From 8787ad51b5206692859df9b84e836a01e7a91c02 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 26 Oct 2006 09:37:58 +0000
Subject: [PATCH] Known bugs fixed

---
 src/jalview/commands/RemoveGapColCommand.java |   10 ++-------
 src/jalview/commands/RemoveGapsCommand.java   |   29 +++++++++++++------------
 2 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index dfcfc47..5bf5b61 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -36,7 +36,7 @@ public class RemoveGapColCommand  extends EditCommand
     edits = new Edit[0];
 
     boolean delete = true;
-    for (int i = start; i <= end; i++)
+    for (int i = start; i < end; i++)
     {
       delete = true;
 
@@ -78,15 +78,9 @@ public class RemoveGapColCommand  extends EditCommand
     {
        //This is for empty columns at the
        //end of the alignment
-       int width = end-endCol;
-
-      if(endCol==-1)
-        width = end-start+1;
-
-
       this.appendEdit(DELETE_GAP, seqs,
                         startCol - deletedCols,
-                        width,
+                        end-startCol+1,
                         gapChar,
                         false);
     }
diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 9343ec2..ddd6b76 100644
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -48,37 +48,44 @@ public class RemoveGapsCommand  extends EditCommand
     int startCol = -1, endCol = -1;
     int deletedCols = 0;
 
+    int j, jSize;
+
     edits = new Edit[0];
 
     boolean delete = true;
     char [] sequence;
+
     for(int s=0; s<seqs.length; s++)
     {
       deletedCols = 0;
       startCol = -1;
       endCol = -1;
-      sequence = seqs[s].getSequence().toCharArray();
-      for (int i = start; i < end; i++)
+      sequence = seqs[s].getSequence(start, end+1).toCharArray();
+
+      jSize = sequence.length;
+      for (j=0; j<jSize; j++)
       {
         delete = true;
 
-        if (!jalview.util.Comparison.isGap(sequence[i]))
+
+        if (!jalview.util.Comparison.isGap(sequence[j]))
         {
           if (delete)
-            endCol = i;
+            endCol = j;
 
           delete = false;
         }
 
+
         if (delete && startCol == -1)
         {
-          startCol = i;
+          startCol = j;
         }
 
         if (!delete && startCol > -1)
         {
           this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},
-                          startCol - deletedCols,
+                          start + startCol - deletedCols,
                           endCol - startCol,
                           gapChar,
                           false);
@@ -90,15 +97,9 @@ public class RemoveGapsCommand  extends EditCommand
       }
       if (delete && startCol > -1)
       {
-        int width = end - endCol;
-
-        if (endCol == -1)
-          width = end - start + 1;
-
-        //This is the end of the region.
         this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]},
-                        startCol - deletedCols,
-                        width,
+                        start + startCol - deletedCols,
+                        jSize - startCol,
                         gapChar,
                         false);
       }
-- 
1.7.10.2