From a87f4c6fd568ccf29aaf3af0ad528da442ea921d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:44:33 +0000
Subject: [PATCH] Retrieves PFAM alignments

---
 src/jalview/gui/SequenceFetcher.java |   26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 0884d44..6d49d12 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -44,6 +44,7 @@ public class SequenceFetcher
     database.addItem("EMBL");
     database.addItem("EMBLCDS");
     database.addItem("PDB");
+    database.addItem("PFAM");
 
     try
     {
@@ -64,8 +65,7 @@ public class SequenceFetcher
 
   private String getFrameTitle()
   {
-    return ( (alignFrame == null) ? "New " : "Additional ") +
-        "Sequence Fetcher (WSDBfetch@EBI)";
+    return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
   }
 
   private void jbInit()
@@ -142,7 +142,6 @@ public class SequenceFetcher
 
   public void ok_actionPerformed(ActionEvent e)
   {
-    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
     database.setEnabled(false);
     textfield.setEnabled(false);
     ok.setEnabled(false);
@@ -158,7 +157,6 @@ public class SequenceFetcher
     textfield.setEnabled(true);
     ok.setEnabled(true);
     close.setEnabled(true);
-    frame.setTitle(getFrameTitle());
   }
 
   public void run()
@@ -214,13 +212,27 @@ public class SequenceFetcher
       if (result.length()>0)
         parseResult(result.toString());
     }
+    else if( database.getSelectedItem().equals("PFAM"))
+    {
+      try{
+        result.append(new FastaFile(
+           "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+           +  textfield.getText().toUpperCase(), "URL").print()
+           );
+
+         if(result.length()>0)
+           parseResult( result.toString() );
+
+      }catch(java.io.IOException ex)
+      {   result = null;    }
+    }
 
     if (result == null || result.length() == 0)
       showErrorMessage("Error retrieving " + textfield.getText()
                        + " from " + database.getSelectedItem());
-    else
-      textfield.setText("");
+
     resetDialog();
+    return;
   }
 
   void getUniprotFile(String id)
@@ -433,9 +445,11 @@ public class SequenceFetcher
 
   void showErrorMessage(String error)
   {
+    resetDialog();
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                           error, "Error Retrieving Data",
                                           JOptionPane.WARNING_MESSAGE);
+    return;
   }
 }
 
-- 
1.7.10.2