Author: rodche
Date: 2011-11-22 13:45:59 -0800 (Tue, 22 Nov 2011)
New Revision: 27558
Modified:
core3/impl/trunk/biopax-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
Log:
Updated paxtools/biopax versions; fixed a compilation issue (due to a core
interface recently changed).
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2011-11-22 21:28:48 UTC (rev
27557)
+++ core3/impl/trunk/biopax-impl/pom.xml 2011-11-22 21:45:59 UTC (rev
27558)
@@ -48,7 +48,7 @@
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.0.0b3</version>
+ <version>4.0.1</version>
</dependency>
<dependency>
<groupId>cytoscape-temp</groupId>
@@ -73,7 +73,7 @@
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>biopax-converter</artifactId>
- <version>4.0.0b3</version>
+ <version>4.0.1</version>
</dependency>
</dependencies>
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-11-22
21:28:48 UTC (rev 27557)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-11-22
21:45:59 UTC (rev 27558)
@@ -109,7 +109,7 @@
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.0.1-SNAPSHOT</version>
+ <version>4.0.1</version>
</dependency>
<dependency>
<groupId>pathwaycommons.cpath</groupId>
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
2011-11-22 21:28:48 UTC (rev 27557)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
2011-11-22 21:45:59 UTC (rev 27558)
@@ -104,7 +104,7 @@
// Complexes are Hexagons.
DiscreteMapping<String, NodeShape> function =
(DiscreteMapping<String, NodeShape>) discreteFactory
.createVisualMappingFunction(
-
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class,
+
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class, null,
RichVisualLexicon.NODE_SHAPE);
function.putMapValue(COMPLEX, NodeShapeVisualProperty.HEXAGON);
style.addVisualMappingFunction(function);
@@ -118,7 +118,7 @@
Color lightBlue = new Color(153, 153, 255);
DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
.createVisualMappingFunction(
-
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class,
+
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE, String.class, null,
RichVisualLexicon.NODE_FILL_COLOR);
function.putMapValue(COMPLEX, lightBlue);
style.addVisualMappingFunction(function);
@@ -129,7 +129,7 @@
// to a particular node color
style.setDefaultValue(MinimalVisualLexicon.EDGE_PAINT,
Color.BLACK);
DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
- .createVisualMappingFunction(INTERACTION,
String.class,
+ .createVisualMappingFunction(INTERACTION,
String.class, null,
RichVisualLexicon.EDGE_PAINT);
function.putMapValue(PARTICIPATES_CONVERSION,
@@ -181,7 +181,7 @@
// create pass through mapper for node labels
style.addVisualMappingFunction(passthroughFactory
.createVisualMappingFunction(
- CyNode.NAME, String.class,
+ CyNode.NAME, String.class, null,
MinimalVisualLexicon.NODE_LABEL));
}
}
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