X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=0480ffa6c6314f136df9fc37f5892c7442b32c22;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=f5cf03cb46d965a71a7720be3025979b08181092;hpb=0fc3643ce8b41726665f13af0d400a0601a098f7;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index f5cf03c..0480ffa 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,25 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program is free software; you can redistribute it and/or
+ * 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
+ *
+ * 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 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
+ * 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/>.
  */
 package jalview.gui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.*;
@@ -29,7 +29,7 @@ import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -43,8 +43,9 @@ public class IdPanel extends JPanel implements MouseListener,
   protected AlignmentPanel alignPanel;
 
   ScrollThread scrollThread = null;
+
   String linkImageURL;
-  
+
   int offy;
 
   // int width;
@@ -54,11 +55,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * Creates a new IdPanel object.
-   * 
+   *
    * @param av
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param parent
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -76,18 +77,19 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     SeqPanel sp = alignPanel.seqPanel;
     int seq = Math.max(0, sp.findSeq(e));
     String tmp;
-    if (seq > -1 && seq < av.alignment.getHeight())
+    if (seq > -1 && seq < av.getAlignment().getHeight())
     {
-      SequenceI sequence = av.alignment.getSequenceAt(seq);
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
       StringBuffer tip = new StringBuffer();
       tip.append("<i>");
 
@@ -123,8 +125,9 @@ public class IdPanel extends JPanel implements MouseListener,
           {
             int sz = -tip.length();
             tfeat[0] = features[i];
-            sp.appendFeatures(tip, linkImageURL, 0, tfeat,sp.seqCanvas.fr.minmax);
-            sz+=tip.length();
+            sp.appendFeatures(tip, linkImageURL, 0, tfeat,
+                    sp.seqCanvas.fr.minmax);
+            sz += tip.length();
             maxWidth = Math.max(maxWidth, sz);
           }
         }
@@ -138,17 +141,18 @@ public class IdPanel extends JPanel implements MouseListener,
 
       tip.append("</html>");
 
-      setToolTipText("<html>" + sequence.getDisplayId(true)
+      setToolTipText("<html>" + sequence.getDisplayId(true) + " "
               + tip.toString());
     }
   }
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent e)
   {
     mouseDragging = true;
@@ -163,11 +167,12 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeqs(lastid + 1, seq);
     }
-    
+
     lastid = seq;
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
@@ -183,10 +188,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
@@ -255,10 +261,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -269,10 +276,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -286,7 +294,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.alignment.getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -294,10 +302,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent e)
   {
     if (e.getClickCount() == 2)
@@ -309,28 +318,27 @@ public class IdPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
-      Sequence sq = (Sequence) av
-      .getAlignment().getSequenceAt(seq);
-      // build a new links menu based on the current links + any non-positional features
+      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++)
+      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].begin == sf[sl].end && sf[sl].begin == 0)
         {
-          if (sf[sl].links!=null && sf[sl].links.size()>0)
+          if (sf[sl].links != null && sf[sl].links.size() > 0)
           {
-            for (int l=0, lSize=sf[sl].links.size(); l<lSize; l++)
-            { 
+            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);
+
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
+              nlinks, new Vector(Preferences.getGroupURLLinks()));
       pop.show(this, e.getX(), e.getY());
 
       return;
@@ -342,7 +350,7 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
     if (e.isShiftDown() && (lastid != -1))
@@ -353,15 +361,14 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeq(seq);
     }
-    av.sendSelection();
     alignPanel.paintAlignment(true);
   }
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -373,11 +380,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param start
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param end
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   void selectSeqs(int start, int end)
   {
@@ -407,45 +414,43 @@ public class IdPanel extends JPanel implements MouseListener,
               av.getAlignment().getSequenceAt(i), true);
     }
   }
+
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent e)
   {
     if (scrollThread != null)
     {
       scrollThread.running = false;
     }
-    if (mouseDragging)
-    {
-     
-      av.sendSelection();
-      
-    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param found
-   *                DOCUMENT ME!
+   *
+   * @param list
+   *          DOCUMENT ME!
    */
-  public void highlightSearchResults(java.util.Vector found)
+  public void highlightSearchResults(List<SequenceI> list)
   {
-    idCanvas.setHighlighted(found);
+    idCanvas.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))
@@ -472,6 +477,7 @@ public class IdPanel extends JPanel implements MouseListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;