Author: pwang
Date: 2013-03-04 15:54:29 -0800 (Mon, 04 Mar 2013)
New Revision: 31148
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOplugin.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BingoPluginAction.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/CyActivator.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/GOlorize/ZSelectNodes.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/HelpButtonActionListener.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
Log:
Updated
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOplugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOplugin.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BiNGOplugin.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -63,20 +63,22 @@
public class BiNGOplugin extends AbstractCySwingApp {
- private static final String CURRENT_WORKING_DIRECTORY = "user.dir";
- private static final String MENU_NAME = "Start bingo Plugin";
- private static final String MENU_CATEGORY = "Tools";
-
- private static final String WINDOW_TITLE = "bingo Settings";
+// private static final String CURRENT_WORKING_DIRECTORY = "user.dir";
+// private static final String MENU_NAME = "Start bingo Plugin";
+// private static final String MENU_CATEGORY = "Tools";
+//
+// private static final String WINDOW_TITLE = "bingo Settings";
+//
+//
+// private String bingoDir;
-
- private String bingoDir;
-
public BiNGOplugin(final CySwingAppAdapter adapter) {
super(adapter);
- adapter.getCySwingApplication().addAction(new
BingoPluginAction(adapter));
- String cwd = System.getProperty(CURRENT_WORKING_DIRECTORY);
- bingoDir = new File(cwd, "plugins").toString();
+// //Note: this class is NOT used, it was used as simple App only.
+
+// adapter.getCySwingApplication().addAction(new
BingoPluginAction(adapter));
+// String cwd = System.getProperty(CURRENT_WORKING_DIRECTORY);
+// bingoDir = new File(cwd, "plugins").toString();
}
}
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BingoPluginAction.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BingoPluginAction.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/BingoPluginAction.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -5,6 +5,8 @@
import javax.swing.JFrame;
import org.cytoscape.app.swing.CySwingAppAdapter;
import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.util.swing.OpenBrowser;
+
import bingo.internal.ui.SettingsPanel;
@@ -15,13 +17,15 @@
private static final String MENU_CATEGORY = "Tools";
private static final String WINDOW_TITLE = "bingo Settings";
private final CySwingAppAdapter adapter;
+ private final OpenBrowser openBrowserService;
private String bingoDir;
private static final long serialVersionUID = 4190390703299860130L;
// The constructor sets the text that should appear on the menu item.
- public BingoPluginAction(final CySwingAppAdapter adapter) {
+ public BingoPluginAction(final CySwingAppAdapter adapter, final
OpenBrowser openBrowserService) {
super(MENU_NAME);
this.adapter = adapter;
+ this.openBrowserService = openBrowserService;
setPreferredMenu(MENU_CATEGORY);
String cwd = System.getProperty(CURRENT_WORKING_DIRECTORY);
@@ -37,7 +41,7 @@
*/
public void actionPerformed(ActionEvent event) {
final JFrame window = new JFrame(WINDOW_TITLE);
- final SettingsPanel settingsPanel = new SettingsPanel(bingoDir,
(CySwingAppAdapter)adapter);
+ final SettingsPanel settingsPanel = new SettingsPanel(bingoDir,
(CySwingAppAdapter)adapter, openBrowserService);
window.getContentPane().add(settingsPanel);
window.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
window.pack();
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/CyActivator.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/CyActivator.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/CyActivator.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -6,6 +6,7 @@
import org.cytoscape.service.util.AbstractCyActivator;
import java.util.Properties;
import org.cytoscape.app.swing.CySwingAppAdapter;
+import org.cytoscape.util.swing.OpenBrowser;
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
@@ -15,8 +16,9 @@
public void start(BundleContext bc) {
CySwingAppAdapter adapter =
getService(bc,CySwingAppAdapter.class);
+ OpenBrowser openBrowserService =
getService(bc,OpenBrowser.class);
- BingoPluginAction bingoPluginAction = new
BingoPluginAction(adapter);
+ BingoPluginAction bingoPluginAction = new
BingoPluginAction(adapter, openBrowserService);
registerService(bc,bingoPluginAction,CyAction.class, new
Properties());
}
}
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/GOlorize/ZSelectNodes.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/GOlorize/ZSelectNodes.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/GOlorize/ZSelectNodes.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -80,7 +80,7 @@
final List<CyNode> nodes = model.getNodeList();
for (final CyNode node : nodes){
//node.getCyRow().set(CyNetwork.SELECTED,
false);
-
model.getDefaultNodeTable().getRow(node).set(CyNetwork.SELECTED, false);
+
model.getDefaultNodeTable().getRow(node.getSUID()).set(CyNetwork.SELECTED,
false);
}
final Set<CyNode> selectedNodesSet = new
HashSet<CyNode>();
@@ -93,7 +93,7 @@
final CyNode node = nodeView.getModel();
//final String nodeName =
node.getCyRow().get(CyNetwork.NAME, String.class);
- final String nodeName =
currentNetwork.getDefaultNodeTable().getRow(node).get(CyNetwork.NAME,
String.class);
+ final String nodeName =
currentNetwork.getDefaultNodeTable().getRow(node.getSUID()).get(CyNetwork.NAME,
String.class);
Set identifiers = alias.get(nodeName);
if (identifiers != null) {
@@ -122,7 +122,7 @@
for(final CyNode node: selectedNodesSet){
//node.getCyRow().set(CyNetwork.SELECTED, true);
-
currentNetwork.getDefaultNodeTable().getRow(node).set(CyNetwork.SELECTED, true);
+
currentNetwork.getDefaultNodeTable().getRow(node.getSUID()).set(CyNetwork.SELECTED,
true);
}
adapter.getCyEventHelper().flushPayloadEvents();
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/HelpButtonActionListener.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/HelpButtonActionListener.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/HelpButtonActionListener.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -36,6 +36,9 @@
import javax.swing.*;
+import org.cytoscape.app.swing.CySwingAppAdapter;
+import org.cytoscape.util.swing.OpenBrowser;
+
import bingo.internal.ui.SettingsPanel;
@@ -61,13 +64,17 @@
FIELD.
--------------------------------------------------------------*/
private SettingsPanel settingsPanel;
+ //private final CySwingAppAdapter adapter;
+ private final OpenBrowser openBrowserService;
/*--------------------------------------------------------------
CONSTRUCTOR.
--------------------------------------------------------------*/
- public HelpButtonActionListener(SettingsPanel settingsPanel) {
+ public HelpButtonActionListener(SettingsPanel settingsPanel, OpenBrowser
openBrowserService) {
this.settingsPanel = settingsPanel;
+ //this.adapter = adapter;
+ this.openBrowserService = openBrowserService;
}
@@ -85,13 +92,15 @@
/*JOptionPane.showMessageDialog(settingsPanel,
"For help, see website \n" +
"http://www.psb.ugent.be/cbd/papers/bingo";);*/
- try {
- //Browser link = new Browser() ;
- Browser.init();
- Browser.displayURL("http://www.psb.ugent.be/cbd/papers/bingo";);
- }
- catch (IOException ee) {
- JOptionPane.showMessageDialog(settingsPanel, "Could not open
website :" + ee);
- }
+// try {
+// //Browser link = new Browser() ;
+// Browser.init();
+// Browser.displayURL("http://www.psb.ugent.be/cbd/papers/bingo";);
+// }
+// catch (IOException ee) {
+// JOptionPane.showMessageDialog(settingsPanel, "Could not open
website :" + ee);
+// }
+
this.openBrowserService.openURL("http://www.psb.ugent.be/cbd/papers/BiNGO";);
+
}
}
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/SettingsPanelActionListener.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -777,7 +777,7 @@
for (CyNode node: nodes) {
// gets the canonical name of the given node from the
attributes object
//String canonicalName =
node.getCyRow().get(CyNetwork.NAME, String.class);
- String canonicalName =
network.getDefaultNodeTable().getRow(node).get(CyNetwork.NAME, String.class);
+ String canonicalName =
network.getDefaultNodeTable().getRow(node.getSUID()).get(CyNetwork.NAME,
String.class);
if (canonicalName != null && (canonicalName.length() !=
0) && !canonicalNameVector.contains(canonicalName)) {
if
(mapNames.contains(params.getAlias().get(canonicalName))) {
Modified:
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
===================================================================
---
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
2013-03-01 22:17:06 UTC (rev 31147)
+++
csplugins/trunk/ucsd/kono/bingo-impl/src/main/java/bingo/internal/ui/SettingsPanel.java
2013-03-04 23:54:29 UTC (rev 31148)
@@ -52,6 +52,7 @@
import javax.swing.JTextField;
import org.cytoscape.app.swing.CySwingAppAdapter;
+import org.cytoscape.util.swing.OpenBrowser;
import bingo.internal.BingoAlgorithm;
import bingo.internal.BingoParameters;
@@ -229,14 +230,16 @@
String ec_label = "Discard the following evidence codes:";
private final CySwingAppAdapter adapter;
+ private final OpenBrowser openBrowserService;
/**
* This constructor creates the panel with its swing-components.
*/
- public SettingsPanel(final String bingoDir, final CySwingAppAdapter
adapter) {
+ public SettingsPanel(final String bingoDir, final CySwingAppAdapter
adapter, OpenBrowser openBrowserService) {
super();
this.bingoDir = bingoDir;
this.adapter= adapter;
+ this.openBrowserService = openBrowserService;
// Create a new bingo parameter set
try {
@@ -404,7 +407,7 @@
helpButton = new JButton("Help");
helpButton.setMnemonic(KeyEvent.VK_H);
- helpButton.addActionListener(new
HelpButtonActionListener(this));
+ helpButton.addActionListener(new HelpButtonActionListener(this,
openBrowserService));
saveSettingsButton = new JButton("Save settings as default");
saveSettingsButton.setMnemonic(KeyEvent.VK_S);
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