src/jalview/ws/Jemboss.java

   1 package jalview.ws;
   2
   3 /**
   4  * <p>Title: JalviewX</p>
   5  * <p>Description: Jalview Re-engineered</p>
   6  * <p>Copyright: Copyright (c) 2004</p>
   7  * <p>Company: Dundee University</p>
   8  * @author not attributable
   9  * @version 1.0
  10  * Commenced 14th January 2005, Jim Procter
  11  * Contains and depends on GPL-2 jemboss classes
  12  * see http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/index.html
  13  */
  14
  15 /**
  16  * Philosophy
  17  * Jemboss webservices are implemented here as re-entrant synchronous SOAP
  18  * exchanges. It is up to the user of the class whether these exchanges
  19  * are executed in their own thread to effect background processing
  20  * functionality.
  21  *
  22  * Things to do
  23  * Standardise the exceptions (currently errors are output on stdout)
  24  * Allow server configuration
  25  * Throw away JembossParams and Jemboss dependence
  26  * Generalise results to return collections of objects - alignments, trees, annotations, etc.
  27  */
  28
  29 import java.net.*;
  30 import java.security.*;
  31 import java.util.*;
  32
  33 import ext.jemboss.*;
  34 import ext.jemboss.soap.*;
  35 import jalview.datamodel.*;
  36 import jalview.io.*;
  37
  38
  39 public class Jemboss
  40 {
  41   private static ext.jemboss.JembossParams vamsas_server;
  42
  43   public Jemboss()
  44   {
  45     // Set up default jalview-jemboss server properties
  46     //
  47     vamsas_server = new JembossParams();
  48     vamsas_server.setCurrentMode("interactive");
  49     System.out.println("Jemboss Server Init\n"
  50                        + vamsas_server.serverDescription()
  51                        + "\nUser Authorisation ? "
  52                        + vamsas_server.getUseAuth()
  53                        +"\n");
  54   }
  55
  56   /* public void updateServer(JembossParams props)
  57   {
  58     vamsas_server.updateJembossPropStrings (
  59       props.getEmbossEnvironmentArray());
  60   }
  61   */
  62     public SequenceI[] clustalW(SequenceI[] sequences) {
  63       // Does the same as below but keeps initial sequence order.
  64       return (this.clustalW(sequences, true));
  65     }
  66   public SequenceI[] clustalW(SequenceI[] sequences, boolean PreserveOrder)
  67   {
  68
  69     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  70     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  71     {
  72       //SSL settings
  73       //    System.setProperty ("javax.net.debug", "all");
  74       com.sun.net.ssl.internal.ssl.Provider p =
  75           new com.sun.net.ssl.internal.ssl.Provider();
  76       Security.addProvider(p);
  77
  78       //have to do it this way to work with JNLP
  79       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
  80       {
  81         public URLStreamHandler createURLStreamHandler(final String protocol)
  82         {
  83           if(protocol != null && protocol.compareTo("https") == 0)
  84           {
  85             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
  86           }
  87           return null;
  88         }
  89       });
  90
  91       //location of keystore
  92       System.setProperty("javax.net.ssl.trustStore",
  93                          "resources/client.keystore");
  94
  95       String jembossClientKeyStore = System.getProperty("user.home") +
  96           "/.jembossClientKeystore";
  97
  98       try
  99       {
 100         new JembossJarUtil("resources/client.jar").writeByteFile(
 101       "client.keystore",jembossClientKeyStore);
 102         System.setProperty("javax.net.ssl.trustStore",
 103                            jembossClientKeyStore);
 104       }
 105       catch(Exception exp){}
 106
 107     }
 108
 109     Hashtable filesToMove = new Hashtable();
 110     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 111     // Duplicate
 112     SequenceI[] myseq = new SequenceI[sequences.length];
 113     for (int i=0; i<sequences.length; i++) {
 114         myseq[i] = new Sequence(sequences[i]);
 115     }
 116     // Uniqueify, and
 117     Hashtable namemap = jalview.analysis.SeqsetUtils.uniquify(myseq);
 118     // Load sequence file into hash
 119
 120     filesToMove.put("jalseqs.fasta",
 121                     jalview.io.FastaFile.print(myseq,124,false, false).getBytes());
 122
 123     if(vamsas_server.getUseAuth() == true)
 124       if(vamsas_server.getServiceUserName() == null)
 125         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 126
 127     // submit to private server
 128     try
 129     {
 130       JembossRun thisrun = new JembossRun(embossCommand,"",
 131                                           filesToMove,vamsas_server);
 132       Hashtable h = thisrun.hash();
 133       Enumeration enumerator = h.keys();
 134       // Find the alignment generated and parse it
 135       while (enumerator.hasMoreElements())
 136       {
 137         String thiskey = (String)enumerator.nextElement().toString();
 138         if (thiskey.endsWith(".aln"))
 139         {
 140           // FormatAdapter, and IdentifyFile use a protocol string
 141           // to work out what 'file' is - file/url/Alignmentasastring
 142           String alfile = h.get(thiskey).toString();
 143           String format = IdentifyFile.Identify(alfile, "Paste");
 144           SequenceI[] alignment = null;
 145
 146           if (FormatAdapter.formats.contains(format))
 147             alignment = FormatAdapter.readFile(alfile, "Paste", format);
 148           else
 149             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 150           if (alignment == null)
 151             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 152                                + alfile + "\n---EOF\n");
 153           else {
 154             if (PreserveOrder) {
 155               jalview.analysis.AlignmentSorter.recoverOrder(alignment);
 156             }
 157             if (!jalview.analysis.SeqsetUtils.deuniquify(namemap, alignment)) {
 158                   System.out.println("jalview.Jemboss: Warning: Some of the "
 159                                      +"original sequence names have not been recovered!\n");
 160             }
 161             return alignment;
 162           }
 163         }
 164
 165       }
 166
 167     }
 168     catch (JembossSoapException eae)
 169     {
 170       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 171                          + "\n" + eae);
 172     }
 173     catch (Exception e) {
 174       System.out.println("jalview.Jemboss: Some other failure :\n"
 175                          +e.getMessage()+"\n");
 176     }
 177
 178     return null;
 179   }
 180 }
 181