Merge branch 'JAL-1601-direct-jpred4-rest-service' into development/Release_2_12_Branch

[jalview.git] / src / jalview / ws2 / actions / secstructpred / SecStructPredMsaTask.java

diff --git a/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java b/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java
new file mode 100644 (file)
index 0000000..21d8807
--- /dev/null
+++ b/src/jalview/ws2/actions/secstructpred/SecStructPredMsaTask.java
@@ -0,0 +1,147 @@
+package jalview.ws2.actions.secstructpred;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
+import jalview.api.AlignViewportI;
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.ws.params.ArgumentI;
+import jalview.ws2.actions.BaseJob;
+import jalview.ws2.actions.BaseTask;
+import jalview.ws2.actions.ServiceInputInvalidException;
+import jalview.ws2.api.Credentials;
+import jalview.ws2.api.JobStatus;
+import jalview.ws2.client.api.SecStructPredWebServiceClientI;
+
+public class SecStructPredMsaTask
+        extends BaseTask<SecStructPredMsaTask.SecStructPredJob, AlignmentI>
+{
+  private final SecStructPredWebServiceClientI client;
+
+  private final AlignmentView alignmentView;
+
+  private final AlignmentI currentView;
+
+  private final char gapChar;
+
+  SecStructPredMsaTask(SecStructPredWebServiceClientI client,
+          List<ArgumentI> args, Credentials credentials,
+          AlignViewportI viewport)
+  {
+    super(client, args, credentials);
+    this.client = client;
+    this.alignmentView = viewport.getAlignmentView(true);
+    this.currentView = viewport.getAlignment();
+    this.gapChar = viewport.getGapCharacter();
+  }
+
+  @Override
+  protected List<SecStructPredJob> prepareJobs()
+          throws ServiceInputInvalidException
+  {
+    SeqCigar[] msf = alignmentView.getSequences();
+    SequenceI referenceSeq = msf[0].getSeq('-');
+    int[] delMap = alignmentView
+            .getVisibleContigMapFor(referenceSeq.gapMap());
+
+    // TODO: assume MSA for now
+    SequenceI[] sequences = new SequenceI[msf.length];
+    for (int i = 0; i < msf.length; i++)
+      sequences[i] = msf[i].getSeq('-');
+    var sequenceInfo = SeqsetUtils.uniquify(sequences, true);
+    referenceSeq.setSequence(alignmentView.getASequenceString('-', 0));
+    for (int i = 0; i < sequences.length; i++)
+      sequences[i].setSequence(alignmentView.getASequenceString('-', i));
+    var nonEmptySeqs = SeqsetUtils.getNonEmptySequenceSet(sequences);
+    var job = new SecStructPredJob(Arrays.asList(nonEmptySeqs),
+            referenceSeq, delMap, sequenceInfo);
+    job.setStatus(JobStatus.READY);
+    return List.of(job);
+  }
+
+  @Override
+  protected AlignmentI collectResult(List<SecStructPredJob> jobs)
+          throws IOException
+  {
+    var job = jobs.get(0); // There shouldn't be more than one job
+    var status = job.getStatus();
+    Console.info(
+            String.format("sec str pred job \"%s\" finished with status %s",
+                    job.getServerJob().getJobId(), status));
+    if (status != JobStatus.COMPLETED)
+      return null;
+    JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
+    AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
+
+    Object[] alnAndHiddenCols = alignmentView
+            .getAlignmentAndHiddenColumns(gapChar);
+    Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]);
+    aln.setDataset(currentView.getDataset());
+    aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]);
+    try
+    {
+      JnetAnnotationMaker.add_annotation(predictionFile, aln, 0, false,
+              job.getDelMap());
+    } catch (Exception e)
+    {
+      throw new IOException(e);
+    }
+
+    for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
+    {
+      if (alnAnnot.sequenceRef != null)
+      {
+        AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot,
+                alnAnnot.label, getClass().getSimpleName());
+      }
+    }
+    aln.setSeqrep(aln.getSequenceAt(0));
+    return aln;
+  }
+
+  public static class SecStructPredJob extends BaseJob
+  {
+    private final int[] delMap;
+
+    private final SequenceI refSeq;
+
+    final Map<String, SequenceInfo> seqNames;
+
+    SecStructPredJob(List<SequenceI> sequences, SequenceI refSeq,
+            int[] delMap, Map<String, SequenceInfo> seqNames)
+    {
+      super(sequences);
+      this.refSeq = refSeq;
+      this.delMap = delMap;
+      this.seqNames = seqNames;
+    }
+
+    @Override
+    public boolean isInputValid()
+    {
+      return true;
+    }
+
+    public int[] getDelMap()
+    {
+      return this.delMap;
+    }
+  }
+
+}