From 0f31ab4d7d3c5fdf3af01f3f2f497962d9602725 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 22 May 2005 18:18:38 +0000
Subject: [PATCH] include MsaWS ordering but not perfect (undo destroys
 ordering efficacy).

---
 src/jalview/gui/AlignFrame.java |   50 +--------------------------------------
 1 file changed, 1 insertion(+), 49 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1ff77e6..b60ee62 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1062,6 +1062,7 @@ public class AlignFrame extends GAlignFrame
       public void actionPerformed(ActionEvent e)
       {
         addHistoryItem("sort");
+        // TODO: JBPNote - have to map order entries to curent SequenceI pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
         alignPanel.repaint();
       }
@@ -1128,55 +1129,6 @@ public class AlignFrame extends GAlignFrame
           jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
         }
   }
-/* Old cLustalW
-       WebserviceInfo info = new WebserviceInfo("Clustal web service",
-     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
-     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
-    +" Nucleic Acids Research, submitted, June 1994.",
-     450, 150);
-
-    ClustalThread thread = new ClustalThread(info);
-    thread.start();
-  }
-
-    class ClustalThread extends Thread
-    {
-      WebserviceInfo info;
-      public ClustalThread(WebserviceInfo info)
-      {this.info = info; }
-
-      public void run()
-      {
-        info.setStatus(WebserviceInfo.STATE_RUNNING);
-        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-        Vector sv = viewport.getAlignment().getSequences();
-        SequenceI[] seqs = new SequenceI[sv.size()];
-
-        int i = 0;
-        do
-        {
-          seqs[i] = (SequenceI) sv.elementAt(i);
-        }
-        while (++i < sv.size());
-
-        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-        if (alignment != null)
-        {
-          AlignFrame af = new AlignFrame(new Alignment(alignment));
-          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
-                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-          af.clustalColour_actionPerformed(null);
-          af.clustalColour.setSelected(true);
-          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else
-        {
-            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-            info.appendProgressText("Problem obtaining clustal alignment");
-        }
-      }
-    }
-*/
 
   protected void jpred_actionPerformed(ActionEvent e)
 {
-- 
1.7.10.2