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

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import java.io.IOException;
   4 import java.util.List;
   5
   6 import jalview.analysis.AlignmentAnnotationUtils;
   7 import jalview.api.AlignViewportI;
   8 import jalview.bin.Console;
   9 import jalview.datamodel.Alignment;
  10 import jalview.datamodel.AlignmentAnnotation;
  11 import jalview.datamodel.AlignmentI;
  12 import jalview.datamodel.AlignmentView;
  13 import jalview.io.AlignFile;
  14 import jalview.io.JPredFile;
  15 import jalview.io.JnetAnnotationMaker;
  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.SecStructPredWebServiceClientI;
  24
  25 public class SecStructPredTask extends BaseTask<BaseJob, AlignmentI>
  26 {
  27   private final SecStructPredWebServiceClientI client;
  28
  29   private final AlignmentView alignmentView;
  30
  31   private final AlignmentI currentView;
  32
  33   private final char gapChar;
  34
  35   SecStructPredTask(SecStructPredWebServiceClientI client, List<ArgumentI> args,
  36       Credentials credentials, AlignViewportI viewport)
  37   {
  38     super(client, args, credentials);
  39     this.client = client;
  40     this.alignmentView = viewport.getAlignmentView(true);
  41     this.currentView = viewport.getAlignment();
  42     this.gapChar = viewport.getGapCharacter();
  43   }
  44
  45   @Override
  46   protected List<BaseJob> prepareJobs() throws ServiceInputInvalidException
  47   {
  48     AlignmentI alignment = alignmentView
  49         .getVisibleAlignment(Comparison.GAP_DASH);
  50     var job = new BaseJob(alignment.getSequences())
  51     {
  52       @Override
  53       public boolean isInputValid()
  54       {
  55         return true;
  56       }
  57     };
  58     job.setStatus(JobStatus.READY);
  59     return List.of(job);
  60   }
  61
  62   @Override
  63   protected AlignmentI collectResult(List<BaseJob> jobs) throws IOException
  64   {
  65     var job = jobs.get(0); // There shouldn't be more than one job
  66     var status = job.getStatus();
  67     Console
  68         .info(String
  69             .format("sec str pred job \"%s\" finished with status %s",
  70                 job.getServerJob().getJobId(), status));
  71     if (status != JobStatus.COMPLETED)
  72       return null;
  73     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  74     AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
  75     // Object[] alnAndHiddenCols =
  76     // alignmentView.getAlignmentAndHiddenColumns(gapChar);
  77     // SequenceI[] sequences = (SequenceI[]) alnAndHiddenCols[0];
  78     var sequences = alignmentFile.getSeqsAsArray();
  79     // HiddenColumns hiddenCols = (HiddenColumns) alnAndHiddenCols[1];
  80     var aln = new Alignment(sequences);
  81     int firstSeq = 0;
  82     aln.setDataset(currentView.getDataset());
  83     try
  84     {
  85       JnetAnnotationMaker.add_annotation(predictionFile, aln, firstSeq, false);
  86     } catch (Exception e)
  87     {
  88       throw new IOException(e);
  89     }
  90
  91     for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
  92     {
  93       if (alnAnnot.sequenceRef != null)
  94       {
  95         AlignmentAnnotationUtils
  96             .replaceAnnotationOnAlignmentWith(alnAnnot, alnAnnot.label,
  97                 getClass().getSimpleName());
  98       }
  99     }
 100     aln.setSeqrep(aln.getSequenceAt(firstSeq));
 101     return aln;
 102   }
 103
 104 }