X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;fp=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=4c1dea0f26420edc314b79792864768bcfb356f0;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=37518bcadb09f4d25e76ee7c28ae3345267abbef;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 37518bc..4c1dea0 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,6 +1,6 @@
 /*
  * 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
@@ -18,9 +18,10 @@
  */
 package jalview.commands;
 
-import jalview.util.ShiftList;
+import java.util.*;
+
 import jalview.datamodel.*;
-import java.util.Vector;
+import jalview.util.*;
 
 public class TrimRegionCommand
     extends EditCommand
@@ -30,7 +31,7 @@ public class TrimRegionCommand
 
   public ColumnSelection colSel = null;
 
-  int [] start;
+  int[] start;
 
   ShiftList shiftList;
 
@@ -41,45 +42,52 @@ public class TrimRegionCommand
   int columnsDeleted;
 
   public TrimRegionCommand(String description,
-                     String command,
-                     SequenceI[] seqs,
-                     int column,
-                     AlignmentI al,
-                     ColumnSelection colSel,
-                     SequenceGroup selectedRegion)
+                           String command,
+                           SequenceI[] seqs,
+                           int column,
+                           AlignmentI al,
+                           ColumnSelection colSel,
+                           SequenceGroup selectedRegion)
   {
     this.description = description;
     this.selectionGroup = selectedRegion;
     this.colSel = colSel;
     if (command.equalsIgnoreCase(TRIM_LEFT))
     {
-      if(column==0)
+      if (column == 0)
+      {
         return;
+      }
 
       columnsDeleted = column;
 
-      edits = new Edit[] { new Edit(CUT, seqs, 0, column, al)};
+      edits = new Edit[]
+          {
+          new Edit(CUT, seqs, 0, column, al)};
     }
     else if (command.equalsIgnoreCase(TRIM_RIGHT))
     {
-      int width = al.getWidth()-column-1;
-      if(width<2)
+      int width = al.getWidth() - column - 1;
+      if (width < 2)
       {
         return;
       }
 
-      columnsDeleted = width-1;
+      columnsDeleted = width - 1;
 
       edits = new Edit[]
-          { new Edit(CUT, seqs, column+1, width, al)};
+          {
+          new Edit(CUT, seqs, column + 1, width, al)};
     }
 
     //We need to keep a record of the sequence start
     //in order to restore the state after a redo
     int i, isize = edits[0].seqs.length;
     start = new int[isize];
-    for(i=0; i<isize; i++)
+    for (i = 0; i < isize; i++)
+    {
       start[i] = edits[0].seqs[i].getStart();
+    }
 
     performEdit(0);
   }
@@ -89,7 +97,7 @@ public class TrimRegionCommand
     int column, j, jSize = command.seqs.length;
     for (j = 0; j < jSize; j++)
     {
-      if(command.position==0)
+      if (command.position == 0)
       {
         //This is a TRIM_LEFT command
         column = command.seqs[j].findPosition(command.number);
@@ -98,7 +106,7 @@ public class TrimRegionCommand
       else
       {
         //This is a TRIM_RIGHT command
-        column = command.seqs[j].findPosition(command.position)-1;
+        column = command.seqs[j].findPosition(command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -108,14 +116,19 @@ public class TrimRegionCommand
     if (command.position == 0)
     {
       deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
-      if(selectionGroup!=null)
+      if (selectionGroup != null)
+      {
         selectionGroup.adjustForRemoveLeft(command.number);
+      }
     }
     else
     {
-      deletedHiddenColumns = colSel.compensateForEdit(command.position, command.number);
-      if(selectionGroup!=null)
+      deletedHiddenColumns = colSel.compensateForEdit(command.position,
+          command.number);
+      if (selectionGroup != null)
+      {
         selectionGroup.adjustForRemoveRight(command.position);
+      }
     }
   }
 
@@ -125,14 +138,14 @@ public class TrimRegionCommand
     int column, j, jSize = command.seqs.length;
     for (j = 0; j < jSize; j++)
     {
-      if(command.position==0)
+      if (command.position == 0)
       {
         command.seqs[j].setStart(start[j]);
       }
       else
       {
         column = command.seqs[j]
-            .findPosition(command.number+command.position)-1;
+            .findPosition(command.number + command.position) - 1;
         command.seqs[j].setEnd(column);
       }
     }
@@ -140,8 +153,10 @@ public class TrimRegionCommand
     if (command.position == 0)
     {
       colSel.compensateForEdit(0, -command.number);
-      if(selectionGroup!=null)
-        selectionGroup.adjustForRemoveLeft(-command.number);
+      if (selectionGroup != null)
+      {
+        selectionGroup.adjustForRemoveLeft( -command.number);
+      }
     }
 
     if (deletedHiddenColumns != null)