Author: kono
Date: 2012-07-27 14:38:45 -0700 (Fri, 27 Jul 2012)
New Revision: 30027
Modified:
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/ValueEditor.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ObjectPositionValueEditor.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
core3/impl/trunk/swing-application-impl/pom.xml
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/AttributeTypeDialog.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/NetworkImportOptionsPanel.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/URLUtil.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/AbstractValueEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/BooleanValueEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/CyColorChooser.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/DiscreteValueEditor.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/FontEditor.java
Log:
Problems on Java 7 environment had been fixed.
Modified:
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/ValueEditor.java
===================================================================
---
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/ValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/ValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -27,6 +27,6 @@
*
* @return the type of value returned by the value editor.
*/
- Class<V> getType();
+ Class<V> getValueType();
}
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ObjectPositionValueEditor.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ObjectPositionValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/ObjectPositionValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -156,7 +156,7 @@
@Override
- public Class<ObjectPosition> getType() {
+ public Class<ObjectPosition> getValueType() {
return ObjectPosition.class;
}
}
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/editor/EdgeBendValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -180,7 +180,7 @@
}
@Override
- public Class<Bend> getType() {
+ public Class<Bend> getValueType() {
return Bend.class;
}
}
Modified: core3/impl/trunk/swing-application-impl/pom.xml
===================================================================
--- core3/impl/trunk/swing-application-impl/pom.xml 2012-07-27 19:56:05 UTC
(rev 30026)
+++ core3/impl/trunk/swing-application-impl/pom.xml 2012-07-27 21:38:45 UTC
(rev 30027)
@@ -92,6 +92,41 @@
</executions>
</plugin>
</plugins>
+ <pluginManagement>
+ <plugins>
+ <!--This plugin's configuration is used to
store Eclipse m2e settings only. It has no influence on the Maven build
itself.-->
+ <plugin>
+ <groupId>org.eclipse.m2e</groupId>
+
<artifactId>lifecycle-mapping</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <lifecycleMappingMetadata>
+ <pluginExecutions>
+
<pluginExecution>
+
<pluginExecutionFilter>
+
<groupId>
+
org.apache.maven.plugins
+
</groupId>
+
<artifactId>
+
maven-dependency-plugin
+
</artifactId>
+
<versionRange>
+
[2.1,)
+
</versionRange>
+
<goals>
+
<goal>unpack</goal>
+
</goals>
+
</pluginExecutionFilter>
+ <action>
+
<ignore></ignore>
+
</action>
+
</pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
</build>
<repositories>
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportAttributeTableReaderTask.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -6,6 +6,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.nio.channels.IllegalSelectorException;
import java.util.Set;
@@ -77,13 +78,14 @@
amp = new AttributeMappingParameters(new
FileInputStream(tempFile), fileType);
this.is = new FileInputStream(tempFile);
} catch (IOException e) {
- e.printStackTrace();
+ try {
+ is.close();
+ } catch (IOException e1) {
+ }
+
this.is = null;
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ throw new IllegalStateException("Could not initialize
object", e);
}
-
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/AttributeTypeDialog.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/AttributeTypeDialog.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/AttributeTypeDialog.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -457,7 +457,7 @@
*
* @return DOCUMENT ME!
*/
- public byte getType() {
+ byte getAttributeType() {
if
(delimiterButtonGroup.getSelection().equals(stringRadioButton.getModel())) {
return AttributeTypes.TYPE_STRING;
} else if
(delimiterButtonGroup.getSelection().equals(integerRadioButton.getModel())) {
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportTablePanel.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -1928,9 +1928,9 @@
try {
workbook = WorkbookFactory.create(tempIs);
} catch (InvalidFormatException e) {
- e.printStackTrace();
- throw new IllegalArgumentException("Could not
read Excel file. Maybe the file is broken?");
- }
+ tempIs.close();
+ throw new IllegalArgumentException("Could not
read Excel file. Maybe the file is broken?", e);
+ }
}
@@ -2101,11 +2101,19 @@
if (sourceURL.toString().startsWith("file:")) {
int fileSize = 0;
+ BufferedInputStream fis = null;
try {
- BufferedInputStream fis = (BufferedInputStream)
sourceURL.openStream();
+ fis = (BufferedInputStream)
sourceURL.openStream();
fileSize = fis.available();
+ fis.close();
} catch (IOException e) {
- e.printStackTrace();
+ if(fis!= null)
+ try {
+ fis.close();
+ } catch (IOException e1) {
+ // TODO Auto-generated catch
block
+ e1.printStackTrace();
+ }
}
if ((fileSize / 1000) == 0) {
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/NetworkImportOptionsPanel.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/NetworkImportOptionsPanel.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/NetworkImportOptionsPanel.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -147,7 +147,8 @@
public void
actionPerformed(java.awt.event.ActionEvent evt) {
networkColumnsComboBoxActionPerformed(evt);
- props.put("action", "set target interaction column");
+ final Map<String,String> props = new
HashMap<String,String>();
+ props.put("action", "set target
interaction column");
props.put("column", targetComboBox.getSelectedItem() ==
null ? null : targetComboBox.getSelectedItem().toString());
CytoscapeServices.eventAdmin.postEvent(new
Event("org/cytoscape/gettingstarted", props));
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/PreviewTablePanel.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -1140,7 +1140,7 @@
atd.setVisible(true);
final String name = atd.getName();
- final byte newType = atd.getType();
+ final byte newType = atd.getAttributeType();
final byte newListType = atd.getListDataType();
if (name != null) {
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/CytoscapeServices.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -2,24 +2,23 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyTableFactory;
import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
-import org.cytoscape.event.CyEventHelper;
import org.cytoscape.property.CyProperty;
-import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
+import org.cytoscape.util.swing.FileUtil;
+import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.swing.DialogTaskManager;
-import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.task.edit.MapGlobalToLocalTableTaskFactory;
-import org.cytoscape.util.swing.OpenBrowser;
-import org.cytoscape.util.swing.FileUtil;
-import org.cytoscape.io.util.StreamUtil;
import org.osgi.service.event.EventAdmin;
public class CytoscapeServices {
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/URLUtil.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/URLUtil.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/util/URLUtil.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -28,15 +28,12 @@
//import cytoscape.task.ui.JTask;
import java.io.File;
-import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
-
import java.net.MalformedURLException;
import java.net.Proxy;
import java.net.URL;
import java.net.URLConnection;
-
import java.util.jar.JarInputStream;
import java.util.zip.GZIPInputStream;
import java.util.zip.ZipInputStream;
@@ -45,10 +42,9 @@
*
*/
public class URLUtil {
+
private static final String GZIP = ".gz";
-
private static final String ZIP = ".zip";
-
private static final String JAR = ".jar";
private static int msConnectionTimeout = 2000;
@@ -235,11 +231,11 @@
while ((c = is.read()) != -1) {
buffer.append((char) c);
}
+ is.close();
}
finally {
- if (is != null) {
+ if (is != null)
is.close();
- }
}
return buffer.toString();
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/EditorManagerImpl.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -153,13 +153,13 @@
@Override
public void addValueEditor(ValueEditor<?> ve,
@SuppressWarnings("rawtypes") Map properties) {
- logger.debug("Got Value Editor " + ve.toString() + ", this is
for " + ve.getType() + "\n\n\n");
- this.valueEditors.put(ve.getType(), ve);
+ logger.debug("Got Value Editor " + ve.toString() + ", this is
for " + ve.getValueType() + "\n\n\n");
+ this.valueEditors.put(ve.getValueType(), ve);
}
public void removeValueEditor(ValueEditor<?> valueEditor,
@SuppressWarnings("rawtypes") Map properties) {
logger.debug("************* Removing Value Editor
****************");
- valueEditors.remove(valueEditor.getType());
+ valueEditors.remove(valueEditor.getValueType());
}
public void addVisualPropertyEditor(VisualPropertyEditor<?> ve,
@SuppressWarnings("rawtypes") Map properties) {
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/AbstractValueEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/AbstractValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/AbstractValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -12,7 +12,7 @@
protected final JOptionPane pane;
protected JDialog editorDialog;
- public AbstractValueEditor(Class<V> type) {
+ public AbstractValueEditor(final Class<V> type) {
this.type = type;
pane = new JOptionPane();
@@ -20,7 +20,7 @@
pane.setOptionType(JOptionPane.OK_CANCEL_OPTION);
}
- @Override public Class<V> getType() {
+ @Override public Class<V> getValueType() {
return type;
}
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/BooleanValueEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/BooleanValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/BooleanValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -26,7 +26,7 @@
}
@Override
- public Class<Boolean> getType() {
+ public Class<Boolean> getValueType() {
return Boolean.class;
}
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/CyColorChooser.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/CyColorChooser.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/CyColorChooser.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -73,7 +73,7 @@
}
}
- public Class<Paint> getType() {
+ public Class<Paint> getValueType() {
return Paint.class;
}
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/DiscreteValueEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/DiscreteValueEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/DiscreteValueEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -327,7 +327,7 @@
}
@Override
- public Class<T> getType() {
+ public Class<T> getValueType() {
return type;
}
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/FontEditor.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/FontEditor.java
2012-07-27 19:56:05 UTC (rev 30026)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/editor/valueeditor/FontEditor.java
2012-07-27 21:38:45 UTC (rev 30027)
@@ -120,7 +120,7 @@
return font;
}
- public Class<Font> getType() {
+ public Class<Font> getValueType() {
return Font.class;
}
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