Author: paperwing
Date: 2012-01-25 11:48:17 -0800 (Wed, 25 Jan 2012)
New Revision: 28105
Added:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/gui-distribution.patch
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
Log:
updated cytoscape core patches needed for the renderer to run, likely will need
a patch for a RenderingEngineAboutToBeRemoved event to be fired before the
bird's eye rendering engine is removed to fix crashing when switching network
windows
Added:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/gui-distribution.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/gui-distribution.patch
(rev 0)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/gui-distribution.patch
2012-01-25 19:48:17 UTC (rev 28105)
@@ -0,0 +1,38 @@
+Index: gui-distribution/features/src/main/resources/features.xml
+===================================================================
+--- gui-distribution/features/src/main/resources/features.xml (revision 27967)
++++ gui-distribution/features/src/main/resources/features.xml (working copy)
+@@ -49,6 +49,9 @@
+ <bundle
start-level="103">mvn:cytoscape-temp/biopax-converter/4.0.1</bundle>
+ <bundle
start-level="103">mvn:com.googlecode.guava-osgi/guava-osgi/9.0.0</bundle>
+
++ <bundle
start-level="103">mvn:cytoscape-temp/jogl/2.0-b23-20110303</bundle>
++ <bundle
start-level="103">mvn:cytoscape-temp/jogl-natives/2.0-b23-20110303</bundle>
++
+ <bundle
start-level="103">mvn:org.apache.commons/com.springsource.org.apache.commons.io/1.4.0</bundle>
+ <bundle start-level="103">mvn:psidev.psi.tools/xxindex/0.11</bundle>
+
+@@ -58,7 +61,7 @@
+ <bundle
start-level="103">mvn:javax.xml.stream/com.springsource.javax.xml.stream/1.0.1</bundle>
+
+ <bundle
start-level="103">mvn:psidev.psi.mi/psi25-xml/1.7.10-SNAPSHOT</bundle>
+-
++
+ <bundle
start-level="110">mvn:org.cytoscape/cmdline/${cytoscape.support.version}</bundle>
+ <bundle
start-level="110">mvn:org.cytoscape/equations-api/${cytoscape.api.version}</bundle>
+ <bundle
start-level="110">mvn:org.cytoscape/model-api/${cytoscape.api.version}</bundle>
+@@ -105,10 +108,13 @@
+
+ <bundle
start-level="140">mvn:org.cytoscape/datasource-biogrid-impl/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="140">mvn:org.cytoscape/session-impl/${cytoscape.impl.version}</bundle>
++
++ <!--
+ <bundle
start-level="140">mvn:org.cytoscape/ding-customgraphics-manager-impl/${cytoscape.impl.version}</bundle>
+-
+ <bundle
start-level="145">mvn:org.cytoscape/ding-presentation-impl/${cytoscape.impl.version}</bundle>
++ -->
+
++ <bundle
start-level="145">mvn:org.cytoscape/paperwing-impl/1.0-SNAPSHOT</bundle>
+ <bundle
start-level="150">mvn:org.cytoscape/io-impl/${cytoscape.impl.version}</bundle>
+
+ <bundle
start-level="155">mvn:org.cytoscape/core-task-impl/${cytoscape.impl.version}</bundle>
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
2012-01-25 19:46:42 UTC (rev 28104)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
2012-01-25 19:48:17 UTC (rev 28105)
@@ -1,8 +1,8 @@
-Index:
src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
+Index:
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
===================================================================
----
src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(revision 27647)
-+++
src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(working copy)
-@@ -15,7 +15,7 @@
+---
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(revision 28020)
++++
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(working copy)
+@@ -19,7 +19,7 @@
private final Map<View<?>, RenderingEngine<?>> renderingEngineMap;
private static final String FACTORY_ID_TAG = "id";
@@ -11,3 +11,15 @@
private VisualLexicon defaultLexicon;
+Index:
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
+===================================================================
+---
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(revision 28020)
++++
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(working copy)
+@@ -25,7 +25,6 @@
+
registerService(bc,renderingEngineManager,RenderingEngineManager.class,
renderingEngineManagerProps);
+
+
registerServiceListener(bc,renderingEngineManager,"addRenderingEngineFactory","removeRenderingEngineFactory",RenderingEngineFactory.class);
+-
+ }
+ }
+
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
2012-01-25 19:46:42 UTC (rev 28104)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
2012-01-25 19:48:17 UTC (rev 28105)
@@ -1,8 +1,8 @@
-Index: src/main/java/org/cytoscape/internal/CyActivator.java
+Index:
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
===================================================================
---- src/main/java/org/cytoscape/internal/CyActivator.java (revision 27647)
-+++ src/main/java/org/cytoscape/internal/CyActivator.java (working copy)
-@@ -175,10 +175,10 @@
+---
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
(revision 28020)
++++
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
(working copy)
+@@ -169,10 +169,10 @@
SubmenuTaskManager submenuTaskManagerServiceRef =
getService(bc, SubmenuTaskManager.class);
RenderingEngineFactory dingRenderingEngineFactoryServiceRef =
getService(bc,
RenderingEngineFactory.class,
@@ -15,16 +15,17 @@
CyProperty bookmarkServiceRef = getService(bc, CyProperty.class,
"(cyPropertyName=bookmarks)");
BookmarksUtil bookmarksUtilServiceRef = getService(bc,
BookmarksUtil.class);
-Index: src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
+Index:
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
---- src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(revision 27647)
-+++ src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(working copy)
-@@ -128,7 +128,7 @@
+---
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(revision 28020)
++++
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(working copy)
+@@ -123,7 +123,7 @@
// TODO: for now, use this as default. But in the future, we should
provide
// UI to select presentation.
- private static final String DEFAULT_PRESENTATION = "ding";
+ private static final String DEFAULT_PRESENTATION = "wind";
- private final Map<CyTable, CyNetwork> nameTables;
private final CyNetworkViewManager networkViewManager;
+ private final CyApplicationManager applicationManager;
+
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
2012-01-25 19:46:42 UTC (rev 28104)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
2012-01-25 19:48:17 UTC (rev 28105)
@@ -1,17 +1,30 @@
-Index:
src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
+Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
===================================================================
----
src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(revision 27648)
-+++
src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(working copy)
-@@ -26,7 +26,7 @@
- .getLogger(BypassManager.class);
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
(revision 28020)
++++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
(working copy)
+@@ -201,7 +201,7 @@
- // TODO: how can we display compatible VP only?
-- private static final String DEF_RENDERER = "ding";
-+ private static final String DEF_RENDERER = "wind";
+ for (VisualLexicon lexicon : lexSet) {
+ for (VisualProperty<?> vp : props) {
+- if
(lexicon.getVisualLexiconNode(vp).getChildren().size() == 0)
++ if (lexicon.getVisualLexiconNode(vp) != null &&
(lexicon.getVisualLexiconNode(vp).getChildren().size() == 0))
+ propSet.add(vp);
+ }
+ }
+@@ -218,7 +218,7 @@
- // TODO: this should be a public string or enum managed in swing app.
- private static final String MENU_KEY = "preferredMenu";
-@@ -48,7 +48,7 @@
+ for (VisualLexicon lexicon : lexSet) {
+ for (VisualProperty<?> vp : props) {
+- if
(lexicon.getVisualLexiconNode(vp).getChildren().size() == 0
++ if (lexicon.getVisualLexiconNode(vp) != null &&
lexicon.getVisualLexiconNode(vp).getChildren().size() == 0
+ &&
lexicon.getVisualLexiconNode(vp).getParent()
+
.getVisualProperty() == MinimalVisualLexicon.NETWORK)
+ propSet.add(vp);
+Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
+===================================================================
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(revision 28020)
++++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(working copy)
+@@ -44,7 +44,7 @@
}
public void addBypass(RenderingEngineFactory<?> factory, Map props) {
@@ -20,10 +33,10 @@
return;
final VisualLexicon lexicon = factory.getVisualLexicon();
-Index: src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
+Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
===================================================================
---- src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(revision 27648)
-+++ src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(working copy)
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(revision 28020)
++++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(working copy)
@@ -74,8 +74,8 @@
CyApplicationConfiguration cyApplicationConfigurationServiceRef
= getService(bc,CyApplicationConfiguration.class);
DialogTaskManager dialogTaskManagerServiceRef =
getService(bc,DialogTaskManager.class);
@@ -35,3 +48,31 @@
VisualMappingManager vmmServiceRef =
getService(bc,VisualMappingManager.class);
CyNetworkManager cyNetworkManagerServiceRef =
getService(bc,CyNetworkManager.class);
CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
+Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
+===================================================================
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
(revision 28020)
++++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
(working copy)
+@@ -12,8 +12,8 @@
+
+ // Visual Properties which are not compatible with current rendering
engine.
+ static {
+- INCOMPATIBLE_VP_SET.add(RichVisualLexicon.NODE_DEPTH);
+- INCOMPATIBLE_VP_SET.add(RichVisualLexicon.NODE_Z_LOCATION);
++ // INCOMPATIBLE_VP_SET.add(RichVisualLexicon.NODE_DEPTH);
++ // INCOMPATIBLE_VP_SET.add(RichVisualLexicon.NODE_Z_LOCATION);
+ }
+
+
+Index: vizmap-gui-impl/src/main/resources/default_vizmap.xml
+===================================================================
+--- vizmap-gui-impl/src/main/resources/default_vizmap.xml (revision 28020)
++++ vizmap-gui-impl/src/main/resources/default_vizmap.xml (working copy)
+@@ -458,7 +458,7 @@
+ <visualProperty name="NODE_TRANSPARENCY" default="255"/>
+ <visualProperty name="NODE_SIZE" default="35.0"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_2"/>
+- <visualProperty name="NODE_FILL_COLOR" default="#00acad"/>
++ <visualProperty name="NODE_FILL_COLOR" default="#797979"/>
+ <visualProperty name="NODE_CUSTOMPAINT_5"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
+ <visualProperty name="NODE_CUSTOMPAINT_6"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
+ <visualProperty name="NODE_CUSTOMPAINT_7"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
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