X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=f0aefb1438fc998ff375e38abc873b7797f864dc;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=a325618e324fc24a90f56fe31756d553a78bcc39;hpb=21f3e784749a8eb93cd716fca379d50732f08827;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a325618..f0aefb1 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,49 +1,66 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 java.util.Vector;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
+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.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 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
+public class IdPanel extends JPanel
+        implements MouseListener, MouseMotionListener, MouseWheelListener
 {
-  protected IdCanvas idCanvas;
+  private IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
   ScrollThread scrollThread = null;
 
+  String linkImageURL;
+
   int offy;
 
   // int width;
@@ -51,21 +68,23 @@ public class IdPanel extends JPanel implements MouseListener,
 
   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);
@@ -73,91 +92,41 @@ 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!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseMoved(MouseEvent e)
   {
-    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
-    String tmp;
-    if (seq > -1 && seq < av.alignment.getHeight())
+    SeqPanel sp = alignPanel.getSeqPanel();
+    int seq = Math.max(0, sp.findSeq(e));
+    if (seq > -1 && seq < av.getAlignment().getHeight())
     {
-      SequenceI sequence = av.alignment.getSequenceAt(seq);
-      StringBuffer tip = new StringBuffer();
-      tip.append("<i>");
-
-      int maxWidth = 0;
-      if (sequence.getDescription() != null)
-      {
-        tmp = sequence.getDescription();
-        tip.append("<br>" + tmp);
-        maxWidth = Math.max(maxWidth, tmp.length());
-      }
-
-      DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
-      if (av.isShowDbRefs() && dbrefs != null)
-      {
-        for (int i = 0; i < dbrefs.length; i++)
-        {
-          tip.append("<br>");
-          tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
-          tip.append(tmp);
-          maxWidth = Math.max(maxWidth, tmp.length());
-        }
-      }
-
-      // ADD NON POSITIONAL SEQUENCE INFO
-      SequenceFeature[] features = sequence.getDatasetSequence()
-              .getSequenceFeatures();
-      if (av.isShowNpFeats() && features != null)
-      {
-        for (int i = 0; i < features.length; i++)
-        {
-          if (features[i].begin == 0 && features[i].end == 0)
-          {
-            tip.append("<br>");
-            int sz = -tip.length();
-            boolean nl=false;
-            if (features[i].getFeatureGroup()!=null) { tip.append(features[i].getFeatureGroup()); nl=true;};
-            if (features[i].getType()!=null) { tip.append(" "); tip.append(features[i].getType()); nl=true;};
-            if (features[i].getDescription()!=null) { tip.append(" "); tip.append(features[i].getDescription()); nl=true;};
-            if (features[i].getScore()!=Float.NaN && features[i].getScore()!=0f) { tip.append(" Score = "); tip.append(features[i].getScore()); nl=true;};
-            if (features[i].getStatus()!=null && features[i].getStatus().length()>0) { tip.append(" ("); tip.append(features[i].getStatus()); tip.append(")");nl=true;};
-            if (nl) {
-              sz+=tip.length();
-              tip.append("<br>");
-              maxWidth = Math.max(maxWidth, sz);
-            }
-          }
-        }
-      }
-
-      if (maxWidth > 60)
-      {
-        tip.insert(0, "<table width=350 border=0><tr><td><i>");
-        tip.append("</i></td></tr></table>");
-      }
-
-      tip.append("</html>");
-
-      setToolTipText("<html>" + sequence.getDisplayId(true)
-              + tip.toString());
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+      StringBuilder tip = new StringBuilder(64);
+      seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
+              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)
     {
@@ -169,100 +138,88 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
+  /**
+   * Response to the mouse wheel by scrolling the alignment panel.
+   */
+  @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
     if (e.getWheelRotation() > 0)
     {
-      alignPanel.scrollUp(false);
+      if (e.isShiftDown())
+      {
+        av.getRanges().scrollRight(true);
+      }
+      else if (!av.getWrapAlignment())
+      {
+        av.getRanges().scrollUp(false);
+      }
     }
     else
     {
-      alignPanel.scrollUp(true);
+      if (e.isShiftDown())
+      {
+        av.getRanges().scrollRight(false);
+      }
+      else if (!av.getWrapAlignment())
+      {
+        av.getRanges().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)
-    {
-      return;
-    }
-
-    java.util.Vector links = Preferences.sequenceURLLinks;
-    if (links == null || links.size() < 1)
+    /*
+     * 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;
     }
 
-    int seq = alignPanel.seqPanel.findSeq(e);
-    String url = null;
-    int i = 0;
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    while (url == null && i < links.size())
-    {
-      // DEFAULT LINK IS FIRST IN THE LINK LIST
-      // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
-      url = links.elementAt(i++).toString();
-      jalview.util.UrlLink urlLink = null;
-      try
-      {
-        urlLink = new UrlLink(url);
-      } catch (Exception foo)
-      {
-        jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
-                foo);
-        url = null;
-        continue;
-      }
-      ;
-      if (!urlLink.isValid())
-      {
-        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
-        url = null;
-        continue;
-      }
+    String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
-      String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0] == null || urls[0].length() < 4)
-      {
-        url = null;
-        continue;
-      }
-      // just take first URL made from regex
-      url = urls[1];
-    }
     try
     {
       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);
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.web_browser_not_found_unix"),
+              MessageManager.getString("label.web_browser_not_found"),
+              JvOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
-
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -275,8 +232,9 @@ public class IdPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -284,71 +242,66 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.alignment.getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
   }
 
   /**
-   * 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.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);
-      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
-                    .getSelectionGroup() != null))
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+                    && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
+    int seq = alignPanel.getSeqPanel().findSeq(e);
     if (e.isShiftDown() && (lastid != -1))
     {
       selectSeqs(lastid, seq);
@@ -358,14 +311,47 @@ public class IdPanel extends JPanel implements MouseListener,
       selectSeq(seq);
     }
 
-    alignPanel.paintAlignment(true);
+    av.isSelectionGroupChanged(true);
+
+    alignPanel.paintAlignment(false);
   }
 
   /**
-   * 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
+     *  and any non-positional features
+     */
+    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+    for (SequenceFeature sf : features)
+    {
+      if (sf.links != null)
+      {
+        for (String link : sf.links)
+        {
+          nlinks.add(link);
+        }
+      }
+    }
+
+    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
+            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)
   {
@@ -376,12 +362,11 @@ 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)
   {
@@ -407,17 +392,18 @@ public class IdPanel extends JPanel implements MouseListener,
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), true);
+      av.getSelectionGroup().addSequence(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)
   {
     if (scrollThread != null)
@@ -427,32 +413,50 @@ public class IdPanel extends JPanel implements MouseListener,
 
     mouseDragging = false;
     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 found
-   *                DOCUMENT ME!
+   * @param list
    */
-  public void highlightSearchResults(java.util.Vector found)
+  public void highlightSearchResults(List<SequenceI> list)
   {
-    idCanvas.setHighlighted(found);
+    getIdCanvas().setHighlighted(list);
 
-    if (found == null)
+    if (list == null)
     {
       return;
     }
 
-    int index = av.alignment.findIndex((SequenceI) found.get(0));
+    int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
+  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
   {
@@ -471,20 +475,21 @@ public class IdPanel extends JPanel implements MouseListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
 
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)