Author: jm
Date: 2011-07-08 06:46:07 -0700 (Fri, 08 Jul 2011)
New Revision: 26117
Modified:
core3/cpath2-impl/trunk/pom.xml
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
fixes #303: Ported Binary SIF visual style
Modified: core3/cpath2-impl/trunk/pom.xml
===================================================================
--- core3/cpath2-impl/trunk/pom.xml 2011-07-08 13:32:45 UTC (rev 26116)
+++ core3/cpath2-impl/trunk/pom.xml 2011-07-08 13:46:07 UTC (rev 26117)
@@ -69,6 +69,11 @@
<artifactId>biopax-impl</artifactId>
<version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>vizmap-api</artifactId>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
+ </dependency>
<dependency>
<groupId>cytoscape-temp</groupId>
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/CPath2Factory.java
2011-07-08 13:46:07 UTC (rev 26117)
@@ -13,6 +13,7 @@
import org.cytoscape.biopax.BioPaxContainer;
import org.cytoscape.biopax.MapBioPaxToCytoscapeFactory;
import org.cytoscape.biopax.NetworkListener;
+import org.cytoscape.cpath2.internal.cytoscape.BinarySifVisualStyleUtil;
import org.cytoscape.cpath2.internal.cytoscape.MergeNetworkEdit;
import org.cytoscape.cpath2.internal.mapping.MapCPathToCytoscape;
import org.cytoscape.cpath2.internal.schemas.summary_response.BasicRecordType;
@@ -42,6 +43,7 @@
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.undo.UndoSupport;
@@ -64,8 +66,10 @@
private final BioPaxContainer bpContainer;
private final MapBioPaxToCytoscapeFactory mapperFactory;
private final NetworkListener networkListener;
+ private final BinarySifVisualStyleUtil binarySifVisualStyleUtil;
+ private final VisualMappingManager mappingManager;
- public CPath2Factory(CySwingApplication application, TaskManager
taskManager, OpenBrowser openBrowser, CyNetworkManager networkManager,
CyApplicationManager applicationManager, CyNetworkViewManager
networkViewManager, CyNetworkReaderManager networkViewReaderManager,
CyNetworkNaming naming, CyNetworkFactory networkFactory,
CyLayoutAlgorithmManager layouts, UndoSupport undoSupport, BioPaxContainer
bpContainer, MapBioPaxToCytoscapeFactory mapperFactory, NetworkListener
networkListener) {
+ public CPath2Factory(CySwingApplication application, TaskManager
taskManager, OpenBrowser openBrowser, CyNetworkManager networkManager,
CyApplicationManager applicationManager, CyNetworkViewManager
networkViewManager, CyNetworkReaderManager networkViewReaderManager,
CyNetworkNaming naming, CyNetworkFactory networkFactory,
CyLayoutAlgorithmManager layouts, UndoSupport undoSupport, BioPaxContainer
bpContainer, MapBioPaxToCytoscapeFactory mapperFactory, NetworkListener
networkListener, BinarySifVisualStyleUtil binarySifVisualStyleUtil,
VisualMappingManager mappingManager) {
this.application = application;
this.taskManager = taskManager;
this.openBrowser = openBrowser;
@@ -80,15 +84,17 @@
this.bpContainer = bpContainer;
this.mapperFactory = mapperFactory;
this.networkListener = networkListener;
+ this.binarySifVisualStyleUtil = binarySifVisualStyleUtil;
+ this.mappingManager = mappingManager;
}
public ExecuteGetRecordByCPathIdTaskFactory
createExecuteGetRecordByCPathIdTaskFactory(CPathWebService webApi, long[] ids,
CPathResponseFormat format, String networkTitle, CyNetwork networkToMerge) {
- return new ExecuteGetRecordByCPathIdTaskFactory(webApi, ids,
format, networkTitle, networkToMerge, this, bpContainer, mapperFactory,
networkListener);
+ return new ExecuteGetRecordByCPathIdTaskFactory(webApi, ids,
format, networkTitle, networkToMerge, this, bpContainer, mapperFactory,
networkListener, mappingManager);
}
public ExecuteGetRecordByCPathIdTaskFactory
createExecuteGetRecordByCPathIdTaskFactory(
CPathWebService webApi, long[] ids, CPathResponseFormat
format, String title) {
- return new ExecuteGetRecordByCPathIdTaskFactory(webApi, ids,
format, title, null, this, bpContainer, mapperFactory, networkListener);
+ return new ExecuteGetRecordByCPathIdTaskFactory(webApi, ids,
format, title, null, this, bpContainer, mapperFactory, networkListener,
mappingManager);
}
public SearchBoxPanel createSearchBoxPanel(CPathWebService webApi) {
@@ -200,4 +206,8 @@
public CyLayoutAlgorithmManager getCyLayoutAlgorithmManager() {
return layoutManager;
}
+
+ public BinarySifVisualStyleUtil getBinarySifVisualStyleUtil() {
+ return binarySifVisualStyleUtil;
+ }
}
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2011-07-08 13:46:07 UTC (rev 26117)
@@ -1,161 +1,187 @@
package org.cytoscape.cpath2.internal.cytoscape;
import java.awt.Color;
+import java.awt.Paint;
+import org.cytoscape.biopax.MapBioPaxToCytoscape;
+import org.cytoscape.biopax.util.BioPaxVisualStyleUtil;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
+import org.cytoscape.view.presentation.property.RichVisualLexicon;
+import org.cytoscape.view.presentation.property.values.NodeShape;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
/**
* Binary SIF Visual Style.
- *
+ *
* @author Ethan Cerami.
*/
public class BinarySifVisualStyleUtil {
- public final static String BINARY_SIF_VISUAL_STYLE =
"Binary_SIF_Version_1";
- public final static String BINARY_NETWORK = "BINARY_NETWORK";
- public final static String COMPONENT_OF = "COMPONENT_OF";
- public final static String COMPONENT_IN_SAME = "IN_SAME_COMPONENT";
- public final static String SEQUENTIAL_CATALYSIS = "SEQUENTIAL_CATALYSIS";
- public final static String CONTROLS_STATE_CHANGE = "STATE_CHANGE";
- public final static String CONTROLS_METABOLIC_CHANGE =
"METABOLIC_CATALYSIS";
- public final static String PARTICIPATES_CONVERSION = "REACTS_WITH";
- public final static String PARTICIPATES_INTERACTION = "INTERACTS_WITH";
- public final static String CO_CONTROL_INDEPENDENT_SIMILAR =
"CO_CONTROL_INDEPENDENT_SIMILAR";
- public final static String CO_CONTROL_INDEPENDENT_ANTI =
"CO_CONTROL_INDEPENDENT_ANTI";
- public final static String CO_CONTROL_DEPENDENT_SIMILAR =
"CO_CONTROL_DEPENDENT_SIMILAR";
- public final static String CO_CONTROL_DEPENDENT_ANTI =
"CO_CONTROL_DEPENDENT_ANTI";
- private final static String COMPLEX = "Complex";
+ public final static String BINARY_SIF_VISUAL_STYLE =
"Binary_SIF_Version_1";
+ public final static String BINARY_NETWORK = "BINARY_NETWORK";
+ public final static String COMPONENT_OF = "COMPONENT_OF";
+ public final static String COMPONENT_IN_SAME = "IN_SAME_COMPONENT";
+ public final static String SEQUENTIAL_CATALYSIS =
"SEQUENTIAL_CATALYSIS";
+ public final static String CONTROLS_STATE_CHANGE = "STATE_CHANGE";
+ public final static String CONTROLS_METABOLIC_CHANGE =
"METABOLIC_CATALYSIS";
+ public final static String PARTICIPATES_CONVERSION = "REACTS_WITH";
+ public final static String PARTICIPATES_INTERACTION = "INTERACTS_WITH";
+ public final static String CO_CONTROL_INDEPENDENT_SIMILAR =
"CO_CONTROL_INDEPENDENT_SIMILAR";
+ public final static String CO_CONTROL_INDEPENDENT_ANTI =
"CO_CONTROL_INDEPENDENT_ANTI";
+ public final static String CO_CONTROL_DEPENDENT_SIMILAR =
"CO_CONTROL_DEPENDENT_SIMILAR";
+ public final static String CO_CONTROL_DEPENDENT_ANTI =
"CO_CONTROL_DEPENDENT_ANTI";
+ private final static String COMPLEX = "Complex";
+ private static final String INTERACTION = "interaction"; // TODO:
Double check this constant
-// /**
-// * Constructor.
-// * If an existing BioPAX Viz Mapper already exists, we use it.
-// * Otherwise, we create a new one.
-// *
-// * @return VisualStyle Object.
-// */
-// public static VisualStyle getVisualStyle() {
-// VisualMappingManager manager =
Cytoscape.getVisualMappingManager();
-// CalculatorCatalog catalog = manager.getCalculatorCatalog();
-//
-// VisualStyle visualStyle =
catalog.getVisualStyle(BINARY_SIF_VISUAL_STYLE);
-// if (visualStyle == null) {
-// visualStyle = new VisualStyle(BINARY_SIF_VISUAL_STYLE);
-//
-// NodeAppearanceCalculator nac =
visualStyle.getNodeAppearanceCalculator();
-//
-// // set node opacity
-//
nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_OPACITY,
125);
-// // unlock node size
-//
visualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
-//
-// createNodeShapes(nac);
-// createNodeColors(nac);
-// createNodeLabel(nac);
-//
-// EdgeAppearanceCalculator eac =
visualStyle.getEdgeAppearanceCalculator();
-//
eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH,4.0);
-// createEdgeColor (eac);
-// createDirectedEdges (eac);
-//
-// visualStyle.setNodeAppearanceCalculator(nac);
-// visualStyle.setEdgeAppearanceCalculator(eac);
-// GlobalAppearanceCalculator gac = new
GlobalAppearanceCalculator();
-// gac.setDefaultBackgroundColor(Color.WHITE);
-// visualStyle.setGlobalAppearanceCalculator(gac);
-//
-// // The visual style must be added to the Global Catalog
-// // in order for it to be written out to vizmap.props upon user
exit
-// catalog.addVisualStyle(visualStyle);
-// }
-// return visualStyle;
-// }
-//
-// private static void createNodeShapes(NodeAppearanceCalculator nac) {
-// // Default shape is an ellipse.
-// nac.getDefaultAppearance().set(VisualPropertyType.NODE_SHAPE,
NodeShape.ELLIPSE);
-//
-// // Complexes are Hexagons.
-// DiscreteMapping discreteMapping = new
DiscreteMapping(NodeShape.ELLIPSE,
-// MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE,
ObjectMapping.NODE_MAPPING);
-// discreteMapping.putMapValue(COMPLEX, NodeShape.HEXAGON);
-// Calculator nodeShapeCalculator = new BasicCalculator("Node Shape",
-// discreteMapping, VisualPropertyType.NODE_SHAPE);
-// nac.setCalculator(nodeShapeCalculator);
-// }
-//
-// private static void createNodeColors(NodeAppearanceCalculator nac) {
-// Color color = new Color (255, 153, 153);
-// nac.getDefaultAppearance().set(VisualPropertyType.NODE_FILL_COLOR,
color);
-//
-// // Complexes are a Different Color.
-// Color lightBlue = new Color (153, 153, 255);
-// DiscreteMapping discreteMapping = new DiscreteMapping(color,
-// MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE,
ObjectMapping.NODE_MAPPING);
-// discreteMapping.putMapValue(COMPLEX, lightBlue);
-//
-// Calculator nodeShapeCalculator = new BasicCalculator("Node Color",
-// discreteMapping, VisualPropertyType.NODE_FILL_COLOR);
-// nac.setCalculator(nodeShapeCalculator);
-// }
-//
-// private static void createEdgeColor(EdgeAppearanceCalculator eac) {
-// // create a discrete mapper, for mapping biopax node type
-// // to a particular node color
-// DiscreteMapping discreteMapping = new
DiscreteMapping(Color.BLACK,
-// Semantics.INTERACTION, ObjectMapping.EDGE_MAPPING);
-//
-// discreteMapping.putMapValue(PARTICIPATES_CONVERSION,
Color.decode("#ccc1da"));
-// discreteMapping.putMapValue(PARTICIPATES_INTERACTION,
Color.decode("#7030a0"));
-// discreteMapping.putMapValue(CONTROLS_STATE_CHANGE,
Color.decode("#0070c0"));
-// discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE,
Color.decode("#00b0f0"));
-// discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS,
Color.decode("#7f7f7f"));
-// discreteMapping.putMapValue(CO_CONTROL_DEPENDENT_ANTI,
Color.decode("#ff0000"));
-// discreteMapping.putMapValue(CO_CONTROL_INDEPENDENT_ANTI,
Color.decode("#fd95a6"));
-// discreteMapping.putMapValue(CO_CONTROL_DEPENDENT_SIMILAR,
Color.decode("#00b050"));
-// discreteMapping.putMapValue(CO_CONTROL_INDEPENDENT_SIMILAR,
Color.decode("#92d050"));
-// discreteMapping.putMapValue(COMPONENT_IN_SAME,
Color.decode("#ffff00"));
-// discreteMapping.putMapValue(COMPONENT_OF, Color.decode("#ffc000"));
-//
-// // create and set edge label calculator in edge appearance calculator
-// Calculator edgeColorCalculator = new BasicCalculator("Edge
Color",
-// discreteMapping, VisualPropertyType.EDGE_COLOR);
-// eac.setCalculator(edgeColorCalculator);
-//
-// // set default color
-//
eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_COLOR,
-// Color.BLACK);
-// }
-//
-// private static void createDirectedEdges(EdgeAppearanceCalculator eac) {
+ static VisualStyle binarySifStyle;
+
+ private final VisualStyleFactory styleFactory;
+ private final VisualMappingManager mappingManager;
+ private final VisualMappingFunctionFactory discreteFactory;
+ private final VisualMappingFunctionFactory passthroughFactory;
+
+ public BinarySifVisualStyleUtil(VisualStyleFactory styleFactory,
+ VisualMappingManager mappingManager,
+ VisualMappingFunctionFactory discreteMappingFactory,
+ VisualMappingFunctionFactory passthroughFactory) {
+ this.styleFactory = styleFactory;
+ this.mappingManager = mappingManager;
+ this.discreteFactory = discreteMappingFactory;
+ this.passthroughFactory = passthroughFactory;
+ }
+
+ // /**
+ // * Constructor.
+ // * If an existing BioPAX Viz Mapper already exists, we use it.
+ // * Otherwise, we create a new one.
+ // *
+ // * @return VisualStyle Object.
+ // */
+ public VisualStyle getVisualStyle() {
+ synchronized (BinarySifVisualStyleUtil.class) {
+ if (binarySifStyle == null) {
+ binarySifStyle = styleFactory
+
.getInstance(BINARY_SIF_VISUAL_STYLE);
+
+ // set node opacity
+ binarySifStyle.setDefaultValue(
+
RichVisualLexicon.NODE_TRANSPARENCY, 125);
+ // unlock node size
+ //
binarySifStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
+
+ createNodeShapes(binarySifStyle);
+ createNodeColors(binarySifStyle);
+ createNodeLabel(binarySifStyle);
+
+
binarySifStyle.setDefaultValue(MinimalVisualLexicon.EDGE_WIDTH,
+ 4.0);
+ createEdgeColor(binarySifStyle);
+ createDirectedEdges(binarySifStyle);
+
+ binarySifStyle
+ .setDefaultValue(
+
MinimalVisualLexicon.NETWORK_BACKGROUND_PAINT,
+ Color.WHITE);
+
+ // The visual style must be added to the Global
Catalog
+ // in order for it to be written out to
vizmap.props upon user
+ // exit
+ mappingManager.addVisualStyle(binarySifStyle);
+ }
+ }
+ return binarySifStyle;
+ }
+
+ private void createNodeShapes(VisualStyle style) {
+ // Default shape is an ellipse.
+ style.setDefaultValue(RichVisualLexicon.NODE_SHAPE,
+ NodeShapeVisualProperty.ELLIPSE);
+
+ // Complexes are Hexagons.
+ DiscreteMapping<String, NodeShape> function =
(DiscreteMapping<String, NodeShape>) discreteFactory
+ .createVisualMappingFunction(
+
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class,
+ RichVisualLexicon.NODE_SHAPE);
+ function.putMapValue(COMPLEX, NodeShapeVisualProperty.HEXAGON);
+ style.addVisualMappingFunction(function);
+ }
+
+ private void createNodeColors(VisualStyle style) {
+ Color color = new Color(255, 153, 153);
+ style.setDefaultValue(MinimalVisualLexicon.NODE_FILL_COLOR,
color);
+
+ // Complexes are a Different Color.
+ Color lightBlue = new Color(153, 153, 255);
+ DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
+ .createVisualMappingFunction(
+
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class,
+
RichVisualLexicon.NODE_FILL_COLOR);
+ function.putMapValue(COMPLEX, lightBlue);
+ style.addVisualMappingFunction(function);
+ }
+
+ private void createEdgeColor(VisualStyle style) {
+ // create a discrete mapper, for mapping biopax node type
+ // to a particular node color
+ style.setDefaultValue(MinimalVisualLexicon.EDGE_PAINT,
Color.BLACK);
+ DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
+ .createVisualMappingFunction(INTERACTION,
String.class,
+ RichVisualLexicon.EDGE_PAINT);
+
+ function.putMapValue(PARTICIPATES_CONVERSION,
+ Color.decode("#ccc1da"));
+ function.putMapValue(PARTICIPATES_INTERACTION,
+ Color.decode("#7030a0"));
+ function.putMapValue(CONTROLS_STATE_CHANGE,
+ Color.decode("#0070c0"));
+ function.putMapValue(CONTROLS_METABOLIC_CHANGE,
+ Color.decode("#00b0f0"));
+ function.putMapValue(SEQUENTIAL_CATALYSIS,
+ Color.decode("#7f7f7f"));
+ function.putMapValue(CO_CONTROL_DEPENDENT_ANTI,
+ Color.decode("#ff0000"));
+ function.putMapValue(CO_CONTROL_INDEPENDENT_ANTI,
+ Color.decode("#fd95a6"));
+ function.putMapValue(CO_CONTROL_DEPENDENT_SIMILAR,
+ Color.decode("#00b050"));
+ function.putMapValue(CO_CONTROL_INDEPENDENT_SIMILAR,
+ Color.decode("#92d050"));
+ function.putMapValue(COMPONENT_IN_SAME,
Color.decode("#ffff00"));
+ function.putMapValue(COMPONENT_OF, Color.decode("#ffc000"));
+ }
+
+ private static void createDirectedEdges(VisualStyle style) {
+ // TODO: Arrow shape isn't part of the RichVisualLexicon yet...
// DiscreteMapping discreteMapping = new
DiscreteMapping(ArrowShape.NONE,
-// Semantics.INTERACTION, ObjectMapping.EDGE_MAPPING);
+// Semantics.INTERACTION,
ObjectMapping.EDGE_MAPPING);
//
-// discreteMapping.putMapValue(COMPONENT_OF, ArrowShape.ARROW);
-// discreteMapping.putMapValue(CONTROLS_STATE_CHANGE, ArrowShape.ARROW);
-// discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE,
ArrowShape.ARROW);
-// discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS, ArrowShape.ARROW);
+// discreteMapping.putMapValue(COMPONENT_OF, ArrowShape.ARROW);
+// discreteMapping.putMapValue(CONTROLS_STATE_CHANGE,
ArrowShape.ARROW);
+// discreteMapping
+// .putMapValue(CONTROLS_METABOLIC_CHANGE,
ArrowShape.ARROW);
+// discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS,
ArrowShape.ARROW);
//
-// // create and set edge label calculator in edge appearance calculator
-// Calculator edgeColorCalculator = new BasicCalculator("Edge
Source Arrow Shape",
-// discreteMapping, VisualPropertyType.EDGE_TGTARROW_SHAPE);
+// // create and set edge label calculator in edge appearance
calculator
+// Calculator edgeColorCalculator = new BasicCalculator(
+// "Edge Source Arrow Shape", discreteMapping,
+// VisualPropertyType.EDGE_TGTARROW_SHAPE);
// eac.setCalculator(edgeColorCalculator);
//
// // set default color
-//
eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE,
-// ArrowShape.NONE);
-// }
-//
-// private static void createNodeLabel(NodeAppearanceCalculator nac) {
-// // create pass through mapper for node labels
-// PassThroughMapping passThroughMapping = new
PassThroughMapping("",
-//
ObjectMapping.NODE_MAPPING);
-//
passThroughMapping.setControllingAttributeName(BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL,
-// null, false);
-//
-// // create and set node label calculator in node appearance
calculator
-// Calculator nodeLabelCalculator = new BasicCalculator("BioPAX
Node Label",
-//
passThroughMapping,
-//
VisualPropertyType.NODE_LABEL);
-// nac.setCalculator(nodeLabelCalculator);
-// }
+// eac.getDefaultAppearance().set(
+//
cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE,
+// ArrowShape.NONE);
+ }
+
+ private void createNodeLabel(VisualStyle style) {
+ // create pass through mapper for node labels
+ style.addVisualMappingFunction(passthroughFactory
+ .createVisualMappingFunction(
+
BioPaxVisualStyleUtil.BIOPAX_NODE_LABEL, String.class,
+
MinimalVisualLexicon.NODE_LABEL));
+ }
}
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2011-07-08 13:46:07 UTC (rev 26117)
@@ -42,6 +42,8 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskFactory;
@@ -69,8 +71,9 @@
private final BioPaxContainer bpContainer;
private final MapBioPaxToCytoscapeFactory mapperFactory;
private final NetworkListener networkListener;
+ private final VisualMappingManager mappingManager;
- /**
+ /**.
* Constructor.
*
* @param webApi
@@ -86,7 +89,7 @@
*/
public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
String networkTitle, CPath2Factory cPathFactory,
BioPaxContainer bpContainer,
- MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener) {
+ MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener, VisualMappingManager mappingManager) {
this.webApi = webApi;
this.ids = ids;
this.format = format;
@@ -95,6 +98,7 @@
this.bpContainer = bpContainer;
this.mapperFactory = mapperFactory;
this.networkListener = networkListener;
+ this.mappingManager = mappingManager;
}
/**
@@ -117,7 +121,7 @@
*/
public ExecuteGetRecordByCPathId(CPathWebService webApi, long ids[],
CPathResponseFormat format,
String networkTitle, CyNetwork mergedNetwork,
CPath2Factory cPathFactory, BioPaxContainer bpContainer,
- MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener) {
+ MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener, VisualMappingManager mappingManager) {
this.webApi = webApi;
this.ids = ids;
this.format = format;
@@ -127,6 +131,7 @@
this.bpContainer = bpContainer;
this.mapperFactory = mapperFactory;
this.networkListener = networkListener;
+ this.mappingManager = mappingManager;
}
/**
@@ -308,10 +313,6 @@
taskMonitor.setProgress(0);
}
- // Set up the right visual style
- // VisualStyle visualStyle =
- // BinarySifVisualStyleUtil.getVisualStyle();
-
// Set up the right layout algorithm.
// LayoutUtil layoutAlgorithm = new
LayoutUtil();
@@ -322,6 +323,8 @@
// (cyNetwork,
cyNetwork.getCyRow().get(CyNetwork.NAME,
// String.class), layoutAlgorithm, null);
+ VisualStyle visualStyle =
cPathFactory.getBinarySifVisualStyleUtil().getVisualStyle();
+ mappingManager.setVisualStyle(visualStyle,
view);
networkListener.registerNetwork(view);
SwingUtilities.invokeLater(new Runnable() {
Modified:
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
===================================================================
---
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
2011-07-08 13:46:07 UTC (rev 26117)
@@ -7,6 +7,7 @@
import org.cytoscape.cpath2.internal.web_service.CPathResponseFormat;
import org.cytoscape.cpath2.internal.web_service.CPathWebService;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
@@ -21,11 +22,12 @@
private final BioPaxContainer bpContainer;
private final MapBioPaxToCytoscapeFactory mapperFactory;
private final NetworkListener networkListener;
+ private final VisualMappingManager mappingManager;
public ExecuteGetRecordByCPathIdTaskFactory(CPathWebService webApi,
long[] ids, CPathResponseFormat format, String
networkTitle,
CyNetwork networkToMerge, CPath2Factory cPathFactory,
BioPaxContainer bpContainer,
- MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener) {
+ MapBioPaxToCytoscapeFactory mapperFactory,
NetworkListener networkListener, VisualMappingManager mappingManager) {
this.webApi = webApi;
this.ids = ids;
this.format = format;
@@ -35,11 +37,12 @@
this.bpContainer = bpContainer;
this.mapperFactory = mapperFactory;
this.networkListener = networkListener;
+ this.mappingManager = mappingManager;
}
@Override
public TaskIterator getTaskIterator() {
- return new TaskIterator(new ExecuteGetRecordByCPathId(webApi,
ids, format, networkTitle, networkToMerge, cPathFactory, bpContainer,
mapperFactory, networkListener));
+ return new TaskIterator(new ExecuteGetRecordByCPathId(webApi,
ids, format, networkTitle, networkToMerge, cPathFactory, bpContainer,
mapperFactory, networkListener, mappingManager));
}
}
Modified:
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-07-08 13:46:07 UTC (rev 26117)
@@ -48,6 +48,20 @@
<osgi:reference id="networkListenerRef"
interface="org.cytoscape.biopax.NetworkListener" />
+
+ <osgi:reference id="visualMappingManagerRef"
+ interface="org.cytoscape.view.vizmap.VisualMappingManager"/>
+ <osgi:reference id="visualStyleFactoryRef"
+ interface="org.cytoscape.view.vizmap.VisualStyleFactory"/>
+
+ <osgi:reference id="discreteMappingFactoryRef"
+
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
+ filter="(mapping.type=discrete)"/>
+
+ <osgi:reference id="passthroughMappingFactoryRef"
+
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
+ filter="(mapping.type=passthrough)"/>
+
<osgi:service ref="cPathWebService" auto-export="interfaces" />
</beans>
Modified:
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-07-08 13:32:45 UTC (rev 26116)
+++
core3/cpath2-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-07-08 13:46:07 UTC (rev 26117)
@@ -31,9 +31,18 @@
<constructor-arg ref="bioPaxContainerRef" />
<constructor-arg ref="mapBioPaxToCytoscapeFactoryRef" />
<constructor-arg ref="networkListenerRef" />
+ <constructor-arg ref="binarySifVisualStyleUtil" />
+ <constructor-arg ref="visualMappingManagerRef" />
</bean>
<bean id="cPathWebService"
class="org.cytoscape.cpath2.internal.web_service.CytoscapeCPathWebService">
<constructor-arg ref="cPath2Factory" />
</bean>
+
+ <bean id="binarySifVisualStyleUtil"
class="org.cytoscape.cpath2.internal.cytoscape.BinarySifVisualStyleUtil">
+ <constructor-arg ref="visualStyleFactoryRef" />
+ <constructor-arg ref="visualMappingManagerRef" />
+ <constructor-arg ref="discreteMappingFactoryRef" />
+ <constructor-arg ref="passthroughMappingFactoryRef" />
+ </bean>
</beans>
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