Author: mes
Date: 2011-09-16 15:41:55 -0700 (Fri, 16 Sep 2011)
New Revision: 26845
Added:
core3/impl/branches/no-spring/presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
Modified:
core3/impl/branches/no-spring/application-impl/src/main/java/org/cytoscape/application/internal/CyActivator.java
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
core3/impl/branches/no-spring/io-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
core3/impl/branches/no-spring/manual-layout-impl/osgi.bnd
core3/impl/branches/no-spring/manual-layout-impl/pom.xml
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
core3/impl/branches/no-spring/table-browser-impl/osgi.bnd
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/CyActivator.java
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
Log:
various tweaks to get things working
Modified:
core3/impl/branches/no-spring/application-impl/src/main/java/org/cytoscape/application/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/application-impl/src/main/java/org/cytoscape/application/internal/CyActivator.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/application-impl/src/main/java/org/cytoscape/application/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -17,6 +17,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.events.NetworkAboutToBeDestroyedListener;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener;
+import org.cytoscape.property.CyProperty;
import org.osgi.framework.BundleContext;
@@ -42,7 +43,7 @@
CyApplicationManagerImpl cyApplicationManager = new
CyApplicationManagerImpl(cyEventHelperServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef);
ShutdownHandler cytoscapeShutdown = new
ShutdownHandler(cyEventHelperServiceRef);
CyApplicationConfigurationImpl cyApplicationConfiguration = new
CyApplicationConfigurationImpl();
- CyApplicationCoreProperty cyApplicationCoreProperty = new
CyApplicationCoreProperty(cyApplicationConfiguration);
+ CyProperty cyApplicationCoreProperty =
getService(bc,CyProperty.class,"(cyPropertyName=cytoscape3.props)");
CyVersion cytoscapeVersion = new
CyVersion(cyApplicationCoreProperty);
registerService(bc,cyApplicationManager,CyApplicationManager.class, new
Properties());
@@ -52,10 +53,10 @@
registerAllServices(bc,cytoscapeVersion, new Properties());
registerAllServices(bc,cyApplicationConfiguration, new
Properties());
- Properties cyApplicationCorePropertyProps = new Properties();
-
cyApplicationCorePropertyProps.setProperty("cyPropertyName","cytoscape3.props");
-
cyApplicationCorePropertyProps.setProperty("serviceType","property");
- registerAllServices(bc,cyApplicationCoreProperty,
cyApplicationCorePropertyProps);
+// Properties cyApplicationCorePropertyProps = new Properties();
+//
cyApplicationCorePropertyProps.setProperty("cyPropertyName","cytoscape3.props");
+//
cyApplicationCorePropertyProps.setProperty("serviceType","property");
+// registerAllServices(bc,cyApplicationCoreProperty,
cyApplicationCorePropertyProps);
Modified:
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -626,6 +626,7 @@
quickStartTaskFactory2Props.setProperty("scope","startup");
quickStartTaskFactory2Props.setProperty("id","QuickStart2");
registerService(bc,quickStartTaskFactory2,TaskFactory.class,
quickStartTaskFactory2Props);
+
registerAllServices(bc,bioGridPreprocessor, new Properties());
Properties connectSelectedNodesTaskFactoryProps = new
Properties();
Modified:
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
===================================================================
---
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -50,7 +50,7 @@
this.processors = processors;
if (processors.size() == 0)
- throw new NullPointerException("Could not found data
preprocessor.");
+ throw new NullPointerException("No data processors
available.");
final List<String> sourceList = new ArrayList<String>();
for (InteractionFilePreprocessor processor : processors) {
Modified:
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
===================================================================
---
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -120,7 +120,7 @@
}
}
- void removeFactory(VisualMappingFunctionFactory factory, Map props) {
+ public void removeFactory(VisualMappingFunctionFactory factory, Map
props) {
}
Modified:
core3/impl/branches/no-spring/io-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/io-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/io-impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -96,6 +96,7 @@
import org.cytoscape.io.write.CyNetworkViewWriterFactory;
import org.cytoscape.io.write.VizmapWriterFactory;
import org.cytoscape.io.write.CySessionWriterFactory;
+import org.cytoscape.io.write.CyWriterFactory;
import org.osgi.framework.BundleContext;
@@ -236,14 +237,13 @@
registerServiceListener(bc,cySessionReaderManager,"addInputStreamTaskFactory","removeInputStreamTaskFactory",InputStreamTaskFactory.class);
registerServiceListener(bc,cyPropertyReaderManager,"addInputStreamTaskFactory","removeInputStreamTaskFactory",InputStreamTaskFactory.class);
registerServiceListener(bc,vizmapReaderManager,"addInputStreamTaskFactory","removeInputStreamTaskFactory",InputStreamTaskFactory.class);
-
registerServiceListener(bc,viewWriterManager,"addCyWriterFactory","removeCyWriterFactory",PresentationWriterFactory.class);
-
registerServiceListener(bc,networkViewWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyNetworkViewWriterFactory.class);
-
registerServiceListener(bc,sessionWriterManager,"addCyWriterFactory","removeCyWriterFactory",CySessionWriterFactory.class);
-
registerServiceListener(bc,propertyWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyPropertyWriterFactory.class);
-
registerServiceListener(bc,tableWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyTableWriterFactory.class);
-
registerServiceListener(bc,vizmapWriterManager,"addCyWriterFactory","removeCyWriterFactory",VizmapWriterFactory.class);
+
registerServiceListener(bc,viewWriterManager,"addCyWriterFactory","removeCyWriterFactory",PresentationWriterFactory.class,CyWriterFactory.class);
+
registerServiceListener(bc,networkViewWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyNetworkViewWriterFactory.class,CyWriterFactory.class);
+
registerServiceListener(bc,sessionWriterManager,"addCyWriterFactory","removeCyWriterFactory",CySessionWriterFactory.class,CyWriterFactory.class);
+
registerServiceListener(bc,propertyWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyPropertyWriterFactory.class,CyWriterFactory.class);
+
registerServiceListener(bc,tableWriterManager,"addCyWriterFactory","removeCyWriterFactory",CyTableWriterFactory.class,CyWriterFactory.class);
+
registerServiceListener(bc,vizmapWriterManager,"addCyWriterFactory","removeCyWriterFactory",VizmapWriterFactory.class,CyWriterFactory.class);
-
}
}
Modified: core3/impl/branches/no-spring/manual-layout-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/manual-layout-impl/osgi.bnd 2011-09-16
22:41:29 UTC (rev 26844)
+++ core3/impl/branches/no-spring/manual-layout-impl/osgi.bnd 2011-09-16
22:41:55 UTC (rev 26845)
@@ -2,5 +2,6 @@
# Use this file to add customized Bnd instructions for the bundle
#-----------------------------------------------------------------
+Export-Package: !org.cytoscape.math.*
Private-Package:
${bundle.namespace},${bundle.namespace}.*,org.cytoscape.math,org.cytoscape.math.*
-Bundle-Activator: ${bundle.namespace}.internal.CyActivator
+Bundle-Activator: ${bundle.namespace}.CyActivator
Modified: core3/impl/branches/no-spring/manual-layout-impl/pom.xml
===================================================================
--- core3/impl/branches/no-spring/manual-layout-impl/pom.xml 2011-09-16
22:41:29 UTC (rev 26844)
+++ core3/impl/branches/no-spring/manual-layout-impl/pom.xml 2011-09-16
22:41:55 UTC (rev 26845)
@@ -53,7 +53,6 @@
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
- <Private-Package>org.cytoscape.*</Private-Package>
<_include>-osgi.bnd</_include>
</instructions>
</configuration>
Added:
core3/impl/branches/no-spring/presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(rev 0)
+++
core3/impl/branches/no-spring/presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -0,0 +1,31 @@
+
+package org.cytoscape.view.presentation.internal;
+
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.view.presentation.internal.RenderingEngineManagerImpl;
+import org.cytoscape.view.presentation.RenderingEngineManager;
+import org.cytoscape.view.presentation.RenderingEngineFactory;
+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) {
+
+ CyEventHelper cyEventHelperServiceRef =
getService(bc,CyEventHelper.class);
+
+ RenderingEngineManagerImpl renderingEngineManager = new
RenderingEngineManagerImpl();
+
+ Properties renderingEngineManagerProps = new Properties();
+
renderingEngineManagerProps.setProperty("service.type","manager");
+
registerService(bc,renderingEngineManager,RenderingEngineManager.class,
renderingEngineManagerProps);
+
+
registerServiceListener(bc,renderingEngineManager,"addRenderingEngineFactory","removeRenderingEngineFactory",RenderingEngineFactory.class);
+
+ }
+}
+
Modified:
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -31,6 +31,12 @@
Properties bookmarksUtilProps = new Properties();
bookmarksUtilProps.setProperty("serviceType","property.util");
registerService(bc,bookmarksUtil,BookmarksUtil.class,
bookmarksUtilProps);
+
+ PropsReader cyApplicationCoreProperty = new
PropsReader("cytoscape3.props");
+ Properties cyApplicationCorePropertyProps = new Properties();
+
cyApplicationCorePropertyProps.setProperty("cyPropertyName","cytoscape3.props");
+ cyApplicationCorePropertyProps.setProperty("serviceType","property");
+ registerAllServices(bc,cyApplicationCoreProperty,
cyApplicationCorePropertyProps);
}
}
Modified:
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
===================================================================
---
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/property-impl/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -38,7 +38,7 @@
if (is == null)
throw new IllegalArgumentException("Failed to
open resource: " + resourceLocation);
- final JAXBContext jaxbContext =
JAXBContext.newInstance(BOOKMARK_PACKAGE);
+ final JAXBContext jaxbContext =
JAXBContext.newInstance(BOOKMARK_PACKAGE,getClass().getClassLoader());
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
Modified: core3/impl/branches/no-spring/table-browser-impl/osgi.bnd
===================================================================
--- core3/impl/branches/no-spring/table-browser-impl/osgi.bnd 2011-09-16
22:41:29 UTC (rev 26844)
+++ core3/impl/branches/no-spring/table-browser-impl/osgi.bnd 2011-09-16
22:41:55 UTC (rev 26845)
@@ -3,6 +3,6 @@
#-----------------------------------------------------------------
-Bundle-Activator: ${bundle.namespace}.internal.CyActivator
-Private-Package: ${bundle.namespace}.*
+Bundle-Activator: ${bundle.namespace}.CyActivator
+Private-Package: ${bundle.namespace},${bundle.namespace}.*
Modified:
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/CyActivator.java
===================================================================
---
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/CyActivator.java
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/java/org/cytoscape/work/internal/CyActivator.java
2011-09-16 22:41:55 UTC (rev 26845)
@@ -20,6 +20,7 @@
import org.cytoscape.work.undo.UndoSupport;
import org.cytoscape.work.swing.GUITunableHandlerFactory;
import org.cytoscape.work.TunableInterceptor;
+import org.cytoscape.work.TunableHandlerFactory;
import org.cytoscape.work.swing.GUITaskManager;
import org.cytoscape.work.swing.GUITunableInterceptor;
import org.cytoscape.work.util.*;
@@ -91,7 +92,7 @@
registerServiceListener(bc,supportedFileTypesManager,"addInputStreamTaskFactory","removeInputStreamTaskFactory",InputStreamTaskFactory.class);
registerServiceListener(bc,supportedFileTypesManager,"addCyWriterTaskFactory","removeCyWriterTaskFactory",CyWriterFactory.class);
registerServiceListener(bc,swingTaskManager,"addTunableInterceptor","removeTunableInterceptor",TunableInterceptor.class);
-
registerServiceListener(bc,guiTunableInterceptor,"addTunableHandlerFactory","removeTunableHandlerFactory",GUITunableHandlerFactory.class);
+
registerServiceListener(bc,guiTunableInterceptor,"addTunableHandlerFactory","removeTunableHandlerFactory",TunableHandlerFactory.class);
}
Modified:
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
===================================================================
---
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-16 22:41:29 UTC (rev 26844)
+++
core3/impl/branches/no-spring/work-swing-impl/impl/src/main/resources/META-INF/spring/bundle-context-osgi.xml-legacy
2011-09-16 22:41:55 UTC (rev 26845)
@@ -104,7 +104,7 @@
</osgi:set>
<osgi:set id="tunableHandlerFactories"
- interface="org.cytoscape.work.swing.GUITunableHandlerFactory"
+ interface="org.cytoscape.work.swing.TunableHandlerFactory"
cardinality="0..N">
<osgi:listener bind-method="addTunableHandlerFactory"
unbind-method="removeTunableHandlerFactory"
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