X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d80c4b86144bc03388f143e62c974c1afaea856c;hb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;hp=939a65effad7f8e993120b2b82e37f936137b9dc;hpb=80d695371530259d7530566f0e46a8df10ff2377;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 939a65e..d80c4b8 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,150 +1,436 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
+ */
 package jalview.gui;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import jalview.datamodel.*;
-
 import javax.swing.*;
 
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {
+import jalview.datamodel.*;
 
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel
+    extends JPanel implements MouseListener,
+    MouseMotionListener, MouseWheelListener
+{
+  protected IdCanvas idCanvas;
+  protected AlignViewport av;
   protected AlignmentPanel alignPanel;
-
-  protected int            offy;
-  public    int            width;
-  public    int            lastid;
-
-  SequenceGroup selectedSequenceGroup;
-
+  ScrollThread scrollThread = null;
+  int offy;
+  int width;
+  int lastid = -1;
+  boolean mouseDragging = false;
+
+  /**
+   * Creates a new IdPanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param parent DOCUMENT ME!
+   */
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
-    this.av         = av;
+    this.av = av;
     alignPanel = parent;
     idCanvas = new IdCanvas(av);
     setLayout(new BorderLayout());
     add(idCanvas, BorderLayout.CENTER);
     addMouseListener(this);
     addMouseMotionListener(this);
+    addMouseWheelListener(this);
+    ToolTipManager.sharedInstance().registerComponent(this);
   }
 
-  public void mouseMoved(MouseEvent e) {}
-
-  public void selectSeqs(int start, int end) {
-     if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-     }
-
-     for (int i = start; i <= end; i++)
-     {
-       SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
-       if (av.getSelection().contains(pickedSeq))
-       {
-         av.getSelection().removeElement(pickedSeq);
-         selectedSequenceGroup.deleteSequence(pickedSeq);
-       }
-       else
-       {
-         av.getSelection().addElement(pickedSeq);
-         if(selectedSequenceGroup==null)
-         {
-           selectedSequenceGroup = new SequenceGroup();
-           av.setRubberbandGroup( selectedSequenceGroup );
-          // av.alignment.addGroup( selectedSequenceGroup );
-           selectedSequenceGroup.setStartRes(0);
-           selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());
-         }
-
-         selectedSequenceGroup.addSequence( pickedSeq );
-       }
-
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag=true;
-     alignPanel.repaint();
-     repaint();
-
-   }
-
-  public void mouseDragged(MouseEvent e) {
-    int y = e.getY();
-    int seq = av.getIndex(y);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent e)
+  {
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+    if (seq > -1 && seq < av.alignment.getHeight())
+    {
+      SequenceI sequence = av.alignment.getSequenceAt(seq);
+      StringBuffer tip = new StringBuffer("<html>");
+      tip.append(sequence.getDisplayId(true));
+      if (sequence.getDescription() != null)
+      {
+        tip.append("<table width=250 border=0><tr><td><i>");
+        tip.append(sequence.getDescription());
+
+        //ADD NON POSITIONAL SEQUENCE INFO
+        SequenceFeature[] features = sequence.getDatasetSequence().
+            getSequenceFeatures();
+        if (features != null)
+        {
+          for (int i = 0; i < features.length; i++)
+          {
+            if (features[i].begin == 0 && features[i].end == 0)
+            {
+              tip.append("<br>" + features[i].featureGroup
+                         + " " + features[i].getType() + " " +
+                         features[i].description);
+            }
+          }
+        }
+        tip.append("</i></td></tr></table>");
+      }
+
+      DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+      if (dbrefs != null)
+      {
+        tip.append("<i>");
+        for (int i = 0; i < dbrefs.length; i++)
+        {
+          tip.append("<br>");
+          tip.append(dbrefs[i].getSource() + " "
+                     + dbrefs[i].getAccessionId());
+        }
+        tip.append("</i>");
+      }
+
+      tip.append("</html>");
+      setToolTipText(tip.toString());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
+
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
 
     if (seq < lastid)
+    {
       selectSeqs(lastid - 1, seq);
+    }
     else if (seq > lastid)
+    {
       selectSeqs(lastid + 1, seq);
+    }
 
     lastid = seq;
+    alignPanel.paintAlignment(true);
+  }
 
-    return;
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    e.consume();
+      if (e.getWheelRotation() > 0)
+      {
+        alignPanel.scrollUp(false);
+      }
+      else
+      {
+        alignPanel.scrollUp(true);
+      }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() < 2)
     {
-       int seq = av.getIndex(e.getY());
-       String id = av.getAlignment().getSequenceAt(seq).getName();
+      return;
+    }
 
-       try{
-         jalview.util.BrowserLauncher.openURL(
-             "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
-             "]+-vn+2");
-       }catch(Exception ex){ex.printStackTrace();}
+    java.util.Vector links = Preferences.sequenceURLLinks;
+    if (links == null || links.size() < 1)
+    {
+      return;
     }
 
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
+
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+    if (id.indexOf("|") > -1)
+    {
+      id = id.substring(id.lastIndexOf("|") + 1);
+    }
+
+    String url = links.elementAt(0).toString();
+    url = url.substring(url.indexOf("|") + 1);
+
+    int index = url.indexOf("$SEQUENCE_ID$");
+    url = url.substring(0, index) + id + url.substring(index + 13);
+
+    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);
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
+    }
+
+    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    {
+      scrollThread = new ScrollThread(true);
+    }
+
+    if (mouseDragging && (e.getY() >= getHeight()) &&
+        (av.alignment.getHeight() > av.getEndSeq()))
+    {
+      scrollThread = new ScrollThread(false);
+    }
   }
-  public void mouseEntered(MouseEvent e) { }
-  public void mouseExited (MouseEvent e) { }
 
-  public void mousePressed(MouseEvent e) {
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent e)
+  {
     if (e.getClickCount() == 2)
+    {
       return;
+    }
 
-    int y = e.getY();
-    int seq = av.getIndex(y);
+    int seq = alignPanel.seqPanel.findSeq(e);
 
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          av.getAlignment().getSequenceAt(seq));
-      pop.show(this, e.getX(), y);
+          (Sequence) av.getAlignment().getSequenceAt(seq),
+          Preferences.sequenceURLLinks);
+      pop.show(this, e.getX(), e.getY());
+
       return;
     }
 
+    if ( (av.getSelectionGroup() == null) ||
+        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    {
+      av.setSelectionGroup(new SequenceGroup());
+      av.getSelectionGroup().setStartRes(0);
+      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+    }
+
+    if (e.isShiftDown() && (lastid != -1))
+    {
+      selectSeqs(lastid, seq);
+    }
+    else
+    {
+      selectSeq(seq);
+    }
+
+    alignPanel.paintAlignment(true);
+  }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  void selectSeq(int seq)
+  {
+    lastid = seq;
 
-    if(av.getRubberbandGroup()!=null && (av.getRubberbandGroup().getSize() == av.getSelection().size()))
-          selectedSequenceGroup = av.getRubberbandGroup();
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
 
-    if (selectedSequenceGroup == null)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   */
+  void selectSeqs(int start, int end)
+  {
+    if (av.getSelectionGroup() == null)
     {
-      selectedSequenceGroup = new SequenceGroup();
-      av.setRubberbandGroup(selectedSequenceGroup);
+      return;
     }
 
-    selectedSequenceGroup.setStartRes(0);
-    selectedSequenceGroup.setEndRes(av.getAlignment().getWidth() - 1);
-
-    if (seq != -1)
-      selectSeqs(seq, seq);
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
 
-    lastid = seq;
+    lastid = start;
 
+    if (end < start)
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
 
-    return;
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+                                         true);
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void mouseReleased(MouseEvent e)
   {
-    lastid = -1;
-    PaintRefresher.Refresh(this);
-    selectedSequenceGroup = null;
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+
+    mouseDragging = false;
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param found DOCUMENT ME!
+   */
+  public void highlightSearchResults(java.util.Vector found)
+  {
+    idCanvas.setHighlighted(found);
+
+    if (found == null)
+    {
+      return;
+    }
+
+    int index = av.alignment.findIndex( (SequenceI) found.get(0));
+
+    // do we need to scroll the panel?
+    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
+    }
+  }
+
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread
+      extends Thread
+  {
+    boolean running = false;
+    boolean up = true;
+
+    public ScrollThread(boolean up)
+    {
+      this.up = up;
+      start();
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+
+      while (running)
+      {
+        if (alignPanel.scrollUp(up))
+        {
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getStartSeq();
+
+          if (!up)
+          {
+            seq = av.getEndSeq();
+          }
+
+          if (seq < lastid)
+          {
+            selectSeqs(lastid - 1, seq);
+          }
+          else if (seq > lastid)
+          {
+            selectSeqs(lastid + 1, seq);
+          }
+
+          lastid = seq;
+        }
+        else
+        {
+          running = false;
+        }
+
+        alignPanel.paintAlignment(true);
+
+        try
+        {
+          Thread.sleep(100);
+        }
+        catch (Exception ex)
+        {
+        }
+      }
+    }
   }
 }