Author: pwang
Date: 2011-10-20 16:04:42 -0700 (Thu, 20 Oct 2011)
New Revision: 27257
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
2011-10-20 23:03:50 UTC (rev 27256)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActiveModulesUI.java
2011-10-20 23:04:42 UTC (rev 27257)
@@ -1,6 +1,5 @@
package csplugins.jActiveModules;
-
import java.awt.event.ActionEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
@@ -8,7 +7,6 @@
import javax.help.HelpSet;
import javax.swing.AbstractAction;
-import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.SwingConstants;
@@ -16,21 +14,36 @@
import csplugins.jActiveModules.data.ActivePathFinderParameters;
import csplugins.jActiveModules.dialogs.ActivePathsParameterPanel;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.CytoscapeInit;
-import cytoscape.data.attr.MultiHashMapDefinitionListener;
-import cytoscape.logger.CyLogger;
-import cytoscape.plugin.CytoscapePlugin;
-import cytoscape.view.cytopanels.CytoPanel;
-import cytoscape.view.cytopanels.CytoPanelState;
-import cytoscape.view.CyHelpBroker;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.events.CytoscapeStartEvent;
+import org.cytoscape.application.events.CytoscapeStartListener;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.application.swing.CytoPanel;
+import org.cytoscape.application.swing.CytoPanelName;
+import org.cytoscape.application.swing.CytoPanelState;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.work.TaskManager;
+//import cytoscape.data.attr.MultiHashMapDefinitionListener;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import java.util.Properties;
+
/**
* UI for Active Modules. Manages the various menu items
*/
-public class ActiveModulesUI extends CytoscapePlugin {
+public class ActiveModulesUI extends AbstractCyAction implements
CytoscapeStartListener {
protected ActivePaths activePaths;
protected ActivePathFinderParameters apfParams;
protected ThreadExceptionHandler xHandler;
@@ -40,62 +53,124 @@
public static String JACTIVEMODULES_TOP_N_MODULE =
"jactivemodules_top_n_modules";
public static String JACTIVEMODULES_TOP_N_MODULE_DEFAULT = "5";
- public ActiveModulesUI() {
- final JMenuItem menuItem = new JMenuItem("jActiveModules...");
- menuItem.addActionListener(new SetParametersAction());
+ private CySwingApplication desktopApp;
+ private final CytoPanel cytoPanelWest;
+ private static final Logger logger =
LoggerFactory.getLogger(ActiveModulesUI.class);
+ private CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
- Cytoscape.getDesktop().getCyMenus().getMenuBar().
- getMenu("Plugins.Module Finders...").add(menuItem);
-
- /* initialize variables */
- apfParams = new ActivePathFinderParameters(CytoscapeInit
- .getProperties());
- apfParams.reloadExpressionAttributes();
+ private CyProperty<Properties> cytoscapeProperties;
+ private CyNetworkManager cyNetworkManager;
+ private CyNetworkViewManager cyNetworkViewManager;
+ private VisualMappingManager visualMappingManager;
+ private CyRootNetworkFactory cyRootNetworkFactory;
+ private CyNetworkViewFactory cyNetworkViewFactory;
+ private CyNetworkFactory cyNetworkFactory;
+ private CyLayoutAlgorithmManager cyLayoutsService;
+ private TaskManager taskManagerService;
+ private CyApplicationManager cyApplicationManagerService;
+ private CyEventHelper cyEventHelperService;
+
+ public ActiveModulesUI(CyApplicationManager appMgr, CySwingApplication
desktopApp,CyProperty<Properties> cytoscapeProperties,
+ CyNetworkManager cyNetworkManager, CyNetworkViewManager
cyNetworkViewManager, VisualMappingManager visualMappingManager,
+ CyNetworkFactory cyNetworkFactory, CyRootNetworkFactory
cyRootNetworkFactory,
+ CyNetworkViewFactory
cyNetworkViewFactory,CyLayoutAlgorithmManager cyLayoutsService,
+ TaskManager taskManagerService, CyEventHelper
cyEventHelperService,
+ ActivePathFinderParameters apfParams,
ActivePathsParameterPanel mainPanel) {
+
+ super("jActiveModules...", appMgr);
+ setPreferredMenu("Plugins.jActiveModules");
+ //setMenuGravity(2.0f);
+
+ this.desktopApp = desktopApp;
+ this.cyNetworkManager = cyNetworkManager;
+ this.cyNetworkViewManager = cyNetworkViewManager;
+ this.visualMappingManager = visualMappingManager;
+ this.cyNetworkFactory = cyNetworkFactory;
+ this.cyRootNetworkFactory = cyRootNetworkFactory;
+ this.cyNetworkViewFactory = cyNetworkViewFactory;
+ this.cyLayoutsService = cyLayoutsService;
+ this.taskManagerService = taskManagerService;
+ this.cyApplicationManagerService = appMgr;
+ this.cyEventHelperService = cyEventHelperService;
+
+ this.cytoscapeProperties = cytoscapeProperties;
+ this.mainPanel = mainPanel;
+ this.mainPanel.setPluginMainClass(this);
+
+ this.apfParams = apfParams;
+ this.apfParams.reloadExpressionAttributes();
+
AttrChangeListener acl = new AttrChangeListener();
- Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
- Cytoscape.ATTRIBUTES_CHANGED, acl);
- Cytoscape.getNodeAttributes().getMultiHashMapDefinition()
- .addDataDefinitionListener(acl);
- xHandler = new ThreadExceptionHandler();
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
-
+
//Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
+ // Cytoscape.ATTRIBUTES_CHANGED, acl);
+ //Cytoscape.getNodeAttributes().getMultiHashMapDefinition()
+ // .addDataDefinitionListener(acl);
+ //xHandler = new ThreadExceptionHandler();
+
//Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+
+ cytoPanelWest = desktopApp.getCytoPanel(CytoPanelName.WEST);
addHelp();
}
+
/**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent e) {
+ // If the state of the cytoPanelEast is HIDE, show it
+ if (cytoPanelWest.getState() == CytoPanelState.HIDE) {
+ cytoPanelWest.setState(CytoPanelState.DOCK);
+ }
+
+ // Select the jActiveModules panel
+ int index = cytoPanelWest.indexOfComponent(mainPanel);
+ if (index == -1) {
+ return;
+ }
+
+ cytoPanelWest.setSelectedIndex(index);
+ }
+
+ /**
* Hook plugin help into the Cytoscape main help system:
*/
private void addHelp() {
final String HELP_SET_NAME = "/help/jhelpset";
final ClassLoader classLoader =
ActiveModulesUI.class.getClassLoader();
URL helpSetURL;
- final CyLogger logger =
CyLogger.getLogger(ActiveModulesUI.class);
try {
helpSetURL = HelpSet.findHelpSet(classLoader,
HELP_SET_NAME);
final HelpSet newHelpSet = new HelpSet(classLoader,
helpSetURL);
- CyHelpBroker.getHelpSet().add(newHelpSet);
+ cyHelpBroker.getHelpSet().add(newHelpSet);
} catch (final Exception e) {
logger.warn("Could not find help set: \"" +
HELP_SET_NAME + "!");
}
}
- public void propertyChange(PropertyChangeEvent evt) {
- if (evt.getPropertyName() == Cytoscape.CYTOSCAPE_INITIALIZED
- && apfParams.getRun()) {
+ public void handleEvent(CytoscapeStartEvent e){
+ //evt.getPropertyName() == Cytoscape.CYTOSCAPE_INITIALIZED
+ if ( apfParams.getRun()) {
if (apfParams.getRandomizeExpression()) {
startRandomizeAndRun(mainPanel.getTargetNetwork());
} else {
activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
- apfParams, this);
+ apfParams, this,
ActiveModulesUI.this.desktopApp, ActiveModulesUI.this.cytoscapeProperties,
+ this.cyNetworkManager,
this.cyNetworkViewManager, this.visualMappingManager,
+ this.cyNetworkFactory,
this.cyRootNetworkFactory,
+ this.cyNetworkViewFactory,
this.cyLayoutsService, this.taskManagerService,
+
this.cyApplicationManagerService, this.cyEventHelperService);
Thread t = new Thread(activePaths);
t.start();
}
}
}
+
/**
* Action to allow the user to change the current options for running
- * jActiveModules, wiht a gui interface
+ * jActiveModules, with a gui interface
*/
protected class SetParametersAction extends AbstractAction {
private static final long serialVersionUID =
-7836213413255212288L;
@@ -108,7 +183,7 @@
if (apfParams.getPossibleExpressionAttributes().size()
== 0) {
JOptionPane
.showMessageDialog(
-
Cytoscape.getDesktop(),
+
ActiveModulesUI.this.desktopApp.getJFrame(),
"JActiveModules
cannot start because it cannot find\n"
+ "any p-value attributes! JActiveModules requires at\n"
+ "least one node attribute with values ranging between\n"
@@ -117,28 +192,32 @@
"jActiveModules", JOptionPane.ERROR_MESSAGE);
return;
}
- final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
- SwingConstants.WEST);
- if (mainPanel == null) {
- mainPanel = new
ActivePathsParameterPanel(apfParams,
- ActiveModulesUI.this);
- }
- int index = cytoPanel.indexOfComponent(mainPanel);
- if (index < 0) {
- cytoPanel.add("jActiveModules", mainPanel);
- index = cytoPanel.indexOfComponent(mainPanel);
- }
- cytoPanel.setSelectedIndex(index);
- cytoPanel.setState(CytoPanelState.DOCK);
+
+
+// final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(
+// SwingConstants.WEST);
+//
+// if (mainPanel == null) {
+// mainPanel = new
ActivePathsParameterPanel(apfParams,
+// ActiveModulesUI.this);
+// }
+// int index = cytoPanel.indexOfComponent(mainPanel);
+// if (index < 0) {
+// cytoPanel.add("jActiveModules", mainPanel);
+// index = cytoPanel.indexOfComponent(mainPanel);
+// }
+// cytoPanel.setSelectedIndex(index);
+// //cytoPanel.setState(CytoPanelState.DOCK);
+
}
}
public void startFindActivePaths(CyNetwork network) {
try {
- activePaths = new ActivePaths(network, apfParams, this);
+ //activePaths = new ActivePaths(network, apfParams,
this);
} catch (final Exception e) {
e.printStackTrace(System.err);
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+
JOptionPane.showMessageDialog(this.desktopApp.getJFrame(),
"Error running jActiveModules (1)! " +
e.getMessage(),
"Error", JOptionPane.ERROR_MESSAGE);
return;
@@ -166,10 +245,9 @@
Thread.UncaughtExceptionHandler {
public void uncaughtException(Thread t, Throwable e) {
e.printStackTrace(System.err);
- CyLogger logger =
CyLogger.getLogger(ActiveModulesUI.class);
logger.warn("Non-fatal exception in Thread " +
t.getName(), e);
logger.warn("The previous exception was non-fatal -
Don't panic!");
- JOptionPane.showMessageDialog(Cytoscape.getDesktop(),
+
JOptionPane.showMessageDialog(ActiveModulesUI.this.desktopApp.getJFrame(),
"Error running jActiveModules (2)! " +
e.getMessage(),
"Error", JOptionPane.ERROR_MESSAGE);
}
@@ -186,15 +264,24 @@
}
public void actionPerformed(ActionEvent e) {
- activePaths = new
ActivePaths(mainPanel.getTargetNetwork(),
- apfParams, ActiveModulesUI.this);
+ activePaths = new
ActivePaths(mainPanel.getTargetNetwork(), apfParams, ActiveModulesUI.this,
+ ActiveModulesUI.this.desktopApp,
ActiveModulesUI.this.cytoscapeProperties,
+ ActiveModulesUI.this.cyNetworkManager,
ActiveModulesUI.this.cyNetworkViewManager,
+
ActiveModulesUI.this.visualMappingManager,
ActiveModulesUI.this.cyNetworkFactory,
ActiveModulesUI.this.cyRootNetworkFactory,
+
ActiveModulesUI.this.cyNetworkViewFactory,
ActiveModulesUI.this.cyLayoutsService,
+
ActiveModulesUI.this.taskManagerService,
ActiveModulesUI.this.cyApplicationManagerService,
+
ActiveModulesUI.this.cyEventHelperService);
activePaths.scoreActivePath();
}
}
public void startRandomizeAndRun(CyNetwork network) {
- activePaths = new ActivePaths(network, apfParams,
ActiveModulesUI.this);
- Thread t = new ScoreDistributionThread(network, activePaths,
apfParams);
+ activePaths = new ActivePaths(network, apfParams,
ActiveModulesUI.this, ActiveModulesUI.this.desktopApp,
ActiveModulesUI.this.cytoscapeProperties,
+ this.cyNetworkManager,
this.cyNetworkViewManager, ActiveModulesUI.this.visualMappingManager,
+ ActiveModulesUI.this.cyNetworkFactory,
ActiveModulesUI.this.cyRootNetworkFactory,
ActiveModulesUI.this.cyNetworkViewFactory,
+ ActiveModulesUI.this.cyLayoutsService,
this.taskManagerService, this.cyApplicationManagerService,
+ ActiveModulesUI.this.cyEventHelperService);
+ Thread t = new ScoreDistributionThread(desktopApp.getJFrame(),
network, activePaths, apfParams);
t.setUncaughtExceptionHandler(xHandler);
t.start();
}
@@ -214,12 +301,12 @@
* This is used to update the expression attributes in the params
object so
* that they match those that exist in CyAttributes.
*/
- protected class AttrChangeListener implements PropertyChangeListener,
- MultiHashMapDefinitionListener {
+ protected class AttrChangeListener implements PropertyChangeListener {
//,
+ //MultiHashMapDefinitionListener {
public void propertyChange(PropertyChangeEvent e) {
- if
(e.getPropertyName().equals(Cytoscape.ATTRIBUTES_CHANGED))
- apfParams.reloadExpressionAttributes();
+ //if
(e.getPropertyName().equals(Cytoscape.ATTRIBUTES_CHANGED))
+ // apfParams.reloadExpressionAttributes();
}
/**
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-10-20 23:03:50 UTC (rev 27256)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-10-20 23:04:42 UTC (rev 27257)
@@ -8,8 +8,10 @@
//------------------------------------------------------------------------------
package csplugins.jActiveModules;
//------------------------------------------------------------------------------
-import giny.model.Node;
-
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyNode;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
@@ -19,6 +21,7 @@
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Properties;
import java.util.Set;
import java.util.Vector;
@@ -28,28 +31,40 @@
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import csplugins.jActiveModules.data.ActivePathFinderParameters;
import csplugins.jActiveModules.util.Scaler;
import csplugins.jActiveModules.util.ScalerFactory;
-import cytoscape.CyEdge;
-import cytoscape.CyNetwork;
-import cytoscape.CyNode;
-import cytoscape.Cytoscape;
-import cytoscape.CytoscapeInit;
-import cytoscape.data.CyAttributes;
-import cytoscape.data.SelectFilter;
-import cytoscape.data.Semantics;
-import cytoscape.layout.CyLayoutAlgorithm;
-import cytoscape.layout.CyLayouts;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.PropUtil;
-import cytoscape.view.CyNetworkView;
-import cytoscape.visual.VisualStyle;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.property.CyProperty;
+//import cytoscape.data.Semantics;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.work.TaskManager;
+import csplugins.jActiveModules.util.SelectUtil;
+import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CySubNetwork;
+import org.cytoscape.model.CyRow;
+import java.util.Collection;
+
//-----------------------------------------------------------------------------------
public class ActivePaths implements ActivePathViewer, Runnable {
- private static CyLogger logger = CyLogger.getLogger(ActivePaths.class);
+ private static final Logger logger =
LoggerFactory.getLogger(ActivePaths.class);
protected boolean showTable = true;
protected boolean hideOthers = true;
@@ -72,15 +87,15 @@
protected static int resultsCount = 1;
protected ActiveModulesUI parentUI;
- private static int MAX_NETWORK_VIEWS =
PropUtil.getInt(CytoscapeInit.getProperties(),
"moduleNetworkViewCreationThreshold", 5);
+ private static int MAX_NETWORK_VIEWS; // =
PropUtil.getInt(CytoscapeInit.getProperties(),
"moduleNetworkViewCreationThreshold", 5);
private static int runCount = 0;
private static final URL vizmapPropsLocation =
ActiveModulesUI.class.getResource("/jActiveModules_VS.props");
private static final String VS_OVERVIEW_NAME = "jActiveModules Overview
Style";
private static final String VS_MODULE_NAME = "jActiveModules Module
Style";
- private static final VisualStyle overviewVS;
- private static final VisualStyle moduleVS;
+ private static VisualStyle overviewVS;
+ private static VisualStyle moduleVS;
// This is common prefix for all finders.
private static final String MODULE_FINDER_PREFIX = "jActiveModules.";
@@ -88,21 +103,72 @@
private static final String NODE_SCORE = MODULE_FINDER_PREFIX +
"activepathScore";
- static {
-
- // Create visualStyles based on the definition in property files
- Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null,
vizmapPropsLocation);
- overviewVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME);
- moduleVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME);
- }
+// static {
+//
+// // Create visualStyles based on the definition in property files
+// Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null,
vizmapPropsLocation);
+// //overviewVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME);
+// //moduleVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME);
+// }
+ private static boolean eventFired = false;
+ private static CyLayoutAlgorithm layoutAlgorithm; // =
CyLayouts.getLayout("force-directed");
- private static final CyLayoutAlgorithm layoutAlgorithm =
CyLayouts.getLayout("force-directed");
+ private CySwingApplication desktopApp;
+ private CyProperty<Properties> cytoscapeProperties;
+ private CyNetworkManager cyNetworkManager;
+ private CyNetworkViewManager cyNetworkViewManager;
+ private VisualMappingManager visualMappingManager;
+ private CyNetworkFactory cyNetworkFactory;
+ private CyRootNetworkFactory cyRootNetworkFactory;
+ private final CyNetworkViewFactory cyNetworkViewFactory;
+ private final CyLayoutAlgorithmManager cyLayoutsService;
+ private TaskManager taskManagerService;
+ private CyApplicationManager cyApplicationManagerService;
+ private CyEventHelper cyEventHelperService;
// ----------------------------------------------------------------
- public ActivePaths(CyNetwork cyNetwork, ActivePathFinderParameters
apfParams, ActiveModulesUI parentUI) {
+ public ActivePaths(CyNetwork cyNetwork, ActivePathFinderParameters
apfParams, ActiveModulesUI parentUI,
+ CySwingApplication desktopApp,CyProperty<Properties>
cytoscapeProperties, CyNetworkManager cyNetworkManager,
+ CyNetworkViewManager cyNetworkViewManager,
VisualMappingManager visualMappingManager,
+ CyNetworkFactory cyNetworkFactory, CyRootNetworkFactory
cyRootNetworkFactory, CyNetworkViewFactory cyNetworkViewFactory,
+ CyLayoutAlgorithmManager cyLayoutsService, TaskManager
taskManagerService,
+ CyApplicationManager cyApplicationManagerService,
CyEventHelper cyEventHelperService) {
this.apfParams = apfParams;
+ this.cytoscapeProperties = cytoscapeProperties;
+ this.desktopApp = desktopApp;
+
+ this.cyNetworkManager = cyNetworkManager;
+ this.cyNetworkViewManager = cyNetworkViewManager;
+ this.visualMappingManager = visualMappingManager;
+ this.cyNetworkFactory = cyNetworkFactory;
+ this.cyRootNetworkFactory = cyRootNetworkFactory;
+ this.cyNetworkViewFactory = cyNetworkViewFactory;
+ this.cyLayoutsService = cyLayoutsService;
+ this.taskManagerService = taskManagerService;
+ this.cyApplicationManagerService = cyApplicationManagerService;
+ this.cyEventHelperService = cyEventHelperService;
+
+ MAX_NETWORK_VIEWS = new
Integer(this.cytoscapeProperties.getProperties().getProperty("defaultPluginDownloadUrl")).intValue();
+ layoutAlgorithm =
this.cyLayoutsService.getLayout("force-directed");
+ //if (!eventFired){
+ // this.cyEventHelperService.fireEvent();
+ //}
+
+ Set<VisualStyle> visualStyles =
this.visualMappingManager.getAllVisualStyles();
+ Iterator<VisualStyle> it = visualStyles.iterator();
+ while (it.hasNext()){
+ VisualStyle vs = it.next();
+ if (vs.getTitle().equalsIgnoreCase(VS_OVERVIEW_NAME)){
+ overviewVS = vs;
+ }
+ if (vs.getTitle().equalsIgnoreCase(VS_MODULE_NAME)){
+ moduleVS = vs;
+ }
+ }
+
+
if (cyNetwork == null || cyNetwork.getNodeCount() == 0) {
throw new IllegalArgumentException("Please select a
network");
}
@@ -112,8 +178,8 @@
if (attrNames.length == 0) {
throw new RuntimeException("No expression data
selected!");
}
- menubar = Cytoscape.getDesktop().getCyMenus().getMenuBar();
- mainFrame = Cytoscape.getDesktop();
+ menubar = desktopApp.getJMenuBar();
+ mainFrame = desktopApp.getJFrame(); //Cytoscape.getDesktop();
this.cyNetwork = cyNetwork;
this.parentUI = parentUI;
@@ -144,75 +210,101 @@
CyNetwork[] subnetworks = createSubnetworks();
//2. create an overview network for all nested network
+ final CyNetwork overview = this.cyNetworkFactory.getInstance();
+ overview.getCyRow().set("name", "jActiveModules Search Result
"+ runCount++);
+
Set<CyNode> path_nodes = new HashSet<CyNode>();
for (int i=0; i< subnetworks.length; i++){
- CyNode newNode
=Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
+ CyNode newNode = overview.addNode();
//Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
+ newNode.getCyRow().set("name",
subnetworks[i].getCyRow().get("name", String.class));
path_nodes.add(newNode);
- newNode.setNestedNetwork(subnetworks[i]);
+ newNode.setNetwork(subnetworks[i]);
// create an attribute for this new node
-
Cytoscape.getNodeAttributes().setAttribute(newNode.getIdentifier(), NODE_SCORE,
new Double(activePaths[i].getScore()));
+
//Cytoscape.getNodeAttributes().setAttribute(newNode.getIdentifier(),
NODE_SCORE, new Double(activePaths[i].getScore()));
+ newNode.getCyRow().set(NODE_SCORE, new
Double(activePaths[i].getScore()));
}
//Edges indicate that nodes in nested networks exist in both
nested networks
- Set<CyEdge> path_edges = getPathEdges(path_nodes); //new
HashSet<CyEdge>();
- final CyNetwork overview = Cytoscape.createNetwork(path_nodes,
path_edges, "jActiveModules Search Result "+ runCount++, cyNetwork, false);
+ Set<CyEdge> path_edges = getPathEdges(overview, path_nodes);
//new HashSet<CyEdge>();
+ //final CyNetwork overview =
Cytoscape.createNetwork(path_nodes, path_edges, "jActiveModules Search Result
"+ runCount++, cyNetwork, false);
//3. Create an edge attribute "overlapScore", which is defined
as NumberOfSharedNodes/min(two network sizes)
- CyAttributes cyEdgeAttrs = Cytoscape.getEdgeAttributes();
+ CyTable cyEdgeAttrs = this.cyNetwork.getDefaultEdgeTable();
//Cytoscape.getEdgeAttributes();
Iterator it = path_edges.iterator();
while(it.hasNext()){
CyEdge aEdge = (CyEdge) it.next();
- int NumberOfSharedNodes =
getNumberOfSharedNodes((CyNetwork)aEdge.getSource().getNestedNetwork(),
-
(CyNetwork)aEdge.getTarget().getNestedNetwork());
+ int NumberOfSharedNodes =
getNumberOfSharedNodes((CyNetwork)aEdge.getSource().getNetwork(),
+
(CyNetwork)aEdge.getTarget().getNetwork());
- int minNodeCount =
Math.min(aEdge.getSource().getNestedNetwork().getNodeCount(),
-
aEdge.getTarget().getNestedNetwork().getNodeCount());
+ int minNodeCount =
Math.min(aEdge.getSource().getNetwork().getNodeCount(),
+
aEdge.getTarget().getNetwork().getNodeCount());
- cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeCount_min_two", minNodeCount);
- cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeOverlapCount", NumberOfSharedNodes);
+ //cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeCount_min_two", minNodeCount);
+
aEdge.getCyRow().set("jActiveModules_nodeCount_min_two", minNodeCount);
+
+ //cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeOverlapCount", NumberOfSharedNodes);
+ aEdge.getCyRow().set("jActiveModules_nodeOverlapCount",
NumberOfSharedNodes);
double overlapScore =
(double)NumberOfSharedNodes/minNodeCount;
- cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
EDGE_SCORE, overlapScore);
+ //cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
EDGE_SCORE, overlapScore);
+ aEdge.getCyRow().set(EDGE_SCORE, overlapScore);
}
//4. Create an view for overview network and apply visual style
- final CyNetworkView newView =
Cytoscape.createNetworkView(overview, overview.getIdentifier(), tuning(), null);
- newView.setVisualStyle(overviewVS.getName());
- Cytoscape.getVisualMappingManager().setVisualStyle(overviewVS);
- newView.redrawGraph(false, true);
+ //Cytoscape.createNetworkView(overview,
overview.getIdentifier(), tuning(), null);
+ final CyNetworkView newView =
this.cyNetworkViewFactory.getNetworkView(overview);
+ this.visualMappingManager.setVisualStyle(overviewVS, newView);
+ newView.updateView();
+
// Create view for top n modules
- int n =
Integer.valueOf(CytoscapeInit.getProperties().getProperty(ActiveModulesUI.JACTIVEMODULES_TOP_N_MODULE)).intValue();
-
+ int n = new
Integer(this.cytoscapeProperties.getProperties().getProperty(ActiveModulesUI.JACTIVEMODULES_TOP_N_MODULE)).intValue();
+
if (n> subnetworks.length){
n = subnetworks.length;
}
for (int i=0; i<n; i++){
- CyNetworkView theView =
Cytoscape.createNetworkView(subnetworks[i]);
- newView.setVisualStyle(moduleVS.getName());
-
Cytoscape.getVisualMappingManager().setVisualStyle(moduleVS);
- theView.redrawGraph(false, true);
+ CyNetworkView theView =
this.cyNetworkViewFactory.getNetworkView(subnetworks[i]);
- CyLayoutAlgorithm alg =
cytoscape.layout.CyLayouts.getLayout("force-directed");
- theView.applyLayout(alg);
+
this.visualMappingManager.setVisualStyle(moduleVS, theView);
+ theView.updateView();
+
+ CyLayoutAlgorithm alg =
this.cyLayoutsService.getLayout("force-directed");
+ alg.setNetworkView(theView);
+
+ this.taskManagerService.execute(alg);
}
}
private static int getNumberOfSharedNodes(CyNetwork networkA, CyNetwork
networkB){
- int[] nodeIndicesA = networkA.getNodeIndicesArray();
- int[] nodeIndicesB = networkB.getNodeIndicesArray();
+ Long[] nodeIndicesA = new Long[networkA.getNodeCount()];
+ Long[] nodeIndicesB = new Long[networkB.getNodeCount()];
- HashSet<Integer> hashSet = new HashSet<Integer>();
+ Iterator<CyNode> it = networkA.getNodeList().iterator();
+ int iA=0;
+ while (it.hasNext()){
+ nodeIndicesA[iA] = it.next().getSUID();
+ iA++;
+ }
+
+ Iterator<CyNode> it2 = networkB.getNodeList().iterator();
+ int iB=0;
+ while (it2.hasNext()){
+ nodeIndicesB[iB] = it2.next().getSUID();
+ iB++;
+ }
+
+ HashSet<Long> hashSet = new HashSet<Long>();
for (int i=0; i< nodeIndicesA.length; i++){
- hashSet.add( new Integer(nodeIndicesA[i]));
+ hashSet.add( new Long(nodeIndicesA[i]));
}
int sharedNodeCount =0;
for (int i=0; i< nodeIndicesB.length; i++){
- if (hashSet.contains(new Integer(nodeIndicesB[i]))){
+ if (hashSet.contains(new Long(nodeIndicesB[i]))){
sharedNodeCount++;
}
}
@@ -221,22 +313,23 @@
}
- private Set<CyEdge> getPathEdges(Set path_nodes) {
+ private Set<CyEdge> getPathEdges(CyNetwork overview, Set path_nodes) {
HashSet<CyEdge> edgeSet = new HashSet<CyEdge>();
Object[] nodes = path_nodes.toArray();
HashSet[] hashSet = new HashSet[nodes.length];
for (int i=0; i< nodes.length; i++){
- hashSet[i] = new
HashSet<CyNode>(((CyNode)nodes[i]).getNestedNetwork().nodesList());
+ hashSet[i] = new
HashSet<CyNode>(((CyNode)nodes[i]).getNetwork().getNodeList());
}
for (int i=0; i< nodes.length-1; i++){
for (int j=i+1; j<nodes.length; j++){
// determine if there are overlap between
nested networks
if (hasTwoSetOverlap(hashSet[i], hashSet[j])){
- CyEdge edge =
Cytoscape.getCyEdge((CyNode)nodes[i], (CyNode)nodes[j], Semantics.INTERACTION,
"overlap", true);
- edgeSet.add(edge);
+ //CyEdge edge =
Cytoscape.getCyEdge((CyNode)nodes[i], (CyNode)nodes[j], Semantics.INTERACTION,
"overlap", true);
+ CyEdge newEdge =
overview.addEdge((CyNode)nodes[i], (CyNode)nodes[j], false);
+ edgeSet.add(newEdge);
}
}
}
@@ -256,9 +349,13 @@
}
- private CyNetwork[] createSubnetworks() {
- CyNetwork[] subnetworks = new CyNetwork[activePaths.length];
+ private CySubNetwork[] createSubnetworks() {
+ //CyNetwork[] subnetworks = new CyNetwork[activePaths.length];
+ CySubNetwork[] subnetworks2 = new
CySubNetwork[activePaths.length];
+
+ CyRootNetwork rootNetwork =
this.cyRootNetworkFactory.convert(cyNetwork);
+
for (int i = 0; i < activePaths.length; i++) {
Component thePath = activePaths[i];
String pathName = "Module_" + runCount + "_" + (i + 1);
@@ -274,23 +371,27 @@
// get edges for this path
Set edgeSet = new HashSet();
- Iterator iterator = cyNetwork.edgesIterator();
+ Iterator iterator = cyNetwork.getEdgeList().iterator();
//.edgesIterator();
while (iterator.hasNext()) {
CyEdge edge = (CyEdge) iterator.next();
if (nodeSet.contains(edge.getSource()) &&
nodeSet.contains(edge.getTarget()))
edgeSet.add(edge);
}
+
+ //subnetworks[i] = Cytoscape.createNetwork(nodeSet,
edgeSet, pathName, cyNetwork, false);
+ subnetworks2[i] = rootNetwork.addSubNetwork(nodeSet,
edgeSet);
+ subnetworks2[i].getCyRow().set("name", pathName);
- subnetworks[i] = Cytoscape.createNetwork(nodeSet,
edgeSet, pathName, cyNetwork, false);
if(i < MAX_NETWORK_VIEWS) {
- final CyNetworkView moduleView =
Cytoscape.createNetworkView(subnetworks[i], subnetworks[i].getTitle(),
tuning());
- moduleView.setVisualStyle(moduleVS.getName());
-
Cytoscape.getVisualMappingManager().setVisualStyle(moduleVS);
- moduleView.redrawGraph(false, true);
+ //final CyNetworkView moduleView =
Cytoscape.createNetworkView(subnetworks[i], subnetworks[i].getTitle(),
tuning());
+ final CyNetworkView moduleView =
this.cyNetworkViewManager.getNetworkView(subnetworks2[i].getSUID());
+
//moduleView.setVisualStyle(moduleVS.getTitle()); //.getName());
+
this.visualMappingManager.setVisualStyle(moduleVS, moduleView);
//Cytoscape.getVisualMappingManager().setVisualStyle(moduleVS);
+ moduleView.updateView(); //.redrawGraph(false,
true);
}
}
- return subnetworks;
+ return subnetworks2;
}
/**
@@ -315,13 +416,13 @@
logger.info("Processing Expression Data into Hash");
HashMap tempHash = new HashMap();
logger.info("Do some testing of the ExpressionData object");
- CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ CyTable nodeAttributes = this.cyNetwork.getDefaultNodeTable();
//Cytoscape.getNodeAttributes();
// Create two identical lists of genes
- List<Node> geneList = new ArrayList<Node>();
- List<Node> shuffledList = new ArrayList<Node>();
- for (Iterator nodeIt = cyNetwork.nodesIterator();
nodeIt.hasNext();) {
- Node n = (Node) nodeIt.next();
+ List<CyNode> geneList = new ArrayList<CyNode>();
+ List<CyNode> shuffledList = new ArrayList<CyNode>();
+ for (Iterator nodeIt = cyNetwork.getNodeList().iterator()
/*.nodesIterator()*/; nodeIt.hasNext();) {
+ CyNode n = (CyNode) nodeIt.next();
geneList.add(n);
shuffledList.add(n);
}
@@ -333,10 +434,16 @@
final Double[][] attribValues = new
Double[attrNames.length][geneList.size()];
final Map<String, Integer> geneNameToIndexMap = new
HashMap<String, Integer>();
for (int i = 0; i < geneList.size(); i++) {
- final String geneName = geneList.get(i).getIdentifier();
+ final String geneName =
geneList.get(i).getCyRow().get("name", String.class); //.getIdentifier();
geneNameToIndexMap.put(geneName, new Integer(i));
for (int j = 0; j < attrNames.length; j++)
- attribValues[j][i] =
nodeAttributes.getDoubleAttribute(geneName, attrNames[j]);
+ {
+ //attribValues[j][i] =
nodeAttributes.get.getDoubleAttribute(geneName, attrNames[j]);
+ Collection<CyRow> rows =
nodeAttributes.getMatchingRows(attrNames[j], geneName);
+ Object[] objs = rows.toArray();
+ CyRow row = (CyRow) objs[0];
+ attribValues[j][i] = row.get(attrNames[j],
Double.class);
+ }
}
// Perform the scaling:
@@ -349,11 +456,11 @@
for (int i = 0; i < geneList.size(); i++) {
// If not randomizing these will be identical.
- Node current = geneList.get(i);
- Node shuffle = shuffledList.get(i);
+ CyNode current = geneList.get(i);
+ CyNode shuffle = shuffledList.get(i);
// If randomizing, you'll get p-values for a different
gene.
- String canonicalName = shuffle.getIdentifier();
+ String canonicalName = shuffle.getCyRow().get("name",
String.class); //.getIdentifier();
double[] tempArray = new double[attrNames.length];
for (int j = 0; j < attrNames.length; j++) {
@@ -364,12 +471,12 @@
double sigValue = d.doubleValue();
if (sigValue < MIN_SIG) {
sigValue = MIN_SIG;
- logger.warn("Warning: value for
" + current.getIdentifier() +
+ logger.warn("Warning: value for
" + current.getCyRow().get("name", String.class)+ //.getIdentifier() +
" (" +
canonicalName + ") adjusted to " + MIN_SIG);
}
if (sigValue > MAX_SIG) {
sigValue = MAX_SIG;
- logger.warn("Warning: value for
" + current.getIdentifier() +
+ logger.warn("Warning: value for
" + current.getCyRow().get("name", String.class)+ //.getIdentifier() +
" (" +
canonicalName + ") adjusted to " + MAX_SIG);
}
@@ -454,7 +561,7 @@
long start = System.currentTimeMillis();
Vector result = new Vector();
- Iterator it = cyNetwork.getSelectedNodes().iterator();
+ Iterator it = SelectUtil.getSelectedNodes(cyNetwork).iterator();
while (it.hasNext()) {
result.add(it.next());
}
@@ -504,16 +611,28 @@
//
------------------------------------------------------------------------------
public void displayPath(Component activePath, boolean clearOthersFirst,
String pathTitle) {
titleForCurrentSelection = pathTitle;
- SelectFilter filter = cyNetwork.getSelectFilter();
+ //SelectFilter filter = cyNetwork.getSelectFilter();
// cytoscapeWindow.selectNodesByName (activePath.getNodes (),
// clearOthersFirst);
if (clearOthersFirst) {
// cyNetwork.unFlagAllNodes();
- filter.unselectAllNodes();
+ //filter.unselectAllNodes();
+ Iterator<CyNode> it =
this.cyNetwork.getNodeList().iterator();
+ while (it.hasNext()){
+ CyNode node = it.next();
+ node.getCyRow().set(CyNetwork.SELECTED, false);
+ }
}
- filter.setSelectedNodes(activePath.getDisplayNodesGeneric(),
true);
+ //filter.setSelectedNodes(activePath.getDisplayNodesGeneric(),
true);
+ Iterator<CyNode> it2 =
activePath.getDisplayNodesGeneric().iterator();
+ while (it2.hasNext()){
+ CyNode node2 = it2.next();
+ node2.getCyRow().set(CyNetwork.SELECTED, true);
+ }
+
// cyNetwork.setFlaggedNodes(activePath.getNodes(),true);
- Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+
this.cyNetworkViewManager.getNetworkView(this.cyApplicationManagerService.getCurrentNetwork().getSUID()).updateView();
+ //Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
}
//
------------------------------------------------------------------------------
public void displayPath(Component activePath,
@@ -522,7 +641,7 @@
}
//
------------------------------------------------------------------------------
-
+ /*
private CyLayoutAlgorithm tuning() {
final CyLayoutAlgorithm fd = layoutAlgorithm;
@@ -533,5 +652,5 @@
return fd;
}
-
+*/
} // class ActivePaths (a CytoscapeWindow plugin)
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