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     public SequenceI[] clustalW(SequenceI[] sequences) {
  87       // Does the same as below but keeps initial sequence order.
  88       return (this.clustalW(sequences, true));
  89     }
  90   public SequenceI[] clustalW(SequenceI[] sequences, boolean PreserveOrder)
  91   {
  92
  93     // Simplest client call - with gumph from jemboss.server.TestPrivateServer
  94     if (vamsas_server.getPublicSoapURL().startsWith("https"))
  95     {
  96       //SSL settings
  97       //    System.setProperty ("javax.net.debug", "all");
  98       com.sun.net.ssl.internal.ssl.Provider p =
  99           new com.sun.net.ssl.internal.ssl.Provider();
 100       Security.addProvider(p);
 101
 102       //have to do it this way to work with JNLP
 103       URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
 104       {
 105         public URLStreamHandler createURLStreamHandler(final String protocol)
 106         {
 107           if(protocol != null && protocol.compareTo("https") == 0)
 108           {
 109             return new com.sun.net.ssl.internal.www.protocol.https.Handler();
 110           }
 111           return null;
 112         }
 113       });
 114
 115       //location of keystore
 116       System.setProperty("javax.net.ssl.trustStore",
 117                          "resources/client.keystore");
 118
 119       String jembossClientKeyStore = System.getProperty("user.home") +
 120           "/.jembossClientKeystore";
 121
 122       try
 123       {
 124         new JembossJarUtil("resources/client.jar").writeByteFile(
 125       "client.keystore",jembossClientKeyStore);
 126         System.setProperty("javax.net.ssl.trustStore",
 127                            jembossClientKeyStore);
 128       }
 129       catch(Exception exp){}
 130
 131     }
 132
 133     Hashtable filesToMove = new Hashtable();
 134     String embossCommand = "emma -sequence jalseqs.fasta -auto";
 135     // Duplicate
 136     SequenceI[] myseq = new SequenceI[sequences.length];
 137     for (int i=0; i<sequences.length; i++) {
 138         myseq[i] = new Sequence(sequences[i]);
 139     }
 140     // Uniqueify, and
 141     Hashtable namemap = uniquify(myseq);
 142     // Load sequence file into hash
 143
 144     filesToMove.put("jalseqs.fasta",
 145                     jalview.io.FastaFile.print(myseq,124,false, false).getBytes());
 146
 147     if(vamsas_server.getUseAuth() == true)
 148       if(vamsas_server.getServiceUserName() == null)
 149         System.out.println("jalview.Jemboss: OOPS! Authentication required!");
 150
 151     // submit to private server
 152     try
 153     {
 154       JembossRun thisrun = new JembossRun(embossCommand,"",
 155                                           filesToMove,vamsas_server);
 156       Hashtable h = thisrun.hash();
 157       Enumeration enum = h.keys();
 158       // Find the alignment generated and parse it
 159       while (enum.hasMoreElements())
 160       {
 161         String thiskey = (String)enum.nextElement().toString();
 162         if (thiskey.endsWith(".aln"))
 163         {
 164           // FormatAdapter, and IdentifyFile use a protocol string
 165           // to work out what 'file' is - file/url/Alignmentasastring
 166           String alfile = h.get(thiskey).toString();
 167           String format = IdentifyFile.Identify(alfile, "Paste");
 168           SequenceI[] alignment = null;
 169
 170           if (FormatProperties.contains(format))
 171             alignment = FormatAdapter.read(alfile, "Paste", format);
 172           else
 173             System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
 174           if (alignment == null)
 175             System.out.println("jalview.Jemboss: Couldn't read response:\n"
 176                                + alfile + "\n---EOF\n");
 177           else {
 178             if (PreserveOrder) {
 179               float[] ids = new float[alignment.length];
 180               for (int i=0; i<alignment.length; i++)
 181                 ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
 182               jalview.util.QuickSort.sort(ids, alignment);
 183             }
 184             if (!deuniquify(namemap, alignment)) {
 185                   System.out.println("jalview.Jemboss: Warning: Some of the "
 186                                      +"original sequence names have not been recovered!\n");
 187             }
 188             return alignment;
 189           }
 190         }
 191
 192       }
 193
 194     }
 195     catch (JembossSoapException eae)
 196     {
 197       System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
 198                          + "\n" + eae);
 199     }
 200     catch (Exception e) {
 201       System.out.println("jalview.Jemboss: Some other failure :\n"
 202                          +e.getMessage()+"\n");
 203     }
 204
 205     return null;
 206   }
 207 }
 208