From 8030eb1b0676c7ffe57f90d8131525ab7ff4b243 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Feb 2005 13:23:09 +0000
Subject: [PATCH] check that mouse is over sequence if unaligned

---
 src/jalview/gui/SeqPanel.java |   28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 83dceef..35c5aef 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -170,6 +170,9 @@ public class SeqPanel extends JPanel
       return;
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    if(res>sequence.getLength())
+      return;
+
     Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
     String aa = "";
     if(obj!=null)
@@ -181,7 +184,8 @@ public class SeqPanel extends JPanel
 
     ap.alignFrame.statusBar.setText(text.toString());
 
-    if(av.showSequenceFeatures)
+    // use aa to see if the mouse pointer is on a
+    if(  av.showSequenceFeatures)
     {
       Vector features = sequence.getSequenceFeatures();
       Enumeration e = features.elements();
@@ -213,6 +217,9 @@ public class SeqPanel extends JPanel
   public void doMouseDragged(MouseEvent evt) {
     // If we're dragging we're editing
 
+    if(lastres==-1)
+      return;
+
     int x = evt.getX();
 
     int res = x/av.getCharWidth() + av.getStartRes();
@@ -361,24 +368,25 @@ public class SeqPanel extends JPanel
     int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
     oldSeq = seq;
 
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+    if(res>sequence.getLength())
+      return;
+
     stretchGroup = av.getRubberbandGroup();
 
     if(stretchGroup == null)
      {
-       stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment().
-                                             getSequenceAt(seq));
+       stretchGroup = av.alignment.findGroup( sequence );
        av.setRubberbandGroup( stretchGroup );
      }
 
-    else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
+    else if(!stretchGroup.sequences.contains(sequence)
             || stretchGroup.getStartRes()>res
             || stretchGroup.getEndRes()<res)
      {
        stretchGroup = null;
 
-       SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.
-           getAlignment().
-           getSequenceAt(seq));
+       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
 
        if (allGroups != null)
          for (int i = 0; i < allGroups.length; i++)
@@ -397,7 +405,7 @@ public class SeqPanel extends JPanel
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
+      sg.addSequence( sequence );
       av.setRubberbandGroup( sg );
       stretchGroup = sg;
 
@@ -442,6 +450,8 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
+    if(stretchGroup==null)
+      return;
 
     if(stretchGroup.cs instanceof ClustalxColourScheme)
     {
@@ -495,6 +505,8 @@ public class SeqPanel extends JPanel
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
     int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
 
+    if(stretchGroup==null)
+      return;
 
     if(stretchGroup.getEndRes()==res)
       // Edit end res position of selected group
-- 
1.7.10.2