run pfam search option

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10796 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/RunMenu.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/RunMenu.java,v 1.12 2008-09-11 10:51:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/RunMenu.java,v 1.13 2009-05-13 15:53:14 tjc Exp $
  **/
 
 package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.JOptionPane;
  *  A JMenu of external commands/functions.
  *
  *  @author Kim Rutherford
- *  @version $Id: RunMenu.java,v 1.12 2008-09-11 10:51:53 tjc Exp $
+ *  @version $Id: RunMenu.java,v 1.13 2009-05-13 15:53:14 tjc Exp $
  **/
 
 public class RunMenu extends SelectionMenu 
@@ -71,7 +71,7 @@ public class RunMenu extends SelectionMenu
     super(frame, menu_name, selection);
 
     addNCBISearches(selection);
-    
+    addPfamSearches(selection);
     if(Options.isUnixHost())
     {
       final ExternalProgramVector external_programs = Options.getOptions()
@@ -103,6 +103,31 @@ public class RunMenu extends SelectionMenu
     this(frame, selection, "Run");
   }
 
+  private void addPfamSearches(final Selection selection)
+  {
+    final JMenuItem ncbiSearchLinks = new JMenuItem("Pfam Search");
+    add(ncbiSearchLinks);
+    ncbiSearchLinks.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent arg0)
+      {
+        final FeatureVector features = selection.getAllFeatures();
+        
+        if(features.size() != 1)
+        {
+          JOptionPane.showMessageDialog(RunMenu.this,
+              "Selected a single feature to send to NCBI for searching.", 
+              "NCBI Search", JOptionPane.INFORMATION_MESSAGE);
+          return; 
+        }
+        final String residues = features.elementAt(0).getTranslation().toString().toUpperCase();
+
+        RunPfamSearchThread pfamSearch = new RunPfamSearchThread(residues);
+        pfamSearch.start();
+      }
+    });
+  }
+  
   /**
    * Add menu for NCBI web searches
    * @param selection

uk/ac/sanger/artemis/components/RunPfamSearchThread.java

+/* RunPfamSearch.java
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ **/
+
+package uk.ac.sanger.artemis.components;
+
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.URLConnection;
+import java.net.URLEncoder;
+
+import javax.swing.JOptionPane;
+
+import uk.ac.sanger.artemis.editor.BrowserControl;
+
+public class RunPfamSearchThread extends Thread
+{
+  private static String pfamUrl = "http://pfam.sanger.ac.uk/search/sequence";
+
+  private String residues;
+  
+  public RunPfamSearchThread(final String residues)
+  {
+    this.residues = residues;
+  }
+  
+  public void run()
+  {
+    try
+    {
+      // Construct data
+      String data = URLEncoder.encode("seq", "UTF-8") + "="
+          + URLEncoder.encode(residues, "UTF-8");
+      data += "&" + URLEncoder.encode("output", "UTF-8") + "="
+          + URLEncoder.encode("xml", "UTF-8");
+
+      // Send data
+      URL url = new URL(pfamUrl);
+      URLConnection conn = url.openConnection();
+      conn.setDoOutput(true);
+      OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream());
+      wr.write(data);
+      wr.flush();
+
+      // Get the response
+      BufferedReader rd = new BufferedReader(
+          new InputStreamReader(conn.getInputStream()));
+      String urlResults = pfamUrl+"/results?";
+      String line;
+      String eta = "10";
+      while ((line = rd.readLine()) != null)
+      {
+        int index;
+        if((index = line.indexOf("jobId=")) > -1)
+        {
+          urlResults = urlResults.concat(line.substring(index));
+        }
+        else if((index = line.indexOf("<estimated_time>")) > -1)
+        {
+          eta = line.substring(index+16);
+          index = eta.indexOf("<");
+          if(index > -1)
+            eta = eta.substring(0, index);
+        }
+        else if((index = line.indexOf("<error>")) > -1)
+        {
+          line = line.substring(index+7);
+          index = line.indexOf("<");
+          if(index > -1)
+            line = line.substring(0, index);
+          JOptionPane.showMessageDialog(null,
+              line, "Pfam search error", JOptionPane.INFORMATION_MESSAGE);
+          return;
+        }
+      }
+      wr.close();
+      rd.close();
+      
+      int waitTime = Integer.parseInt(eta);
+      ProgressBarFrame progress = new ProgressBarFrame(waitTime, "Pfam");
+      URL result = new URL(urlResults);
+      Thread.sleep(waitTime*1000);
+      
+      int cnt = 0;
+      while(((HttpURLConnection) result.openConnection()).getResponseCode() == 204 &&
+            cnt < 500)
+      {
+        cnt++;
+        Thread.sleep(500);
+      }
+
+      BrowserControl.displayURL(urlResults);
+      progress.dispose();
+    }
+    catch (Exception e){}
+  }
+}
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