Author: kono
Date: 2012-07-03 18:08:20 -0700 (Tue, 03 Jul 2012)
New Revision: 29752
Added:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualStyleBuilder.java
Removed:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/VisualStyleBuilder.java
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
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/ConnComponentAction.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/LoadNetstatsAction.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
Log:
fixes #1201 Visualization function enabled.
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalysisExecutor.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -32,6 +32,7 @@
import org.slf4j.LoggerFactory;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
/**
* Initializer and starter of a separate thread dedicated to network analysis.
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
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/AnalyzeNetworkAction.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -35,6 +35,7 @@
import de.mpg.mpi_inf.bioinf.netanalyzer.data.NetworkStatus;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.InterpretationDialog;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
/**
* Action handler for the menu item "Analyze Network".
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ConnComponentAction.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -23,6 +23,8 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFatory;
+import org.cytoscape.work.TaskManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.CCInfo;
@@ -40,11 +42,17 @@
private static final Logger logger =
LoggerFactory.getLogger(ConnComponentAction.class);
+ private final NewNetworkSelectedNodesAndEdgesTaskFatory tf;
+ private final TaskManager<?, ?> tm;
+
/**
* Initializes a new instance of <code>ConnComponentAction</code>.
*/
- public ConnComponentAction(CyApplicationManager
appMgr,CySwingApplication swingApp) {
+ public ConnComponentAction(CyApplicationManager
appMgr,CySwingApplication swingApp, final
NewNetworkSelectedNodesAndEdgesTaskFatory tf, final TaskManager<?, ?> tm) {
super(Messages.AC_CONNCOMP,appMgr,swingApp);
+ this.tf = tf;
+ this.tm = tm;
+
setPreferredMenu(NetworkAnalyzer.PARENT_MENU +
Messages.AC_MENU_MODIFICATION);
}
@@ -72,7 +80,7 @@
Utils.showInfoBox(swingApp.getJFrame(),Messages.DT_CONNCOMP, msg);
} else {
Arrays.sort(comps, new CCInfoInvComparator());
- ConnComponentsDialog d = new
ConnComponentsDialog(swingApp.getJFrame(), network, comps);
+ ConnComponentsDialog d = new
ConnComponentsDialog(swingApp.getJFrame(), network, comps, tf, tm);
d.setVisible(true);
}
} catch (InnerException ex) {
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
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -1,7 +1,3 @@
-
-
-
-
package de.mpg.mpi_inf.bioinf.netanalyzer;
import org.cytoscape.application.swing.CySwingApplication;
@@ -22,6 +18,7 @@
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;
@@ -29,10 +26,12 @@
import org.osgi.framework.BundleContext;
import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFatory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.swing.DialogTaskManager;
import java.util.Properties;
@@ -43,7 +42,8 @@
super();
}
-
+
+ @Override
public void start(BundleContext bc) {
CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
@@ -58,6 +58,10 @@
VisualMappingFunctionFactory continupousMappingFactoryRef =
getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=continuous)");
VisualMappingFunctionFactory passthroughMappingFactoryRef =
getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=passthrough)");
+ // Create network from selection
+ NewNetworkSelectedNodesAndEdgesTaskFatory
newNetworkSelectedNodesEdgesTaskFactoryServiceRef =
getService(bc,NewNetworkSelectedNodesAndEdgesTaskFatory.class);
+ DialogTaskManager taskManager = getService(bc,
DialogTaskManager.class);
+
// FIXME refactor this code
Plugin plugin = new Plugin(cySwingApplicationServiceRef);
@@ -71,17 +75,16 @@
AboutAction aboutAction = new
AboutAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
AnalyzeSubsetAction analyzeSubsetAction = new
AnalyzeSubsetAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
analyzeNetworkAction);
BatchAnalysisAction batchAnalysisAction = new
BatchAnalysisAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef,cyNetworkViewReaderManagerServiceRef,
loadNetstatsAction);
- CompareAction compareAction = new
CompareAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
- ConnComponentAction connComponentAction = new
ConnComponentAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ // Disabled because similar function is available from Network
Merge
+ //CompareAction compareAction = new
CompareAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
+ ConnComponentAction connComponentAction = new
ConnComponentAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
newNetworkSelectedNodesEdgesTaskFactoryServiceRef, taskManager);
PlotParameterAction plotParameterAction = new
PlotParameterAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
analyzeNetworkAction);
RemDupEdgesAction remDupEdgesAction = new
RemDupEdgesAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
RemoveSelfLoopsAction removeSelfLoopsAction = new
RemoveSelfLoopsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
SettingsAction settingsAction = new
SettingsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
-
-
registerService(bc,analyzeNetworkAction,CyAction.class, new
Properties());
registerService(bc,analyzeSubsetAction,CyAction.class, new
Properties());
registerService(bc,batchAnalysisAction,CyAction.class, new
Properties());
@@ -89,11 +92,10 @@
registerService(bc,plotParameterAction,CyAction.class, new
Properties());
registerService(bc,mapParameterAction,CyAction.class, new
Properties());
registerService(bc,settingsAction,CyAction.class, new
Properties());
- registerService(bc,compareAction,CyAction.class, new
Properties());
+ //registerService(bc,compareAction,CyAction.class, new
Properties());
registerService(bc,connComponentAction,CyAction.class, new
Properties());
registerService(bc,remDupEdgesAction,CyAction.class, new
Properties());
registerService(bc,removeSelfLoopsAction,CyAction.class, new
Properties());
registerService(bc,aboutAction,CyAction.class, new
Properties());
}
-}
-
+}
\ No newline at end of file
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/LoadNetstatsAction.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -36,6 +36,7 @@
import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.StatsSerializer;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.AnalysisDialog;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.Utils;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
/**
* Action handler for the menu item "Load Network Statistics".
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/MapParameterAction.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -31,6 +31,7 @@
import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.settings.PluginSettings;
import de.mpg.mpi_inf.bioinf.netanalyzer.ui.MapParameterDialog;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ui.VisualStyleBuilder;
/**
* Action handler for the menu item "Visualize Parameters".
Deleted:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/VisualStyleBuilder.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/VisualStyleBuilder.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/VisualStyleBuilder.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -1,140 +0,0 @@
-package de.mpg.mpi_inf.bioinf.netanalyzer;
-
-import java.awt.Color;
-
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
-import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
-import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
-import org.cytoscape.view.vizmap.VisualStyle;
-import org.cytoscape.view.vizmap.VisualStyleFactory;
-import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
-
-import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
-
-public class VisualStyleBuilder {
-
- private static final String VS_NAME_PREFIX = "Network Analyzer Style: ";
-
- // Preset defaults
- private static final Color NODE_COLOR = Color.WHITE;
- private static final Color NODE_LABEL_COLOR = new Color(100, 100, 100);
- private static final Color EDGE_COLOR = new Color(100, 100, 100);
-
- private final VisualStyleFactory vsFactory;
-
- private final VisualMappingFunctionFactory passthroughFactory;
- private final VisualMappingFunctionFactory continuousFactory;
-
- public VisualStyleBuilder(final VisualStyleFactory vsFactory,
- final VisualMappingFunctionFactory passthroughFactory,
final VisualMappingFunctionFactory continuousFactory) {
- this.vsFactory = vsFactory;
- this.passthroughFactory = passthroughFactory;
- this.continuousFactory = continuousFactory;
- }
-
- /**
- * Creates a new visual style in Cytoscape's VizMapper depending on the
by
- * the user defined mappings of computed attributes.
- *
- * @return New visual style.
- **/
- public VisualStyle createVisualStyle(final CyNetworkView networkView) {
-
- final CyNetwork network = networkView.getModel();
- // Create new visual style
- final String name = network.getRow(network).get(CyNetwork.NAME,
String.class);
- final VisualStyle visualStyle =
vsFactory.createVisualStyle(VS_NAME_PREFIX + name);
-
- // Network VP
- final Color backGroundColor =
SettingsSerializer.getPluginSettings().getBackgroundColor();
-
visualStyle.setDefaultValue(BasicVisualLexicon.NETWORK_BACKGROUND_PAINT,
backGroundColor);
-
- // Node Label Mapping
- final PassthroughMapping<String, String> labelPassthrough =
(PassthroughMapping<String, String>) passthroughFactory
- .createVisualMappingFunction(CyNetwork.NAME,
String.class, BasicVisualLexicon.NODE_LABEL);
- visualStyle.addVisualMappingFunction(labelPassthrough);
-
- // Node View Defaults
- visualStyle.setDefaultValue(BasicVisualLexicon.NODE_SHAPE,
NodeShapeVisualProperty.ELLIPSE);
- visualStyle.setDefaultValue(BasicVisualLexicon.NODE_FILL_COLOR,
NODE_COLOR);
-
visualStyle.setDefaultValue(BasicVisualLexicon.NODE_LABEL_COLOR,
NODE_LABEL_COLOR);
-
-
visualStyle.setDefaultValue(BasicVisualLexicon.NODE_BORDER_WIDTH, 0.0d);
- visualStyle.setDefaultValue(BasicVisualLexicon.NODE_WIDTH, 30d);
- visualStyle.setDefaultValue(BasicVisualLexicon.NODE_HEIGHT,
30d);
- visualStyle.setDefaultValue(BasicVisualLexicon.NODE_SIZE, 30d);
-
- // Edge View Defaults
- visualStyle.setDefaultValue(BasicVisualLexicon.EDGE_WIDTH,
3.0d);
- visualStyle.setDefaultValue(BasicVisualLexicon.EDGE_PAINT,
EDGE_COLOR);
-
- // // Apply new visual settings
- // if (attrNodeColor.length() > 0) {
- // // Continuous Mapping - set node color
- // name += "_NodeColor_" + attrNodeColor;
- // ContinuousMapping conMapNodeColor =
getColorMapping(attrNodeColor,
- // ObjectMapping.NODE_MAPPING);
- // conMapNodeColor = addBoundaries(conMapNodeColor,
attrNodeColor,
- // mapNodeColor, SettingsSerializer
- // .getPluginSettings().getBrightColor(),
- // SettingsSerializer.getPluginSettings().getMiddleColor(),
- // SettingsSerializer.getPluginSettings().getDarkColor());
- // Calculator nodeColorCalculator = new
- // BasicCalculator("NetworkAnalyzer Node Color Calc",
conMapNodeColor,
- // VisualPropertyType.NODE_FILL_COLOR);
- // nodeAppCalc.setCalculator(nodeColorCalculator);
- // }
- // if (attrNodeSize.length() > 0) {
- // // Continuous Mapping - set node size
- // name += "_NodeSize_" + attrNodeSize;
- //
visualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,
- // false);
- // ContinuousMapping conMapNodeSize =
getSizeMapping(attrNodeSize,
- // ObjectMapping.NODE_MAPPING);
- // conMapNodeSize = addBoundaries(conMapNodeSize, attrNodeSize,
- // mapNodeSize, new Double(10.0),
- // new Double(50.0), new Double(100.0));
- // Calculator nodeHeightCalculator = new
- // BasicCalculator("NetworkAnalyzer Node Height Calc",
conMapNodeSize,
- // VisualPropertyType.NODE_HEIGHT);
- // Calculator nodeWidthCalculator = new
- // BasicCalculator("NetworkAnalyzer Node Width Calc",
conMapNodeSize,
- // VisualPropertyType.NODE_WIDTH);
- // nodeAppCalc.setCalculator(nodeHeightCalculator);
- // nodeAppCalc.setCalculator(nodeWidthCalculator);
- // }
- // if (attrEdgeColor.length() > 0) {
- // // Continuous Mapping - set edge color
- // name += "_EdgeColor_" + attrEdgeColor;
- // ContinuousMapping conMapEdgeColor =
getColorMapping(attrEdgeColor,
- // ObjectMapping.EDGE_MAPPING);
- // conMapEdgeColor = addBoundaries(conMapEdgeColor,
attrEdgeColor,
- // mapEdgeColor, SettingsSerializer
- // .getPluginSettings().getBrightColor(),
- // SettingsSerializer.getPluginSettings().getMiddleColor(),
- // SettingsSerializer.getPluginSettings().getDarkColor());
- // Calculator edgeColorCalculator = new
- // BasicCalculator("NetworkAnalyzer Edge Color Calc",
conMapEdgeColor,
- // VisualPropertyType.EDGE_COLOR);
- // edgeAppCalc.setCalculator(edgeColorCalculator);
- // }
- // if (attrEdgeSize.length() > 0) {
- // // Continuous Mapping - set line width
- // name += "_EdgeSize_" + attrEdgeSize;
- // ContinuousMapping conMapEdgeSize =
getSizeMapping(attrEdgeSize,
- // ObjectMapping.EDGE_MAPPING);
- // conMapEdgeSize = addBoundaries(conMapEdgeSize, attrEdgeSize,
- // mapEdgeSize, new Double(1.0), new Double(4.0),
- // new Double(8.0));
- // Calculator edgeSizeCalculator = new
- // BasicCalculator("NetworkAnalyzer Edge Size Calc",
conMapEdgeSize,
- // VisualPropertyType.EDGE_LINE_WIDTH);
- // edgeAppCalc.setCalculator(edgeSizeCalculator);
- // }
-
- return visualStyle;
- }
-
-}
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/data/Messages.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -215,7 +215,10 @@
public static String SM_CHOOSEINTERPR = "Please choose an
interpretation for the edges.";
- public static String SM_CLOSEWARN = "<html>You have not saved the
network statistics. They will be lost when you close this window.<br>Are you
sure you want to close the window?";
+ public static String SM_CLOSEWARN = "<html>You have not saved the
network statistics. " +
+ "They will be lost when you close this window." +
+ "<br /><br />Are you sure you want to close the
window?<br /><br />" +
+ "(Note: Statistics will be saved as normal table data,
not the Network Analyzer property file)</html>";
public static String SM_CONNECTED = " is connected, i.e. has a single
connected component.";
@@ -332,7 +335,7 @@
public static String AC_COMPARE = "Compare Two Networks";
- public static String AC_CONNCOMP = "Connected Components";
+ public static String AC_CONNCOMP = "Extract Connected Components...";
public static String AC_LOAD = "Load Network Statistics";
@@ -344,7 +347,7 @@
/**
* Name of Submenu in Cytoscape's menubar, where network modification
actions are added.
*/
- public static String AC_MENU_MODIFICATION = "Network Modifications";
+ public static String AC_MENU_MODIFICATION = "Subnetwork Creation";
public static String AC_PLOTPARAM = "Plot Parameters";
@@ -354,7 +357,7 @@
public static String AC_REMSELFLOOPS = "Remove Self-Loops";
- public static String AC_MAPPARAM = "Visualize Parameters";
+ public static String AC_MAPPARAM = "Generate Visual Style from
Statistics...";
// Labels of items in dialogs
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/AnalysisDialog.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -47,7 +47,6 @@
import de.mpg.mpi_inf.bioinf.netanalyzer.InnerException;
import de.mpg.mpi_inf.bioinf.netanalyzer.NetworkAnalyzer;
import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
-import de.mpg.mpi_inf.bioinf.netanalyzer.VisualStyleBuilder;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.ComplexParam;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Decorators;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/ConnComponentsDialog.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -49,6 +49,12 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.task.create.NewNetworkSelectedNodesAndEdgesTaskFatory;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.TaskMonitor;
import de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAnalyzer;
import de.mpg.mpi_inf.bioinf.netanalyzer.CyNetworkUtils;
@@ -64,6 +70,9 @@
public class ConnComponentsDialog extends JDialog
implements ActionListener, DocumentListener, ListSelectionListener {
+ private final NewNetworkSelectedNodesAndEdgesTaskFatory tf;
+ private final TaskManager<?, ?> tm;
+
/**
* Initializes a new instance of <code>ConnComponentsDialog</code>.
*
@@ -73,11 +82,15 @@
* @throws HeadlessException if
<code>GraphicsEnvironment.isHeadless()</code> returns
* <code>true</code>.
*/
- public ConnComponentsDialog(Frame aOwner, CyNetwork aNetwork, CCInfo[]
aComponents)
+ public ConnComponentsDialog(Frame aOwner, CyNetwork aNetwork, CCInfo[]
aComponents,
+ final NewNetworkSelectedNodesAndEdgesTaskFatory tf,
final TaskManager<?, ?> tm)
throws HeadlessException {
super(aOwner, Messages.DT_CONNCOMP, true);
network = aNetwork;
components = aComponents;
+ this.tf = tf;
+ this.tm = tm;
+
initControls();
pack();
setResizable(false);
@@ -95,13 +108,24 @@
setVisible(false);
dispose();
} else if (btnExtract == src) {
+ // Reset
+ for(CyNode node: network.getNodeList())
+ network.getRow(node).set(CyNetwork.SELECTED,
false);
+ for(CyEdge edge: network.getEdgeList())
+ network.getRow(edge).set(CyNetwork.SELECTED,
false);
+
CCInfo comp = components[listComp.getSelectedIndex()];
- ArrayList<CyNode> nodes = new
ArrayList<CyNode>(ConnComponentAnalyzer.getNodesOf(network, comp));
- Set<CyEdge> edges =
CyNetworkUtils.getAllConnectingEdges(network,nodes);
- // TODO figure out what the procedure should be for
creating new networks from selected nodes/edges.
- // This should be resolved in the
NewNetworkFromNodesAndEdges tasks in core-task-impl, not here.
-// Cytoscape.createNetwork(nodes, edges,
fieldNetName.getText());
- JOptionPane.showMessageDialog(getOwner(), "This
functionality is not yet implemented");
+ final List<CyNode> nodes = new
ArrayList<CyNode>(ConnComponentAnalyzer.getNodesOf(network, comp));
+ final Set<CyEdge> edges =
CyNetworkUtils.getAllConnectingEdges(network,nodes);
+
+ for(CyNode node: nodes)
+ network.getRow(node).set(CyNetwork.SELECTED,
true);
+ for(CyEdge edge: edges)
+ network.getRow(edge).set(CyNetwork.SELECTED,
true);
+
+ final TaskIterator itr = tf.createTaskIterator(network);
+ tm.execute(itr);
+ //fieldNetName.getText();
}
}
@@ -124,7 +148,7 @@
} else {
title = title + "_" + i;
}
- fieldNetName.setText(title);
+ //fieldNetName.setText(title);
}
}
@@ -194,22 +218,23 @@
panList.add(scrollList);
contentPane.add(panList);
- JPanel panExtract = new JPanel(new BorderLayout());
-
panExtract.setBorder(BorderFactory.createTitledBorder(Messages.DI_EXTRCOMP));
- panExtract.add(new JLabel(Messages.DI_EXTRCOMPLONG),
BorderLayout.NORTH);
- fieldNetName = new JTextField();
- fieldNetName.getDocument().addDocumentListener(this);
- panExtract.add(fieldNetName, BorderLayout.CENTER);
+// JPanel panExtract = new JPanel(new BorderLayout());
+//
panExtract.setBorder(BorderFactory.createTitledBorder(Messages.DI_EXTRCOMP));
+// panExtract.add(new JLabel(Messages.DI_EXTRCOMPLONG),
BorderLayout.NORTH);
+// fieldNetName = new JTextField();
+// fieldNetName.getDocument().addDocumentListener(this);
+// panExtract.add(fieldNetName, BorderLayout.CENTER);
btnExtract = Utils.createButton(Messages.DI_EXTR, null, this);
btnExtract.setEnabled(false);
- JPanel panExtr = new JPanel(new
FlowLayout(FlowLayout.TRAILING));
- panExtr.add(btnExtract);
- panExtract.add(panExtr, BorderLayout.SOUTH);
- contentPane.add(panExtract);
+// JPanel panExtr = new JPanel(new
FlowLayout(FlowLayout.TRAILING));
+// panExtr.add(btnExtract);
+// panExtract.add(panExtr, BorderLayout.SOUTH);
+// contentPane.add(panExtract);
JPanel panButtons = new JPanel();
panButtons.setAlignmentX(Component.CENTER_ALIGNMENT);
btnClose = Utils.createButton(Messages.DI_CLOSE, null, this);
+ panButtons.add(btnExtract);
panButtons.add(btnClose);
contentPane.add(panButtons);
setContentPane(contentPane);
@@ -219,7 +244,7 @@
* Updates the "enabled" status of the Extract button.
*/
private void updateBtnExtract() {
- if ("".equals(fieldNetName.getText()) ||
listComp.getSelectedIndex() == -1) {
+ if (listComp.getSelectedIndex() == -1) {
btnExtract.setEnabled(false);
} else {
btnExtract.setEnabled(true);
@@ -251,8 +276,8 @@
*/
private JList listComp;
- /**
- * Text field for entering the name of a new network.
- */
- private JTextField fieldNetName;
+// /**
+// * Text field for entering the name of a new network.
+// */
+// private JTextField fieldNetName;
}
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
2012-07-03 23:57:12 UTC (rev 29751)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -45,7 +45,6 @@
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
-import de.mpg.mpi_inf.bioinf.netanalyzer.VisualStyleBuilder;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
@@ -164,7 +163,7 @@
}
// Create a new style and register it
- final VisualStyle newStyle =
vsBuilder.createVisualStyle(networkView);
+ final VisualStyle newStyle =
vsBuilder.createVisualStyle(networkView, this);
vmm.addVisualStyle(newStyle);
vmm.setVisualStyle(newStyle, networkView);
@@ -458,93 +457,6 @@
}
/**
- * Creates a continuous mapping of a node or edge attribute to the
color of the nodes/edges.
- *
- * @param attr
- * Attribute to be mapped to the color of nodes/edges.
- * @param objectMapping
- * Contains the information whether a node or edge attribute
is mapped.
- * @return A continuous mapping ot an attribute to the color of
nodes/edges.
-
- private ContinuousMapping getColorMapping(String attr, byte
objectMapping) {
- ContinuousMapping conMapColor = new
ContinuousMapping(Color.WHITE, objectMapping);
- conMapColor.setControllingAttributeName(attr, network, false);
-
- Interpolator numToColor = new LinearNumberToColorInterpolator();
- conMapColor.setInterpolator(numToColor);
-
- return conMapColor;
- }
- */
-
- /**
- * Creates a continuous mapping of a node or edge attribute to the size
of the nodes (width &
- * height)/edges(tickness).
- *
- * @param attr
- * Attribute to be mapped to the size of nodes/edges.
- * @param objectMapping
- * Contains the information whether a node or edge attribute
is mapped.
- * @return A continuous mapping ot an attribute to the size of
nodes/edges.
-
- private ContinuousMapping getSizeMapping(String attr, byte
objectMapping) {
- ContinuousMapping conMapSize = new ContinuousMapping(new
Double(1.0), objectMapping);
- conMapSize.setControllingAttributeName(attr, network, false);
-
- Interpolator numToNum = new LinearNumberToNumberInterpolator();
- conMapSize.setInterpolator(numToNum);
-
- return conMapSize;
- }
- */
-
- /**
- * Adds boundaries to the continuous mapping by defining minimal,
maximal and middle values for both color
- * and size mapping.
- *
- * @param conMap
- * Continuous mapping for which boundaries are set.
- * @param attr
- * Node/Edge attribute that is mapped.
- * @param mapType
- * Type of the mapping, i.e. low values to small sizes or
otherwise or low values to bright
- * colors and otherwise respectively.
- * @param min
- * Minimal value of size/color for the mapping.
- * @param mid
- * Middle value of size/color for the mapping.
- * @param max
- * Maximal value of size/color for the mapping.
- * @return The value of the <code>conMap</code> parameter.
-
- private ContinuousMapping addBoundaries(ContinuousMapping conMap,
String attr, String mapType,
- Object min, Object mid, Object max) {
- Object min_ = min;
- Object mid_ = mid;
- Object max_ = max;
- if (min instanceof Color &&
mapType.equals(Messages.DI_LOWTODARK)) {
- min_ = max;
- max_ = min;
- }
- if (min instanceof Double &&
mapType.equals(Messages.DI_LOWTOLARGE)) {
- min_ = max;
- max_ = min;
- }
-
- // Create boundary conditions less than, equals, greater than
- BoundaryRangeValues bv0 = new BoundaryRangeValues(min_, min_,
min_);
- BoundaryRangeValues bv1 = new BoundaryRangeValues(mid_, mid_,
mid_);
- BoundaryRangeValues bv2 = new BoundaryRangeValues(max_, max_,
max_);
-
- // Set the attribute point values associated with the boundary
values
- conMap.addPoint(minAttrValue.get(attr).doubleValue(), bv0);
- conMap.addPoint(meanAttrValue.get(attr).doubleValue(), bv1);
- conMap.addPoint(maxAttrValue.get(attr).doubleValue(), bv2);
-
- return conMap;
- }
-*/
- /**
* Unique ID for this version of this class. It is used in
serialization.
*/
private static final long serialVersionUID = 1514650388927387666L;
@@ -625,55 +537,55 @@
/**
* Attribute that is mapped to node size.
*/
- private String attrNodeSize;
+ protected String attrNodeSize;
/**
* Type of mapping the node attributes, i.e. low values to small sizes
or otherwise.
*/
- private String mapNodeSize;
+ protected String mapNodeSize;
/**
* Attribute that is mapped to node color.
*/
- private String attrNodeColor;
+ protected String attrNodeColor;
/**
* Type of mapping the node attributes, i.e. low values to bright
colors or otherwise.
*/
- private String mapNodeColor;
+ protected String mapNodeColor;
/**
* Attribute that is mapped to edge size.
*/
- private String attrEdgeSize;
+ protected String attrEdgeSize;
/**
* Type of mapping the edge attributes, i.e. low values to small sizes
or otherwise.
*/
- private String mapEdgeSize;
+ protected String mapEdgeSize;
/**
* Attribute that is mapped to edge color.
*/
- private String attrEdgeColor;
+ protected String attrEdgeColor;
/**
* Type of mapping the edge attributes, i.e. low values to bright
colors or otherwise.
*/
- private String mapEdgeColor;
+ protected String mapEdgeColor;
/**
* Map with the minimal computed value for each attribute.
*/
- private HashMap<String, Double> minAttrValue;
+ protected HashMap<String, Double> minAttrValue;
/**
* Map with the maximal computed value for each attribute.
*/
- private HashMap<String, Double> maxAttrValue;
+ protected HashMap<String, Double> maxAttrValue;
/**
* Map with the mean computed value for each attribute.
*/
- private HashMap<String, Double> meanAttrValue;
+ protected HashMap<String, Double> meanAttrValue;
}
Copied:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualStyleBuilder.java
(from rev 29740,
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/VisualStyleBuilder.java)
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualStyleBuilder.java
(rev 0)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/VisualStyleBuilder.java
2012-07-04 01:08:20 UTC (rev 29752)
@@ -0,0 +1,172 @@
+package de.mpg.mpi_inf.bioinf.netanalyzer.ui;
+
+import java.awt.Color;
+import java.awt.Paint;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
+import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.view.vizmap.mappings.BoundaryRangeValues;
+import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.Messages;
+import de.mpg.mpi_inf.bioinf.netanalyzer.data.io.SettingsSerializer;
+
+public class VisualStyleBuilder {
+
+ private static final String VS_NAME_PREFIX = "Network Analyzer Style: ";
+
+ // Preset defaults
+ private static final Color NODE_COLOR = Color.WHITE;
+ private static final Color NODE_LABEL_COLOR = new Color(130, 130, 130);
+ private static final Color EDGE_COLOR = new Color(100, 100, 100);
+
+ private final VisualStyleFactory vsFactory;
+
+ private final VisualMappingFunctionFactory passthroughFactory;
+ private final VisualMappingFunctionFactory continuousFactory;
+
+ public VisualStyleBuilder(final VisualStyleFactory vsFactory,
+ final VisualMappingFunctionFactory passthroughFactory,
final VisualMappingFunctionFactory continuousFactory) {
+ this.vsFactory = vsFactory;
+ this.passthroughFactory = passthroughFactory;
+ this.continuousFactory = continuousFactory;
+ }
+
+ /**
+ * Creates a new visual style in Cytoscape's VizMapper depending on the
by
+ * the user defined mappings of computed attributes.
+ *
+ * @return New visual style.
+ **/
+ public VisualStyle createVisualStyle(final CyNetworkView networkView,
final MapParameterDialog parameterDialog) {
+
+ final CyNetwork network = networkView.getModel();
+ // Create new visual style
+ final String name = network.getRow(network).get(CyNetwork.NAME,
String.class);
+ final VisualStyle visualStyle =
vsFactory.createVisualStyle(VS_NAME_PREFIX + name);
+
+ // Network VP
+ final Color backGroundColor =
SettingsSerializer.getPluginSettings().getBackgroundColor();
+
visualStyle.setDefaultValue(BasicVisualLexicon.NETWORK_BACKGROUND_PAINT,
backGroundColor);
+
+ // Node Label Mapping
+ final PassthroughMapping<String, String> labelPassthrough =
(PassthroughMapping<String, String>) passthroughFactory
+ .createVisualMappingFunction(CyNetwork.NAME,
String.class, BasicVisualLexicon.NODE_LABEL);
+ visualStyle.addVisualMappingFunction(labelPassthrough);
+
+ // Node View Defaults
+ visualStyle.setDefaultValue(BasicVisualLexicon.NODE_SHAPE,
NodeShapeVisualProperty.ELLIPSE);
+ visualStyle.setDefaultValue(BasicVisualLexicon.NODE_FILL_COLOR,
NODE_COLOR);
+
visualStyle.setDefaultValue(BasicVisualLexicon.NODE_LABEL_COLOR,
NODE_LABEL_COLOR);
+
+
visualStyle.setDefaultValue(BasicVisualLexicon.NODE_BORDER_WIDTH, 0.0d);
+ visualStyle.setDefaultValue(BasicVisualLexicon.NODE_WIDTH, 30d);
+ visualStyle.setDefaultValue(BasicVisualLexicon.NODE_HEIGHT,
30d);
+ visualStyle.setDefaultValue(BasicVisualLexicon.NODE_SIZE, 30d);
+
visualStyle.setDefaultValue(BasicVisualLexicon.NODE_TRANSPARENCY, 200);
+
+ // Edge View Defaults
+
visualStyle.setDefaultValue(BasicVisualLexicon.EDGE_TRANSPARENCY, 100);
+ visualStyle.setDefaultValue(BasicVisualLexicon.EDGE_WIDTH,
3.0d);
+ visualStyle.setDefaultValue(BasicVisualLexicon.EDGE_PAINT,
EDGE_COLOR);
+
+ // Apply new visual settings
+ if (parameterDialog.attrNodeColor.length() > 0) {
+ // Continuous Mapping - set node color
+ final CyColumn col =
network.getDefaultNodeTable().getColumn(parameterDialog.attrNodeColor);
+ Class<?> attrValueType = col.getType();
+ final VisualMappingFunction<?, Paint> conMapNodeColor =
continuousFactory.createVisualMappingFunction(
+ parameterDialog.attrNodeColor,
attrValueType, BasicVisualLexicon.NODE_FILL_COLOR);
+ addBoundaries(parameterDialog, conMapNodeColor,
parameterDialog.attrNodeColor,
+ parameterDialog.mapNodeColor,
SettingsSerializer.getPluginSettings().getBrightColor(),
+
SettingsSerializer.getPluginSettings().getMiddleColor(),
SettingsSerializer.getPluginSettings()
+ .getDarkColor());
+ visualStyle.addVisualMappingFunction(conMapNodeColor);
+ }
+
+ if (parameterDialog.attrNodeSize.length() > 0) {
+ final CyColumn col =
network.getDefaultNodeTable().getColumn(parameterDialog.attrNodeSize);
+ Class<?> attrValueType = col.getType();
+ VisualMappingFunction<?, Double> conMapNodeSize =
continuousFactory.createVisualMappingFunction(
+ parameterDialog.attrNodeSize,
attrValueType, BasicVisualLexicon.NODE_SIZE);
+ addBoundaries(parameterDialog, conMapNodeSize,
parameterDialog.attrNodeSize, parameterDialog.mapNodeSize, new Double(10.0),
+ new Double(50.0), new Double(100.0));
+ visualStyle.addVisualMappingFunction(conMapNodeSize);
+ }
+ if (parameterDialog.attrEdgeColor.length() > 0) {
+ final CyColumn col =
network.getDefaultEdgeTable().getColumn(parameterDialog.attrEdgeColor);
+ Class<?> attrValueType = col.getType();
+ final VisualMappingFunction<?, Paint> conMapEdgeColor =
continuousFactory.createVisualMappingFunction(
+ parameterDialog.attrEdgeColor,
attrValueType, BasicVisualLexicon.EDGE_STROKE_UNSELECTED_PAINT);
+ addBoundaries(parameterDialog, conMapEdgeColor,
parameterDialog.attrEdgeColor, parameterDialog.mapEdgeColor, SettingsSerializer
+ .getPluginSettings().getBrightColor(),
SettingsSerializer.getPluginSettings().getMiddleColor(),
+
SettingsSerializer.getPluginSettings().getDarkColor());
+ visualStyle.addVisualMappingFunction(conMapEdgeColor);
+ }
+ if (parameterDialog.attrEdgeSize.length() > 0) {
+ final CyColumn col =
network.getDefaultEdgeTable().getColumn(parameterDialog.attrEdgeSize);
+ Class<?> attrValueType = col.getType();
+ VisualMappingFunction<?, Double> conMapEdgeSize =
continuousFactory.createVisualMappingFunction(
+ parameterDialog.attrEdgeSize,
attrValueType, BasicVisualLexicon.EDGE_WIDTH);
+ addBoundaries(parameterDialog, conMapEdgeSize,
parameterDialog.attrEdgeSize, parameterDialog.mapEdgeSize, new Double(1.0), new
Double(4.0),
+ new Double(8.0));
+ visualStyle.addVisualMappingFunction(conMapEdgeSize);
+ }
+
+ return visualStyle;
+ }
+
+ /**
+ * Adds boundaries to the continuous mapping by defining minimal,
maximal
+ * and middle values for both color and size mapping.
+ *
+ * @param conMapNodeColor
+ * Continuous mapping for which boundaries are set.
+ * @param attr
+ * Node/Edge attribute that is mapped.
+ * @param mapType
+ * Type of the mapping, i.e. low values to small sizes or
+ * otherwise or low values to bright colors and otherwise
+ * respectively.
+ * @param min
+ * Minimal value of size/color for the mapping.
+ * @param mid
+ * Middle value of size/color for the mapping.
+ * @param max
+ * Maximal value of size/color for the mapping.
+ * @return The value of the <code>conMap</code> parameter.
+ **/
+ private void addBoundaries(final MapParameterDialog parameterDialog,
+ VisualMappingFunction<?, ?> conMapNodeColor, String
attr, String mapType, Object min, Object mid,
+ Object max) {
+ Object min_ = min;
+ Object mid_ = mid;
+ Object max_ = max;
+ if (min instanceof Color &&
mapType.equals(Messages.DI_LOWTODARK)) {
+ min_ = max;
+ max_ = min;
+ }
+ if (min instanceof Double &&
mapType.equals(Messages.DI_LOWTOLARGE)) {
+ min_ = max;
+ max_ = min;
+ }
+
+ // Create boundary conditions less than, equals, greater than
+ BoundaryRangeValues bv0 = new BoundaryRangeValues(min_, min_,
min_);
+ BoundaryRangeValues bv1 = new BoundaryRangeValues(mid_, mid_,
mid_);
+ BoundaryRangeValues bv2 = new BoundaryRangeValues(max_, max_,
max_);
+
+ // Set the attribute point values associated with the boundary
values
+ ((ContinuousMapping)
conMapNodeColor).addPoint(parameterDialog.minAttrValue.get(attr).doubleValue(),
bv0);
+ ((ContinuousMapping)
conMapNodeColor).addPoint(parameterDialog.meanAttrValue.get(attr).doubleValue(),
bv1);
+ ((ContinuousMapping)
conMapNodeColor).addPoint(parameterDialog.maxAttrValue.get(attr).doubleValue(),
bv2);
+ }
+}
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