X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=a65be7b1175dc42fc2920699ab96b43e73c0d773;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=a42251ef66b59081db3078de9ee8d874f7abbda2;hpb=e33b171845992fd21094ba754498f9ab3d29f110;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a42251e..a65be7b 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,45 +1,62 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
+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 $Revision$
  */
 public class IdPanel extends JPanel implements MouseListener,
         MouseMotionListener, MouseWheelListener
 {
-  protected IdCanvas idCanvas;
+  private IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
@@ -53,65 +70,66 @@ public class IdPanel extends JPanel implements MouseListener,
   int lastid = -1;
 
   boolean mouseDragging = false;
+
   private final SequenceAnnotationReport seqAnnotReport;
 
   /**
    * Creates a new IdPanel object.
-   *
+   * 
    * @param av
-   *          DOCUMENT ME!
    * @param parent
-   *          DOCUMENT ME!
    */
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
     this.av = av;
     alignPanel = parent;
-    idCanvas = new IdCanvas(av);
+    setIdCanvas(new IdCanvas(av));
     linkImageURL = getClass().getResource("/images/link.gif").toString();
     seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
     setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
+    add(getIdCanvas(), BorderLayout.CENTER);
     addMouseListener(this);
     addMouseMotionListener(this);
     addMouseWheelListener(this);
     ToolTipManager.sharedInstance().registerComponent(this);
   }
+
   /**
-   * DOCUMENT ME!
-   *
+   * Respond to mouse movement by constructing tooltip text for the sequence id
+   * under the mouse.
+   * 
    * @param e
    *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent e)
   {
-    SeqPanel sp = alignPanel.seqPanel;
+    SeqPanel sp = alignPanel.getSeqPanel();
     int seq = Math.max(0, sp.findSeq(e));
     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(),
-              sp.seqCanvas.fr.minmax);
-      setToolTipText("<html>" + sequence.getDisplayId(true) + " "
-              + tip.toString()+"</html>");
+              av.isShowDBRefs(), av.isShowNPFeats(),
+              sp.seqCanvas.fr.getMinMax());
+      setToolTipText(JvSwingUtils.wrapTooltip(true,
+              sequence.getDisplayId(true) + " " + tip.toString()));
     }
   }
 
   /**
-   * 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)
   {
     mouseDragging = true;
 
-    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+    int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
 
     if (seq < lastid)
     {
@@ -126,6 +144,9 @@ 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)
   {
@@ -135,8 +156,9 @@ public class IdPanel extends JPanel implements MouseListener,
       if (e.isShiftDown())
       {
         alignPanel.scrollRight(true);
-        
-      } else {
+      }
+      else
+      {
         alignPanel.scrollUp(false);
       }
     }
@@ -145,33 +167,45 @@ public class IdPanel extends JPanel implements MouseListener,
       if (e.isShiftDown())
       {
         alignPanel.scrollRight(false);
-      } else {
+      }
+      else
+      {
         alignPanel.scrollUp(true);
       }
     }
   }
 
   /**
-   * 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))
     {
+      // reinstate isRightMouseButton check to ignore mouse-related popup events
+      // note - this does nothing on default MacBookPro force-trackpad config!
       return;
     }
 
-    java.util.Vector links = Preferences.sequenceURLLinks;
+    Vector links = Preferences.sequenceURLLinks;
     if (links == null || links.size() < 1)
     {
       return;
     }
 
-    int seq = alignPanel.seqPanel.findSeq(e);
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     String url = null;
     int i = 0;
     String id = av.getAlignment().getSequenceAt(seq).getName();
@@ -213,20 +247,17 @@ public class IdPanel extends JPanel implements MouseListener,
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane
-              .showInternalMessageDialog(
-                      Desktop.desktop,
-                      "Unixers: Couldn't find default web browser."
-                              + "\nAdd the full path to your browser in Preferences.",
-                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.web_browser_not_found_unix"),
+              MessageManager.getString("label.web_browser_not_found"),
+              JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
-
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -241,7 +272,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -266,51 +297,44 @@ 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 (e.isPopupTrigger()) // Mac reports this in mousePressed
     {
-      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
-      // build a new links menu based on the current links + any non-positional
-      // features
-      Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
-      {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
-        {
-          if (sf[sl].links != null && sf[sl].links.size() > 0)
-          {
-            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
-            {
-              nlinks.addElement(sf[sl].links.elementAt(l));
-            }
-          }
-        }
-      }
-
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
-              nlinks, new Vector(Preferences.getGroupURLLinks()));
-      pop.show(this, e.getX(), e.getY());
+      showPopupMenu(e);
+      return;
+    }
 
+    /*
+     * defer right-mouse click handling to mouseReleased on Windows
+     * (where isPopupTrigger() will answer true)
+     * NB isRightMouseButton is also true for Cmd-click on Mac
+     */
+    if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac())
+    {
       return;
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!e.isControlDown() && !e.isShiftDown()) && av
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
                     .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
@@ -318,6 +342,7 @@ public class IdPanel extends JPanel implements MouseListener,
       av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     if (e.isShiftDown() && (lastid != -1))
     {
       selectSeqs(lastid, seq);
@@ -326,14 +351,51 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeq(seq);
     }
+
+    av.isSelectionGroupChanged(true);
+
     alignPanel.paintAlignment(true);
   }
 
   /**
-   * DOCUMENT ME!
-   *
+   * Build and show the popup-menu at the right-click mouse position
+   * 
+   * @param e
+   */
+  void showPopupMenu(MouseEvent e)
+  {
+    int seq2 = alignPanel.getSeqPanel().findSeq(e);
+    Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
+    // build a new links menu based on the current links + any non-positional
+    // features
+    Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
+    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
+    if (sfs != null)
+    {
+      for (SequenceFeature sf : sfs)
+      {
+        if (sf.begin == sf.end && sf.begin == 0)
+        {
+          if (sf.links != null && sf.links.size() > 0)
+          {
+            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
+            {
+              nlinks.addElement(sf.links.elementAt(l));
+            }
+          }
+        }
+      }
+    }
+
+    PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+            Preferences.getGroupURLLinks());
+    pop.show(this, e.getX(), e.getY());
+  }
+
+  /**
+   * Toggle whether the sequence is part of the current selection group.
+   * 
    * @param seq
-   *          DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -344,12 +406,11 @@ 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)
   {
@@ -376,15 +437,15 @@ public class IdPanel extends JPanel implements MouseListener,
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), true);
+              av.getAlignment().getSequenceAt(i), i == end);
     }
   }
 
   /**
-   * 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)
@@ -398,17 +459,22 @@ public class IdPanel extends JPanel implements MouseListener,
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     // always send selection message when mouse is released
     av.sendSelection();
+
+    if (e.isPopupTrigger()) // Windows reports this in mouseReleased
+    {
+      showPopupMenu(e);
+    }
   }
 
   /**
-   * 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)
   {
-    idCanvas.setHighlighted(list);
+    getIdCanvas().setHighlighted(list);
 
     if (list == null)
     {
@@ -424,6 +490,16 @@ public class IdPanel extends JPanel implements MouseListener,
     }
   }
 
+  public IdCanvas getIdCanvas()
+  {
+    return idCanvas;
+  }
+
+  public void setIdCanvas(IdCanvas idCanvas)
+  {
+    this.idCanvas = idCanvas;
+  }
+
   // this class allows scrolling off the bottom of the visible alignment
   class ScrollThread extends Thread
   {