Author: rodche
Date: 2011-12-07 10:35:53 -0800 (Wed, 07 Dec 2011)
New Revision: 27733
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPathCytoscapeWebService.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/CPathNetworkImportTask.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecutePhysicalEntitySearchTaskFactory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTaskFactory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/LoadNetworkFromUrlTaskFactory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTaskFactory.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
Log:
Updated to the latest Cy3 api and to use new biopax-api core bundle instead of
separate (wrapped) paxtools modules, etc.
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-12-07
17:15:38 UTC (rev 27732)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2011-12-07
18:35:53 UTC (rev 27733)
@@ -66,19 +66,9 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>biopax-impl</artifactId>
+ <artifactId>biopax-api</artifactId>
<version>${parent.version}</version>
<scope>provided</scope>
- <exclusions>
- <exclusion>
- <artifactId>paxtools-core</artifactId>
- <groupId>cytoscape-temp</groupId>
- </exclusion>
- <exclusion>
-
<artifactId>biopax-converter</artifactId>
- <groupId>cytoscape-temp</groupId>
- </exclusion>
- </exclusions>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
@@ -96,11 +86,6 @@
<scope>test</scope>
</dependency>
<dependency>
- <groupId>org.biopax.paxtools</groupId>
- <artifactId>paxtools-core</artifactId>
- <version>4.0.1</version>
- </dependency>
- <dependency>
<groupId>pathwaycommons.cpath</groupId>
<artifactId>cpath-api</artifactId>
<version>4.0.0-SNAPSHOT</version>
@@ -158,7 +143,7 @@
<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>
<Export-Package>
!${bundle.namespace}.internal.*,
-
${bundle.namespace}.*;version="${pom.version}"
+
${bundle.namespace}.*;version="${project.version}"
</Export-Package>
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
<Embed-Dependency>
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPathCytoscapeWebService.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPathCytoscapeWebService.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/CPathCytoscapeWebService.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -75,7 +75,7 @@
}
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
String query = "";
CPathNetworkImportTask task =
factory.createCPathNetworkImportTask(query, webApi, OutputFormat.BINARY_SIF);
return new TaskIterator(task);
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/CPathNetworkImportTask.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/CPathNetworkImportTask.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/CPathNetworkImportTask.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -34,7 +34,7 @@
// Create the task
ExecuteGetRecordByCPathIdTaskFactory taskFactory = factory
.createExecuteGetRecordByCPathIdTaskFactory(client, ids,
format, CPathProperties.serverName);
- TaskIterator iterator = taskFactory.getTaskIterator();
+ TaskIterator iterator = taskFactory.createTaskIterator();
while (iterator.hasNext()) {
Task task = iterator.next();
task.run(taskMonitor);
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathId.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -188,7 +188,7 @@
CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
TaskFactory tf = layoutManager.getDefaultLayout();
- TaskIterator ti = tf.getTaskIterator();
+ TaskIterator ti = tf.createTaskIterator();
Task task = ti.next();
insertTasksAfterCurrentTask(new Task[] {task});
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTaskFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -38,8 +38,9 @@
this.mappingManager = mappingManager;
}
+
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
return new TaskIterator(new ExecuteGetRecordByCPathId(webApi,
ids, format, networkTitle, cPathFactory, bpContainer, mapperFactory,
networkListener, mappingManager));
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecutePhysicalEntitySearchTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecutePhysicalEntitySearchTaskFactory.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecutePhysicalEntitySearchTaskFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -19,7 +19,7 @@
}
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
task = new ExecutePhysicalEntitySearchTask(webApi, keyword,
ncbiTaxonomyId, result);
return new TaskIterator(task);
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTaskFactory.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/GetParentInteractionsTaskFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -15,7 +15,7 @@
}
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
CyNetwork network = netView.getModel();
CyNode node = nodeView.getModel();
return new TaskIterator(new GetParentInteractionsTask(network,
node, factory));
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/LoadNetworkFromUrlTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/LoadNetworkFromUrlTaskFactory.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/LoadNetworkFromUrlTaskFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -17,7 +17,7 @@
}
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
return new TaskIterator(new LoadNetworkFromUrlTask(url,
factory));
}
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTaskFactory.java
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ViewNetworkNeighborhoodTaskFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -19,7 +19,7 @@
}
@Override
- public TaskIterator getTaskIterator() {
+ public TaskIterator createTaskIterator() {
return new TaskIterator(new
ViewNetworkNeighborhoodTask(nodeView, networkView));
}
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
2011-12-07 17:15:38 UTC (rev 27732)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/view/BinarySifVisualStyleFactory.java
2011-12-07 18:35:53 UTC (rev 27733)
@@ -64,8 +64,7 @@
public VisualStyle getVisualStyle() {
synchronized (this) {
if (binarySifStyle == null) {
- binarySifStyle = styleFactory
-
.getInstance(BINARY_SIF_VISUAL_STYLE);
+ binarySifStyle =
styleFactory.createVisualStyle(BINARY_SIF_VISUAL_STYLE);
// set node opacity
binarySifStyle.setDefaultValue(
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