JAL-1360 Javadoc, Vector replaced with ArrayList, code formatted

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 1f23338..43c648e 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -40,9 +40,9 @@ import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 import javax.swing.JButton;
 import javax.swing.JInternalFrame;
@@ -51,23 +51,26 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
 /**
- * DOCUMENT ME!
+ * This panel allows the user to assign colours to Amino Acid residue codes, and
+ * save the colour scheme.
  * 
- * @author $author$
- * @version $Revision$
+ * @author Andrew Waterhouse
+ * @author Mungo Carstairs
  */
 public class UserDefinedColours extends GUserDefinedColours implements
         ChangeListener
 {
   private static final int MY_FRAME_HEIGHT = 420;
+
   private static final int MY_FRAME_WIDTH = 810;
+
   private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
 
-AlignmentPanel ap;
+  AlignmentPanel ap;
 
   SequenceGroup seqGroup;
 
-  Vector selectedButtons;
+  ArrayList<JButton> selectedButtons;
 
   ColourSchemeI oldColourScheme;
 
@@ -75,9 +78,9 @@ AlignmentPanel ap;
 
   JalviewStructureDisplayI jmol;
 
-  Vector upperCaseButtons;
+  ArrayList<JButton> upperCaseButtons;
 
-  Vector lowerCaseButtons;
+  ArrayList<JButton> lowerCaseButtons;
 
   /**
    * Creates a new UserDefinedColours object.
@@ -127,7 +130,8 @@ AlignmentPanel ap;
     showFrame();
   }
 
-  public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs)
+  public UserDefinedColours(JalviewStructureDisplayI jmol,
+          ColourSchemeI oldcs)
   {
     super();
     this.jmol = jmol;
@@ -152,9 +156,9 @@ AlignmentPanel ap;
     colorChooser.getSelectionModel().addChangeListener(this);
     frame = new JInternalFrame();
     frame.setContentPane(this);
-               Desktop.addInternalFrame(frame,
-                               MessageManager.getString("label.user_defined_colours"), MY_FRAME_WIDTH,
-                               MY_FRAME_HEIGHT, true);
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.user_defined_colours"),
+            MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
 
     if (seqGroup != null)
     {
@@ -168,7 +172,7 @@ AlignmentPanel ap;
 
     if (upperCaseButtons == null)
     {
-      upperCaseButtons = new Vector();
+      upperCaseButtons = new ArrayList<JButton>();
     }
 
     JButton button;
@@ -209,7 +213,7 @@ AlignmentPanel ap;
 
       if (lowerCaseButtons == null)
       {
-        lowerCaseButtons = new Vector();
+        lowerCaseButtons = new ArrayList<JButton>();
       }
 
       for (int i = 0; i < 20; i++)
@@ -230,12 +234,15 @@ AlignmentPanel ap;
       buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
     }
 
-    // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA codes
-    if (this.frame != null) {
-       int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE : MY_FRAME_WIDTH;
-       this.frame.setSize(newWidth, this.frame.getHeight());
+    // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
+    // codes
+    if (this.frame != null)
+    {
+      int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+              : MY_FRAME_WIDTH;
+      this.frame.setSize(newWidth, this.frame.getHeight());
     }
-    
+
     buttonPanel.validate();
     validate();
   }
@@ -246,15 +253,16 @@ AlignmentPanel ap;
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void stateChanged(ChangeEvent evt)
   {
     if (selectedButtons != null)
     {
       JButton button = null;
-         final Color newColour = colorChooser.getColor();
-         for (int i = 0; i < selectedButtons.size(); i++)
+      final Color newColour = colorChooser.getColor();
+      for (int i = 0; i < selectedButtons.size(); i++)
       {
-        button = (JButton) selectedButtons.elementAt(i);
+        button = selectedButtons.get(i);
         button.setBackground(newColour);
         button.setForeground(ColorUtils.brighterThan(newColour));
       }
@@ -262,25 +270,38 @@ AlignmentPanel ap;
       {
         for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
-          button = (JButton) lowerCaseButtons.elementAt(i);
+          button = lowerCaseButtons.get(i);
           button.setBackground(newColour);
-          button.setForeground(ColorUtils.brighterThan(button.getBackground()));
+          button.setForeground(ColorUtils.brighterThan(button
+                  .getBackground()));
         }
       }
     }
   }
 
   /**
-   * DOCUMENT ME!
+   * Performs actions when a residue button is clicked. This manages the button
+   * selection set (highlighted by brighter foreground text).
+   * <p>
+   * On select button(s) with Ctrl/click or Shift/click: set button foreground
+   * text to brighter than background.
+   * <p>
+   * On unselect button(s) with Ctrl/click on selected, or click to release
+   * current selection: reset foreground text to darker than background.
+   * <p>
+   * Simple click: clear selection (resetting foreground to darker); set clicked
+   * button foreground to brighter
+   * <p>
+   * Finally, synchronize the colour chooser to the colour of the first button
+   * in the selected set.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   public void colourButtonPressed(MouseEvent e)
   {
     if (selectedButtons == null)
     {
-      selectedButtons = new Vector();
+      selectedButtons = new ArrayList<JButton>();
     }
 
     JButton pressed = (JButton) e.getSource();
@@ -290,8 +311,7 @@ AlignmentPanel ap;
       JButton start, end = (JButton) e.getSource();
       if (selectedButtons.size() > 0)
       {
-        start = (JButton) selectedButtons
-                .elementAt(selectedButtons.size() - 1);
+        start = selectedButtons.get(selectedButtons.size() - 1);
       }
       else
       {
@@ -323,7 +343,8 @@ AlignmentPanel ap;
         JButton button = (JButton) buttonPanel.getComponent(b);
         if (!selectedButtons.contains(button))
         {
-          button.setForeground(ColorUtils.brighterThan(button.getBackground()));
+          button.setForeground(ColorUtils.brighterThan(button
+                  .getBackground()));
           selectedButtons.add(button);
         }
       }
@@ -332,12 +353,12 @@ AlignmentPanel ap;
     {
       for (int b = 0; b < selectedButtons.size(); b++)
       {
-        JButton button = (JButton) selectedButtons.elementAt(b);
+        JButton button = selectedButtons.get(b);
         button.setForeground(ColorUtils.darkerThan(button.getBackground()));
       }
       selectedButtons.clear();
       pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
-      selectedButtons.addElement(pressed);
+      selectedButtons.add(pressed);
 
     }
     else if (e.isControlDown())
@@ -349,15 +370,15 @@ AlignmentPanel ap;
       }
       else
       {
-        pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
-        selectedButtons.addElement(pressed);
+        pressed.setForeground(ColorUtils.brighterThan(pressed
+                .getBackground()));
+        selectedButtons.add(pressed);
       }
     }
 
     if (selectedButtons.size() > 0)
     {
-      colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
-              .getBackground());
+      colorChooser.setColor((selectedButtons.get(0)).getBackground());
     }
   }
 
@@ -369,15 +390,15 @@ AlignmentPanel ap;
    * @param aa
    *          DOCUMENT ME!
    */
-  JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
-          int buttonIndex)
+  JButton makeButton(String label, String aa,
+          ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
   {
     final JButton button;
     Color col;
 
     if (buttonIndex < caseSensitiveButtons.size())
     {
-      button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+      button = caseSensitiveButtons.get(buttonIndex);
       col = button.getBackground();
     }
     else
@@ -385,13 +406,14 @@ AlignmentPanel ap;
       button = new JButton();
       button.addMouseListener(new java.awt.event.MouseAdapter()
       {
+        @Override
         public void mouseClicked(MouseEvent e)
         {
           colourButtonPressed(e);
         }
       });
 
-      caseSensitiveButtons.addElement(button);
+      caseSensitiveButtons.add(button);
 
       col = Color.white;
       if (oldColourScheme != null)
@@ -414,7 +436,7 @@ AlignmentPanel ap;
       button.setMargin(new java.awt.Insets(2, 14, 2, 14));
     }
 
-    button.setOpaque(true);    // required for the next line to have effect
+    button.setOpaque(true); // required for the next line to have effect
     button.setBackground(col);
     button.setText(label);
     button.setForeground(ColorUtils.darkerThan(col));
@@ -429,6 +451,7 @@ AlignmentPanel ap;
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void okButton_actionPerformed(ActionEvent e)
   {
     applyButton_actionPerformed(null);
@@ -447,6 +470,7 @@ AlignmentPanel ap;
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void applyButton_actionPerformed(ActionEvent e)
   {
     UserColourScheme ucs = getSchemeFromButtons();
@@ -474,7 +498,7 @@ AlignmentPanel ap;
 
     for (int i = 0; i < 24; i++)
     {
-      JButton button = (JButton) upperCaseButtons.elementAt(i);
+      JButton button = upperCaseButtons.get(i);
       newColours[i] = button.getBackground();
     }
 
@@ -485,7 +509,7 @@ AlignmentPanel ap;
       newColours = new Color[23];
       for (int i = 0; i < 23; i++)
       {
-        JButton button = (JButton) lowerCaseButtons.elementAt(i);
+        JButton button = lowerCaseButtons.get(i);
         newColours[i] = button.getBackground();
       }
       ucs.setLowerCaseColours(newColours);
@@ -505,10 +529,11 @@ AlignmentPanel ap;
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void loadbutton_actionPerformed(ActionEvent e)
   {
-    upperCaseButtons = new Vector();
-    lowerCaseButtons = new Vector();
+    upperCaseButtons = new ArrayList<JButton>();
+    lowerCaseButtons = new ArrayList<JButton>();
 
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
@@ -546,7 +571,7 @@ AlignmentPanel ap;
         resetButtonPanel(true);
         for (int i = 0; i < lowerCaseButtons.size(); i++)
         {
-          JButton button = (JButton) lowerCaseButtons.elementAt(i);
+          JButton button = lowerCaseButtons.get(i);
           button.setBackground(ucs.getLowerCaseColours()[i]);
         }
 
@@ -560,7 +585,7 @@ AlignmentPanel ap;
 
       for (int i = 0; i < upperCaseButtons.size(); i++)
       {
-        JButton button = (JButton) upperCaseButtons.elementAt(i);
+        JButton button = upperCaseButtons.get(i);
         button.setBackground(colors[i]);
       }
 
@@ -685,7 +710,7 @@ AlignmentPanel ap;
 
         jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
 
-        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+        jucs = jucs.unmarshal(in);
 
         newColours = new Color[jucs.getColourCount()];
 
@@ -719,6 +744,7 @@ AlignmentPanel ap;
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void savebutton_actionPerformed(ActionEvent e)
   {
     if (schemeName.getText().trim().length() < 1)
@@ -735,7 +761,7 @@ AlignmentPanel ap;
     {
       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
               MessageManager.formatMessage(
-                      "label.colour_scheme_exists_overwrite", new String[]
+                      "label.colour_scheme_exists_overwrite", new Object[]
                       { schemeName.getText(), schemeName.getText() }),
               MessageManager.getString("label.duplicate_scheme_name"),
               JOptionPane.YES_NO_OPTION);
@@ -810,6 +836,7 @@ AlignmentPanel ap;
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cancelButton_actionPerformed(ActionEvent e)
   {
     if (ap != null)
@@ -939,17 +966,19 @@ AlignmentPanel ap;
 
   }
 
+  @Override
   public void caseSensitive_actionPerformed(ActionEvent e)
   {
     resetButtonPanel(caseSensitive.isSelected());
     lcaseColour.setEnabled(caseSensitive.isSelected());
   }
 
+  @Override
   public void lcaseColour_actionPerformed(ActionEvent e)
   {
     if (selectedButtons == null)
     {
-      selectedButtons = new Vector();
+      selectedButtons = new ArrayList<JButton>();
     }
     else
     {
@@ -957,5 +986,4 @@ AlignmentPanel ap;
     }
     selectedButtons.add(lcaseColour);
   }
-
 }