From 46897ebed0492bccdce44872277a3e4c3d9f0e07 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sat, 15 Jan 2005 15:04:16 +0000
Subject: [PATCH] Implemented clustal alignment via jemboss.

---
 src/jalview/gui/AlignFrame.java |   34 ++++++++++++++++++++++++++++------
 1 file changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f7b4ac5..96ba962 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -16,6 +16,7 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
+import jalview.ws.*;
 import MCview.*;
 import java.awt.*;
 import java.awt.event.*;
@@ -23,6 +24,7 @@ import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
+import jalview.datamodel.SequenceI;
 
 public class AlignFrame extends GAlignFrame
 {
@@ -456,7 +458,7 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-  public void clustalColour_actionPerformed(ActionEvent e)
+  public void Colour_actionPerformed(ActionEvent e)
   {
     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
     conservationMenuItem.setSelected(false);
@@ -795,15 +797,35 @@ public class AlignFrame extends GAlignFrame
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
-                                  +"\nwithin the Barton Group, Dundee University."
-                                  +"\nThis will be available as a web service 2005",
-                                  "Web service", JOptionPane.INFORMATION_MESSAGE);
+    // JBPNote
+    // Should check to see if the server settings are valid
+    // Need visual-delay indication here.
+    Jemboss jemboss = new 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, getTitle().concat(" - ClustalW Alignment"), 
+                               700, 500); // JBPNote - is there a new window geom. property ?
+    }
   }
 
   public void pdbTest_actionPerformed(ActionEvent e)
   {
-   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
+   String reply = 
+       JOptionPane.showInternalInputDialog(this, "Enter pdb code", 
+                                           "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
 
    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
    if (reply.length()>1)
-- 
1.7.10.2