rename

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10797 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/RunPfamSearch.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 uk.ac.sanger.artemis.editor.BrowserControl;
-
-public class RunPfamSearch
-{
-  private static String pfamUrl = "http://pfam.sanger.ac.uk/search/sequence";
-  
-  public RunPfamSearch(final String residues)
-  {
-    postData(residues);
-  }
-  
-  public void postData(final String residues)
-  {
-    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 = "http://pfam.sanger.ac.uk/search/sequence/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);
-        }
-      }
-      wr.close();
-      rd.close();
-      
-      URL result = new URL(urlResults);
-      Thread.sleep(Integer.parseInt(eta)*1000);
-      
-      while(((HttpURLConnection) result.openConnection()).getResponseCode() == 204)
-        Thread.sleep(1000);
-
-      BrowserControl.displayURL(urlResults);
-    }
-    catch (Exception e)
-    {
-    }
-
-  }
-}
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