src/jalview/ws2/actions/hmmer/PhmmerTask.java

   1 package jalview.ws2.actions.hmmer;
   2
   3 import static jalview.util.Comparison.GapChars;
   4
   5 import java.io.IOException;
   6 import java.util.List;
   7
   8 import jalview.analysis.AlignSeq;
   9 import jalview.bin.Console;
  10 import jalview.datamodel.AlignmentAnnotation;
  11 import jalview.datamodel.AlignmentI;
  12 import jalview.datamodel.AlignmentView;
  13 import jalview.datamodel.Annotation;
  14 import jalview.datamodel.Sequence;
  15 import jalview.datamodel.SequenceI;
  16 import jalview.util.Comparison;
  17 import jalview.ws.params.ArgumentI;
  18 import jalview.ws2.actions.BaseJob;
  19 import jalview.ws2.actions.BaseTask;
  20 import jalview.ws2.actions.ServiceInputInvalidException;
  21 import jalview.ws2.api.Credentials;
  22 import jalview.ws2.api.JobStatus;
  23 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  24
  25 class PhmmerTask extends BaseTask<BaseJob, AlignmentI>
  26 {
  27   private final AlignmentWebServiceClientI client;
  28   private final AlignmentView view;
  29
  30   PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
  31           Credentials credentials, AlignmentView view)
  32   {
  33     super(client, args, credentials);
  34     this.client = client;
  35     this.view = view;
  36   }
  37
  38   @Override
  39   protected List<BaseJob> prepareJobs() throws ServiceInputInvalidException
  40   {
  41     Console.info("Preparing sequence for phmmer job");
  42     var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
  43     var seq = new Sequence(sequence.getName(),
  44             AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
  45     var job = new BaseJob(List.of(seq))
  46     {
  47       @Override
  48       public boolean isInputValid()
  49       {
  50         return true;
  51       }
  52     };
  53     job.setStatus(JobStatus.READY);
  54     return List.of(job);
  55   }
  56
  57   @Override
  58   protected AlignmentI collectResult(List<BaseJob> jobs) throws IOException
  59   {
  60     var job = jobs.get(0);
  61     var status = job.getStatus();
  62     Console.info(String.format("phmmer finished job \"%s\" with status %s",
  63             job.getServerJob().getJobId(), status));
  64     if (status != JobStatus.COMPLETED)
  65       return null;
  66     var outputAlignment = client.getAlignment(job.getServerJob());
  67     var querySeq = job.getInputSequences().get(0).deriveSequence();
  68     {
  69       AlignmentAnnotation refpos = null;
  70       for (var annot : outputAlignment.getAlignmentAnnotation())
  71       {
  72         if (annot.sequenceRef == null && annot.label.equals("Reference Positions"))
  73         {
  74           refpos = annot;
  75           break;
  76         }
  77       }
  78       if (refpos != null)
  79       {
  80         querySeq = alignQeuryToReferencePositions(querySeq, refpos);
  81       }
  82     }
  83     outputAlignment.insertSequenceAt(0, querySeq);
  84     return outputAlignment;
  85   }
  86
  87   private SequenceI alignQeuryToReferencePositions(SequenceI query, AlignmentAnnotation refpos)
  88   {
  89     var sequenceBuilder = new StringBuilder();
  90     var index = 0;
  91     for (Annotation a : refpos.annotations)
  92     {
  93       // TODO: we assume that the number of "x" annotations is equal to the number
  94       // of residues. may need a safeguard against invalid input
  95       if (a != null && a.displayCharacter.equals("x"))
  96       {
  97         char c;
  98         do
  99           c = query.getCharAt(index++);
 100         while (Comparison.isGap(c));
 101         sequenceBuilder.append(c);
 102       }
 103       else
 104       {
 105         sequenceBuilder.append(Comparison.GAP_DASH);
 106       }
 107     }
 108     query.setSequence(sequenceBuilder.toString());
 109     return query;
 110   }
 111 }