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     if (msf.length > 1)
  57       throw new ServiceInputInvalidException(MessageManager.getString(
  58               "error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
  59     SequenceI seq = msf[0].getSeq('-');
  60     if (seq == null)
  61       throw new ServiceInputInvalidException("Missing sequence.");
  62     int[] delMap = alignmentView.getVisibleContigMapFor(seq.gapMap());
  63     var seqInfo = SeqsetUtils.SeqCharacterHash(seq);
  64     seq.setSequence(AlignSeq.extractGaps(Comparison.GapChars,
  65             alignmentView.getASequenceString('-', 0)));
  66     if (seq.getLength() < 20)
  67       throw new ServiceInputInvalidException(
  68               "Sequence is too short to predict with JPred - need at least 20 amino acids.");
  69     var job = new SecStructPredJob(seq, delMap, seqInfo);
  70     job.setStatus(JobStatus.READY);
  71     return List.of(job);
  72   }
  73
  74   public static final int MSA_INDEX = 0;
  75
  76   @Override
  77   protected AlignmentI collectResult(List<SecStructPredJob> jobs)
  78           throws IOException
  79   {
  80     var job = jobs.get(0);  // There should be exactly one job
  81     var status = job.getStatus();
  82     Console.info(
  83             String.format("sec str pred job \"%s\" finished with status %s",
  84                     job.getServerJob().getJobId(), status));
  85     JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
  86     SequenceI[] preds = predictionFile.getSeqsAsArray();
  87     Alignment aln = new Alignment(preds);
  88     int queryPosition = predictionFile.getQuerySeqPosition();
  89     SequenceI profileSeq = aln.getSequenceAt(queryPosition);
  90     if (job.delMap != null)
  91     {
  92       SequenceI[] seqs = (SequenceI[]) alignmentView.getAlignmentAndHiddenColumns(gapChar)[0];
  93       if (MSA_INDEX >= seqs.length)
  94         throw new Error(MessageManager.getString(
  95                 "error.implementation_error_invalid_msa_index_for_job"));
  96       new RemoveGapsCommand(
  97               MessageManager.getString("label.remove_gaps"),
  98               new SequenceI[] { seqs[MSA_INDEX] }, currentView);
  99       profileSeq.setSequence(seqs[MSA_INDEX].getSequenceAsString());
 100     }
 101     if (!SeqsetUtils.SeqCharacterUnhash(aln.getSequenceAt(queryPosition), job.info))
 102       throw new IOException(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query"));
 103     aln.setDataset(currentView.getDataset());
 104     try
 105     {
 106       JnetAnnotationMaker.add_annotation(predictionFile, aln, queryPosition, true,
 107               job.delMap);
 108     } catch (Exception e)
 109     {
 110       throw new IOException(e);
 111     }
 112     alignToProfileSequence(aln, profileSeq);
 113     if (job.delMap != null)
 114       aln.setHiddenColumns(aln.propagateInsertions(profileSeq, alignmentView));
 115
 116     for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
 117     {
 118       if (alnAnnot.sequenceRef != null)
 119       {
 120         AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot,
 121                 alnAnnot.label, getClass().getSimpleName());
 122       }
 123     }
 124     aln.setSeqrep(profileSeq);
 125     return aln;
 126   }
 127
 128   /**
 129    * Given an alignment where all other sequences except profileseq are
 130    * aligned to the ungapped profileseq, insert gaps in the other sequences to
 131    * realign them with the residues in profileseq.
 132    *
 133    * Shamelessly copied from JPredThread.
 134    *
 135    * @param al
 136    * @param profileseq
 137    */
 138   private static void alignToProfileSequence(AlignmentI al, SequenceI profileseq)
 139   {
 140     char gc = al.getGapCharacter();
 141     int[] gapMap = profileseq.gapMap();
 142     // insert gaps into profile
 143     for (int lp = 0, r = 0; r < gapMap.length; r++)
 144     {
 145       if (gapMap[r] - lp > 1)
 146       {
 147         StringBuffer sb = new StringBuffer();
 148         for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
 149         {
 150           sb.append(gc);
 151         }
 152         for (int s = 1, ns = al.getHeight(); s < ns; s++)
 153         {
 154           String sq = al.getSequenceAt(s).getSequenceAsString();
 155           int diff = gapMap[r] - sq.length();
 156           if (diff > 0)
 157           {
 158             // pad gaps
 159             sq = sq + sb;
 160             while ((diff = gapMap[r] - sq.length()) > 0)
 161             {
 162               sq = sq + ((diff >= sb.length()) ? sb.toString()
 163                       : sb.substring(0, diff));
 164             }
 165             al.getSequenceAt(s).setSequence(sq);
 166           }
 167           else
 168           {
 169             al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
 170                     + sb.toString() + sq.substring(gapMap[r]));
 171           }
 172         }
 173       }
 174       lp = gapMap[r];
 175     }
 176   }
 177
 178   public static class SecStructPredJob extends BaseJob
 179   {
 180     private final SequenceInfo info;
 181
 182     private final int[] delMap;
 183
 184     SecStructPredJob(SequenceI querySequence, int[] delMap,
 185             SequenceInfo info)
 186     {
 187       super(List.of(querySequence));
 188       this.delMap = delMap;
 189       this.info = info;
 190     }
 191
 192     @Override
 193     public boolean isInputValid()
 194     {
 195       return true;
 196     }
 197   }
 198
 199 }