From 7931bc3242f86a9fbd36f9910ba5fd3551bc6e0b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 26 Oct 2006 13:09:20 +0000
Subject: [PATCH] Returns number of columns deleted

---
 src/jalview/commands/RemoveGapColCommand.java |   24 ++++++++++++++++++------
 src/jalview/commands/TrimRegionCommand.java   |   22 ++++++++++++++++++++--
 2 files changed, 38 insertions(+), 8 deletions(-)

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;
+  }
+
 }
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 5a5dcd1..8166ed6 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -38,6 +38,8 @@ public class TrimRegionCommand
 
   Vector deletedHiddenColumns;
 
+  int columnsDeleted;
+
   public TrimRegionCommand(String description,
                      String command,
                      SequenceI[] seqs,
@@ -51,12 +53,25 @@ public class TrimRegionCommand
     this.colSel = colSel;
     if (command.equalsIgnoreCase(TRIM_LEFT))
     {
+      if(column==0)
+        return;
+
+      columnsDeleted = column;
+
       edits = new Edit[] { new Edit(CUT, seqs, 0, column, al)};
     }
     else if (command.equalsIgnoreCase(TRIM_RIGHT))
     {
+      int width = al.getWidth()-column;
+      if(width<2)
+      {
+        return;
+      }
+
+      columnsDeleted = width-1;
+
       edits = new Edit[]
-          { new Edit(CUT, seqs, column+1, al.getWidth() - column, al)};
+          { new Edit(CUT, seqs, column+1, width, al)};
     }
 
     //We need to keep a record of the sequence start
@@ -138,8 +153,11 @@ public class TrimRegionCommand
         colSel.hideColumns(region[0], region[1]);
       }
     }
+  }
 
-
+  public int getSize()
+  {
+    return columnsDeleted;
   }
 
 }
-- 
1.7.10.2