v2

[jalview.git] / src / jalview / gui / IdPanel.java

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 38912fd..0480ffa 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,24 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
+ * 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 
+ * 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 
+ *
+ * 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.*;
@@ -28,7 +29,7 @@ import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -54,7 +55,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * Creates a new IdPanel object.
-   * 
+   *
    * @param av
    *          DOCUMENT ME!
    * @param parent
@@ -76,18 +77,19 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          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>");
 
@@ -146,10 +148,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent e)
   {
     mouseDragging = true;
@@ -169,6 +172,7 @@ public class IdPanel extends JPanel implements MouseListener,
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
@@ -184,10 +188,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
@@ -256,10 +261,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -270,10 +276,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -287,7 +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);
     }
@@ -295,10 +302,11 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent e)
   {
     if (e.getClickCount() == 2)
@@ -314,7 +322,7 @@ public class IdPanel extends JPanel implements MouseListener,
       // 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();
+      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)
@@ -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))
@@ -358,7 +366,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param seq
    *          DOCUMENT ME!
    */
@@ -372,7 +380,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param start
    *          DOCUMENT ME!
    * @param end
@@ -409,43 +417,40 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent e)
   {
     if (scrollThread != null)
     {
       scrollThread.running = false;
     }
-    // if (mouseDragging)
-    {
-      // always send selection message when mouse is released
-      av.sendSelection();
-
-    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param found
+   *
+   * @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;