src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java

   1 package jalview.ws.jws2.jabaws2;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.datamodel.Sequence;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.ws.api.CancellableI;
   7 import jalview.ws.api.JobId;
   8 import jalview.ws.api.MultipleSequenceAlignmentI;
   9 import jalview.ws.jws2.JabaParamStore;
  10 import jalview.ws.jws2.JabaPreset;
  11 import jalview.ws.params.ArgumentI;
  12 import jalview.ws.params.InvalidArgumentException;
  13 import jalview.ws.params.WsParamSetI;
  14
  15 import java.io.IOError;
  16 import java.rmi.ServerError;
  17 import java.util.ArrayList;
  18 import java.util.List;
  19
  20 import compbio.data.sequence.Alignment;
  21 import compbio.data.sequence.FastaSequence;
  22 import compbio.metadata.ResultNotAvailableException;
  23
  24 public class JabawsMsaInstance
  25         extends JabawsServiceInstance<compbio.data.msa.MsaWS>
  26         implements MultipleSequenceAlignmentI, CancellableI
  27 {
  28   @Override
  29   public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
  30           List<ArgumentI> arguments) throws Throwable
  31   {
  32     List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
  33     for (SequenceI seq : toalign)
  34     {
  35       seqs.add(new FastaSequence(seq.getName(), seq.getSequenceAsString()));
  36     }
  37     String jobid = null;
  38     if (parameters != null)
  39     {
  40       if (parameters instanceof JabaPreset)
  41       {
  42         jobid = service.presetAlign(seqs,
  43                 ((JabaPreset) parameters).getJabaPreset());
  44       }
  45       else
  46       {
  47         jobid = service.customAlign(seqs, JabaParamStore
  48                 .getJabafromJwsArgs(parameters.getArguments()));
  49       }
  50     }
  51     else if (arguments != null && arguments.size() > 0)
  52     {
  53       jobid = service.customAlign(seqs,
  54               JabaParamStore.getJabafromJwsArgs(arguments));
  55     }
  56     else
  57     {
  58       jobid = service.align(seqs);
  59     }
  60
  61     if (jobid == null)
  62     {
  63       return null;
  64     }
  65     return new JobId(our.getServiceType(), our.getName(), jobid);
  66   }
  67
  68   @Override
  69   public AlignmentI getAlignmentFor(JobId jobId)
  70           throws InvalidArgumentException, ServerError, IOError
  71   {
  72     Alignment alignment = null;
  73     try
  74     {
  75       alignment = service.getResult(jobId.getJobId());
  76     } catch (ResultNotAvailableException rnotav)
  77     {
  78
  79       // TODO - migrate JABA exception
  80       // throw new ServerError("Couldn't get result for job",rnotav);
  81     }
  82     SequenceI[] alseqs;
  83     int alseq_l = 0;
  84     if (alignment.getSequences().size() == 0)
  85     {
  86       return null;
  87     }
  88
  89     alseqs = new SequenceI[alignment.getSequences().size()];
  90     for (compbio.data.sequence.FastaSequence seq : alignment.getSequences())
  91     {
  92       alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
  93     }
  94     AlignmentI jv_al = new jalview.datamodel.Alignment(alseqs);
  95     jv_al.setGapCharacter(alignment.getMetadata().getGapchar());
  96     return jv_al;
  97
  98   }
  99
 100   public JabawsMsaInstance(Jws2Instance handle)
 101   {
 102     super(handle);
 103   }
 104
 105 }