Author: clopes
Date: 2012-07-13 13:18:14 -0700 (Fri, 13 Jul 2012)
New Revision: 29890
Modified:
csplugins/trunk/toronto/clopes/mcode/pom.xml
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/CyActivator.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
Log:
Fixed MCODE for Cy3 Milestone 5:
- Fixed a couple of compilation errors.
- Added OSGI Core dependency and "Cytoscape-API-Compatibility" manifest entry.
Modified: csplugins/trunk/toronto/clopes/mcode/pom.xml
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/pom.xml 2012-07-13 20:17:17 UTC
(rev 29889)
+++ csplugins/trunk/toronto/clopes/mcode/pom.xml 2012-07-13 20:18:14 UTC
(rev 29890)
@@ -5,7 +5,7 @@
<properties>
<bundle.symbolicName>org.cytoscape.mcode.mcode-plugin</bundle.symbolicName>
<bundle.namespace>org.cytoscape.mcode</bundle.namespace>
-
<cytoscape.api.version>3.0.0-alpha8-SNAPSHOT</cytoscape.api.version>
+
<cytoscape.api.version>3.0.0-beta3-SNAPSHOT</cytoscape.api.version>
<maven.build.timestamp.format>MMMM
yyyy</maven.build.timestamp.format>
<buildDate>${maven.build.timestamp}</buildDate>
</properties>
@@ -13,7 +13,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.cytoscape.mcode</groupId>
<artifactId>mcode-app</artifactId>
- <version>1.4.0-alpha3-SNAPSHOT</version>
+ <version>1.4.0-beta1-SNAPSHOT</version>
<name>${bundle.symbolicName} [${bundle.namespace}]</name>
@@ -79,6 +79,18 @@
</instructions>
</configuration>
</plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.3.1</version>
+ <configuration>
+ <archive>
+ <manifestEntries>
+
<Cytoscape-API-Compatibility>3.0</Cytoscape-API-Compatibility>
+ </manifestEntries>
+ </archive>
+ </configuration>
+ </plugin>
</plugins>
<pluginManagement>
<plugins>
@@ -142,6 +154,13 @@
<!-- Dependencies needed to compile this project. -->
<dependencies>
+ <!-- OSGI -->
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>org.osgi.core</artifactId>
+ <version>4.2.0</version>
+ </dependency>
+
<!-- Cytoscape -->
<dependency>
<groupId>org.cytoscape</groupId>
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/CyActivator.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/CyActivator.java
2012-07-13 20:17:17 UTC (rev 29889)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/CyActivator.java
2012-07-13 20:18:14 UTC (rev 29890)
@@ -33,6 +33,7 @@
super();
}
+ @Override
@SuppressWarnings("unchecked")
public void start(BundleContext bc) {
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-07-13 20:17:17 UTC (rev 29889)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-07-13 20:18:14 UTC (rev 29890)
@@ -499,7 +499,7 @@
}
public CyNetworkView createNetworkView(final CyNetwork net, VisualStyle
vs) {
- final CyNetworkView view =
networkViewFactory.createNetworkView(net, false);
+ final CyNetworkView view =
networkViewFactory.createNetworkView(net);
if (vs == null) vs = visualMappingMgr.getDefaultVisualStyle();
visualMappingMgr.setVisualStyle(vs, view);
@@ -577,7 +577,7 @@
// Node Shape:
DiscreteMapping<String, NodeShape> nodeShapeDm =
(DiscreteMapping<String, NodeShape>) discreteMappingFactory
-
.createVisualMappingFunction("MCODE_Node_Status", String.class, null,
NODE_SHAPE);
+
.createVisualMappingFunction("MCODE_Node_Status", String.class, NODE_SHAPE);
nodeShapeDm.putMapValue("Clustered",
NodeShapeVisualProperty.ELLIPSE);
nodeShapeDm.putMapValue("Seed",
NodeShapeVisualProperty.RECTANGLE);
@@ -594,7 +594,7 @@
// The lower the score the darker the color
ContinuousMapping<Double, Paint> nodeColorCm =
(ContinuousMapping<Double, Paint>) continuousMappingFactory
- .createVisualMappingFunction("MCODE_Score",
Double.class, null, NODE_FILL_COLOR);
+ .createVisualMappingFunction("MCODE_Score",
Double.class, NODE_FILL_COLOR);
final Color MIN_COLOR = Color.BLACK;
final Color MAX_COLOR = Color.RED;
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