Author: mes
Date: 2011-09-12 16:54:51 -0700 (Mon, 12 Sep 2011)
New Revision: 26769
Added:
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
Removed:
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml
Modified:
core3/impl/branches/no-spring/biopax-impl/osgi.bnd
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainerImpl.java
Log:
removed use of spring
Modified: core3/impl/branches/no-spring/biopax-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/biopax-impl/osgi.bnd 2011-09-12 23:49:28 UTC
(rev 26768)
+++ core3/impl/branches/no-spring/biopax-impl/osgi.bnd 2011-09-12 23:54:51 UTC
(rev 26769)
@@ -2,6 +2,6 @@
# Use this file to add customized Bnd instructions for the bundle
#-----------------------------------------------------------------
-Spring-Context: META-INF/spring/*.xml
+Bundle-Activator: ${bundle.namespace}.internal.CyActivator
Private-Package: ${bundle.namespace}.internal.*
Export-Package:
!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${pom.version}"
Added:
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
(rev 0)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2011-09-12 23:54:51 UTC (rev 26769)
@@ -0,0 +1,87 @@
+package org.cytoscape.biopax.internal;
+
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.util.swing.OpenBrowser;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.util.swing.FileUtil;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+
+import org.cytoscape.biopax.internal.BioPaxFilter;
+import org.cytoscape.biopax.internal.action.NetworkListenerImpl;
+import org.cytoscape.biopax.internal.BioPaxNetworkViewTaskFactory;
+import org.cytoscape.biopax.internal.BioPaxFactory;
+import org.cytoscape.biopax.util.BioPaxVisualStyleUtil;
+import org.cytoscape.biopax.internal.view.BioPaxContainerImpl;
+import org.cytoscape.biopax.internal.MapBioPaxToCytoscapeFactoryImpl;
+import org.cytoscape.biopax.internal.view.BioPaxDetailsPanel;
+import org.cytoscape.biopax.internal.view.BioPaxCytoPanelComponent;
+import org.cytoscape.biopax.internal.action.LaunchExternalBrowser;
+
+import org.cytoscape.application.swing.CytoPanelComponent;
+import org.cytoscape.biopax.MapBioPaxToCytoscapeFactory;
+import org.cytoscape.model.events.RowsSetListener;
+import org.cytoscape.biopax.BioPaxContainer;
+import org.cytoscape.io.read.InputStreamTaskFactory;
+import org.cytoscape.biopax.NetworkListener;
+
+
+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) {
+
+ CySwingApplication cySwingApplicationRef =
getService(bc,CySwingApplication.class);
+ TaskManager taskManagerRef = getService(bc,TaskManager.class);
+ OpenBrowser openBrowserRef = getService(bc,OpenBrowser.class);
+ CyApplicationManager cyApplicationManagerRef =
getService(bc,CyApplicationManager.class);
+ CyNetworkViewManager cyNetworkViewManagerRef =
getService(bc,CyNetworkViewManager.class);
+ CyNetworkNaming cyNetworkNamingRef =
getService(bc,CyNetworkNaming.class);
+ CyNetworkFactory cyNetworkFactoryRef =
getService(bc,CyNetworkFactory.class);
+ CyNetworkViewFactory cyNetworkViewFactoryRef =
getService(bc,CyNetworkViewFactory.class);
+ FileUtil fileUtilRef = getService(bc,FileUtil.class);
+ StreamUtil streamUtilRef = getService(bc,StreamUtil.class);
+ VisualMappingManager visualMappingManagerRef =
getService(bc,VisualMappingManager.class);
+ VisualStyleFactory visualStyleFactoryRef =
getService(bc,VisualStyleFactory.class);
+ VisualMappingFunctionFactory discreteMappingFunctionFactoryRef
= getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=discrete)");
+ VisualMappingFunctionFactory
passthroughMappingFunctionFactoryRef =
getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=passthrough)");
+
+ MapBioPaxToCytoscapeFactoryImpl mapBioPaxToCytoscapeFactory =
new MapBioPaxToCytoscapeFactoryImpl();
+ BioPaxFilter bioPaxFilter = new BioPaxFilter(streamUtilRef);
+ LaunchExternalBrowser launchExternalBrowser = new
LaunchExternalBrowser(openBrowserRef);
+ BioPaxFactory bioPaxFactory = new
BioPaxFactory(cyNetworkViewManagerRef,fileUtilRef,cyApplicationManagerRef,bioPaxFilter,taskManagerRef,launchExternalBrowser,cySwingApplicationRef);
+ BioPaxDetailsPanel bioPaxDetailsPanel = new
BioPaxDetailsPanel(launchExternalBrowser);
+ BioPaxContainerImpl bioPaxContainer = new
BioPaxContainerImpl(launchExternalBrowser,cyApplicationManagerRef,cyNetworkViewManagerRef,bioPaxDetailsPanel,cySwingApplicationRef);
+ NetworkListenerImpl networkListener = new
NetworkListenerImpl(bioPaxDetailsPanel,bioPaxContainer,mapBioPaxToCytoscapeFactory,cyNetworkViewManagerRef);
+ BioPaxCytoPanelComponent bioPaxCytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
+ BioPaxVisualStyleUtil bioPaxVisualStyleUtil = new
BioPaxVisualStyleUtil(visualStyleFactoryRef,visualMappingManagerRef,discreteMappingFunctionFactoryRef,passthroughMappingFunctionFactoryRef);
+ BioPaxNetworkViewTaskFactory bioPaxNetworkViewTaskFactory = new
BioPaxNetworkViewTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,bioPaxContainer,networkListener,visualMappingManagerRef,bioPaxVisualStyleUtil);
+
+
registerService(bc,mapBioPaxToCytoscapeFactory,MapBioPaxToCytoscapeFactory.class,
new Properties());
+
registerService(bc,bioPaxNetworkViewTaskFactory,InputStreamTaskFactory.class,
new Properties());
+ registerService(bc,bioPaxContainer,BioPaxContainer.class, new
Properties());
+
registerService(bc,bioPaxCytoPanelComponent,CytoPanelComponent.class, new
Properties());
+ registerService(bc,networkListener,NetworkListener.class, new
Properties());
+ registerService(bc,networkListener,RowsSetListener.class, new
Properties());
+
+ }
+}
+
Modified:
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainerImpl.java
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainerImpl.java
2011-09-12 23:49:28 UTC (rev 26768)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/java/org/cytoscape/biopax/internal/view/BioPaxContainerImpl.java
2011-09-12 23:54:51 UTC (rev 26769)
@@ -85,7 +85,7 @@
* @param factory
* @param applicationManager
*/
- private BioPaxContainerImpl(LaunchExternalBrowser browser,
CyApplicationManager applicationManager, CyNetworkViewManager viewManager,
BioPaxDetailsPanel bpDetailsPanel, CySwingApplication application) {
+ public BioPaxContainerImpl(LaunchExternalBrowser browser,
CyApplicationManager applicationManager, CyNetworkViewManager viewManager,
BioPaxDetailsPanel bpDetailsPanel, CySwingApplication application) {
this.applicationManager = applicationManager;
cards = new JPanel(new CardLayout());
Deleted:
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-12 23:49:28 UTC (rev 26768)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-09-12 23:54:51 UTC (rev 26769)
@@ -1,72 +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">
-
-
- <!-- Import services -->
- <osgi:reference id="cySwingApplicationRef"
- interface="org.cytoscape.application.swing.CySwingApplication"
/>
-
- <osgi:reference id="taskManagerRef"
- interface="org.cytoscape.work.TaskManager" />
-
- <osgi:reference id="openBrowserRef"
- interface="org.cytoscape.util.swing.OpenBrowser" />
-
- <osgi:reference id="cyApplicationManagerRef"
- interface="org.cytoscape.application.CyApplicationManager" />
-
- <osgi:reference id="cyNetworkViewManagerRef"
- interface="org.cytoscape.view.model.CyNetworkViewManager" />
-
- <osgi:reference id="cyNetworkNamingRef"
- interface="org.cytoscape.session.CyNetworkNaming" />
-
- <osgi:reference id="cyNetworkFactoryRef"
- interface="org.cytoscape.model.CyNetworkFactory" />
-
- <osgi:reference id="cyNetworkViewFactoryRef"
- interface="org.cytoscape.view.model.CyNetworkViewFactory" />
-
- <osgi:reference id="fileUtilRef"
- interface="org.cytoscape.util.swing.FileUtil" />
-
- <osgi:reference id="streamUtilRef"
- interface="org.cytoscape.io.util.StreamUtil" />
-
- <osgi:reference id="visualMappingManagerRef"
- interface="org.cytoscape.view.vizmap.VisualMappingManager" />
-
- <osgi:reference id="visualStyleFactoryRef"
- interface="org.cytoscape.view.vizmap.VisualStyleFactory" />
-
- <osgi:reference id="discreteMappingFunctionFactoryRef"
-
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
- filter="(mapping.type=discrete)" />
-
- <osgi:reference id="passthroughMappingFunctionFactoryRef"
-
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
- filter="(mapping.type=passthrough)" />
-
- <osgi:service ref="mapBioPaxToCytoscapeFactory"
- interface="org.cytoscape.biopax.MapBioPaxToCytoscapeFactory" />
-
- <osgi:service ref="bioPaxNetworkViewTaskFactory"
- interface="org.cytoscape.io.read.InputStreamTaskFactory" />
-
- <osgi:service ref="bioPaxContainer"
- interface="org.cytoscape.biopax.BioPaxContainer" />
-
- <osgi:service ref="bioPaxCytoPanelComponent"
- interface="org.cytoscape.application.swing.CytoPanelComponent"
/>
-
- <osgi:service ref="networkListener">
- <osgi:interfaces>
- <value>org.cytoscape.biopax.NetworkListener</value>
-
<value>org.cytoscape.model.events.RowsSetListener</value>
- </osgi:interfaces>
- </osgi:service>
-</beans>
Copied:
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml)
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-12 23:54:51 UTC (rev 26769)
@@ -0,0 +1,72 @@
+<?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">
+
+
+ <!-- Import services -->
+ <osgi:reference id="cySwingApplicationRef"
+ interface="org.cytoscape.application.swing.CySwingApplication"
/>
+
+ <osgi:reference id="taskManagerRef"
+ interface="org.cytoscape.work.TaskManager" />
+
+ <osgi:reference id="openBrowserRef"
+ interface="org.cytoscape.util.swing.OpenBrowser" />
+
+ <osgi:reference id="cyApplicationManagerRef"
+ interface="org.cytoscape.application.CyApplicationManager" />
+
+ <osgi:reference id="cyNetworkViewManagerRef"
+ interface="org.cytoscape.view.model.CyNetworkViewManager" />
+
+ <osgi:reference id="cyNetworkNamingRef"
+ interface="org.cytoscape.session.CyNetworkNaming" />
+
+ <osgi:reference id="cyNetworkFactoryRef"
+ interface="org.cytoscape.model.CyNetworkFactory" />
+
+ <osgi:reference id="cyNetworkViewFactoryRef"
+ interface="org.cytoscape.view.model.CyNetworkViewFactory" />
+
+ <osgi:reference id="fileUtilRef"
+ interface="org.cytoscape.util.swing.FileUtil" />
+
+ <osgi:reference id="streamUtilRef"
+ interface="org.cytoscape.io.util.StreamUtil" />
+
+ <osgi:reference id="visualMappingManagerRef"
+ interface="org.cytoscape.view.vizmap.VisualMappingManager" />
+
+ <osgi:reference id="visualStyleFactoryRef"
+ interface="org.cytoscape.view.vizmap.VisualStyleFactory" />
+
+ <osgi:reference id="discreteMappingFunctionFactoryRef"
+
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
+ filter="(mapping.type=discrete)" />
+
+ <osgi:reference id="passthroughMappingFunctionFactoryRef"
+
interface="org.cytoscape.view.vizmap.VisualMappingFunctionFactory"
+ filter="(mapping.type=passthrough)" />
+
+ <osgi:service ref="mapBioPaxToCytoscapeFactory"
+ interface="org.cytoscape.biopax.MapBioPaxToCytoscapeFactory" />
+
+ <osgi:service ref="bioPaxNetworkViewTaskFactory"
+ interface="org.cytoscape.io.read.InputStreamTaskFactory" />
+
+ <osgi:service ref="bioPaxContainer"
+ interface="org.cytoscape.biopax.BioPaxContainer" />
+
+ <osgi:service ref="bioPaxCytoPanelComponent"
+ interface="org.cytoscape.application.swing.CytoPanelComponent"
/>
+
+ <osgi:service ref="networkListener">
+ <osgi:interfaces>
+ <value>org.cytoscape.biopax.NetworkListener</value>
+
<value>org.cytoscape.model.events.RowsSetListener</value>
+ </osgi:interfaces>
+ </osgi:service>
+</beans>
Deleted:
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-12 23:49:28 UTC (rev 26768)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-12 23:54:51 UTC (rev 26769)
@@ -1,81 +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:aop="http://www.springframework.org/schema/aop";
- xmlns:context="http://www.springframework.org/schema/context";
- xmlns:lang="http://www.springframework.org/schema/lang";
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/aop
- http://www.springframework.org/schema/aop/spring-aop-3.0.xsd
- http://www.springframework.org/schema/context
- http://www.springframework.org/schema/context/spring-context-3.0.xsd
- http://www.springframework.org/schema/lang
http://www.springframework.org/schema/lang/spring-lang-3.0.xsd
- http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
- default-lazy-init="true">
-
- <context:annotation-config />
-
- <bean id="mapBioPaxToCytoscapeFactory"
class="org.cytoscape.biopax.internal.MapBioPaxToCytoscapeFactoryImpl" />
-
- <bean id="bioPaxFilter"
class="org.cytoscape.biopax.internal.BioPaxFilter">
- <constructor-arg ref="streamUtilRef" />
- </bean>
-
- <bean id="launchExternalBrowser"
class="org.cytoscape.biopax.internal.action.LaunchExternalBrowser">
- <constructor-arg ref="openBrowserRef" />
- </bean>
-
- <bean id="bioPaxFactory"
class="org.cytoscape.biopax.internal.BioPaxFactory">
- <constructor-arg ref="cyNetworkViewManagerRef" />
- <constructor-arg ref="fileUtilRef" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="bioPaxFilter" />
- <constructor-arg ref="taskManagerRef" />
- <constructor-arg ref="launchExternalBrowser" />
- <constructor-arg ref="cySwingApplicationRef" />
- </bean>
-
- <bean id="bioPaxDetailsPanel"
class="org.cytoscape.biopax.internal.view.BioPaxDetailsPanel">
- <constructor-arg ref="launchExternalBrowser" />
- </bean>
-
- <bean id="bioPaxContainer"
class="org.cytoscape.biopax.internal.view.BioPaxContainerImpl">
- <constructor-arg ref="launchExternalBrowser" />
- <constructor-arg ref="cyApplicationManagerRef" />
- <constructor-arg ref="cyNetworkViewManagerRef" />
- <constructor-arg ref="bioPaxDetailsPanel" />
- <constructor-arg ref="cySwingApplicationRef" />
- </bean>
-
- <bean id="networkListener"
class="org.cytoscape.biopax.internal.action.NetworkListenerImpl">
- <constructor-arg ref="bioPaxDetailsPanel"/>
- <constructor-arg ref="bioPaxContainer"/>
- <constructor-arg ref="mapBioPaxToCytoscapeFactory"/>
- <constructor-arg ref="cyNetworkViewManagerRef"/>
- </bean>
-
- <bean id="bioPaxCytoPanelComponent"
class="org.cytoscape.biopax.internal.view.BioPaxCytoPanelComponent">
- <constructor-arg ref="bioPaxContainer" />
- </bean>
-
- <bean id="bioPaxNetworkViewTaskFactory"
class="org.cytoscape.biopax.internal.BioPaxNetworkViewTaskFactory">
- <constructor-arg ref="bioPaxFilter"/>
- <constructor-arg ref="cyNetworkFactoryRef"/>
- <constructor-arg ref="cyNetworkViewFactoryRef"/>
- <constructor-arg ref="cyNetworkNamingRef"/>
- <constructor-arg ref="bioPaxContainer"/>
- <constructor-arg ref="networkListener"/>
- <constructor-arg ref="visualMappingManagerRef"/>
- <constructor-arg ref="bioPaxVisualStyleUtil"/>
- </bean>
-
- <bean id="bioPaxVisualStyleUtil"
class="org.cytoscape.biopax.util.BioPaxVisualStyleUtil">
- <constructor-arg ref="visualStyleFactoryRef" />
- <constructor-arg ref="visualMappingManagerRef" />
- <constructor-arg ref="discreteMappingFunctionFactoryRef" />
- <constructor-arg ref="passthroughMappingFunctionFactoryRef" />
- </bean>
-
-
-</beans>
Copied:
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(from rev 26762,
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml)
===================================================================
---
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
(rev 0)
+++
core3/impl/branches/no-spring/biopax-impl/src/main/resources/META-INF/spring/bundle-context.xml-legacy
2011-09-12 23:54:51 UTC (rev 26769)
@@ -0,0 +1,81 @@
+<?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:aop="http://www.springframework.org/schema/aop";
+ xmlns:context="http://www.springframework.org/schema/context";
+ xmlns:lang="http://www.springframework.org/schema/lang";
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/aop
+ http://www.springframework.org/schema/aop/spring-aop-3.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-3.0.xsd
+ http://www.springframework.org/schema/lang
http://www.springframework.org/schema/lang/spring-lang-3.0.xsd
+ http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="true">
+
+ <context:annotation-config />
+
+ <bean id="mapBioPaxToCytoscapeFactory"
class="org.cytoscape.biopax.internal.MapBioPaxToCytoscapeFactoryImpl" />
+
+ <bean id="bioPaxFilter"
class="org.cytoscape.biopax.internal.BioPaxFilter">
+ <constructor-arg ref="streamUtilRef" />
+ </bean>
+
+ <bean id="launchExternalBrowser"
class="org.cytoscape.biopax.internal.action.LaunchExternalBrowser">
+ <constructor-arg ref="openBrowserRef" />
+ </bean>
+
+ <bean id="bioPaxFactory"
class="org.cytoscape.biopax.internal.BioPaxFactory">
+ <constructor-arg ref="cyNetworkViewManagerRef" />
+ <constructor-arg ref="fileUtilRef" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="bioPaxFilter" />
+ <constructor-arg ref="taskManagerRef" />
+ <constructor-arg ref="launchExternalBrowser" />
+ <constructor-arg ref="cySwingApplicationRef" />
+ </bean>
+
+ <bean id="bioPaxDetailsPanel"
class="org.cytoscape.biopax.internal.view.BioPaxDetailsPanel">
+ <constructor-arg ref="launchExternalBrowser" />
+ </bean>
+
+ <bean id="bioPaxContainer"
class="org.cytoscape.biopax.internal.view.BioPaxContainerImpl">
+ <constructor-arg ref="launchExternalBrowser" />
+ <constructor-arg ref="cyApplicationManagerRef" />
+ <constructor-arg ref="cyNetworkViewManagerRef" />
+ <constructor-arg ref="bioPaxDetailsPanel" />
+ <constructor-arg ref="cySwingApplicationRef" />
+ </bean>
+
+ <bean id="networkListener"
class="org.cytoscape.biopax.internal.action.NetworkListenerImpl">
+ <constructor-arg ref="bioPaxDetailsPanel"/>
+ <constructor-arg ref="bioPaxContainer"/>
+ <constructor-arg ref="mapBioPaxToCytoscapeFactory"/>
+ <constructor-arg ref="cyNetworkViewManagerRef"/>
+ </bean>
+
+ <bean id="bioPaxCytoPanelComponent"
class="org.cytoscape.biopax.internal.view.BioPaxCytoPanelComponent">
+ <constructor-arg ref="bioPaxContainer" />
+ </bean>
+
+ <bean id="bioPaxNetworkViewTaskFactory"
class="org.cytoscape.biopax.internal.BioPaxNetworkViewTaskFactory">
+ <constructor-arg ref="bioPaxFilter"/>
+ <constructor-arg ref="cyNetworkFactoryRef"/>
+ <constructor-arg ref="cyNetworkViewFactoryRef"/>
+ <constructor-arg ref="cyNetworkNamingRef"/>
+ <constructor-arg ref="bioPaxContainer"/>
+ <constructor-arg ref="networkListener"/>
+ <constructor-arg ref="visualMappingManagerRef"/>
+ <constructor-arg ref="bioPaxVisualStyleUtil"/>
+ </bean>
+
+ <bean id="bioPaxVisualStyleUtil"
class="org.cytoscape.biopax.util.BioPaxVisualStyleUtil">
+ <constructor-arg ref="visualStyleFactoryRef" />
+ <constructor-arg ref="visualMappingManagerRef" />
+ <constructor-arg ref="discreteMappingFunctionFactoryRef" />
+ <constructor-arg ref="passthroughMappingFunctionFactoryRef" />
+ </bean>
+
+
+</beans>
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