Author: rodche
Date: 2012-02-28 17:00:14 -0800 (Tue, 28 Feb 2012)
New Revision: 28395
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
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/SearchHitsPanel.java
Log:
Updated to the recent changes in the presentation api.
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-02-29
00:55:15 UTC (rev 28394)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-02-29
01:00:14 UTC (rev 28395)
@@ -91,7 +91,7 @@
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.1.0-SNAPSHOT</version>
+ <version>4.1.1</version>
</dependency>
<!-- Spring Dependencies to embed (temporary; must use/start Spring
EBR bundles instead) -->
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
2012-02-29 00:55:15 UTC (rev 28394)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
2012-02-29 01:00:14 UTC (rev 28395)
@@ -6,9 +6,7 @@
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;
@@ -17,6 +15,8 @@
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+import static org.cytoscape.view.presentation.property.BasicVisualLexicon.*;
+
/**
* Binary SIF Visual Style.
*
@@ -69,7 +69,7 @@
// set node opacity
binarySifStyle.setDefaultValue(
-
RichVisualLexicon.NODE_TRANSPARENCY, 125);
+ NODE_TRANSPARENCY, 125);
// unlock node size
//
binarySifStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
@@ -77,14 +77,14 @@
createNodeColors(binarySifStyle);
createNodeLabel(binarySifStyle);
-
binarySifStyle.setDefaultValue(MinimalVisualLexicon.EDGE_WIDTH,
+ binarySifStyle.setDefaultValue(EDGE_WIDTH,
4.0);
createEdgeColor(binarySifStyle);
createDirectedEdges(binarySifStyle);
binarySifStyle
.setDefaultValue(
-
MinimalVisualLexicon.NETWORK_BACKGROUND_PAINT,
+
NETWORK_BACKGROUND_PAINT,
Color.WHITE);
// The visual style must be added to the Global
Catalog
@@ -98,28 +98,28 @@
private void createNodeShapes(VisualStyle style) {
// Default shape is an ellipse.
- style.setDefaultValue(RichVisualLexicon.NODE_SHAPE,
+ style.setDefaultValue(NODE_SHAPE,
NodeShapeVisualProperty.ELLIPSE);
// Complexes are Hexagons.
DiscreteMapping<String, NodeShape> function =
(DiscreteMapping<String, NodeShape>) discreteFactory
.createVisualMappingFunction(
BioPaxUtil.BIOPAX_ENTITY_TYPE,
String.class, null,
- RichVisualLexicon.NODE_SHAPE);
+ 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);
+ style.setDefaultValue(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(
BioPaxUtil.BIOPAX_ENTITY_TYPE,
String.class, null,
-
RichVisualLexicon.NODE_FILL_COLOR);
+ NODE_FILL_COLOR);
function.putMapValue(COMPLEX, lightBlue);
style.addVisualMappingFunction(function);
}
@@ -127,10 +127,10 @@
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);
+ style.setDefaultValue(EDGE_PAINT, Color.BLACK);
DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
.createVisualMappingFunction(INTERACTION,
String.class, null,
- RichVisualLexicon.EDGE_PAINT);
+ EDGE_PAINT);
function.putMapValue(PARTICIPATES_CONVERSION,
Color.decode("#ccc1da"));
@@ -160,7 +160,7 @@
(DiscreteMapping<String, ArrowShape>) discreteFactory
.createVisualMappingFunction(
INTERACTION, String.class, null,
-
RichVisualLexicon.EDGE_TARGET_ARROW_SHAPE);
+ EDGE_TARGET_ARROW_SHAPE);
discreteMapping.putMapValue(COMPONENT_OF,
ArrowShapeVisualProperty.ARROW);
discreteMapping.putMapValue(CONTROLS_STATE_CHANGE,
ArrowShapeVisualProperty.ARROW);
@@ -175,7 +175,6 @@
// create pass through mapper for node labels
style.addVisualMappingFunction(passthroughFactory
.createVisualMappingFunction(
- CyNode.NAME, String.class, null,
-
MinimalVisualLexicon.NODE_LABEL));
+ CyNode.NAME, String.class,
null, NODE_LABEL));
}
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
2012-02-29 00:55:15 UTC (rev 28394)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/SearchHitsPanel.java
2012-02-29 01:00:14 UTC (rev 28395)
@@ -141,7 +141,7 @@
// Remove all children
rootNode.removeAllChildren();
- // Create Entity Type Filter
+ // Create Filters
if (typeMap.size() > 0) {
typeFilter = new CheckNode("Filter by BioPAX Type");
rootNode.add(typeFilter);
@@ -269,11 +269,8 @@
chainedFilter.addFilter(organismFilter);
List<SearchHit> passedRecordList;
- try {
- passedRecordList =
chainedFilter.filter(model.getRecordList().getHits());
- } catch (NullPointerException e) {
- passedRecordList = null;
- }
+ passedRecordList =
chainedFilter.filter(model.getRecordList().getHits());
+
return passedRecordList;
}
@@ -300,6 +297,7 @@
// detailsFrame.setVisible(true);
+
}
}
});
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