X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=1e9b83299d897e7142c9008b49c84bc1851f8b41;hb=def10fb2252c67e8256ec1fddc6605e34d760c63;hp=5bf5b6100f5d005e47c9ca6ea26e431cfee62397;hpb=8787ad51b5206692859df9b84e836a01e7a91c02;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 5bf5b61..1e9b832 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,7 +1,8 @@
 package jalview.commands;
-  /*
+
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -20,23 +21,25 @@ package jalview.commands;
 
 import jalview.datamodel.*;
 
-public class RemoveGapColCommand  extends EditCommand
+public class RemoveGapColCommand
+    extends EditCommand
 {
+  int columnsDeleted;
   public RemoveGapColCommand(String description,
                              SequenceI[] seqs,
-                             int start, int end, char gapChar)
+                             int start, int end, AlignmentI al)
   {
     this.description = description;
 
     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;
 
@@ -47,7 +50,9 @@ public class RemoveGapColCommand  extends EditCommand
           if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
           {
             if (delete)
+            {
               endCol = i;
+            }
 
             delete = false;
             break;
@@ -63,12 +68,12 @@ public class RemoveGapColCommand  extends EditCommand
       if (!delete && startCol > -1)
       {
         this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
+                        startCol - columnsDeleted,
                         endCol - startCol,
-                        gapChar,
+                        al,
                         false);
 
-        deletedCols += (endCol - startCol);
+        columnsDeleted += (endCol - startCol);
         startCol = -1;
         endCol = -1;
       }
@@ -76,16 +81,26 @@ public class RemoveGapColCommand  extends EditCommand
 
     if (delete && startCol > -1)
     {
-       //This is for empty columns at the
-       //end of the alignment
+      //This is for empty columns at the
+      //end of the alignment
+
       this.appendEdit(DELETE_GAP, seqs,
-                        startCol - deletedCols,
-                        end-startCol+1,
-                        gapChar,
-                        false);
+                      startCol - columnsDeleted,
+                      end - startCol + 1,
+                      al,
+                      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;
+  }
+
 }