Author: kono
Date: 2011-05-09 14:43:36 -0700 (Mon, 09 May 2011)
New Revision: 24976
Added:
core3/biopax-impl/trunk/.classpath
core3/biopax-impl/trunk/.project
core3/biopax-impl/trunk/.settings/
core3/biopax-impl/trunk/.settings/org.eclipse.core.resources.prefs
core3/biopax-impl/trunk/.settings/org.eclipse.jdt.core.prefs
core3/biopax-impl/trunk/.settings/org.maven.ide.eclipse.prefs
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.beans.core.prefs
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.core.prefs
core3/biopax-impl/trunk/.springBeans
core3/biopax-impl/trunk/target/
Modified:
core3/biopax-impl/trunk/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
Log:
Fixed to make this bundle compatible with new network IO API.
Added: core3/biopax-impl/trunk/.classpath
===================================================================
--- core3/biopax-impl/trunk/.classpath (rev 0)
+++ core3/biopax-impl/trunk/.classpath 2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes"
path="src/main/java"/>
+ <classpathentry excluding="**" kind="src" output="target/classes"
path="src/main/resources"/>
+ <classpathentry kind="con"
path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="con"
path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: core3/biopax-impl/trunk/.project
===================================================================
--- core3/biopax-impl/trunk/.project (rev 0)
+++ core3/biopax-impl/trunk/.project 2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>biopax-impl</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+
<name>org.springframework.ide.eclipse.core.springbuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+
<nature>org.springframework.ide.eclipse.core.springnature</nature>
+ <nature>org.eclipse.pde.PluginNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ </natures>
+</projectDescription>
Added: core3/biopax-impl/trunk/.settings/org.eclipse.core.resources.prefs
===================================================================
--- core3/biopax-impl/trunk/.settings/org.eclipse.core.resources.prefs
(rev 0)
+++ core3/biopax-impl/trunk/.settings/org.eclipse.core.resources.prefs
2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,3 @@
+#Mon May 09 14:35:22 PDT 2011
+eclipse.preferences.version=1
+encoding/<project>=UTF-8
Added: core3/biopax-impl/trunk/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- core3/biopax-impl/trunk/.settings/org.eclipse.jdt.core.prefs
(rev 0)
+++ core3/biopax-impl/trunk/.settings/org.eclipse.jdt.core.prefs
2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,3 @@
+#Mon May 09 14:35:30 PDT 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
Added: core3/biopax-impl/trunk/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- core3/biopax-impl/trunk/.settings/org.maven.ide.eclipse.prefs
(rev 0)
+++ core3/biopax-impl/trunk/.settings/org.maven.ide.eclipse.prefs
2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,8 @@
+#Mon May 09 14:35:05 PDT 2011
+activeProfiles=
+eclipse.preferences.version=1
+fullBuildGoals=process-test-resources
+resolveWorkspaceProjects=true
+resourceFilterGoals=process-resources resources\:testResources
+skipCompilerPlugin=true
+version=1
Added:
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.beans.core.prefs
===================================================================
---
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.beans.core.prefs
(rev 0)
+++
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.beans.core.prefs
2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,3 @@
+#Mon May 09 14:35:55 PDT 2011
+eclipse.preferences.version=1
+org.springframework.ide.eclipse.beans.core.ignoreMissingNamespaceHandler=false
Added:
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.core.prefs
===================================================================
---
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.core.prefs
(rev 0)
+++
core3/biopax-impl/trunk/.settings/org.springframework.ide.eclipse.core.prefs
2011-05-09 21:43:36 UTC (rev 24976)
@@ -0,0 +1,41 @@
+#Mon May 09 14:35:55 PDT 2011
+eclipse.preferences.version=1
+org.springframework.ide.eclipse.core.builders.enable.aopreferencemodelbuilder=true
+org.springframework.ide.eclipse.core.builders.enable.beanmetadatabuilder=true
+org.springframework.ide.eclipse.core.enable.project.preferences=false
+org.springframework.ide.eclipse.core.validator.enable.org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.enable.org.springframework.ide.eclipse.core.springvalidator=false
+org.springframework.ide.eclipse.core.validator.enable.org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.autowire.autowire-org.springframework.ide.eclipse.beans.core.beansvalidator=false
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanAlias-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanClass-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanConstructorArgument-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanDefinition-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanDefinitionHolder-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanFactory-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanInitDestroyMethod-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanProperty-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.beanReference-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.methodOverride-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.parsingProblems-org.springframework.ide.eclipse.beans.core.beansvalidator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.requiredProperty-org.springframework.ide.eclipse.beans.core.beansvalidator=false
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.beans.core.toolAnnotation-org.springframework.ide.eclipse.beans.core.beansvalidator=false
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.core.springClasspath-org.springframework.ide.eclipse.core.springvalidator=false
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.action-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.actionstate-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.attribute-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.attributemapper-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.beanaction-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.evaluationaction-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.evaluationresult-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.exceptionhandler-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.import-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.inputattribute-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.mapping-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.outputattribute-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.set-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.state-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.subflowstate-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.transition-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.variable-org.springframework.ide.eclipse.webflow.core.validator=true
+org.springframework.ide.eclipse.core.validator.rule.enable.org.springframework.ide.eclipse.webflow.core.validation.webflowstate-org.springframework.ide.eclipse.webflow.core.validator=true
Added: core3/biopax-impl/trunk/.springBeans
===================================================================
--- core3/biopax-impl/trunk/.springBeans (rev 0)
+++ core3/biopax-impl/trunk/.springBeans 2011-05-09 21:43:36 UTC (rev
24976)
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beansProjectDescription>
+ <version>1</version>
+ <pluginVersion><![CDATA[2.6.0.201103160035-RELEASE]]></pluginVersion>
+ <configSuffixes>
+ <configSuffix><![CDATA[xml]]></configSuffix>
+ </configSuffixes>
+ <enableImports><![CDATA[false]]></enableImports>
+ <configs>
+
<config>src/main/resources/META-INF/spring/bundle-context-osgi.xml</config>
+
<config>src/main/resources/META-INF/spring/bundle-context.xml</config>
+ </configs>
+ <configSets>
+ </configSets>
+</beansProjectDescription>
Modified:
core3/biopax-impl/trunk/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
===================================================================
---
core3/biopax-impl/trunk/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
2011-05-09 21:32:27 UTC (rev 24975)
+++
core3/biopax-impl/trunk/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
2011-05-09 21:43:36 UTC (rev 24976)
@@ -11,7 +11,7 @@
import org.cytoscape.biopax.internal.view.BioPaxContainerImpl;
import org.cytoscape.biopax.util.BioPaxUtil;
import org.cytoscape.biopax.util.BioPaxVisualStyleUtil;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
@@ -19,7 +19,6 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
@@ -32,7 +31,8 @@
* @author Ethan Cerami.
* @author Igor Rodchenkov (re-factoring, using PaxTools API)
*/
-public class BioPaxNetworkViewReaderTask extends AbstractTask implements
CyNetworkViewReader {
+public class BioPaxNetworkViewReaderTask extends AbstractTask implements
CyNetworkReader {
+
public static final Logger log =
LoggerFactory.getLogger(BioPaxNetworkViewReaderTask.class);
private String networkName;
@@ -44,7 +44,7 @@
private final BioPaxContainerImpl bpContainer;
private final NetworkListener networkListener;
- private CyNetworkView view;
+ private CyNetwork network;
private InputStream stream;
@@ -81,19 +81,9 @@
}
@Override
- public CyNetworkView[] getNetworkViews() {
- return new CyNetworkView[] { view };
- }
-
- @Override
public void cancel() {
}
- @Override
- public VisualStyle[] getVisualStyles() {
- // TODO VisualStyles
- return new VisualStyle[0];
- }
public void run(TaskMonitor taskMonitor) throws Exception {
Model model = BioPaxUtil.read(stream);
@@ -107,10 +97,10 @@
+ " BioPAX elements");
networkName = getNetworkName(model);
- CyNetwork network = networkFactory.getInstance();
+ network = networkFactory.getInstance();
AttributeUtil.set(network, CyNetwork.NAME, networkName,
String.class);
- view = viewFactory.getNetworkView(network);
+ //view = viewFactory.getNetworkView(network);
// Map BioPAX Data to Cytoscape Nodes/Edges (run as task)
MapBioPaxToCytoscapeImpl mapper = new
MapBioPaxToCytoscapeImpl(network, taskMonitor);
@@ -214,7 +204,7 @@
// bpContainer.showLegend();
// add network listener
- networkListener.registerNetwork(view);
+// networkListener.registerNetwork(view);
// add node's context menu
// TODO: NodeViewTaskFactory?
@@ -248,4 +238,16 @@
}
}
}
+
+ @Override
+ public CyNetwork[] getCyNetworks() {
+ return new CyNetwork[]{network};
+ }
+
+ @Override
+ public CyNetworkView buildCyNetworkView(CyNetwork network) {
+ CyNetworkView view = viewFactory.getNetworkView(network);
+ networkListener.registerNetwork(view);
+ return view;
+ }
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
