODECurrentParameters.getInstance().getParamsCopy(networkID);
+ params =
mcodeUtil.getCurrentParameters().getParamsCopy(networkID);
this.taskMonitor = taskMonitor;
}
@@ -457,7 +457,7 @@
// This method is similar to the finding method with the
exception of the filtering so that the decrease of the cluster size
// can produce a single node, also the use of the node seen
hash map is differentially applied...
Map<Integer, NodeInfo> nodeInfoHashMap =
nodeInfoResultsMap.get(resultId);
- MCODEParameterSet params =
MCODECurrentParameters.getResultParams(cluster.getResultId());
+ MCODEParameterSet params =
mcodeUtil.getCurrentParameters().getResultParams(cluster.getResultId());
final Map<Integer, Boolean> nodeSeenHashMap;
// If the size slider is below the set node score cutoff we use
the node seen hash map so that clusters
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECurrentParameters.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECurrentParameters.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECurrentParameters.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -46,20 +46,10 @@
*/
public class MCODECurrentParameters {
- private static MCODECurrentParameters ourInstance = new
MCODECurrentParameters();
- private static Map<Long, MCODEParameterSet> currentParams = new
HashMap<Long, MCODEParameterSet>();
- private static Map<Integer, MCODEParameterSet> resultParams = new
HashMap<Integer, MCODEParameterSet>();
+ private Map<Long, MCODEParameterSet> currentParams = new HashMap<Long,
MCODEParameterSet>();
+ private Map<Integer, MCODEParameterSet> resultParams = new
HashMap<Integer, MCODEParameterSet>();
/**
- * Get the one instance of this singleton class that stores the current
parameters internally.
- *
- * @return ourInstance
- */
- public static MCODECurrentParameters getInstance() {
- return ourInstance;
- }
-
- /**
* Get a copy of the current parameters for a particular network. Only
a copy of the current param object is
* returned to avoid side effects. The user should use the following
code to get their
* own copy of the current parameters:
@@ -116,11 +106,11 @@
resultParams.put(resultId, resultParamSet);
}
- public static MCODEParameterSet getResultParams(int resultId) {
+ public MCODEParameterSet getResultParams(int resultId) {
return resultParams.get(resultId).copy();
}
- public static void removeResultParams(int resultId) {
+ public void removeResultParams(int resultId) {
resultParams.remove(resultId);
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/task/MCODEAnalyzeTask.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -130,20 +130,14 @@
// Also create all the images here for the clusters,
since it can be a time consuming operation
clusters = mcodeUtil.sortClusters(clusters);
imageList = new Image[clusters.length];
- int imageSize =
MCODECurrentParameters.getResultParams(resultId).getDefaultRowHeight();
+ int imageSize =
mcodeUtil.getCurrentParameters().getResultParams(resultId).getDefaultRowHeight();
for (int i = 0; i < clusters.length; i++) {
if (interrupted) {
return;
}
- imageList[i] =
mcodeUtil.convertNetworkToImage(network,
-
null,
-
clusters[i],
-
imageSize,
-
imageSize,
-
null,
-
true);
+ imageList[i] =
mcodeUtil.createClusterImage(clusters[i], imageSize, imageSize, null, true,
null);
taskMonitor.setProgress((i * 100) /
clusters.length);
}
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
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -1,7 +1,6 @@
package org.cytoscape.mcode.internal.util;
import java.awt.Color;
-import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics2D;
@@ -13,14 +12,16 @@
import java.io.IOException;
import java.text.DateFormat;
import java.text.NumberFormat;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Comparator;
import java.util.Date;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Map;
import java.util.Set;
-import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
@@ -29,6 +30,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.mcode.internal.model.MCODEAlgorithm;
import org.cytoscape.mcode.internal.model.MCODECluster;
+import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
import org.cytoscape.mcode.internal.view.MCODELoader;
import org.cytoscape.mcode.internal.view.SpringEmbeddedLayouter;
import org.cytoscape.model.CyEdge;
@@ -106,6 +108,9 @@
private boolean interrupted;
private Image placeHolderImage;
private VisualStyle style; // visual style used by the MCODE plugin
+ private MCODECurrentParameters currentParameters;
+ //Keeps track of networks (id is key) and their respective algorithms
+ private Map<Long, MCODEAlgorithm> networkAlgorithms;
public MCODEUtil(final RenderingEngineFactory<CyNetwork>
renderingEngineFactory,
final CyNetworkViewFactory
networkViewFactory,
@@ -127,26 +132,48 @@
this.visualMappingMgr = visualMappingMgr;
this.swingApplication = swingApplication;
this.eventHelper = eventHelper;
+
+ this.reset();
}
+ public void reset() {
+ currentParameters = new MCODECurrentParameters();
+ networkAlgorithms = new HashMap<Long, MCODEAlgorithm>();
+ }
+
+ public MCODECurrentParameters getCurrentParameters() {
+ return currentParameters;
+ }
+
+ public boolean containsNetworkAlgorithm(long suid) {
+ return networkAlgorithms.containsKey(suid);
+ }
+
+ public MCODEAlgorithm getNetworkAlgorithm(long suid) {
+ return networkAlgorithms.get(suid);
+ }
+
+ public void addNetworkAlgorithm(long suid, MCODEAlgorithm alg) {
+ networkAlgorithms.put(suid, alg);
+ }
+
/**
* Convert a network to an image. This is used by the
MCODEResultsPanel.
- *
- * @param loader Graphic loader displaying progress and process
+ *
* @param cluster Input network to convert to an image
* @param height Height that the resulting image should be
* @param width Width that the resulting image should be
* @param layouter Reference to the layout algorithm
* @param layoutNecessary Determinant of cluster size growth or
shrinkage, the former requires layout
+ * @param loader Graphic loader displaying progress and process
* @return The resulting image
*/
- public Image convertNetworkToImage(final CyNetwork network,
-
final MCODELoader loader,
-
final MCODECluster cluster,
-
final int height,
-
final int width,
-
SpringEmbeddedLayouter layouter,
-
boolean layoutNecessary) {
+ public Image createClusterImage(final MCODECluster cluster,
+ final
int height,
+ final
int width,
+
SpringEmbeddedLayouter layouter,
+ boolean
layoutNecessary,
+ final
MCODELoader loader) {
// Progress reporters.
// There are three basic tasks, the progress of each is
calculated and then combined
// using the respective weighting to get an overall progress
global progress
@@ -164,7 +191,7 @@
final VisualStyle vs = getPluginStyle();
final CyNetworkView clusterView =
createNetworkView(cluster.getNetwork(), vs);
-
+
clusterView.setVisualProperty(MinimalVisualLexicon.NETWORK_WIDTH, new
Double(width));
clusterView.setVisualProperty(MinimalVisualLexicon.NETWORK_HEIGHT, new
Double(height));
@@ -255,7 +282,8 @@
@Override
public void run() {
try {
- displayNetworkView(clusterView);
+ // TODO: remove this workaround when
possible to get image off-screen
+ //
displayNetworkView(clusterView);
// Apply style again:
vs.apply(clusterView);
@@ -275,7 +303,8 @@
} catch (Exception ex) {
throw new RuntimeException(ex);
} finally {
- destroyNetworkViewAndModel(clusterView);
+ // TODO: remove this workaround when
possible to get image off-screen
+ //
destroyNetworkViewAndModel(clusterView);
}
}
});
@@ -330,7 +359,7 @@
networkMgr.destroyNetwork(view.getModel());
}
}
-
+
public VisualStyle getPluginStyle() {
if (style == null) {
style = visualStyleFactory.getInstance("MCODE");
@@ -413,15 +442,21 @@
return view != null ? visualMappingMgr.getVisualStyle(view) :
null;
}
- public void setSelected(final Collection<? extends CyTableEntry>
objects, final boolean select, CyNetworkView view) {
- for (final CyTableEntry nodeOrEdge : objects)
+ @SuppressWarnings("unchecked")
+ public void setSelected(final Collection<? extends CyTableEntry>
elements, CyNetwork network, CyNetworkView view) {
+ Collection<? extends CyTableEntry> allElements = new
ArrayList<CyTableEntry>(network.getNodeList());
+ allElements.addAll((Collection) network.getEdgeList());
+
+ for (final CyTableEntry nodeOrEdge : allElements) {
+ boolean select = elements.contains(nodeOrEdge);
nodeOrEdge.getCyRow().set(CyNetwork.SELECTED, select);
+ }
eventHelper.flushPayloadEvents();
-
+
if (view != null) {
view.updateView();
- eventHelper.flushPayloadEvents();
+// eventHelper.flushPayloadEvents();
swingApplication.getJFrame().repaint(); // TODO: remove
this ugly hack!!!
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEMainPanel.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEMainPanel.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEMainPanel.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -2,7 +2,6 @@
import java.awt.BorderLayout;
import java.awt.Component;
-import java.awt.Container;
import java.awt.FlowLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
@@ -34,9 +33,9 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
-import org.cytoscape.mcode.internal.model.MCODECurrentParameters;
import org.cytoscape.mcode.internal.model.MCODEParameterSet;
import org.cytoscape.mcode.internal.util.MCODEResources;
+import org.cytoscape.mcode.internal.util.MCODEUtil;
import org.cytoscape.mcode.internal.util.MCODEResources.ImageName;
/**
@@ -81,6 +80,7 @@
private static final long serialVersionUID = 2655227790686546553L;
private final CySwingApplication swingApplication;
+ private final MCODEUtil mcodeUtil;
private final List<CyAction> actions;
// Panels
@@ -126,22 +126,16 @@
/**
* The actual parameter change panel that builds the UI
- *
- * @param trigger A reference to the action that triggered the
initiation of this class
- * @param MCODEVS Reference to MCODE's visual style
*/
- public MCODEMainPanel(final CySwingApplication swingApplication
- /*MCODEMainPanelAction trigger, final MCODEVisualStyle MCODEVS*/) {
+ public MCODEMainPanel(final CySwingApplication swingApplication, final
MCODEUtil mcodeUtil) {
this.swingApplication = swingApplication;
-
+ this.mcodeUtil = mcodeUtil;
actions = new ArrayList<CyAction>();
-
- // this.trigger = trigger;
- // this.MCODEVS = MCODEVS;
+
setLayout(new BorderLayout());
//get the current parameters
- currentParamsCopy =
MCODECurrentParameters.getInstance().getParamsCopy(null);
+ currentParamsCopy =
mcodeUtil.getCurrentParameters().getParamsCopy(null);
currentParamsCopy.setDefaultParams();
decFormat = new DecimalFormat();
@@ -168,7 +162,7 @@
public void addAction(CyAction action) {
JButton bt = new JButton(action);
getBottomPanel().add(bt);
-
+
this.actions.add(action);
}
@@ -196,7 +190,7 @@
public MCODEParameterSet getCurrentParamsCopy() {
return currentParamsCopy;
}
-
+
/**
* Creates a JPanel containing scope radio buttons
*
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2011-08-25 20:24:28 UTC (rev 26636)
@@ -168,7 +168,7 @@
this.swingApplication = swingApplication;
this.registrar = registrar;
- currentParamsCopy =
MCODECurrentParameters.getResultParams(resultId);
+ currentParamsCopy =
mcodeutil.getCurrentParameters().getResultParams(resultId);
JPanel clusterBrowserPanel =
createClusterBrowserPanel(imageList);
JPanel bottomPanel = createBottomPanel();
@@ -465,13 +465,13 @@
protected Object doInBackground() throws
Exception {
CyNetwork newNetwork =
mcodeutil.createSubNetwork(clusterNetwork, clusterNetwork.getNodeList());
newNetwork.getCyRow().set(CyNetwork.NAME, title);
-
+
VisualStyle vs =
mcodeutil.getNetworkViewStyle(networkView);
CyNetworkView newNetworkView =
mcodeutil.createNetworkView(newNetwork, vs);
-
+
newNetworkView.setVisualProperty(MinimalVisualLexicon.NETWORK_CENTER_X_LOCATION,
0.0);
newNetworkView.setVisualProperty(MinimalVisualLexicon.NETWORK_CENTER_Y_LOCATION,
0.0);
-
+
mcodeutil.displayNetworkView(newNetworkView);
// Layout new cluster and fit it to
window.
@@ -825,7 +825,7 @@
null);
if (result == JOptionPane.YES_OPTION) {
registrar.unregisterService(trigger,
CytoPanelComponent.class);
-
MCODECurrentParameters.removeResultParams(getResultId());
+
mcodeutil.getCurrentParameters().removeResultParams(getResultId());
}
// If there are no more tabs in the cytopanel then we
hide it
@@ -931,15 +931,15 @@
/**
* Selects a cluster in the view that is selected by the user in the
browser table
*
- * @param gpCluster Cluster to be selected
+ * @param custerNetwork Cluster to be selected
*/
- public void selectCluster(final CyNetwork gpCluster) {
- if (gpCluster != null) {
+ public void selectCluster(final CyNetwork custerNetwork) {
+ if (custerNetwork != null) {
// Only do this if a view has been created on this
network
if (networkView != null) {
// start with no selected nodes
-
mcodeutil.setSelected(networkView.getModel().getNodeList(), false, networkView);
- mcodeutil.setSelected(gpCluster.getNodeList(),
true, networkView);
+ //
mcodeutil.setSelected(network.getNodeList(), false, networkView);
+
mcodeutil.setSelected(custerNetwork.getNodeList(), network, networkView);
// TODO: is it still necessary?
// We want the focus to switch to the
appropriate network view but only if the cytopanel is docked
@@ -948,7 +948,6 @@
//
//
Cytoscape.getDesktop().setFocus(networkView.getSUID());
// }
- networkView.fitSelected();
} else {
// Warn user that nothing will happen in this
case because there
// is no view to select nodes with
@@ -957,8 +956,8 @@
"No Network View",
JOptionPane.INFORMATION_MESSAGE);
}
- } else if (networkView != null) {
-
mcodeutil.setSelected(networkView.getModel().getNodeList(), false, networkView);
+ } else {
+ mcodeutil.setSelected(new ArrayList<CyNode>(), network,
networkView); // deselect all
}
}
@@ -1181,13 +1180,12 @@
// process was interrupted by the
slider movement
// In that case the drawing must occur
for a new cluster using the drawGraph method
if (drawGraph && !drawPlaceHolder) {
- Image image =
mcodeutil.convertNetworkToImage(network,
-
loader,
-
cluster,
-
graphPicSize,
-
graphPicSize,
-
layouter,
-
layoutNecessary);
+ Image image =
mcodeutil.createClusterImage(cluster,
+
graphPicSize,
+
graphPicSize,
+
layouter,
+
layoutNecessary,
+
loader);
// If the drawing process was
interrupted, a new cluster must have been found and
// this will have returned
null, the drawing will be recalled (with the new cluster)
// However, if the graphing was
successful, we update
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
2011-08-24 23:35:48 UTC (rev 26635)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
2011-08-25 20:24:28 UTC (rev 26636)
@@ -15,6 +15,7 @@
<constructor-arg ref="cySwingApplicationServiceRef" />
<constructor-arg ref="cyServiceRegistrarServiceRef" />
<constructor-arg ref="analyzeAction" />
+ <constructor-arg ref="mcodeUtil" />
</bean>
<bean id="closeAction"
class="org.cytoscape.mcode.internal.MCODECloseAction">
@@ -22,6 +23,7 @@
<constructor-arg ref="cyApplicationManagerServiceRef" />
<constructor-arg ref="cySwingApplicationServiceRef" />
<constructor-arg ref="cyServiceRegistrarServiceRef" />
+ <constructor-arg ref="mcodeUtil" />
</bean>
<bean id="helpAction"
class="org.cytoscape.mcode.internal.MCODEHelpAction">
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
