From be545261cf6e7225da6f3ac1306b1b2609fd0e70 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:31:36 +0000
Subject: [PATCH] historyItem.restore

---
 src/jalview/gui/AlignFrame.java |   42 +++++----------------------------------
 1 file changed, 5 insertions(+), 37 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b714aea..a4f5e4d 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -450,42 +450,8 @@ public class AlignFrame
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
-    }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -2575,11 +2541,12 @@ public void showTranslation_actionPerformed(ActionEvent e)
  */
 public boolean parseGroupsFile(String file)
 {
+    String line = null;
     try
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
       SequenceI seq = null;
-      String line, type, desc, token;
+      String type, desc, token;
 
       int index, start, end;
       StringTokenizer st;
@@ -2650,8 +2617,9 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
+      System.out.println(line);
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex);
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
       return false;
     }
 
-- 
1.7.10.2