Author: rodche
Date: 2012-06-18 18:04:51 -0700 (Mon, 18 Jun 2012)
New Revision: 29614
Modified:
core3/impl/trunk/biopax-impl/pom.xml
core3/impl/trunk/cpath2-impl/pom.xml
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
Log:
Fixed ConcurrentModificationException bug in the FilterMainPanel. Fixed visual
style related issues.
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2012-06-19 00:41:47 UTC (rev
29613)
+++ core3/impl/trunk/biopax-impl/pom.xml 2012-06-19 01:04:51 UTC (rev
29614)
@@ -66,7 +66,8 @@
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>woodstox-core-lgpl</artifactId>
- <version>4.0.5</version>
+ <version>[4.0.5, 5.0.0)</version>
+ <scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
Modified: core3/impl/trunk/cpath2-impl/pom.xml
===================================================================
--- core3/impl/trunk/cpath2-impl/pom.xml 2012-06-19 00:41:47 UTC (rev
29613)
+++ core3/impl/trunk/cpath2-impl/pom.xml 2012-06-19 01:04:51 UTC (rev
29614)
@@ -66,8 +66,9 @@
<dependency>
<groupId>cytoscape-temp</groupId>
<artifactId>woodstox-core-lgpl</artifactId>
- <version>4.0.5</version>
- </dependency>
+ <version>[4.0.5, 5.0.0)</version>
+ <scope>provided</scope>
+ </dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-06-19 00:41:47 UTC (rev 29613)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/BinarySifVisualStyleUtil.java
2012-06-19 01:04:51 UTC (rev 29614)
@@ -63,6 +63,11 @@
// */
public VisualStyle getVisualStyle() {
synchronized (this) {
+ for(VisualStyle vs :
mappingManager.getAllVisualStyles()) {
+
if(BINARY_SIF_VISUAL_STYLE.equals(vs.getTitle()))
+ binarySifStyle = vs;
+ }
+
if (binarySifStyle == null) {
binarySifStyle =
styleFactory.createVisualStyle(BINARY_SIF_VISUAL_STYLE);
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-06-19 00:41:47 UTC (rev 29613)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-06-19 01:04:51 UTC (rev 29614)
@@ -15,7 +15,6 @@
import javax.swing.SwingUtilities;
-import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.converter.OneTwoThree;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
@@ -247,9 +246,17 @@
*
* @param cyNetwork Cytoscape Network Object.
*/
- private void postProcessingBinarySif(final CyNetworkView view,
TaskMonitor taskMonitor) {
+ private void postProcessingBinarySif(final CyNetworkView view,
TaskMonitor taskMonitor) {
final CyNetwork cyNetwork = view.getModel();
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CyNetworkNaming naming =
cPathFactory.getCyNetworkNaming();
+ String networkTitleWithUnderscores =
naming.getSuggestedNetworkTitle(networkTitle);
+ AttributeUtil.set(cyNetwork, cyNetwork,
CyNetwork.NAME, networkTitleWithUnderscores, String.class);
+ }
+ });
+
// Set the Quick Find Default Index
AttributeUtil.set(cyNetwork, cyNetwork,
"quickfind.default_index", CyNetwork.NAME, String.class);
@@ -270,16 +277,8 @@
VisualStyle visualStyle =
cPathFactory.getBinarySifVisualStyleUtil().getVisualStyle();
mappingManager.setVisualStyle(visualStyle,
view);
-
- SwingUtilities.invokeLater(new Runnable() {
- public void run() {
- String
networkTitleWithUnderscores = networkTitle.replaceAll(": ", "");
- networkTitleWithUnderscores =
networkTitleWithUnderscores.replaceAll(" ", "_");
- CyNetworkNaming naming =
cPathFactory.getCyNetworkNaming();
- networkTitleWithUnderscores =
naming.getSuggestedNetworkTitle(networkTitleWithUnderscores);
- AttributeUtil.set(cyNetwork,
cyNetwork, CyNetwork.NAME, networkTitleWithUnderscores, String.class);
- }
- });
+ visualStyle.apply(view);
+ view.updateView();
}
}
}
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
2012-06-19 00:41:47 UTC (rev 29613)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/LoadNetworkFromUrlTask.java
2012-06-19 01:04:51 UTC (rev 29614)
@@ -59,7 +59,6 @@
*
* Modified version of the original LoadNetworkTask from cytoscape code.
*
- * TODO
*/
public class LoadNetworkFromUrlTask implements Task {
private final URL url;
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2012-06-19 00:41:47 UTC (rev 29613)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2012-06-19 01:04:51 UTC (rev 29614)
@@ -43,6 +43,7 @@
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Vector;
@@ -87,7 +88,6 @@
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.events.ColumnNameChangedEvent;
import org.cytoscape.model.events.ColumnNameChangedListener;
@@ -446,8 +446,7 @@
return Collections.emptyList();
}
- final Collection<CyColumn> columns = table.getColumns();
-
+ final Collection<CyColumn> columns = new
HashSet<CyColumn>(table.getColumns());
for (final CyColumn column : columns) {
if(column!= null){
// Show all attributes, with type of String or
Number
@@ -461,7 +460,6 @@
// Alphabetical sort
Collections.sort(attributeList);
}
-
}
// type conversion
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