X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=2c3aced98760b033ec38d59714d1f1f322657f90;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=5bf5b6100f5d005e47c9ca6ea26e431cfee62397;hpb=8787ad51b5206692859df9b84e836a01e7a91c02;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 5bf5b61..2c3aced 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -22,6 +22,7 @@ import jalview.datamodel.*;
 
 public class RemoveGapColCommand  extends EditCommand
 {
+  int columnsDeleted;
   public RemoveGapColCommand(String description,
                              SequenceI[] seqs,
                              int start, int end, char gapChar)
@@ -31,12 +32,12 @@ public class RemoveGapColCommand  extends EditCommand
     int j, jSize = seqs.length;
 
     int startCol = -1, endCol = -1;
-    int deletedCols = 0;
+    columnsDeleted=0;
 
     edits = new Edit[0];
 
     boolean delete = true;
-    for (int i = start; i < end; i++)
+    for (int i = start; i <= end; i++)
     {
       delete = true;
 
@@ -63,12 +64,12 @@ public class RemoveGapColCommand  extends EditCommand
       if (!delete && startCol > -1)
       {
         this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
+                        startCol - columnsDeleted,
                         endCol - startCol,
                         gapChar,
                         false);
 
-        deletedCols += (endCol - startCol);
+        columnsDeleted += (endCol - startCol);
         startCol = -1;
         endCol = -1;
       }
@@ -78,14 +79,25 @@ public class RemoveGapColCommand  extends EditCommand
     {
        //This is for empty columns at the
        //end of the alignment
+
       this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
-                        end-startCol+1,
+                        startCol - columnsDeleted,
+                        end - startCol +1,
                         gapChar,
                         false);
+
+      columnsDeleted += (end - startCol +1);
     }
 
+
     performEdit(0);
   }
 
+  public int getSize()
+  {
+    //We're interested in the number of columns deleted,
+    //Not the number of sequence edits.
+    return columnsDeleted;
+  }
+
 }