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

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import java.io.IOException;
   4 import java.util.ArrayList;
   5 import java.util.Arrays;
   6 import java.util.List;
   7 import java.util.Map;
   8
   9 import jalview.analysis.AlignmentAnnotationUtils;
  10 import jalview.analysis.SeqsetUtils;
  11 import jalview.analysis.SeqsetUtils.SequenceInfo;
  12 import jalview.api.AlignViewportI;
  13 import jalview.bin.Console;
  14 import jalview.datamodel.Alignment;
  15 import jalview.datamodel.AlignmentAnnotation;
  16 import jalview.datamodel.AlignmentI;
  17 import jalview.datamodel.AlignmentView;
  18 import jalview.datamodel.HiddenColumns;
  19 import jalview.datamodel.SeqCigar;
  20 import jalview.datamodel.SequenceI;
  21 import jalview.io.AlignFile;
  22 import jalview.io.JPredFile;
  23 import jalview.io.JnetAnnotationMaker;
  24 import jalview.ws.params.ArgumentI;
  25 import jalview.ws2.actions.BaseJob;
  26 import jalview.ws2.actions.BaseTask;
  27 import jalview.ws2.actions.ServiceInputInvalidException;
  28 import jalview.ws2.api.Credentials;
  29 import jalview.ws2.api.JobStatus;
  30 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  31
  32 public class SecStructPredMsaTask
  33         extends BaseTask<SecStructPredMsaTask.SecStructPredJob, AlignmentI>
  34 {
  35   private final SecStructPredWebServiceClientI client;
  36
  37   private final AlignmentView alignmentView;
  38
  39   private final AlignmentI currentView;
  40
  41   private final char gapChar;
  42
  43   SecStructPredMsaTask(SecStructPredWebServiceClientI client,
  44           List<ArgumentI> args, Credentials credentials,
  45           AlignViewportI viewport)
  46   {
  47     super(client, args, credentials);
  48     this.client = client;
  49     this.alignmentView = viewport.getAlignmentView(true);
  50     this.currentView = viewport.getAlignment();
  51     this.gapChar = viewport.getGapCharacter();
  52   }
  53
  54   @Override
  55   protected List<SecStructPredJob> prepareJobs()
  56           throws ServiceInputInvalidException
  57   {
  58     SeqCigar[] msf = alignmentView.getSequences();
  59     SequenceI referenceSeq = msf[0].getSeq('-');
  60     int[] delMap = alignmentView
  61             .getVisibleContigMapFor(referenceSeq.gapMap());
  62
  63     // TODO: assume MSA for now
  64     SequenceI[] sequences = new SequenceI[msf.length];
  65     for (int i = 0; i < msf.length; i++)
  66       sequences[i] = msf[i].getSeq('-');
  67     var sequenceInfo = SeqsetUtils.uniquify(sequences, true);
  68     referenceSeq.setSequence(alignmentView.getASequenceString('-', 0));
  69     for (int i = 0; i < sequences.length; i++)
  70       sequences[i].setSequence(alignmentView.getASequenceString('-', i));
  71     var nonEmptySeqs = SeqsetUtils.getNonEmptySequenceSet(sequences);
  72     var job = new SecStructPredJob(Arrays.asList(nonEmptySeqs),
  73             referenceSeq, delMap, sequenceInfo);
  74     job.setStatus(JobStatus.READY);
  75     return List.of(job);
  76   }
  77
  78   @Override
  79   protected AlignmentI collectResult(List<SecStructPredJob> jobs)
  80           throws IOException
  81   {
  82     var job = jobs.get(0); // There shouldn't be more than one job
  83     var status = job.getStatus();
  84     Console.info(
  85             String.format("sec str pred job \"%s\" finished with status %s",
  86                     job.getServerJob().getJobId(), status));
  87     if (status != JobStatus.COMPLETED)
  88       return null;
  89     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  90     AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
  91
  92     Object[] alnAndHiddenCols = alignmentView
  93             .getAlignmentAndHiddenColumns(gapChar);
  94     Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]);
  95     aln.setDataset(currentView.getDataset());
  96     aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]);
  97     try
  98     {
  99       JnetAnnotationMaker.add_annotation(predictionFile, aln, 0, false,
 100               job.getDelMap());
 101     } catch (Exception e)
 102     {
 103       throw new IOException(e);
 104     }
 105
 106     for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
 107     {
 108       if (alnAnnot.sequenceRef != null)
 109       {
 110         AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot,
 111                 alnAnnot.label, getClass().getSimpleName());
 112       }
 113     }
 114     aln.setSeqrep(aln.getSequenceAt(0));
 115     return aln;
 116   }
 117
 118   public static class SecStructPredJob extends BaseJob
 119   {
 120     private final int[] delMap;
 121
 122     private final SequenceI refSeq;
 123
 124     final Map<String, SequenceInfo> seqNames;
 125
 126     SecStructPredJob(List<SequenceI> sequences, SequenceI refSeq,
 127             int[] delMap, Map<String, SequenceInfo> seqNames)
 128     {
 129       super(sequences);
 130       this.refSeq = refSeq;
 131       this.delMap = delMap;
 132       this.seqNames = seqNames;
 133     }
 134
 135     @Override
 136     public boolean isInputValid()
 137     {
 138       return true;
 139     }
 140
 141     public int[] getDelMap()
 142     {
 143       return this.delMap;
 144     }
 145   }
 146
 147 }