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     private Hashtable uniquify(SequenceI[] sequences) {
  63         // Generate a safely named sequence set and a hash to recover the sequence names
  64         Hashtable map = new Hashtable();
  65         for (int i=0; i<sequences.length; i++) {
  66             String safename = new String("Sequence"+i);
  67             map.put(safename, sequences[i].getName());
  68             sequences[i].setName(safename);
  69         }
  70         return map;
  71     }
  72
  73     private boolean deuniquify(Hashtable map, SequenceI[] sequences) {
  74         // recover unsafe sequence names for a sequence set
  75         boolean allfound=true;
  76         for (int i=0; i<sequences.length; i++) {
  77             if (map.containsKey(sequences[i].getName())) {
  78                 String unsafename = (String) map.get(sequences[i].getName());
  79                 sequences[i].setName(unsafename);
  80             } else {
  81                 allfound=false;
  82             }
  83         }
  84         return allfound;
  85     }
  86
  87   public SequenceI[] clustalW(SequenceI[] sequences)
  88   {
  89
  90     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  91     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  92     {
  93       //SSL settings
  94       //    System.setProperty ("javax.net.debug", "all");
  95       com.sun.net.ssl.internal.ssl.Provider p =
  96           new com.sun.net.ssl.internal.ssl.Provider();
  97       Security.addProvider(p);
  98
  99       //have to do it this way to work with JNLP
 100       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
 101       {
 102         public URLStreamHandler createURLStreamHandler(final String protocol)
 103         {
 104           if(protocol != null && protocol.compareTo("https") == 0)
 105           {
 106             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
 107           }
 108           return null;
 109         }
 110       });
 111
 112       //location of keystore
 113       System.setProperty("javax.net.ssl.trustStore",
 114                          "resources/client.keystore");
 115
 116       String jembossClientKeyStore = System.getProperty("user.home") +
 117           "/.jembossClientKeystore";
 118
 119       try
 120       {
 121         new JembossJarUtil("resources/client.jar").writeByteFile(
 122       "client.keystore",jembossClientKeyStore);
 123         System.setProperty("javax.net.ssl.trustStore",
 124                            jembossClientKeyStore);
 125       }
 126       catch(Exception exp){}
 127
 128     }
 129
 130     Hashtable filesToMove = new Hashtable();
 131     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 132     // Duplicate
 133     SequenceI[] myseq = new SequenceI[sequences.length];
 134     for (int i=0; i<sequences.length; i++) {
 135         myseq[i] = new Sequence(sequences[i]);
 136     }
 137     // Uniqueify, and
 138     Hashtable namemap = uniquify(myseq);
 139     // Load sequence file into hash
 140
 141     filesToMove.put("jalseqs.fasta",
 142                     jalview.io.FastaFile.print(myseq,124,false).getBytes());
 143
 144     if(vamsas_server.getUseAuth() == true)
 145       if(vamsas_server.getServiceUserName() == null)
 146         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 147
 148     // submit to private server
 149     try
 150     {
 151       JembossRun thisrun = new JembossRun(embossCommand,"",
 152                                           filesToMove,vamsas_server);
 153       Hashtable h = thisrun.hash();
 154       Enumeration enum = h.keys();
 155       // Find the alignment generated and parse it
 156       while (enum.hasMoreElements())
 157       {
 158         String thiskey = (String)enum.nextElement().toString();
 159         if (thiskey.endsWith(".aln"))
 160         {
 161           // FormatAdapter, and IdentifyFile use a protocol string
 162           // to work out what 'file' is - file/url/Alignmentasastring
 163           String alfile = h.get(thiskey).toString();
 164           String format = IdentifyFile.Identify(alfile, "Paste");
 165           SequenceI[] alignment = null;
 166
 167           if (FormatProperties.contains(format))
 168             alignment = FormatAdapter.read(alfile, "Paste", format);
 169           else
 170             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 171           if (alignment == null)
 172             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 173                                + alfile + "\n---EOF\n");
 174           else {
 175             if (!deuniquify(namemap, alignment)) {
 176                   System.out.println("jalview.Jemboss: Warning: Some of the "
 177                                      +"original sequence names have not been recovered!\n");
 178             }
 179             return alignment;
 180           }
 181         }
 182
 183       }
 184
 185     }
 186     catch (JembossSoapException eae)
 187     {
 188       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 189                          + "\n" + eae);
 190     }
 191     catch (Exception e) {
 192       System.out.println("jalview.Jemboss: Some other failure :\n"
 193                          +e.getMessage()+"\n");
 194     }
 195
 196     return null;
 197   }
 198 }
 199