From b59132cb08bb83359dd7fcb17c50a964d4b162c5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 7 Jul 2005 10:14:03 +0000
Subject: [PATCH] Remove all gaps must check jSize

---
 src/jalview/appletgui/AlignFrame.java |   15 ++++++++++++++-
 src/jalview/gui/AlignFrame.java       |   12 +++++++++++-
 2 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index aeee116..3ab3132 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -397,13 +397,26 @@ public class AlignFrame
       return;
     }
 
+
     SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
+
     for (int i = 0; i < sg.sequences.size(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+                                                     sg.getEndRes() + 1);
+      }
+
+
       if (seq.getSequence().length() < 1)
       {
         viewport.getAlignment().deleteSequence(seq);
@@ -579,7 +592,7 @@ public class AlignFrame
         }
         j++;
       }
-      while(j < end);
+      while(j < end && j < jSize) ;
     }
 
     viewport.updateConservation();
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d154e2e..2f7e5a8 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -680,6 +680,9 @@ public class AlignFrame extends GAlignFrame
                 HistoryItem.HIDE));
 
         SequenceGroup sg = viewport.getSelectionGroup();
+        boolean allSequences = false;
+        if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
 
         for (int i = 0; i < sg.sequences.size(); i++)
         {
@@ -687,6 +690,13 @@ public class AlignFrame extends GAlignFrame
             int index = viewport.getAlignment().findIndex(seq);
             seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+            // If the cut affects all sequences, remove highlighted columns
+            if(allSequences)
+            {
+              viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
+            }
+
+
             if (seq.getSequence().length() < 1)
             {
                 seqsdeleted = true;
@@ -936,7 +946,7 @@ public class AlignFrame extends GAlignFrame
 
                 j++;
             }
-            while (j < end);
+            while (j < end && j < jSize);
         }
 
         viewport.updateConservation();
-- 
1.7.10.2