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.Arrays;
   7 import java.util.List;
   8
   9 import jalview.analysis.AlignSeq;
  10 import jalview.bin.Console;
  11 import jalview.datamodel.AlignmentAnnotation;
  12 import jalview.datamodel.AlignmentI;
  13 import jalview.datamodel.AlignmentView;
  14 import jalview.datamodel.Annotation;
  15 import jalview.datamodel.Sequence;
  16 import jalview.datamodel.SequenceI;
  17 import jalview.util.Comparison;
  18 import jalview.ws.params.ArgumentI;
  19 import jalview.ws2.actions.AbstractPollableTask;
  20 import jalview.ws2.actions.BaseJob;
  21 import jalview.ws2.actions.ServiceInputInvalidException;
  22 import jalview.ws2.actions.api.TaskEventListener;
  23 import jalview.ws2.api.Credentials;
  24 import jalview.ws2.api.JobStatus;
  25 import jalview.ws2.client.api.AlignmentWebServiceClientI;
  26
  27 class PhmmerTask extends AbstractPollableTask<BaseJob, AlignmentI>
  28 {
  29   private final AlignmentWebServiceClientI client;
  30   private final AlignmentView view;
  31
  32   PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,
  33           Credentials credentials, AlignmentView view,
  34           TaskEventListener<AlignmentI> eventListener)
  35   {
  36     super(client, args, credentials, eventListener);
  37     this.client = client;
  38     this.view = view;
  39   }
  40
  41   @Override
  42   protected List<BaseJob> prepare() throws ServiceInputInvalidException
  43   {
  44     Console.info("Preparing sequence for phmmer job");
  45     var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
  46     var seq = new Sequence(sequence.getName(),
  47             AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
  48     var job = new BaseJob(List.of(seq))
  49     {
  50       @Override
  51       public boolean isInputValid()
  52       {
  53         return true;
  54       }
  55     };
  56     job.setStatus(JobStatus.READY);
  57     return List.of(job);
  58   }
  59
  60   @Override
  61   protected AlignmentI done() throws IOException
  62   {
  63     var job = getSubJobs().get(0);
  64     var status = job.getStatus();
  65     Console.info(String.format("phmmer finished job \"%s\" with status %s",
  66             job.getServerJob().getJobId(), status));
  67     if (status != JobStatus.COMPLETED)
  68       return null;
  69     var outputAlignment = client.getAlignment(job.getServerJob());
  70     var querySeq = job.getInputSequences().get(0).deriveSequence();
  71     {
  72       AlignmentAnnotation refpos = null;
  73       for (var annot : outputAlignment.getAlignmentAnnotation())
  74       {
  75         if (annot.sequenceRef == null && annot.label.equals("Reference Positions"))
  76         {
  77           refpos = annot;
  78           break;
  79         }
  80       }
  81       if (refpos != null)
  82       {
  83         querySeq = alignQeuryToReferencePositions(querySeq, refpos);
  84       }
  85     }
  86     outputAlignment.insertSequenceAt(0, querySeq);
  87     return outputAlignment;
  88   }
  89
  90   private SequenceI alignQeuryToReferencePositions(SequenceI query, AlignmentAnnotation refpos)
  91   {
  92     var sequenceBuilder = new StringBuilder();
  93     var index = 0;
  94     for (Annotation a : refpos.annotations)
  95     {
  96       // TODO: we assume that the number of "x" annotations is equal to the number
  97       // of residues. may need a safeguard against invalid input
  98       if (a != null && a.displayCharacter.equals("x"))
  99       {
 100         char c;
 101         do
 102           c = query.getCharAt(index++);
 103         while (Comparison.isGap(c));
 104         sequenceBuilder.append(c);
 105       }
 106       else
 107       {
 108         sequenceBuilder.append(Comparison.GAP_DASH);
 109       }
 110     }
 111     query.setSequence(sequenceBuilder.toString());
 112     return query;
 113   }
 114 }