X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5569c3ba2c9a7ee430475a29847b2cac81fdc4c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=766d5835c0d6f2fd3933ad61e096531759392983;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 766d583..b5569c3 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,36 +1,51 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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.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 $Revision$
@@ -38,9 +53,9 @@ import jalview.util.UrlLink;
 public class IdPanel extends JPanel implements MouseListener,
         MouseMotionListener, MouseWheelListener
 {
-  protected IdCanvas idCanvas;
+  private IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
@@ -61,19 +76,17 @@ 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)
   {
     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);
@@ -81,7 +94,8 @@ 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!
@@ -89,33 +103,32 @@ public class IdPanel extends JPanel implements MouseListener,
   @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();
-      seqAnnotReport
-              .createSequenceAnnotationReport(tip, sequence,
-                      av.isShowDbRefs(), av.isShowNpFeats(),
-                      sp.seqCanvas.fr.minmax);
+      StringBuffer tip = new StringBuffer(64);
+      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+              av.isShowDBRefs(), av.isShowNPFeats(),
+              sp.seqCanvas.fr.getMinMax());
       setToolTipText("<html>" + sequence.getDisplayId(true) + " "
               + tip.toString() + "</html>");
     }
   }
 
   /**
-   * 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)
     {
@@ -130,6 +143,9 @@ 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)
   {
@@ -139,7 +155,6 @@ public class IdPanel extends JPanel implements MouseListener,
       if (e.isShiftDown())
       {
         alignPanel.scrollRight(true);
-
       }
       else
       {
@@ -160,26 +175,34 @@ 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;
     }
 
-    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();
@@ -221,15 +244,12 @@ 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();
     }
-
   }
 
   /**
@@ -274,29 +294,35 @@ 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);
+    int seq = alignPanel.getSeqPanel().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
       // features
       Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
-              .getSequenceFeatures();
+      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -335,14 +361,16 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeq(seq);
     }
+    // TODO is this addition ok here?
+    av.isSelectionGroupChanged(true);
+
     alignPanel.paintAlignment(true);
   }
 
   /**
-   * DOCUMENT ME!
+   * Toggle whether the sequence is part of the current selection group.
    * 
    * @param seq
-   *          DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -353,12 +381,11 @@ 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)
   {
@@ -390,10 +417,10 @@ 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)
@@ -410,14 +437,14 @@ 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)
   {
-    idCanvas.setHighlighted(list);
+    getIdCanvas().setHighlighted(list);
 
     if (list == null)
     {
@@ -433,6 +460,16 @@ 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
   {