src/jalview/ws2/actions/secstructpred/SecStructPredTask.java

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import java.io.IOException;
   4 import java.util.ArrayList;
   5 import java.util.List;
   6
   7 import jalview.analysis.AlignmentAnnotationUtils;
   8 import jalview.analysis.SeqsetUtils;
   9 import jalview.api.AlignViewportI;
  10 import jalview.bin.Console;
  11 import jalview.datamodel.Alignment;
  12 import jalview.datamodel.AlignmentAnnotation;
  13 import jalview.datamodel.AlignmentI;
  14 import jalview.datamodel.AlignmentView;
  15 import jalview.datamodel.HiddenColumns;
  16 import jalview.datamodel.SeqCigar;
  17 import jalview.datamodel.SequenceI;
  18 import jalview.io.AlignFile;
  19 import jalview.io.JPredFile;
  20 import jalview.io.JnetAnnotationMaker;
  21 import jalview.util.Comparison;
  22 import jalview.ws.params.ArgumentI;
  23 import jalview.ws2.actions.BaseJob;
  24 import jalview.ws2.actions.BaseTask;
  25 import jalview.ws2.actions.ServiceInputInvalidException;
  26 import jalview.ws2.api.Credentials;
  27 import jalview.ws2.api.JobStatus;
  28 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  29
  30 public class SecStructPredTask extends BaseTask<SecStructPredJob, AlignmentI>
  31 {
  32   private final SecStructPredWebServiceClientI client;
  33
  34   private final AlignmentView alignmentView;
  35
  36   private final AlignmentI currentView;
  37
  38   private final char gapChar;
  39
  40   SecStructPredTask(SecStructPredWebServiceClientI client, List<ArgumentI> args,
  41       Credentials credentials, AlignViewportI viewport)
  42   {
  43     super(client, args, credentials);
  44     this.client = client;
  45     this.alignmentView = viewport.getAlignmentView(true);
  46     this.currentView = viewport.getAlignment();
  47     this.gapChar = viewport.getGapCharacter();
  48   }
  49
  50   @Override
  51   protected List<SecStructPredJob> prepareJobs()
  52       throws ServiceInputInvalidException
  53   {
  54     SeqCigar[] msf = alignmentView.getSequences();
  55     SequenceI referenceSeq = msf[0].getSeq('-');
  56     int[] delMap = alignmentView.getVisibleContigMapFor(referenceSeq.gapMap());
  57
  58     // TODO: assume MSA for now
  59     SequenceI[] sequences = new SequenceI[msf.length];
  60     for (int i = 0; i < msf.length; i++)
  61       sequences[i] = msf[i].getSeq('-');
  62     var sequenceInfo = SeqsetUtils.uniquify(sequences, true);
  63     referenceSeq.setSequence(alignmentView.getASequenceString('-', 0));
  64     for (int i = 0; i < sequences.length; i++)
  65       sequences[i].setSequence(alignmentView.getASequenceString('-', i));
  66     var sequencesList = filterEmptySequences(sequences);
  67     var job = new SecStructPredJob(sequencesList, referenceSeq, delMap,
  68         sequenceInfo);
  69     job.setStatus(JobStatus.READY);
  70     return List.of(job);
  71   }
  72
  73   private static List<SequenceI> filterEmptySequences(SequenceI[] seqs)
  74   {
  75     var filtered = new ArrayList<SequenceI>();
  76     for (var seq : seqs)
  77       if (seq.getEnd() - seq.getStart() > 0)
  78         filtered.add(seq);
  79     return filtered;
  80   }
  81
  82   @Override
  83   protected AlignmentI collectResult(List<SecStructPredJob> jobs)
  84       throws IOException
  85   {
  86     var job = jobs.get(0); // There shouldn't be more than one job
  87     var status = job.getStatus();
  88     Console
  89         .info(String
  90             .format("sec str pred job \"%s\" finished with status %s",
  91                 job.getServerJob().getJobId(), status));
  92     if (status != JobStatus.COMPLETED)
  93       return null;
  94     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  95     AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
  96
  97     Object[] alnAndHiddenCols = alignmentView
  98         .getAlignmentAndHiddenColumns(gapChar);
  99     Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]);
 100     aln.setDataset(currentView.getDataset());
 101     aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]);
 102     try
 103     {
 104       JnetAnnotationMaker
 105           .add_annotation(predictionFile, aln, 0, false, job.getDelMap());
 106     } catch (Exception e)
 107     {
 108       throw new IOException(e);
 109     }
 110
 111     for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
 112     {
 113       if (alnAnnot.sequenceRef != null)
 114       {
 115         AlignmentAnnotationUtils
 116             .replaceAnnotationOnAlignmentWith(alnAnnot, alnAnnot.label,
 117                 getClass().getSimpleName());
 118       }
 119     }
 120     aln.setSeqrep(aln.getSequenceAt(0));
 121     return aln;
 122   }
 123
 124 }