Author: mmichaud
Date: 2009-03-20 09:50:27 -0700 (Fri, 20 Mar 2009)
New Revision: 16316

Modified:
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/AbstractGuiHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BooleanHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedDoubleHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedFloatHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedIntegerHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedLongHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/DoubleHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FloatHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiHandlerFactory.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiTunableInterceptor.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/Guihandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/InputStreamHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/IntegerHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListMultipleHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListSingleHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/LongHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
   
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
Log:


Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/AbstractGuiHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/AbstractGuiHandler.java
      2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/AbstractGuiHandler.java
      2009-03-20 16:50:27 UTC (rev 16316)
@@ -27,7 +27,7 @@
 
        private java.util.List<Guihandler> deps;
 
-       public AbstractGuiHandler(Field f, Object o, Tunable t) {
+       protected AbstractGuiHandler(Field f, Object o, Tunable t) {
                super(f,o,t);   
         String s = t.dependsOn();
         if ( !s.equals("") ) {

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BooleanHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BooleanHandler.java
  2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BooleanHandler.java
  2009-03-20 16:50:27 UTC (rev 16316)
@@ -18,7 +18,7 @@
        JCheckBox jcb;
        Boolean myBoolean;
        
-       public BooleanHandler(Field f, Object o, Tunable t) {
+       protected BooleanHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
        
                try{

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedDoubleHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedDoubleHandler.java
    2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedDoubleHandler.java
    2009-03-20 16:50:27 UTC (rev 16316)
@@ -21,7 +21,7 @@
        mySlider slider;
        myBoundedSwing boundedField;
        
-       public BoundedDoubleHandler(Field f, Object o, Tunable t) {
+       protected BoundedDoubleHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
                        this.myBounded = (BoundedDouble)f.get(o);

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedFloatHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedFloatHandler.java
     2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedFloatHandler.java
     2009-03-20 16:50:27 UTC (rev 16316)
@@ -26,7 +26,7 @@
        String newline = System.getProperty("line.separator");
        Double value=null;
        
-       public BoundedFloatHandler(Field f, Object o, Tunable t) {
+       protected BoundedFloatHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
                        this.myBounded = (BoundedFloat)f.get(o);

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedIntegerHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedIntegerHandler.java
   2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedIntegerHandler.java
   2009-03-20 16:50:27 UTC (rev 16316)
@@ -22,7 +22,7 @@
        mySlider slider;
        myBoundedSwing boundedField;
        
-       public BoundedIntegerHandler(Field f, Object o, Tunable t) {
+       protected BoundedIntegerHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
                        this.myBounded = (BoundedInteger)f.get(o);

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedLongHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedLongHandler.java
      2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/BoundedLongHandler.java
      2009-03-20 16:50:27 UTC (rev 16316)
@@ -23,7 +23,7 @@
        mySlider slider;
        myBoundedSwing boundedField;
        
-       public BoundedLongHandler(Field f, Object o, Tunable t) {
+       protected BoundedLongHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
                        this.myBounded = (BoundedLong)f.get(o);
@@ -38,7 +38,6 @@
                        label.setFont(new Font(null, Font.PLAIN,12));
                        panel.add(label,BorderLayout.WEST);
                        slider = new 
mySlider(title,myBounded.getLowerBound(),myBounded.getUpperBound(),myBounded.getValue(),myBounded.isLowerBoundStrict(),myBounded.isUpperBoundStrict());
-                       //slider.addChangeListener(this);
                        panel.add(slider,BorderLayout.EAST);
                }
                else{

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/DoubleHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/DoubleHandler.java
   2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/DoubleHandler.java
   2009-03-20 16:50:27 UTC (rev 16316)
@@ -9,7 +9,6 @@
 import org.cytoscape.work.Tunable;
 
 
-
 public class DoubleHandler extends AbstractGuiHandler {
 
        JTextField jtf;
@@ -18,35 +17,32 @@
        String newline = System.getProperty("line.separator");
 
 
-       public DoubleHandler(Field f, Object o, Tunable t) {
+       protected DoubleHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try{
                        this.myDouble=(Double)f.get(o);
                }catch(Exception e){e.printStackTrace();}
-               
                panel = new JPanel(new BorderLayout());
                JLabel label = new JLabel(t.description());
                label.setFont(new Font(null, Font.PLAIN,12));
                panel.add(label,BorderLayout.WEST);
                try {
                        jtf = new JTextField(f.get(o).toString(), 10);
-                       //jtf.addActionListener(this);
-                       jtf.setHorizontalAlignment(JTextField.RIGHT);
-                       panel.add(jtf,BorderLayout.EAST);
                } catch (Exception e) { e.printStackTrace(); }
-                       
+               jtf.setHorizontalAlignment(JTextField.RIGHT);
+               panel.add(jtf,BorderLayout.EAST);                       
        }
 
        public void handle() {
+               jtf.setBackground(Color.white);
                try{
-                       jtf.setBackground(Color.white);
                        value = Double.parseDouble(jtf.getText());
                }catch(NumberFormatException nfe){
+                       jtf.setBackground(Color.red);
                        try{
-                               jtf.setBackground(Color.red);
                                value = Double.parseDouble(f.get(o).toString());
-                               JOptionPane.showMessageDialog(null,"A double 
was Expected"+newline+"Value will be set to default = "+value.doubleValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                        }catch(Exception e){e.printStackTrace();}
+                       JOptionPane.showMessageDialog(null,"A double was 
Expected"+newline+"Value will be set to default = "+value.doubleValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                }
                try {
                        f.set(o,value.doubleValue());

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
     2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FileHandler.java
     2009-03-20 16:50:27 UTC (rev 16316)
@@ -15,17 +15,17 @@
 
 public class FileHandler extends AbstractGuiHandler {
 
-       JButton button;
        File myFile;
-       JFileChooser fileChooser;
-       boolean filechoosen;
-       JTextField networkFileTextField;
+       private JFileChooser fileChooser;
+       private JButton button;
+       private boolean filechoosen;
+       private JTextField networkFileTextField;
+       private ImageIcon image;
+       private JLabel titleLabel;
+       private JSeparator titleSeparator;
        //FileUtil flUtil;
-       ImageIcon image;
-       JLabel titleLabel;
-       JSeparator titleSeparator;
        
-       public FileHandler(Field f, Object o, Tunable t) {
+       protected FileHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                //this.flUtil = flUtil;
                filechoosen = false;
@@ -49,8 +49,7 @@
                GroupLayout layout = new GroupLayout(panel);
                panel.setLayout(layout);
                
layout.setHorizontalGroup(layout.createParallelGroup(GroupLayout.LEADING)
-                               .add(
-                                       layout.createSequentialGroup()
+                               .add(layout.createSequentialGroup()
                                                .addContainerGap()
                                                
.add(layout.createParallelGroup(GroupLayout.LEADING)
                                                        
.add(titleLabel,GroupLayout.PREFERRED_SIZE,350,GroupLayout.PREFERRED_SIZE)
@@ -90,20 +89,19 @@
                                                )
                                                .addContainerGap()));
                
-layout.setVerticalGroup(layout.createParallelGroup(GroupLayout.LEADING)
+               
layout.setVerticalGroup(layout.createParallelGroup(GroupLayout.LEADING)
                                .add(layout.createSequentialGroup()
                                                .addContainerGap()
                                                .add(titleLabel)
                                                .add(8, 8, 8)
                                                
.add(titleSeparator,GroupLayout.PREFERRED_SIZE,GroupLayout.DEFAULT_SIZE,GroupLayout.PREFERRED_SIZE)
-                                                               .add(7, 7, 7)
-                                                               
.addPreferredGap(LayoutStyle.RELATED)
-                                                               
.add(layout.createParallelGroup(GroupLayout.BASELINE)
-                                                                               
.add(button)
-                                                                               
.add(networkFileTextField))
-                                                               
.addPreferredGap(LayoutStyle.RELATED,3, Short.MAX_VALUE)
-                                                               
.addContainerGap()));
-//             panel.add(button);                      
+                                               .add(7, 7, 7)
+                                               
.addPreferredGap(LayoutStyle.RELATED)
+                                               
.add(layout.createParallelGroup(GroupLayout.BASELINE)
+                                                               .add(button)
+                                                               
.add(networkFileTextField))
+                                               
.addPreferredGap(LayoutStyle.RELATED,3, Short.MAX_VALUE)
+                                               .addContainerGap()));
        }
 
        

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FloatHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FloatHandler.java
    2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/FloatHandler.java
    2009-03-20 16:50:27 UTC (rev 16316)
@@ -16,35 +16,32 @@
        String newline = System.getProperty("line.separator");
 
 
-       public FloatHandler(Field f, Object o, Tunable t) {
+       protected FloatHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try{
                        this.myFloat=(Float)f.get(o);
                }catch(Exception e){e.printStackTrace();}
-               
                panel = new JPanel(new BorderLayout());
                JLabel label = new JLabel(t.description());
                label.setFont(new Font(null, Font.PLAIN,12));
                panel.add(label,BorderLayout.WEST);
                try {
                        jtf = new JTextField(f.get(o).toString(), 10);
-                       //jtf.addActionListener(this);
-                       jtf.setHorizontalAlignment(JTextField.RIGHT);
-                       panel.add(jtf,BorderLayout.EAST);
                } catch (Exception e) { e.printStackTrace(); }
-                       
+               jtf.setHorizontalAlignment(JTextField.RIGHT);
+               panel.add(jtf,BorderLayout.EAST);
        }
 
        public void handle() {
+               jtf.setBackground(Color.white);
                try{
-                       jtf.setBackground(Color.white);
                        value = Double.parseDouble(jtf.getText());
                }catch(NumberFormatException nfe){
+                       jtf.setBackground(Color.red);
                        try{
-                               jtf.setBackground(Color.red);
                                value = Double.parseDouble(f.get(o).toString());
-                               JOptionPane.showMessageDialog(null,"A float was 
Expected"+newline+"Value will be set to default = "+value.floatValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                        }catch(Exception e){e.printStackTrace();}
+               JOptionPane.showMessageDialog(null,"A float was 
Expected"+newline+"Value will be set to default = "+value.floatValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                }
                try {
                        f.set(o,value.floatValue());

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiHandlerFactory.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiHandlerFactory.java
       2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiHandlerFactory.java
       2009-03-20 16:50:27 UTC (rev 16316)
@@ -22,6 +22,7 @@
 import cytoscape.util.FileUtil;
 import org.cytoscape.io.util.StreamUtil;
 
+
 public class GuiHandlerFactory implements HandlerFactory<Guihandler> {
 
        private Bookmarks bookmarks;

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiTunableInterceptor.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiTunableInterceptor.java
   2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/GuiTunableInterceptor.java
   2009-03-20 16:50:27 UTC (rev 16316)
@@ -24,7 +24,6 @@
        private Component parent=null;
        private Map<java.util.List<Guihandler>,JPanel> panelMap;
        private java.util.List<Guihandler> lh;
-       private boolean m;
        
        public GuiTunableInterceptor(HandlerFactory<Guihandler> factory) {
                super( factory );
@@ -43,8 +42,6 @@
 
        public boolean createUI(Object... proxyObjs) {
                Object[] objs = convertSpringProxyObjs( proxyObjs );
-
-               //java.util.List<Guihandler> lh = new ArrayList<Guihandler>();
                lh = new ArrayList<Guihandler>();
                for ( Object o : objs ) {
                        if ( !handlerMap.containsKey( o ) )
@@ -98,16 +95,15 @@
 
 
                if(parent==null){
-               //Custom button text
-               Object[] buttons = {"OK","Cancel"};
-               int n = JOptionPane.showOptionDialog(parent,
-                   panelMap.get(lh),
-                   "Set Parameters",
-                   JOptionPane.YES_NO_CANCEL_OPTION,
-                   JOptionPane.PLAIN_MESSAGE,
-                   null,
-                   buttons,
-                   buttons[0]);
+                       Object[] buttons = {"OK","Cancel"};
+                       int n = JOptionPane.showOptionDialog(parent,
+                                       panelMap.get(lh),
+                                       "Set Parameters",
+                                       JOptionPane.YES_NO_CANCEL_OPTION,
+                                       JOptionPane.PLAIN_MESSAGE,
+                                       null,
+                                       buttons,
+                                       buttons[0]);
 
                        if ( n == JOptionPane.OK_OPTION ){
                                for ( Guihandler h : lh ) h.handle();
@@ -115,7 +111,6 @@
                        }
                        else
                                return false;
-               
                }
                else{
                        int nbPanel = ((Container) 
parent).getComponentCount()-1;

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/Guihandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/Guihandler.java
      2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/Guihandler.java
      2009-03-20 16:50:27 UTC (rev 16316)
@@ -6,7 +6,7 @@
 import org.cytoscape.work.Handler;
 
 public interface Guihandler extends Handler{
-       public void handle();
+       void handle();
        JPanel getJPanel();
        String getState();
        String getName();

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/InputStreamHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/InputStreamHandler.java
      2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/InputStreamHandler.java
      2009-03-20 16:50:27 UTC (rev 16316)
@@ -3,6 +3,7 @@
 
 import java.awt.Component;
 import java.awt.Font;
+import java.awt.Insets;
 import java.awt.event.ActionListener;
 import java.io.File;
 import java.io.FileInputStream;
@@ -23,28 +24,22 @@
 
 public class InputStreamHandler extends AbstractGuiHandler {
 
-       Bookmarks theBookmarks;
-       String bookmarkCategory = "network";
-       String urlstr;
-       BookmarkComboBoxEditor bookmarkEditor = new BookmarkComboBoxEditor();
-       JComboBox networkFileComboBox;
-       //FileUtil flUtil;
-       BookmarksUtil bkUtil;
-       //StreamUtil stUtil;
-       
-       InputStream InStream = null;
+       InputStream InStream;
        URL url;
-       JButton button;
        File myFile;
-       JFileChooser fileChooser;
-       boolean filechoosen;
-       JTextField path;
-       private javax.swing.JSeparator titleSeparator;
        
+       private Bookmarks theBookmarks;
+       private BookmarkComboBoxEditor bookmarkEditor;
+       private BookmarksUtil bkUtil;
+       private String bookmarkCategory = "network";
+       private String urlstr;
+       private JComboBox networkFileComboBox;
+       private JFileChooser fileChooser;
+       private boolean filechoosen;
+       private JSeparator titleSeparator;
        private String pleaseMessage = "Please provide URL or select from list";
-       
-       //private JPanel valuePanel;
-       private JLabel titleLabel = new JLabel("Import Network File");
+
+       private JLabel titleLabel;
        private JPanel radioButtonPanel;
        private JButton selectButton;
        private JRadioButton remoteRadioButton;
@@ -53,16 +48,19 @@
        private static final String URL_TOOLTIP = "<html>Enter URL or 
<strong><font color=\"red\">Drag and Drop local/remote 
files.</font></strong></html>";
        private static final String LOCAL_TOOLTIP = "<html>Specify path to 
local files.</html>";
 
+       //FileUtil flUtil;
+       //StreamUtil stUtil;
        
-       public InputStreamHandler(Field f, Object o, Tunable t,Bookmarks 
bookmarks,BookmarksUtil bkUtil) {
+       protected InputStreamHandler(Field f, Object o, Tunable t,Bookmarks 
bookmarks,BookmarksUtil bkUtil) {
                super(f,o,t);
                this.bkUtil=bkUtil;
                //this.flUtil=flUtil;
                //this.stUtil=stUtil;
+               titleLabel = new JLabel("Import Network File");
                this.theBookmarks=bookmarks;
                filechoosen = false;
                fileChooser = new JFileChooser();
-               
+               bookmarkEditor = new BookmarkComboBoxEditor();
                try{
                        this.InStream = (InputStream) f.get(o);
                }catch(Exception e){e.printStackTrace();}
@@ -71,24 +69,12 @@
                if (theCategory == null) {
                        theCategory = new Category();
                        theCategory.setName(bookmarkCategory);
-
                        List<Category> theCategoryList = 
bookmarks.getCategory();
                        theCategoryList.add(theCategory);
                }
-               
-
-               //panel.add(new JLabel("Path :"));
-               //path = new JTextField("select file",12);
-               //path.setFont(new Font(null, Font.ITALIC,10));
-               //panel.add(path);
-
                initComponents();
                addListeners();
-               switchImportView("remote");
-               
-               //panel = new JPanel(new BorderLayout());
-               //panel.add(radioButtonPanel,BorderLayout.NORTH);
-               //panel.add(valuePanel,BorderLayout.SOUTH);
+               switchImportView("local");              
        }
        
        
@@ -139,38 +125,28 @@
     
     
     private void initComponents() {
-               localRadioButton = new javax.swing.JRadioButton();
-               remoteRadioButton = new javax.swing.JRadioButton();
-               networkFileTextField = new javax.swing.JTextField();
-               networkFileComboBox = new javax.swing.JComboBox();
-               selectButton = new javax.swing.JButton();
+               localRadioButton = new JRadioButton();
+               remoteRadioButton = new JRadioButton();
+               networkFileTextField = new JTextField();
+               networkFileComboBox = new JComboBox();
+               selectButton = new JButton();
                titleSeparator = new JSeparator();
-               radioButtonPanel = new javax.swing.JPanel();
-               //valuePanel = new javax.swing.JPanel();
-
+               radioButtonPanel = new JPanel();
                
radioButtonPanel.setBorder(BorderFactory.createTitledBorder("Data Source 
Type"));
                
                localRadioButton.setSelected(true);
                localRadioButton.setText("Local");
-               
localRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 
0));
-               localRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+               localRadioButton.setBorder(BorderFactory.createEmptyBorder(0, 
0, 0, 0));
+               localRadioButton.setMargin(new Insets(0, 0, 0, 0));
                localRadioButton.setToolTipText(LOCAL_TOOLTIP);
 
                remoteRadioButton.setText("Remote/URL");
-               
remoteRadioButton.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 
0, 0));
-               remoteRadioButton.setMargin(new java.awt.Insets(0, 0, 0, 0));
+               remoteRadioButton.setBorder(BorderFactory.createEmptyBorder(0, 
0, 0, 0));
+               remoteRadioButton.setMargin(new Insets(0, 0, 0, 0));
                remoteRadioButton.setToolTipText(URL_TOOLTIP);
-
-       
-               //radioButtonPanel.add(localRadioButton);
-               //radioButtonPanel.add(remoteRadioButton);
-               //valuePanel.add(networkFileTextField);
-               //valuePanel.add(selectButton);
-               //valuePanel.add(networkFileComboBox);
                
                networkFileTextField.setText("Please select a network file...");
                networkFileTextField.setName("networkFileTextField");
-               //networkFileTextField.addFocusListener(this);
 
                selectButton.setText("Select");
 
@@ -305,16 +281,11 @@
                LocalRemoteListener l = new LocalRemoteListener();
                localRadioButton.addActionListener(l);
                remoteRadioButton.addActionListener(l);
-
-               // ButtonActionListener btnActionListener = new 
ButtonActionListener();
                selectButton.addActionListener(this);
-               //bookmarkEditor.addActionListener(this);
        }
 
     
     
-    
-    
        private void switchImportView(String pLocation) {
                if (pLocation.equalsIgnoreCase("Local")) {
                        networkFileComboBox.setVisible(false);
@@ -334,7 +305,7 @@
     
        
        
-       class LocalRemoteListener implements java.awt.event.ActionListener {
+       private class LocalRemoteListener implements ActionListener {
                public void actionPerformed(java.awt.event.ActionEvent e) {
                        Object _actionObject = e.getSource();
 
@@ -353,7 +324,7 @@
        }
     
     
-       class BookmarkComboBoxEditor implements ComboBoxEditor {
+       private class BookmarkComboBoxEditor implements ComboBoxEditor {
                DataSource theDataSource = new DataSource();
                JTextField tfInput = new JTextField(pleaseMessage);
                
@@ -414,7 +385,7 @@
        }
 
        
-       class MyCellRenderer extends JLabel implements ListCellRenderer {
+       private class MyCellRenderer extends JLabel implements ListCellRenderer 
{
                private final static long serialVersionUID = 1202339872997986L;
                public MyCellRenderer() {
                        setOpaque(true);

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/IntegerHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/IntegerHandler.java
  2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/IntegerHandler.java
  2009-03-20 16:50:27 UTC (rev 16316)
@@ -15,37 +15,34 @@
        Double value = null;
        Integer myInteger;
        String newline = System.getProperty("line.separator");
-
-
-       public IntegerHandler(Field f, Object o, Tunable t) {
+       
+       
+       protected IntegerHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try{
                        this.myInteger=(Integer)f.get(o);
                }catch(Exception e){e.printStackTrace();}
-               
                panel = new JPanel(new BorderLayout());
                JLabel label = new JLabel(t.description());
                label.setFont(new Font(null, Font.PLAIN,12));
                panel.add(label,BorderLayout.WEST );
                try {
                        jtf = new JTextField(f.get(o).toString(), 10);
-                       //jtf.addActionListener( this );
-                       jtf.setHorizontalAlignment(JTextField.RIGHT);
-                       panel.add(jtf,BorderLayout.EAST);
                } catch (Exception e) { e.printStackTrace(); }
-                       
+               jtf.setHorizontalAlignment(JTextField.RIGHT);
+               panel.add(jtf,BorderLayout.EAST);                       
        }
 
        public void handle() {
+               jtf.setBackground(Color.white);
                try{
-                       jtf.setBackground(Color.white);
                        value = Double.parseDouble(jtf.getText());
                }catch(NumberFormatException nfe){
+                       jtf.setBackground(Color.red);
                        try{
-                               jtf.setBackground(Color.red);
                                value = Double.parseDouble(f.get(o).toString());
-                               JOptionPane.showMessageDialog(null,"An Integer 
was Expected"+newline+"Value will be set to default = "+value.intValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                        }catch(Exception e){e.printStackTrace();}
+               JOptionPane.showMessageDialog(null,"An Integer was 
Expected"+newline+"Value will be set to default = "+value.intValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                }
                try {
                        f.set(o,value.intValue());

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListMultipleHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListMultipleHandler.java
     2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListMultipleHandler.java
     2009-03-20 16:50:27 UTC (rev 16316)
@@ -23,12 +23,11 @@
 
        
        @SuppressWarnings("unchecked")
-       public ListMultipleHandler(Field f, Object o, Tunable t) {
+       protected ListMultipleHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
             lms = (ListMultipleSelection<T>) f.get(o);
         } catch(Exception e) {e.printStackTrace();}
-       
         panel = new JPanel(new BorderLayout());
         JTextArea jta = new JTextArea(t.description());
         jta.setLineWrap(true);
@@ -58,7 +57,7 @@
        }
        
        
-       public List<T> convertToArray(Object[] in){
+       private List<T> convertToArray(Object[] in){
                List<T> list = new ArrayList<T>();
                if(in.length!=0){
                        for(int i=0;i<in.length;i++){

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListSingleHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListSingleHandler.java
       2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/ListSingleHandler.java
       2009-03-20 16:50:27 UTC (rev 16316)
@@ -17,7 +17,7 @@
        T selected;
 
        @SuppressWarnings("unchecked")
-       public ListSingleHandler(Field f, Object o, Tunable t) {
+       protected ListSingleHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try {
             lss = (ListSingleSelection<T>) f.get(o);
@@ -32,7 +32,6 @@
                jta.setEditable(false);     
                combobox = new JComboBox(lss.getPossibleValues().toArray());
                combobox.setFont(new Font("sansserif",Font.PLAIN,11));
-//             combobox.setSelectedIndex(0);
                combobox.addActionListener(this);
                panel.add(combobox,BorderLayout.EAST);
        }
@@ -47,7 +46,6 @@
                 f.set(o,lss);
             }catch(Exception e){e.printStackTrace();}
         }
-        //System.out.println(lss.getSelectedValue());
        }
 
        public String getState() {

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/LongHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/LongHandler.java
     2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/LongHandler.java
     2009-03-20 16:50:27 UTC (rev 16316)
@@ -15,36 +15,32 @@
        Long myLong;
        String newline = System.getProperty("line.separator");
 
-
-       public LongHandler(Field f, Object o, Tunable t) {
+       protected LongHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
                try{
                        this.myLong=(Long)f.get(o);
                }catch(Exception e){e.printStackTrace();}
-               
                panel = new JPanel(new BorderLayout());
                JLabel label = new JLabel(t.description());
                label.setFont(new Font(null, Font.PLAIN,12));
                panel.add(label,BorderLayout.WEST);
                try {
                        jtf = new JTextField( f.get(o).toString(), 10);
-                       //jtf.addActionListener( this );
-                       jtf.setHorizontalAlignment(JTextField.RIGHT);
-                       panel.add(jtf,BorderLayout.EAST);
                } catch (Exception e) { e.printStackTrace(); }
-                       
+               jtf.setHorizontalAlignment(JTextField.RIGHT);
+               panel.add(jtf,BorderLayout.EAST);                       
        }
 
        public void handle() {
+               jtf.setBackground(Color.white);
                try{
-                       jtf.setBackground(Color.white);
                        value = Double.parseDouble(jtf.getText());
                }catch(NumberFormatException nfe){
+                       jtf.setBackground(Color.red);
                        try{
-                               jtf.setBackground(Color.red);
                                value = Double.parseDouble(f.get(o).toString());
-                               JOptionPane.showMessageDialog(null,"A long was 
Expected"+newline+"Value will be set to default = "+value.longValue(), 
"Error",JOptionPane.ERROR_MESSAGE);
                        }catch(Exception e){e.printStackTrace();}
+               JOptionPane.showMessageDialog(null,"A long was 
Expected"+newline+"Value will be set to default = "+value.longValue(), 
"Error",JOptionPane.ERROR_MESSAGE);       
                }
                try {
                        f.set(o,value.longValue());

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
   2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/StringHandler.java
   2009-03-20 16:50:27 UTC (rev 16316)
@@ -1,4 +1,3 @@
-
 package org.cytoscape.work.internal.tunables;
 
 import java.awt.BorderLayout;
@@ -11,22 +10,19 @@
 
 public class StringHandler extends AbstractGuiHandler {
 
-       JTextField jtf;
+       private JTextField jtf;
 
-       public StringHandler(Field f, Object o, Tunable t) {
+       protected StringHandler(Field f, Object o, Tunable t) {
                super(f,o,t);
-
                panel = new JPanel(new BorderLayout());
+               JLabel label = new JLabel(t.description());
+               label.setFont(new Font(null, Font.PLAIN,12));
+               panel.add(label,BorderLayout.WEST );
                try {
-                       JLabel label = new JLabel(t.description());
-                       label.setFont(new Font(null, Font.PLAIN,12));
-                       panel.add(label,BorderLayout.WEST );
                        jtf = new JTextField( (String)f.get(o), 15);
-                       jtf.setHorizontalAlignment(JTextField.RIGHT);
-                       //jtf.addActionListener(this);
-                       panel.add(jtf,BorderLayout.EAST);
                } catch (Exception e) {e.printStackTrace(); }
-                       
+               jtf.setHorizontalAlignment(JTextField.RIGHT);
+               panel.add(jtf,BorderLayout.EAST);                       
        }
 
        public void handle() {

Modified: 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
===================================================================
--- 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
      2009-03-20 15:35:52 UTC (rev 16315)
+++ 
core3/work-swing-impl/trunk/src/main/java/org/cytoscape/work/internal/tunables/URLHandler.java
      2009-03-20 16:50:27 UTC (rev 16316)
@@ -18,27 +18,24 @@
 import org.jdesktop.layout.GroupLayout;
 import org.jdesktop.layout.LayoutStyle;
 
-import cytoscape.Cytoscape;
-
-
 public class URLHandler extends AbstractGuiHandler {
 
-       URL url;
-       BookmarksUtil bkUtil;
-       Bookmarks theBookmarks;
-       String bookmarkCategory = "network";
-       String urlstr;
-       BookmarkComboBoxEditor bookmarkEditor = new BookmarkComboBoxEditor();
-       JComboBox networkFileComboBox;
-       JLabel titleLabel;
+       public URL url;
+       private BookmarksUtil bkUtil;
+       private Bookmarks theBookmarks;
+       private String bookmarkCategory = "network";
+       private String urlstr;
+       private BookmarkComboBoxEditor bookmarkEditor;
+       private JComboBox networkFileComboBox;
+       private JLabel titleLabel;
        private JSeparator titleSeparator;
-
        private String pleaseMessage = "Please provide URL or select from list";
        
        public URLHandler(Field f, Object o, Tunable t,Bookmarks 
bookmarks,BookmarksUtil bkUtil) {
                super(f,o,t);
                this.bkUtil=bkUtil;
                this.theBookmarks=bookmarks;
+               this.bookmarkEditor = new BookmarkComboBoxEditor();
                titleSeparator = new JSeparator();
                titleLabel = new JLabel("Import URL file");
                try{
@@ -92,7 +89,6 @@
                                                
.addPreferredGap(LayoutStyle.RELATED,3, Short.MAX_VALUE)
                                                .addContainerGap()));
                
-               //panel = new JPanel(new BorderLayout());
                panel.add(new JLabel("URL Path = "));
                panel.add(networkFileComboBox);
                bookmarkEditor.setStr(pleaseMessage);
@@ -101,7 +97,6 @@
 
        public void handle() {
                urlstr = bookmarkEditor.getURLstr();
-               System.out.println("Loading : "+urlstr);
                try{
                        if ( urlstr != null ) {
                                try {
@@ -125,7 +120,8 @@
                return s;
     }
     
-       class BookmarkComboBoxEditor implements ComboBoxEditor {
+    
+       private class BookmarkComboBoxEditor implements ComboBoxEditor {
                DataSource theDataSource = new DataSource();
                JTextField tfInput = new JTextField(pleaseMessage);
                
@@ -186,7 +182,7 @@
        }
 
        
-       class MyCellRenderer extends JLabel implements ListCellRenderer {
+       private class MyCellRenderer extends JLabel implements ListCellRenderer 
{
                private final static long serialVersionUID = 1202339872997986L;
                public MyCellRenderer() {
                        setOpaque(true);


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