Author: mes
Date: 2011-01-24 14:02:34 -0800 (Mon, 24 Jan 2011)
New Revision: 23579
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/CyOperatingContextImpl.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/ShutdownHandler.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/PreferenceAction.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/RedoAction.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/UndoAction.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/dialogs/PreferencesDialogImpl.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CyHelpBrokerImpl.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelImp.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelUtil.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
Log:
cleaned up printlns
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/CyOperatingContextImpl.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/CyOperatingContextImpl.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/CyOperatingContextImpl.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -45,6 +45,9 @@
import org.cytoscape.property.CyProperty;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Basic access to Cytoscape's operating context.
*/
@@ -56,6 +59,8 @@
public static final String CONFIG_DIR = ".cytoscape";
public static final String PROPS = "cytoscape.props";
+ private static final Logger logger =
LoggerFactory.getLogger(CyOperatingContextImpl.class);
+
private CyProperty<Properties> props;
public CyOperatingContextImpl(CyProperty<Properties> props) {
@@ -74,7 +79,7 @@
if (vmp != null)
props.getProperties().load(new FileInputStream(vmp));
else
- System.out.println("couldn't read " + PROPS + " from " +
CONFIG_DIR);
+ logger.warn("couldn't read " + PROPS + " from " + CONFIG_DIR);
} catch (IOException ioe) {
ioe.printStackTrace();
}
@@ -98,11 +103,11 @@
File parent_dir = new File(dirName, CONFIG_DIR);
if (parent_dir.mkdir())
- System.err.println("Parent_Dir: " + parent_dir + " created.");
+ logger.warn("Parent_Dir: " + parent_dir + " created.");
return parent_dir;
} catch (Exception e) {
- System.err.println("error getting config directory");
+ logger.warn("error getting config directory");
}
return null;
@@ -117,11 +122,11 @@
File file = new File(parent_dir, file_name);
if (file.createNewFile())
- System.err.println("Config file: " + file + "
created.");
+ logger.warn("Config file: " + file + "
created.");
return file;
} catch (Exception e) {
- System.err.println("error getting config file:" +
file_name);
+ logger.warn("error getting config file:" + file_name);
}
return null;
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/ShutdownHandler.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/ShutdownHandler.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/ShutdownHandler.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -43,11 +43,15 @@
import org.cytoscape.application.swing.events.CytoscapeShutdownListener;
import org.cytoscape.event.CyEventHelper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
*
*/
public class ShutdownHandler implements CytoscapeShutdown {
+ private static final Logger logger =
LoggerFactory.getLogger(ShutdownHandler.class);
private final CyEventHelper eh;
private boolean actuallyShutdown;
@@ -64,6 +68,6 @@
if ( ev.actuallyShutdown() )
System.exit(retVal);
else
- System.out.println("NOT shutting down, per listener
instruction: " + ev.whyNot() );
+ logger.info("NOT shutting down, per listener
instruction: " + ev.whyNot() );
}
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -50,7 +50,6 @@
public BookmarkAction(CySwingApplication desktop, CyApplicationManager
appMgr, BookmarkDialogFactoryImpl bookmarkDialogFactory) {
super("Bookmarks...", appMgr);
this.bookmarkDialogFactory = bookmarkDialogFactory;
- System.out.println("BookmarkAction()...");
setPreferredMenu("Edit.Preferences");
this.desktop = desktop;
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/PreferenceAction.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/PreferenceAction.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/PreferenceAction.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -66,7 +66,6 @@
super("Properties...",appMgr);
this.desktop = desktop;
this.pdf = pdf;
- System.out.println("PreferenceAction()...");
setPreferredMenu("Edit.Preferences");
setMenuGravity(10.0f);
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/RedoAction.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/RedoAction.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/RedoAction.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -48,6 +48,8 @@
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.work.undo.UndoSupport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* An action that calls redo for the most recent edit in the
@@ -57,6 +59,7 @@
private final static long serialVersionUID = 1202339875203626L;
private final UndoSupport undo;
+ private static final Logger logger =
LoggerFactory.getLogger(RedoAction.class);
/**
* Constructs the action.
@@ -79,7 +82,7 @@
if ( undo.getUndoManager().canRedo() )
undo.getUndoManager().redo();
} catch (CannotUndoException ex) {
- System.out.println("Unable to redo: " + ex);
+ logger.warn("Unable to redo: " + ex);
ex.printStackTrace();
}
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/UndoAction.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/UndoAction.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/actions/UndoAction.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -48,6 +48,8 @@
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.work.undo.UndoSupport;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* An action that calls undo for the most recent edit in the
@@ -56,6 +58,8 @@
public class UndoAction extends AbstractCyAction {
private final static long serialVersionUID = 1202339875212525L;
+ private final static Logger logger =
LoggerFactory.getLogger(UndoAction.class);
+
private UndoSupport undo;
/**
@@ -79,7 +83,7 @@
if ( undo.getUndoManager().canUndo() )
undo.getUndoManager().undo();
} catch (CannotUndoException ex) {
- System.out.println("Unable to undo: " + ex);
+ logger.warn("Unable to undo: " + ex);
ex.printStackTrace();
}
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/dialogs/PreferencesDialogImpl.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/dialogs/PreferencesDialogImpl.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/dialogs/PreferencesDialogImpl.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -70,12 +70,16 @@
import org.cytoscape.internal.CyOperatingContextImpl;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
*
*/
public class PreferencesDialogImpl extends JDialog {
private final static long serialVersionUID = 1202339873396288L;
+ private static final Logger logger =
LoggerFactory.getLogger(PreferencesDialogImpl.class);
int[] selection = null;
private Properties props;
@@ -407,11 +411,11 @@
File file =
context.getConfigFile("cytoscape.props");
FileOutputStream output = new
FileOutputStream(file);
props.store(output, "Cytoscape Property
File");
- System.out.println("wrote Cytoscape
properties file to: "
+ logger.debug("wrote Cytoscape
properties file to: "
+
file.getAbsolutePath());
} catch (Exception ex) {
ex.printStackTrace();
- System.out.println("Could not write
cytoscape.props file!");
+ logger.warn("Could not write
cytoscape.props file!");
}
saveCyPropsAsDefault = false;
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CyHelpBrokerImpl.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CyHelpBrokerImpl.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CyHelpBrokerImpl.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -42,7 +42,10 @@
import org.cytoscape.application.swing.CyHelpBroker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* This class creates the Cytoscape Help Broker for managing the JavaHelp
system
* and help set access
@@ -51,6 +54,7 @@
private HelpBroker hb;
private HelpSet hs;
private static final String HELP_RESOURCE =
"/cytoscape/help/jhelpset.hs";
+ private static final Logger logger =
LoggerFactory.getLogger(CyHelpBrokerImpl.class);
/**
* Creates a new CyHelpBroker object.
@@ -65,8 +69,7 @@
hs = new HelpSet(null, hsURL);
hb = hs.createHelpBroker();
} catch (Exception e) {
- System.out.println("HelpSet " + e.getMessage());
- System.out.println("HelpSet " + hs + " not found.");
+ logger.warn("HelpSet not found!",e);
}
}
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelImp.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelImp.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelImp.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -69,6 +69,8 @@
import org.cytoscape.application.swing.events.CytoPanelStateChangedEvent;
import org.cytoscape.event.CyEventHelper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* The CytoPanel class extends JPanel to provide the following functionality:
@@ -82,6 +84,8 @@
*/
public class CytoPanelImp extends JPanel implements CytoPanel, ChangeListener {
private final static long serialVersionUID = 1202339868245830L;
+ private final static Logger logger =
LoggerFactory.getLogger(CytoPanelImp.class);
+
/**
* The JTabbedPane we hide.
*/
@@ -655,10 +659,7 @@
// add this cytopanel back to cytopanel container
if (cytoPanelContainer == null) {
- System.out.println("CytoPanel::DockCytoPanel()
-"
- + "cytoPanelContainer
reference has not been set!");
- // TODO Is this possibly right?
- //Cytoscape.exit(1);
+ logger.warn("cytoPanelContainer reference has
not been set!");
}
cytoPanelContainer.insertCytoPanel(this,
compassDirection);
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelUtil.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelUtil.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/CytoPanelUtil.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -36,6 +36,7 @@
import java.awt.*;
+
/**
* Contains methods to assist with various
* tasks performed by the CytoPanel API.
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-01-24 21:49:15 UTC (rev 23578)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-01-24 22:02:34 UTC (rev 23579)
@@ -381,7 +381,7 @@
try {
presentationContainerMap.get(view.getModel().getSUID()).dispose();
} catch (Exception e) {
- System.err.println("Network View unable to be killed");
+ logger.error("Network View unable to be killed",e);
}
presentationContainerMap.remove(view.getModel().getSUID());
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