From 24dfc5f9d53c590ad1b5fda82f312d9742ac4d5d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 20 May 2005 09:27:38 +0000
Subject: [PATCH] copy order maintained

---
 src/jalview/appletgui/AlignFrame.java |   24 ++++++++++++++++++++++--
 src/jalview/gui/AlignFrame.java       |   33 +++++++++++++++++++++++++++------
 2 files changed, 49 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 44b163b..711a2f3 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -222,10 +222,30 @@ public class AlignFrame extends GAlignFrame
 
    SequenceGroup sg = viewport.getSelectionGroup();
    copiedSequences = new StringBuffer();
+   Hashtable orderedSeqs = new Hashtable();
+   for(int i=0; i<sg.getSize(); i++)
+   {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.alignment.findIndex(seq);
+      orderedSeqs.put(index+"", seq);
+   }
 
-       for(int i=0; i<sg.getSize(); i++)
+   int index=0;
+   for(int i=0; i<sg.getSize(); i++)
+   {
+     SequenceI seq = null;
+     while( seq == null )
+     {
+       if(orderedSeqs.containsKey(index+""))
        {
-         SequenceI seq = sg.getSequenceAt(i);
+         seq = (SequenceI) orderedSeqs.get(index + "");
+         index++;
+         break;
+       }
+       else
+         index++;
+     }
+
          copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
                         +seq.findPosition( sg.getEndRes() )+ "\t"
                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3302fff..725a702 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -287,21 +287,42 @@ public class AlignFrame extends GAlignFrame
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+     if(viewport.getSelectionGroup()==null)
+       return;
 
-   SequenceGroup sg = viewport.getSelectionGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
 
-       for(int i=0; i<sg.getSize(); i++)
+     Hashtable orderedSeqs = new Hashtable();
+     for(int i=0; i<sg.getSize(); i++)
+     {
+        SequenceI seq = sg.getSequenceAt(i);
+        int index = viewport.alignment.findIndex(seq);
+        orderedSeqs.put(index+"", seq);
+     }
+
+     int index=0;
+     for(int i=0; i<sg.getSize(); i++)
+     {
+       SequenceI seq = null;
+       while( seq == null )
        {
-         SequenceI seq = sg.getSequenceAt(i);
+         if(orderedSeqs.containsKey(index+""))
+         {
+           seq = (SequenceI) orderedSeqs.get(index + "");
+           index++;
+           break;
+         }
+         else
+           index++;
+       }
+
          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
                         +seq.findPosition( sg.getEndRes() )+ "\t"
                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
+     }
      c.setContents( new StringSelection( buffer.toString()) , null ) ;
 
   }
-- 
1.7.10.2