Author: rodche
Date: 2012-02-14 11:27:27 -0800 (Tue, 14 Feb 2012)
New Revision: 28263
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
Log:
Fix for the edge style (arrow shapes) of a SIF formatted network loaded from
Pathway Commons
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-02-14 18:28:56 UTC (rev 28262)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-02-14 19:27:27 UTC (rev 28263)
@@ -5,9 +5,11 @@
import org.cytoscape.cpath2.internal.util.BioPaxUtil;
import org.cytoscape.model.CyNode;
+import org.cytoscape.view.presentation.property.ArrowShapeVisualProperty;
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.ArrowShape;
import org.cytoscape.view.presentation.property.values.NodeShape;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -33,6 +35,7 @@
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 INTERACTION = "interaction";
VisualStyle binarySifStyle;
@@ -149,27 +152,19 @@
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);
-//
-// 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);
-// eac.setCalculator(edgeColorCalculator);
-//
-// // set default color
-// eac.getDefaultAppearance().set(
-//
cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE,
-// ArrowShape.NONE);
+ private void createDirectedEdges(VisualStyle style) {
+ DiscreteMapping<String, ArrowShape> discreteMapping =
+ (DiscreteMapping<String, ArrowShape>)
discreteFactory
+ .createVisualMappingFunction(
+ INTERACTION,
String.class, null,
+
RichVisualLexicon.EDGE_TARGET_ARROW_SHAPE);
+
+ discreteMapping.putMapValue(COMPONENT_OF,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(CONTROLS_STATE_CHANGE,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS,
ArrowShapeVisualProperty.ARROW);
+
+ style.addVisualMappingFunction(discreteMapping);
}
private void createNodeLabel(VisualStyle style) {
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
2012-02-14 18:28:56 UTC (rev 28262)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
2012-02-14 19:27:27 UTC (rev 28263)
@@ -5,9 +5,11 @@
import org.cytoscape.cpathsquared.internal.util.BioPaxUtil;
import org.cytoscape.model.CyNode;
+import org.cytoscape.view.presentation.property.ArrowShapeVisualProperty;
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.ArrowShape;
import org.cytoscape.view.presentation.property.values.NodeShape;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -35,7 +37,7 @@
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
+ private final static String INTERACTION = "interaction"; // TODO:
Double check this constant
VisualStyle binarySifStyle;
@@ -153,29 +155,23 @@
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);
-//
-// 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);
-// eac.setCalculator(edgeColorCalculator);
-//
-// // set default color
-// eac.getDefaultAppearance().set(
-//
cytoscape.visual.VisualPropertyType.EDGE_TGTARROW_SHAPE,
-// ArrowShape.NONE);
+
+ private void createDirectedEdges(VisualStyle style) {
+ DiscreteMapping<String, ArrowShape> discreteMapping =
+ (DiscreteMapping<String, ArrowShape>) discreteFactory
+ .createVisualMappingFunction(
+ INTERACTION, String.class, null,
+
RichVisualLexicon.EDGE_TARGET_ARROW_SHAPE);
+
+ discreteMapping.putMapValue(COMPONENT_OF,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(CONTROLS_STATE_CHANGE,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(CONTROLS_METABOLIC_CHANGE,
ArrowShapeVisualProperty.ARROW);
+ discreteMapping.putMapValue(SEQUENTIAL_CATALYSIS,
ArrowShapeVisualProperty.ARROW);
+
+ style.addVisualMappingFunction(discreteMapping);
}
+
private void createNodeLabel(VisualStyle style) {
// create pass through mapper for node labels
style.addVisualMappingFunction(passthroughFactory
--
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