Author: mes
Date: 2011-09-15 12:40:55 -0700 (Thu, 15 Sep 2011)
New Revision: 26812
Added:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
Removed:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml
Modified:
core3/impl/branches/no-spring/network-analyzer-impl/osgi.bnd
Log:
removed use of spring
Modified: core3/impl/branches/no-spring/network-analyzer-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/network-analyzer-impl/osgi.bnd
2011-09-15 19:36:05 UTC (rev 26811)
+++ core3/impl/branches/no-spring/network-analyzer-impl/osgi.bnd
2011-09-15 19:40:55 UTC (rev 26812)
@@ -3,3 +3,4 @@
#-----------------------------------------------------------------
Private-Package: ${bundle.namespace},${bundle.namespace}.*
+Bundle-Activator: ${bundle.namespace}.CyActivator
Added:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
(rev 0)
+++
core3/impl/branches/no-spring/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/CyActivator.java
2011-09-15 19:40:55 UTC (rev 26812)
@@ -0,0 +1,78 @@
+
+
+
+
+package de.mpg.mpi_inf.bioinf.netanalyzer;
+
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.io.read.CyNetworkReaderManager;
+import org.cytoscape.model.CyNetworkManager;
+
+import de.mpg.mpi_inf.bioinf.netanalyzer.CompareAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.PlotParameterAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.MapParameterAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.RemoveSelfLoopsAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.BatchAnalysisAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.RemDupEdgesAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.SettingsAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeSubsetAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.Plugin;
+import de.mpg.mpi_inf.bioinf.netanalyzer.AboutAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction;
+import de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeNetworkAction;
+
+import org.cytoscape.application.swing.CyAction;
+
+
+import org.osgi.framework.BundleContext;
+
+import org.cytoscape.service.util.AbstractCyActivator;
+
+import java.util.Properties;
+
+
+
+public class CyActivator extends AbstractCyActivator {
+ public CyActivator() {
+ super();
+ }
+
+
+ public void start(BundleContext bc) {
+
+ CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
+ CySwingApplication cySwingApplicationServiceRef =
getService(bc,CySwingApplication.class);
+ CyNetworkManager cyNetworkManagerServiceRef =
getService(bc,CyNetworkManager.class);
+ CyNetworkReaderManager cyNetworkViewReaderManagerServiceRef =
getService(bc,CyNetworkReaderManager.class);
+
+ Plugin plugin = new Plugin(cySwingApplicationServiceRef);
+ AboutAction aboutAction = new
AboutAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ AnalyzeNetworkAction analyzeNetworkAction = new
AnalyzeNetworkAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ AnalyzeSubsetAction analyzeSubsetAction = new
AnalyzeSubsetAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ BatchAnalysisAction batchAnalysisAction = new
BatchAnalysisAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef,cyNetworkViewReaderManagerServiceRef);
+ CompareAction compareAction = new
CompareAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
+ ConnComponentAction connComponentAction = new
ConnComponentAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ LoadNetstatsAction loadNetstatsAction = new
LoadNetstatsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ MapParameterAction mapParameterAction = new
MapParameterAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ PlotParameterAction plotParameterAction = new
PlotParameterAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+ RemDupEdgesAction remDupEdgesAction = new
RemDupEdgesAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
+ RemoveSelfLoopsAction removeSelfLoopsAction = new
RemoveSelfLoopsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
+ SettingsAction settingsAction = new
SettingsAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef);
+
+ registerService(bc,analyzeNetworkAction,CyAction.class, new
Properties());
+ registerService(bc,analyzeSubsetAction,CyAction.class, new
Properties());
+ registerService(bc,batchAnalysisAction,CyAction.class, new
Properties());
+ registerService(bc,loadNetstatsAction,CyAction.class, new
Properties());
+ registerService(bc,plotParameterAction,CyAction.class, new
Properties());
+ registerService(bc,mapParameterAction,CyAction.class, new
Properties());
+ registerService(bc,settingsAction,CyAction.class, new
Properties());
+ registerService(bc,compareAction,CyAction.class, new
Properties());
+ registerService(bc,connComponentAction,CyAction.class, new
Properties());
+ registerService(bc,remDupEdgesAction,CyAction.class, new
Properties());
+ registerService(bc,removeSelfLoopsAction,CyAction.class, new
Properties());
+ registerService(bc,aboutAction,CyAction.class, new
Properties());
+ }
+}
+
Deleted:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 19:36:05 UTC (rev 26811)
+++
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-15 19:40:55 UTC (rev 26812)
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans";
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
- xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
- http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
- default-lazy-init="false">
-
- <osgi:reference id="cyApplicationManagerServiceRef"
- interface="org.cytoscape.application.CyApplicationManager"/>
-
- <osgi:reference id="cySwingApplicationServiceRef"
- interface="org.cytoscape.application.swing.CySwingApplication"
/>
-
- <osgi:reference id="cyNetworkManagerServiceRef"
- interface="org.cytoscape.model.CyNetworkManager"/>
-
- <osgi:reference id="cyNetworkViewReaderManagerServiceRef"
- interface="org.cytoscape.io.read.CyNetworkReaderManager"/>
-
- <osgi:service id="analyzeNetworkActionService"
ref="analyzeNetworkAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="analyzeSubsetActionService" ref="analyzeSubsetAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="batchAnalysisActionService" ref="batchAnalysisAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="loadNetstatsActionService" ref="loadNetstatsAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="plotParameterActionService" ref="plotParameterAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="mapParameterActionService" ref="mapParameterAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="settingsActionService" ref="settingsAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="compareActionService" ref="compareAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="connComponentActionService" ref="connComponentAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="remDupEdgesActionService" ref="remDupEdgesAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="removeSelfLoopsActionService"
ref="removeSelfLoopsAction"
- interface="org.cytoscape.application.swing.CyAction"/>
- <osgi:service id="aboutActionService" ref="aboutAction"
- interface="org.cytoscape.application.swing.CyAction"/>
-
-</beans>
Copied:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml)
===================================================================
---
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-15 19:40:55 UTC (rev 26812)
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+ http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+ <osgi:reference id="cyApplicationManagerServiceRef"
+ interface="org.cytoscape.application.CyApplicationManager"/>
+
+ <osgi:reference id="cySwingApplicationServiceRef"
+ interface="org.cytoscape.application.swing.CySwingApplication"
/>
+
+ <osgi:reference id="cyNetworkManagerServiceRef"
+ interface="org.cytoscape.model.CyNetworkManager"/>
+
+ <osgi:reference id="cyNetworkViewReaderManagerServiceRef"
+ interface="org.cytoscape.io.read.CyNetworkReaderManager"/>
+
+ <osgi:service id="analyzeNetworkActionService"
ref="analyzeNetworkAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="analyzeSubsetActionService" ref="analyzeSubsetAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="batchAnalysisActionService" ref="batchAnalysisAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="loadNetstatsActionService" ref="loadNetstatsAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="plotParameterActionService" ref="plotParameterAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="mapParameterActionService" ref="mapParameterAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="settingsActionService" ref="settingsAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="compareActionService" ref="compareAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="connComponentActionService" ref="connComponentAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="remDupEdgesActionService" ref="remDupEdgesAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="removeSelfLoopsActionService"
ref="removeSelfLoopsAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+ <osgi:service id="aboutActionService" ref="aboutAction"
+ interface="org.cytoscape.application.swing.CyAction"/>
+
+</beans>
Deleted:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 19:36:05 UTC (rev 26811)
+++
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-15 19:40:55 UTC (rev 26812)
@@ -1,70 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans";
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:context="http://www.springframework.org/schema/context";
- xsi:schemaLocation="
- http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context-3.0.xsd";>
-
- <context:annotation-config />
-
- <bean id="plugin" class="de.mpg.mpi_inf.bioinf.netanalyzer.Plugin">
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
-
- <bean id="aboutAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AboutAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="analyzeNetworkAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeNetworkAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="analyzeSubsetAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeSubsetAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="batchAnalysisAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.BatchAnalysisAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="cyNetworkViewReaderManagerServiceRef" />
- </bean>
- <bean id="compareAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.CompareAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- </bean>
- <bean id="connComponentAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="loadNetstatsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="mapParameterAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.MapParameterAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="plotParameterAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.PlotParameterAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
- <bean id="remDupEdgesAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.RemDupEdgesAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- </bean>
- <bean id="removeSelfLoopsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.RemoveSelfLoopsAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- <constructor-arg ref="cyNetworkManagerServiceRef" />
- </bean>
- <bean id="settingsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.SettingsAction">
- <constructor-arg ref="cyApplicationManagerServiceRef" />
- <constructor-arg ref="cySwingApplicationServiceRef" />
- </bean>
-
-</beans>
Copied:
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml)
===================================================================
---
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/network-analyzer-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2011-09-15 19:40:55 UTC (rev 26812)
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:context="http://www.springframework.org/schema/context";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-3.0.xsd";>
+
+ <context:annotation-config />
+
+ <bean id="plugin" class="de.mpg.mpi_inf.bioinf.netanalyzer.Plugin">
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+
+ <bean id="aboutAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AboutAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="analyzeNetworkAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeNetworkAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="analyzeSubsetAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.AnalyzeSubsetAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="batchAnalysisAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.BatchAnalysisAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ <constructor-arg ref="cyNetworkViewReaderManagerServiceRef" />
+ </bean>
+ <bean id="compareAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.CompareAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ </bean>
+ <bean id="connComponentAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.ConnComponentAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="loadNetstatsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.LoadNetstatsAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="mapParameterAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.MapParameterAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="plotParameterAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.PlotParameterAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+ <bean id="remDupEdgesAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.RemDupEdgesAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ </bean>
+ <bean id="removeSelfLoopsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.RemoveSelfLoopsAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ <constructor-arg ref="cyNetworkManagerServiceRef" />
+ </bean>
+ <bean id="settingsAction"
class="de.mpg.mpi_inf.bioinf.netanalyzer.SettingsAction">
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ </bean>
+
+</beans>
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