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.List;
   6 import java.util.Map;
   7
   8 import jalview.analysis.AlignmentAnnotationUtils;
   9 import jalview.analysis.SeqsetUtils;
  10 import jalview.analysis.SeqsetUtils.SequenceInfo;
  11 import jalview.api.AlignViewportI;
  12 import jalview.bin.Console;
  13 import jalview.datamodel.Alignment;
  14 import jalview.datamodel.AlignmentAnnotation;
  15 import jalview.datamodel.AlignmentI;
  16 import jalview.datamodel.AlignmentView;
  17 import jalview.datamodel.HiddenColumns;
  18 import jalview.datamodel.SeqCigar;
  19 import jalview.datamodel.SequenceI;
  20 import jalview.io.AlignFile;
  21 import jalview.io.JPredFile;
  22 import jalview.io.JnetAnnotationMaker;
  23 import jalview.ws.params.ArgumentI;
  24 import jalview.ws2.actions.BaseJob;
  25 import jalview.ws2.actions.BaseTask;
  26 import jalview.ws2.actions.ServiceInputInvalidException;
  27 import jalview.ws2.api.Credentials;
  28 import jalview.ws2.api.JobStatus;
  29 import jalview.ws2.client.api.SecStructPredWebServiceClientI;
  30
  31 public class SecStructPredMsaTask
  32         extends BaseTask<SecStructPredMsaTask.SecStructPredJob, AlignmentI>
  33 {
  34   private final SecStructPredWebServiceClientI client;
  35
  36   private final AlignmentView alignmentView;
  37
  38   private final AlignmentI currentView;
  39
  40   private final char gapChar;
  41
  42   SecStructPredMsaTask(SecStructPredWebServiceClientI client,
  43           List<ArgumentI> args, Credentials credentials,
  44           AlignViewportI viewport)
  45   {
  46     super(client, args, credentials);
  47     this.client = client;
  48     this.alignmentView = viewport.getAlignmentView(true);
  49     this.currentView = viewport.getAlignment();
  50     this.gapChar = viewport.getGapCharacter();
  51   }
  52
  53   @Override
  54   protected List<SecStructPredJob> prepareJobs()
  55           throws ServiceInputInvalidException
  56   {
  57     SeqCigar[] msf = alignmentView.getSequences();
  58     SequenceI referenceSeq = msf[0].getSeq('-');
  59     int[] delMap = alignmentView
  60             .getVisibleContigMapFor(referenceSeq.gapMap());
  61
  62     // TODO: assume MSA for now
  63     SequenceI[] sequences = new SequenceI[msf.length];
  64     for (int i = 0; i < msf.length; i++)
  65       sequences[i] = msf[i].getSeq('-');
  66     var sequenceInfo = SeqsetUtils.uniquify(sequences, true);
  67     referenceSeq.setSequence(alignmentView.getASequenceString('-', 0));
  68     for (int i = 0; i < sequences.length; i++)
  69       sequences[i].setSequence(alignmentView.getASequenceString('-', i));
  70     var sequencesList = filterEmptySequences(sequences);
  71     var job = new SecStructPredJob(sequencesList, referenceSeq, delMap,
  72             sequenceInfo);
  73     job.setStatus(JobStatus.READY);
  74     return List.of(job);
  75   }
  76
  77   private static List<SequenceI> filterEmptySequences(SequenceI[] seqs)
  78   {
  79     var filtered = new ArrayList<SequenceI>();
  80     for (var seq : seqs)
  81       if (seq.getEnd() - seq.getStart() > 0)
  82         filtered.add(seq);
  83     return filtered;
  84   }
  85
  86   @Override
  87   protected AlignmentI collectResult(List<SecStructPredJob> jobs)
  88           throws IOException
  89   {
  90     var job = jobs.get(0); // There shouldn't be more than one job
  91     var status = job.getStatus();
  92     Console.info(
  93             String.format("sec str pred job \"%s\" finished with status %s",
  94                     job.getServerJob().getJobId(), status));
  95     if (status != JobStatus.COMPLETED)
  96       return null;
  97     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  98     AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
  99
 100     Object[] alnAndHiddenCols = alignmentView
 101             .getAlignmentAndHiddenColumns(gapChar);
 102     Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]);
 103     aln.setDataset(currentView.getDataset());
 104     aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]);
 105     try
 106     {
 107       JnetAnnotationMaker.add_annotation(predictionFile, aln, 0, false,
 108               job.getDelMap());
 109     } catch (Exception e)
 110     {
 111       throw new IOException(e);
 112     }
 113
 114     for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
 115     {
 116       if (alnAnnot.sequenceRef != null)
 117       {
 118         AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot,
 119                 alnAnnot.label, getClass().getSimpleName());
 120       }
 121     }
 122     aln.setSeqrep(aln.getSequenceAt(0));
 123     return aln;
 124   }
 125
 126   public static class SecStructPredJob extends BaseJob
 127   {
 128     private final int[] delMap;
 129
 130     private final SequenceI refSeq;
 131
 132     final Map<String, SequenceInfo> seqNames;
 133
 134     SecStructPredJob(List<SequenceI> sequences, SequenceI refSeq,
 135             int[] delMap, Map<String, SequenceInfo> seqNames)
 136     {
 137       super(sequences);
 138       this.refSeq = refSeq;
 139       this.delMap = delMap;
 140       this.seqNames = seqNames;
 141     }
 142
 143     @Override
 144     public boolean isInputValid()
 145     {
 146       return true;
 147     }
 148
 149     public int[] getDelMap()
 150     {
 151       return this.delMap;
 152     }
 153   }
 154
 155 }