X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=cdaa5b949c903dcdc41581c30a1563f9d0afc953;hb=f1cf002d98f35e6d471ebf1af95b37c63cf86d1c;hp=b8902bd0b18aeb1b44b5f863ccdccb9fdad4fdef;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index b8902bd..cdaa5b9 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,23 +1,24 @@
 /*
  * 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.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -31,7 +32,7 @@ import jalview.structure.*;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision: 1.130 $
  */
@@ -97,7 +98,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * Creates a new SeqPanel object.
-   * 
+   *
    * @param avp
    *          DOCUMENT ME!
    * @param p
@@ -297,7 +298,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   void setCursorPosition()
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
@@ -392,7 +393,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
@@ -482,7 +483,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     editSequence(false, false, seqCanvas.cursorX);
     endEditing();
   }
-  
+
   void insertNucAtCursor(boolean group,String nuc){
 	  groupEditing = group;
 	    startseq = seqCanvas.cursorY;
@@ -534,10 +535,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
@@ -554,10 +556,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     lastMousePress = evt.getPoint();
@@ -607,6 +610,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   String lastMessage;
 
+  @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
     String tmp = sequence.hashCode() + " " + index + " " + pos;
@@ -619,6 +623,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     lastMessage = tmp;
   }
 
+  @Override
   public void highlightSequence(SearchResults results)
   {
     if (av.followHighlight)
@@ -631,6 +636,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     seqCanvas.highlightSearchResults(results);
   }
 
+  @Override
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
@@ -639,10 +645,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     if (editingSeqs)
@@ -755,7 +762,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * appends the features at rpos to the given stringbuffer ready for display in
    * a tooltip
-   * 
+   *
    * @param tooltipText2
    * @param linkImageURL
    * @param rpos
@@ -896,7 +903,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * Set status message in alignment panel
-   * 
+   *
    * @param sequence
    *          aligned sequence object
    * @param res
@@ -944,10 +951,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (mouseWheelPressed)
@@ -1101,7 +1109,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       // but the sequence represents a group
       if (sg == null)
       {
-        if (av.isHiddenRepSequence(seq))
+        if (!av.isHiddenRepSequence(seq))
         {
           endEditing();
           return;
@@ -1163,12 +1171,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (groupEditing)
     {
-      Vector vseqs = sg.getSequences(av.getHiddenRepSequences());
+      List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
       int g, groupSize = vseqs.size();
       SequenceI[] groupSeqs = new SequenceI[groupSize];
       for (g = 0; g < groupSeqs.length; g++)
       {
-        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+        groupSeqs[g] = vseqs.get(g);
       }
 
       // drag to right
@@ -1424,10 +1432,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (oldSeq < 0)
@@ -1444,10 +1453,11 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -1461,6 +1471,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     SequenceGroup sg = null;
@@ -1495,6 +1506,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
@@ -1511,7 +1523,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
@@ -1536,7 +1548,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
     if ((sequence == null) || (res > sequence.getLength()))
     {
@@ -1656,7 +1668,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
@@ -1673,9 +1685,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-                stretchGroup.getSequences(av.getHiddenRepSequences()),
-                stretchGroup.getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
+                stretchGroup,av.getHiddenRepSequences());
       }
 
       if (stretchGroup.cs.conservationApplied())
@@ -1700,7 +1711,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
@@ -1857,6 +1868,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
@@ -1899,6 +1911,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * modify current selection according to a received message.
    */
+  @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
           SelectionSource source)
   {