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

   1 package jalview.ws2.actions.secstructpred;
   2
   3 import java.io.IOException;
   4 import java.util.List;
   5
   6 import jalview.analysis.AlignSeq;
   7 import jalview.analysis.AlignmentAnnotationUtils;
   8 import jalview.analysis.SeqsetUtils;
   9 import jalview.analysis.SeqsetUtils.SequenceInfo;
  10 import jalview.api.AlignViewportI;
  11 import jalview.bin.Console;
  12 import jalview.commands.RemoveGapsCommand;
  13 import jalview.datamodel.Alignment;
  14 import jalview.datamodel.AlignmentAnnotation;
  15 import jalview.datamodel.AlignmentI;
  16 import jalview.datamodel.AlignmentView;
  17 import jalview.datamodel.SeqCigar;
  18 import jalview.datamodel.SequenceI;
  19 import jalview.io.JPredFile;
  20 import jalview.io.JnetAnnotationMaker;
  21 import jalview.util.Comparison;
  22 import jalview.util.MessageManager;
  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 SecStructPredPDBSearchTask extends
  32         BaseTask<SecStructPredPDBSearchTask.SecStructPredJob, AlignmentI>
  33 {
  34   private final SecStructPredWebServiceClientI client;
  35
  36   private final AlignmentView alignmentView;
  37   private final AlignmentI currentView;
  38   private final char gapChar;
  39
  40   SecStructPredPDBSearchTask(SecStructPredWebServiceClientI client,
  41           List<ArgumentI> args, Credentials credentials,
  42           AlignViewportI viewport)
  43   {
  44     super(client, args, credentials);
  45     this.client = client;
  46     this.alignmentView = viewport.getAlignmentView(true);
  47     this.currentView = viewport.getAlignment();
  48     this.gapChar = viewport.getGapCharacter();
  49   }
  50
  51   @Override
  52   protected List<SecStructPredJob> prepareJobs()
  53           throws ServiceInputInvalidException
  54   {
  55     SeqCigar[] msf = alignmentView.getSequences();
  56     SequenceI seq = msf[0].getSeq('-');
  57     int[] delMap = alignmentView.getVisibleContigMapFor(seq.gapMap());
  58     if (msf.length > 1)
  59       throw new ServiceInputInvalidException(MessageManager.getString(
  60               "error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
  61     var seqInfo = SeqsetUtils.SeqCharacterHash(seq);
  62     seq.setSequence(AlignSeq.extractGaps(Comparison.GapChars,
  63             alignmentView.getASequenceString('-', 0)));
  64     if (seq.getLength() < 20)
  65       throw new ServiceInputInvalidException(
  66               "Sequence is too short to predict with JPred - need at least 20 amino acids.");
  67     var job = new SecStructPredJob(seq, delMap, seqInfo);
  68     job.setStatus(JobStatus.READY);
  69     return List.of(job);
  70   }
  71
  72   public static final int MSA_INDEX = 0;
  73
  74   @Override
  75   protected AlignmentI collectResult(List<SecStructPredJob> jobs)
  76           throws IOException
  77   {
  78     var job = jobs.get(0);  // There should be exactly one job
  79     var status = job.getStatus();
  80     Console.info(
  81             String.format("sec str pred job \"%s\" finished with status %s",
  82                     job.getServerJob().getJobId(), status));
  83     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  84     SequenceI[] preds = predictionFile.getSeqsAsArray();
  85     Alignment aln = new Alignment(preds);
  86     int queryPosition = predictionFile.getQuerySeqPosition();
  87     SequenceI profileSeq = aln.getSequenceAt(queryPosition);
  88     if (job.delMap != null)
  89     {
  90       SequenceI[] seqs = (SequenceI[]) alignmentView.getAlignmentAndHiddenColumns(gapChar)[0];
  91       if (MSA_INDEX >= seqs.length)
  92         throw new Error(MessageManager.getString(
  93                 "error.implementation_error_invalid_msa_index_for_job"));
  94       new RemoveGapsCommand(
  95               MessageManager.getString("label.remove_gaps"),
  96               new SequenceI[] { seqs[MSA_INDEX] }, currentView);
  97       profileSeq.setSequence(seqs[MSA_INDEX].getSequenceAsString());
  98     }
  99     if (!SeqsetUtils.SeqCharacterUnhash(aln.getSequenceAt(queryPosition), job.info))
 100       throw new IOException(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query"));
 101     aln.setDataset(currentView.getDataset());
 102     try
 103     {
 104       JnetAnnotationMaker.add_annotation(predictionFile, aln, queryPosition, true,
 105               job.delMap);
 106     } catch (Exception e)
 107     {
 108       throw new IOException(e);
 109     }
 110     alignToProfileSequence(aln, profileSeq);
 111     if (job.delMap != null)
 112       aln.setHiddenColumns(aln.propagateInsertions(profileSeq, alignmentView));
 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(profileSeq);
 123     return aln;
 124   }
 125
 126   /**
 127    * Given an alignment where all other sequences except profileseq are
 128    * aligned to the ungapped profileseq, insert gaps in the other sequences to
 129    * realign them with the residues in profileseq.
 130    *
 131    * Shamelessly copied from JPredThread.
 132    *
 133    * @param al
 134    * @param profileseq
 135    */
 136   private static void alignToProfileSequence(AlignmentI al, SequenceI profileseq)
 137   {
 138     char gc = al.getGapCharacter();
 139     int[] gapMap = profileseq.gapMap();
 140     // insert gaps into profile
 141     for (int lp = 0, r = 0; r < gapMap.length; r++)
 142     {
 143       if (gapMap[r] - lp > 1)
 144       {
 145         StringBuffer sb = new StringBuffer();
 146         for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
 147         {
 148           sb.append(gc);
 149         }
 150         for (int s = 1, ns = al.getHeight(); s < ns; s++)
 151         {
 152           String sq = al.getSequenceAt(s).getSequenceAsString();
 153           int diff = gapMap[r] - sq.length();
 154           if (diff > 0)
 155           {
 156             // pad gaps
 157             sq = sq + sb;
 158             while ((diff = gapMap[r] - sq.length()) > 0)
 159             {
 160               sq = sq + ((diff >= sb.length()) ? sb.toString()
 161                       : sb.substring(0, diff));
 162             }
 163             al.getSequenceAt(s).setSequence(sq);
 164           }
 165           else
 166           {
 167             al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
 168                     + sb.toString() + sq.substring(gapMap[r]));
 169           }
 170         }
 171       }
 172       lp = gapMap[r];
 173     }
 174   }
 175
 176   public static class SecStructPredJob extends BaseJob
 177   {
 178     private final SequenceInfo info;
 179
 180     private final int[] delMap;
 181
 182     SecStructPredJob(SequenceI querySequence, int[] delMap,
 183             SequenceInfo info)
 184     {
 185       super(List.of(querySequence));
 186       this.delMap = delMap;
 187       this.info = info;
 188     }
 189
 190     @Override
 191     public boolean isInputValid()
 192     {
 193       return true;
 194     }
 195   }
 196
 197 }