JAL-1554 handle left-then-right click on sequence id

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index ee779f7..7f2e669 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,19 +20,30 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.UrlLink;
+
+import java.awt.BorderLayout;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
 import java.util.List;
 import java.util.Vector;
 
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.SequenceAnnotationReport;
-import jalview.util.UrlLink;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
  * 
  * @author $author$
  * @version $Revision$
@@ -63,9 +74,7 @@ public class IdPanel extends JPanel implements MouseListener,
    * Creates a new IdPanel object.
    * 
    * @param av
-   *          DOCUMENT ME!
    * @param parent
-   *          DOCUMENT ME!
    */
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -83,7 +92,8 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to mouse movement by constructing tooltip text for the sequence id
+   * under the mouse.
    * 
    * @param e
    *          DOCUMENT ME!
@@ -96,7 +106,7 @@ public class IdPanel extends JPanel implements MouseListener,
     if (seq > -1 && seq < av.getAlignment().getHeight())
     {
       SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-      StringBuffer tip = new StringBuffer();
+      StringBuffer tip = new StringBuffer(64);
       seqAnnotReport
               .createSequenceAnnotationReport(tip, sequence,
                       av.isShowDbRefs(), av.isShowNpFeats(),
@@ -107,10 +117,10 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Responds to a mouse drag by selecting the sequences under the dragged
+   * region.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseDragged(MouseEvent e)
@@ -132,6 +142,9 @@ public class IdPanel extends JPanel implements MouseListener,
     alignPanel.paintAlignment(true);
   }
 
+  /**
+   * Response to the mouse wheel by scrolling the alignment panel.
+   */
   @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
@@ -141,7 +154,6 @@ public class IdPanel extends JPanel implements MouseListener,
       if (e.isShiftDown())
       {
         alignPanel.scrollRight(true);
-
       }
       else
       {
@@ -162,20 +174,28 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Handle a mouse click event. Currently only responds to a double-click. The
+   * action is to try to open a browser window at a URL that searches for the
+   * selected sequence id. The search URL is configured in Preferences |
+   * Connections | URL link from Sequence ID. For example:
+   * 
+   * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() < 2)
+    /*
+     * Ignore single click. Ignore 'left' click followed by 'right' click (user
+     * selects a row then its pop-up menu).
+     */
+    if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
     {
       return;
     }
 
-    java.util.Vector links = Preferences.sequenceURLLinks;
+    Vector links = Preferences.sequenceURLLinks;
     if (links == null || links.size() < 1)
     {
       return;
@@ -231,7 +251,6 @@ public class IdPanel extends JPanel implements MouseListener,
                       "Web browser not found", JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
-
   }
 
   /**
@@ -276,22 +295,29 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to a mouse press. Does nothing for (left) double-click as this is
+   * handled by mouseClicked().
+   * 
+   * Right mouse down - construct and show context menu.
+   * 
+   * Ctrl-down or Shift-down - add to or expand current selection group if there
+   * is one.
+   * 
+   * Mouse down - select this sequence.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
     {
       return;
     }
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if (javax.swing.SwingUtilities.isRightMouseButton(e))
+    if (SwingUtilities.isRightMouseButton(e))
     {
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
       // build a new links menu based on the current links + any non-positional
@@ -341,10 +367,9 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Toggle whether the sequence is part of the current selection group.
    * 
    * @param seq
-   *          DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -355,12 +380,11 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Add contiguous rows of the alignment to the current selection group. Does
+   * nothing if there is no selection group.
    * 
    * @param start
-   *          DOCUMENT ME!
    * @param end
-   *          DOCUMENT ME!
    */
   void selectSeqs(int start, int end)
   {
@@ -392,10 +416,10 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Respond to mouse released. Refreshes the display and triggers broadcast of
+   * the new selection group to any listeners.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent e)
@@ -412,10 +436,10 @@ public class IdPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Highlight sequence ids that match the given list, and if necessary scroll
+   * to the start sequence of the list.
    * 
    * @param list
-   *          DOCUMENT ME!
    */
   public void highlightSearchResults(List<SequenceI> list)
   {