Author: mes
Date: 2011-07-22 12:26:33 -0700 (Fri, 22 Jul 2011)
New Revision: 26253
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/pom.xml
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DeleteFileInGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DownloadFileFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/ListFilesInGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadAttrsFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadNetworkFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadOntologyAndAnnotationFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadSessionFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableAttrsFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableNetworkFromGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveNetworkToGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveSessionToGenomeSpace.java
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/UploadFileToGenomeSpace.java
Log:
some minor updates towards 3.0
Modified: csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/pom.xml
===================================================================
--- csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/pom.xml
2011-07-22 19:08:26 UTC (rev 26252)
+++ csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/pom.xml
2011-07-22 19:26:33 UTC (rev 26253)
@@ -89,12 +89,12 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
- <version>3.0.0-alpha2</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
</dependency>
<!-- Logging -->
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DeleteFileInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DeleteFileInGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DeleteFileInGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -2,9 +2,9 @@
import cytoscape.Cytoscape;
-import cytoscape.util.CytoscapeAction;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
-import cytoscape.logger.CyLogger;
+import org.slf4j.Logger;
import java.awt.FileDialog;
import java.awt.event.ActionEvent;
@@ -22,7 +22,7 @@
import org.genomespace.client.ui.GSFileBrowserDialog;
-public class DeleteFileInGenomeSpace extends CytoscapeAction {
+public class DeleteFileInGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 4234432889999989L;
private static final CyLogger logger =
CyLogger.getLogger(DeleteFileInGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DownloadFileFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DownloadFileFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/DownloadFileFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -2,8 +2,8 @@
import cytoscape.Cytoscape;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import java.awt.FileDialog;
import java.awt.event.ActionEvent;
@@ -28,7 +28,7 @@
* then fill in your expected behavior in the actionPerformed()
* method.
*/
-public class DownloadFileFromGenomeSpace extends CytoscapeAction {
+public class DownloadFileFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7777788473487659L;
private static final CyLogger logger =
CyLogger.getLogger(DownloadFileFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/ListFilesInGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/ListFilesInGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/ListFilesInGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -3,9 +3,9 @@
import cytoscape.Cytoscape;
import org.cytoscape.genomespace.internal.filechoosersupport.GenomeSpaceTree;
-import cytoscape.util.CytoscapeAction;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
-import cytoscape.logger.CyLogger;
+import org.slf4j.Logger;
import java.awt.Component;
import java.awt.event.ActionEvent;
@@ -36,7 +36,7 @@
* then fill in your expected behavior in the actionPerformed()
* method.
*/
-public class ListFilesInGenomeSpace extends CytoscapeAction {
+public class ListFilesInGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 1234487711999989L;
private static final CyLogger logger =
CyLogger.getLogger(ListFilesInGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadAttrsFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadAttrsFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadAttrsFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -4,8 +4,8 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.readers.CyAttributesReader;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import java.awt.event.ActionEvent;
import java.io.File;
@@ -21,7 +21,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadAttrsFromGenomeSpace extends CytoscapeAction {
+public class LoadAttrsFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7577788473487659L;
private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadNetworkFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadNetworkFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadNetworkFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -6,8 +6,8 @@
import cytoscape.data.readers.GMLReader;
import cytoscape.data.readers.InteractionsReader;
import cytoscape.data.readers.XGMMLReader;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
import java.awt.event.ActionEvent;
@@ -24,7 +24,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadNetworkFromGenomeSpace extends CytoscapeAction {
+public class LoadNetworkFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7577788473487659L;
private static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadOntologyAndAnnotationFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadOntologyAndAnnotationFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadOntologyAndAnnotationFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -4,8 +4,8 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.readers.CyAttributesReader;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
@@ -24,7 +24,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadOntologyAndAnnotationFromGenomeSpace extends CytoscapeAction {
+public class LoadOntologyAndAnnotationFromGenomeSpace extends AbstractCyAction
{
private static final long serialVersionUID = 7571788473486759L;
private static final CyLogger logger =
CyLogger.getLogger(LoadOntologyAndAnnotationFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadSessionFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadSessionFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadSessionFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -6,12 +6,12 @@
import cytoscape.data.readers.CyAttributesReader;
import cytoscape.data.readers.CytoscapeSessionReader;
import cytoscape.data.readers.XGMMLException;
-import cytoscape.logger.CyLogger;
+import org.slf4j.Logger;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
-import cytoscape.util.CytoscapeAction;
+import org.cytoscape.application.swing.AbstractCyAction;
import java.awt.Frame;
import java.awt.event.ActionEvent;
@@ -31,7 +31,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadSessionFromGenomeSpace extends CytoscapeAction {
+public class LoadSessionFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7577788473487659L;
static final CyLogger logger =
CyLogger.getLogger(LoadNetworkFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableAttrsFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableAttrsFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableAttrsFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -4,8 +4,8 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.readers.CyAttributesReader;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
@@ -24,7 +24,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadTableAttrsFromGenomeSpace extends CytoscapeAction {
+public class LoadTableAttrsFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7572758437487659L;
private static final CyLogger logger =
CyLogger.getLogger(LoadTableAttrsFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableNetworkFromGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableNetworkFromGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/LoadTableNetworkFromGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -4,8 +4,8 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.readers.CyAttributesReader;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import edu.ucsd.bioeng.coreplugin.tableImport.ui.ImportTextTableDialog;
@@ -24,7 +24,7 @@
import org.genomespace.datamanager.core.GSFileMetadata;
-public class LoadTableNetworkFromGenomeSpace extends CytoscapeAction {
+public class LoadTableNetworkFromGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 7577788473487659L;
private static final CyLogger logger =
CyLogger.getLogger(LoadTableNetworkFromGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveNetworkToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveNetworkToGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveNetworkToGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -3,12 +3,12 @@
import cytoscape.Cytoscape;
import cytoscape.data.writers.CytoscapeSessionWriter;
-import cytoscape.logger.CyLogger;
+import org.slf4j.Logger;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
-import cytoscape.util.CytoscapeAction;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
import java.awt.FileDialog;
@@ -31,7 +31,7 @@
* then fill in your expected behavior in the actionPerformed()
* method.
*/
-public class SaveNetworkToGenomeSpace extends CytoscapeAction {
+public class SaveNetworkToGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 9988760123456789L;
private static final CyLogger logger =
CyLogger.getLogger(UploadFileToGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveSessionToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveSessionToGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/SaveSessionToGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -3,12 +3,12 @@
import cytoscape.Cytoscape;
import cytoscape.data.writers.CytoscapeSessionWriter;
-import cytoscape.logger.CyLogger;
+import org.slf4j.Logger;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
-import cytoscape.util.CytoscapeAction;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
import java.awt.FileDialog;
@@ -32,7 +32,7 @@
* then fill in your expected behavior in the actionPerformed()
* method.
*/
-public class SaveSessionToGenomeSpace extends CytoscapeAction {
+public class SaveSessionToGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 9988760123456789L;
private static final CyLogger logger =
CyLogger.getLogger(UploadFileToGenomeSpace.class);
Modified:
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/UploadFileToGenomeSpace.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/UploadFileToGenomeSpace.java
2011-07-22 19:08:26 UTC (rev 26252)
+++
csplugins/trunk/ucsd/ruschein/genomespace-plugin-cytoscape3/src/main/java/org/cytoscape/genomespace/internal/UploadFileToGenomeSpace.java
2011-07-22 19:26:33 UTC (rev 26253)
@@ -2,8 +2,8 @@
import cytoscape.Cytoscape;
-import cytoscape.logger.CyLogger;
-import cytoscape.util.CytoscapeAction;
+import org.slf4j.Logger;
+import org.cytoscape.application.swing.AbstractCyAction;
import cytoscape.util.FileUtil;
import java.awt.FileDialog;
@@ -25,7 +25,7 @@
* then fill in your expected behavior in the actionPerformed()
* method.
*/
-public class UploadFileToGenomeSpace extends CytoscapeAction {
+public class UploadFileToGenomeSpace extends AbstractCyAction {
private static final long serialVersionUID = 9988760123456789L;
private static final CyLogger logger =
CyLogger.getLogger(UploadFileToGenomeSpace.class);
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