X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=8166ed61adf81d35446eeb25c38199c3f1fc3234;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=8ada376dc57ce8d0119188c940e5eca9bc081d9e;hpb=ebb678af128304dc13e1b6ec9e0961489bf83d39;p=jalview.git

diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 8ada376..8166ed6 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -19,8 +19,8 @@
 package jalview.commands;
 
 import jalview.util.ShiftList;
-
 import jalview.datamodel.*;
+import java.util.Vector;
 
 public class TrimRegionCommand
     extends EditCommand
@@ -32,23 +32,46 @@ public class TrimRegionCommand
 
   int [] start;
 
+  ShiftList shiftList;
+
+  SequenceGroup selectionGroup;
+
+  Vector deletedHiddenColumns;
+
+  int columnsDeleted;
+
   public TrimRegionCommand(String description,
                      String command,
                      SequenceI[] seqs,
                      int column,
                      AlignmentI al,
-                     ColumnSelection colSel)
+                     ColumnSelection colSel,
+                     SequenceGroup selectedRegion)
   {
     this.description = description;
+    this.selectionGroup = selectedRegion;
+    this.colSel = colSel;
     if (command.equalsIgnoreCase(TRIM_LEFT))
     {
+      if(column==0)
+        return;
+
+      columnsDeleted = column;
+
       edits = new Edit[] { new Edit(CUT, seqs, 0, column, al)};
-      this.colSel = colSel;
     }
     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
@@ -68,16 +91,32 @@ public class TrimRegionCommand
     {
       if(command.position==0)
       {
+        //This is a TRIM_LEFT command
         column = command.seqs[j].findPosition(command.number);
         command.seqs[j].setStart(column);
       }
       else
       {
+        //This is a TRIM_RIGHT command
         column = command.seqs[j].findPosition(command.position)-1;
         command.seqs[j].setEnd(column);
       }
     }
+
     super.cut(command);
+
+    if (command.position == 0)
+    {
+      deletedHiddenColumns = colSel.compensateForEdit(0, command.number);
+      if(selectionGroup!=null)
+        selectionGroup.adjustForRemoveLeft(command.number);
+    }
+    else
+    {
+      deletedHiddenColumns = colSel.compensateForEdit(command.position, command.number);
+      if(selectionGroup!=null)
+        selectionGroup.adjustForRemoveRight(command.position);
+    }
   }
 
   void paste(Edit command)
@@ -98,12 +137,27 @@ public class TrimRegionCommand
       }
     }
 
-    if(command.position==0)
+    if (command.position == 0)
+    {
+      colSel.compensateForEdit(0, -command.number);
+      if(selectionGroup!=null)
+        selectionGroup.adjustForRemoveLeft(-command.number);
+    }
+
+    if (deletedHiddenColumns != null)
     {
-      ShiftList slist = new ShiftList();
-      slist.addShift(0, -command.number);
-      colSel.compensateForEdits(slist);
+      int[] region;
+      for (int i = 0; i < deletedHiddenColumns.size(); i++)
+      {
+        region = (int[]) deletedHiddenColumns.elementAt(i);
+        colSel.hideColumns(region[0], region[1]);
+      }
     }
   }
 
+  public int getSize()
+  {
+    return columnsDeleted;
+  }
+
 }