X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabawsCalcWorker.java;fp=src%2Fjalview%2Fws%2Fjws2%2FJabawsCalcWorker.java;h=4a78209e0da4ae9cb6d0ca8e79b70852d718934b;hb=44396db56b65458459eb38b399a52e0962b5bdab;hp=0000000000000000000000000000000000000000;hpb=9abf7aa279cedfeff9c8f4752ab911482485f059;p=jalview.git

diff --git a/src/jalview/ws/jws2/JabawsCalcWorker.java b/src/jalview/ws/jws2/JabawsCalcWorker.java
new file mode 100644
index 0000000..4a78209
--- /dev/null
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -0,0 +1,599 @@
+package jalview.ws.jws2;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
+import compbio.metadata.Argument;
+import compbio.metadata.ChunkHolder;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.Option;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.WrongParameterException;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.IProgressIndicator;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+public abstract class JabawsCalcWorker extends AlignCalcWorker
+{
+
+  protected Jws2Instance service;
+  @SuppressWarnings("unchecked")
+  protected SequenceAnnotation aaservice;
+  protected ScoreManager scoremanager;
+  protected WsParamSetI preset;
+  protected List<Argument> arguments;
+  protected IProgressIndicator guiProgress;
+
+  public JabawsCalcWorker(AlignViewportI alignViewport,
+          AlignmentViewPanel alignPanel)
+  {
+    super(alignViewport, alignPanel);
+  }
+
+  public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+          WsParamSetI preset, List<Argument> paramset)
+  {
+    this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+    this.guiProgress = alignFrame;
+    this.preset = preset;
+    this.arguments = paramset;
+    this.service = service;
+    aaservice = (SequenceAnnotation) service.service;
+
+  }
+
+  public WsParamSetI getPreset()
+  {
+    return preset;
+  }
+
+  public List<Argument> getArguments()
+  {
+    return arguments;
+  }
+
+  /**
+   * reconfigure and restart the AAConClient. This method will spawn a new
+   * thread that will wait until any current jobs are finished, modify the
+   * parameters and restart the conservation calculation with the new values.
+   * 
+   * @param newpreset
+   * @param newarguments
+   */
+  public void updateParameters(final WsParamSetI newpreset, final List<Argument> newarguments)
+  {
+    preset = newpreset;
+    arguments = newarguments;
+    calcMan.startWorker(this);
+  }
+
+  public List<Option> getJabaArguments()
+  {
+    List<Option> newargs = new ArrayList<Option>();
+    if (preset != null && preset instanceof JabaWsParamSet)
+    {
+      newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+    }
+    if (arguments != null && arguments.size() > 0)
+    {
+      for (Argument rg : arguments)
+      {
+        if (Option.class.isAssignableFrom(rg.getClass()))
+        {
+          newargs.add((Option) rg);
+        }
+      }
+    }
+    return newargs;
+  }
+
+  @Override
+  public void run()
+  {
+    if (aaservice == null)
+    {
+      return;
+    }
+    long progressId = -1;
+  
+    int serverErrorsLeft = 3;
+  
+    String rslt = "JOB NOT DEFINED";
+    StringBuffer msg = new StringBuffer();
+    try
+    {
+      if (checkDone())
+      {
+        return;
+      }
+      List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
+              .getAlignment());
+  
+      if (seqs == null)
+      {
+        calcMan.workerComplete(this);
+        return;
+      }
+  
+      AlignmentAnnotation[] aa = alignViewport.getAlignment()
+              .getAlignmentAnnotation();
+      if (guiProgress != null)
+      {
+        guiProgress.setProgressBar("JABA " + getServiceActionText(),
+                progressId = System.currentTimeMillis());
+      }
+      if (preset == null && arguments == null)
+      {
+        rslt = aaservice.analize(seqs);
+      }
+      else
+      {
+        try
+        {
+          rslt = aaservice.customAnalize(seqs, getJabaArguments());
+        } catch (WrongParameterException x)
+        {
+          throw new JobSubmissionException(
+                  "Invalid parameter set. Check Jalview implementation.", x);
+  
+        }
+      }
+      boolean finished = false;
+      long rpos = 0;
+      do
+      {
+        JobStatus status = aaservice.getJobStatus(rslt);
+        if (status.equals(JobStatus.FINISHED))
+        {
+          finished = true;
+        }
+        if (calcMan.isPending(this) && this instanceof AAConClient)
+        {
+          finished = true;
+          // cancel this job and yield to the new job
+          try
+          {
+            if (aaservice.cancelJob(rslt))
+            {
+              System.err.println("Cancelled AACon job: " + rslt);
+            }
+            else
+            {
+              System.err.println("FAILED TO CANCEL AACon job: " + rslt);
+            }
+  
+          } catch (Exception x)
+          {
+  
+          }
+  
+          return;
+        }
+        long cpos;
+        ChunkHolder stats = null;
+        do
+        {
+          cpos = rpos;
+          boolean retry = false;
+          do
+          {
+            try
+            {
+              stats = aaservice.pullExecStatistics(rslt, rpos);
+            } catch (Exception x)
+            {
+  
+              if (x.getMessage().contains(
+                      "Position in a file could not be negative!"))
+              {
+                // squash index out of bounds exception- seems to happen for
+                // disorder predictors which don't (apparently) produce any
+                // progress information and JABA server throws an exception
+                // because progress length is -1.
+                stats = null;
+              }
+              else
+              {
+                if (--serverErrorsLeft > 0)
+                {
+                  retry = true;
+                  try
+                  {
+                    Thread.sleep(200);
+                  } catch (InterruptedException q)
+                  {
+                  }
+                  ;
+                }
+                else
+                {
+                  throw x;
+                }
+              }
+            }
+          } while (retry);
+          if (stats != null)
+          {
+            System.out.print(stats.getChunk());
+            msg.append(stats);
+            rpos = stats.getNextPosition();
+          }
+        } while (stats != null && rpos > cpos);
+  
+        if (!finished && status.equals(JobStatus.FAILED))
+        {
+          try
+          {
+            Thread.sleep(200);
+          } catch (InterruptedException x)
+          {
+          }
+          ;
+        }
+      } while (!finished);
+      if (serverErrorsLeft > 0)
+      {
+        try
+        {
+          Thread.sleep(200);
+        } catch (InterruptedException x)
+        {
+        }
+        ;
+        scoremanager = aaservice.getAnnotation(rslt);
+        if (scoremanager != null)
+        {
+          jalview.bin.Cache.log
+                  .debug("Updating result annotation from Job " + rslt
+                          + " at " + service.getUri());
+          updateResultAnnotation(true);
+          ap.adjustAnnotationHeight();
+        }
+      }
+    }
+  
+    catch (JobSubmissionException x)
+    {
+  
+      System.err.println("submission error with " + getServiceActionText()
+              + " :");
+      x.printStackTrace();
+      calcMan.workerCannotRun(this);
+    } catch (ResultNotAvailableException x)
+    {
+      System.err.println("collection error:\nJob ID: " + rslt);
+      x.printStackTrace();
+      calcMan.workerCannotRun(this);
+  
+    } catch (OutOfMemoryError error)
+    {
+      calcMan.workerCannotRun(this);
+  
+      // consensus = null;
+      // hconsensus = null;
+      ap.raiseOOMWarning(getServiceActionText(), error);
+    } catch (Exception x)
+    {
+      calcMan.workerCannotRun(this);
+  
+      // consensus = null;
+      // hconsensus = null;
+      System.err
+              .println("Blacklisting worker due to unexpected exception:");
+      x.printStackTrace();
+    } finally
+    {
+  
+      calcMan.workerComplete(this);
+      if (ap != null)
+      {
+        calcMan.workerComplete(this);
+        if (guiProgress != null && progressId != -1)
+        {
+          guiProgress.setProgressBar("", progressId);
+        }
+        ap.paintAlignment(true);
+      }
+      if (msg.length() > 0)
+      {
+        // TODO: stash message somewhere in annotation or alignment view.
+        // code below shows result in a text box popup
+        /*
+         * jalview.gui.CutAndPasteTransfer cap = new
+         * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
+         * jalview.gui.Desktop.addInternalFrame(cap,
+         * "Job Status for "+getServiceActionText(), 600, 400);
+         */
+      }
+    }
+  
+  }
+
+  @Override
+  public void updateAnnotation()
+  {
+    updateResultAnnotation(false);
+  }
+
+  public abstract void updateResultAnnotation(boolean immediate);
+
+  public abstract String getServiceActionText();
+
+  protected boolean submitGaps = true;
+  protected boolean alignedSeqs = true;
+  protected boolean nucleotidesAllowed = false;
+  protected boolean proteinAllowed = false;
+  /**
+   * record sequences for mapping result back to afterwards
+   */
+  protected boolean bySequence = false;
+  protected Map<String, SequenceI> seqNames;
+  protected boolean[] gapMap;
+  int realw;
+
+  public List<FastaSequence> getInputSequences(AlignmentI alignment)
+  {
+    if (alignment == null || alignment.getWidth() <= 0
+            || alignment.getSequences() == null
+            // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
+            || alignment.isNucleotide() ? !nucleotidesAllowed
+            : !proteinAllowed)
+    {
+      return null;
+    }
+    List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+  
+    int minlen = 10;
+    int ln = -1;
+    if (bySequence)
+    {
+      seqNames = new HashMap<String, SequenceI>();
+    }
+    gapMap = new boolean[0];
+    for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+    {
+      if (sq.getEnd() - sq.getStart() > minlen - 1)
+      {
+        String newname = SeqsetUtils.unique_name(seqs.size() + 1);
+        // make new input sequence with or without gaps
+        if (seqNames != null)
+        {
+          seqNames.put(newname, sq);
+        }
+        FastaSequence seq;
+        if (submitGaps)
+        {
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  sq.getSequenceAsString()));
+          if (gapMap == null || gapMap.length < seq.getSequence().length())
+          {
+            boolean[] tg = gapMap;
+            gapMap = new boolean[seq.getLength()];
+            System.arraycopy(tg, 0, gapMap, 0, tg.length);
+            for (int p = tg.length; p < gapMap.length; p++)
+            {
+              gapMap[p] = false; // init as a gap
+            }
+          }
+          for (int apos : sq.gapMap())
+          {
+            gapMap[apos] = true; // aligned.
+          }
+        }
+        else
+        {
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          sq.getSequenceAsString())));
+        }
+        if (seq.getSequence().length() > ln)
+        {
+          ln = seq.getSequence().length();
+        }
+      }
+    }
+    if (alignedSeqs && submitGaps)
+    {
+      realw = 0;
+      for (int i = 0; i < gapMap.length; i++)
+      {
+        if (gapMap[i])
+        {
+          realw++;
+        }
+      }
+      // try real hard to return something submittable
+      // TODO: some of AAcon measures need a minimum of two or three amino
+      // acids at each position, and AAcon doesn't gracefully degrade.
+      for (int p = 0; p < seqs.size(); p++)
+      {
+        FastaSequence sq = seqs.get(p);
+        int l = sq.getSequence().length();
+        // strip gapped columns
+        char[] padded = new char[realw], orig = sq.getSequence()
+                .toCharArray();
+        for (int i = 0, pp = 0; i < realw; pp++)
+        {
+          if (gapMap[pp])
+          {
+            if (orig.length > pp)
+            {
+              padded[i++] = orig[pp];
+            }
+            else
+            {
+              padded[i++] = '-';
+            }
+          }
+        }
+        seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+                new String(padded)));
+      }
+    }
+    return seqs;
+  }
+
+  /**
+   * notify manager that we have started, and wait for a free calculation slot
+   * 
+   * @return true if slot is obtained and work still valid, false if another
+   *         thread has done our work for us.
+   */
+  boolean checkDone()
+  {
+    calcMan.notifyStart(this);
+    ap.paintAlignment(false);
+    while (!calcMan.notifyWorking(this))
+    {
+      if (calcMan.isWorking(this))
+      {
+        return true;
+      }
+      try
+      {
+        if (ap != null)
+        {
+          ap.paintAlignment(false);
+        }
+  
+        Thread.sleep(200);
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+    }
+    if (alignViewport.isClosed())
+    {
+      abortAndDestroy();
+      return true;
+    }
+    return false;
+  }
+
+  protected void createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String calcId,
+          int alWidth, Score scr)
+  {
+    // simple annotation row
+    AlignmentAnnotation annotation = alignViewport.getAlignment()
+            .findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
+                    null);
+    if (alWidth == gapMap.length) // scr.getScores().size())
+    {
+      constructAnnotationFromScore(annotation, 0, alWidth, scr);
+      ourAnnot.add(annotation);
+    }
+  }
+
+  protected AlignmentAnnotation createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String typeName,
+          String calcId, SequenceI dseq, int base, Score scr)
+  {
+    System.out.println("Creating annotation on dseq:" + dseq.getStart()
+            + " base is " + base + " and length=" + dseq.getLength()
+            + " == " + scr.getScores().size());
+    // AlignmentAnnotation annotation = new AlignmentAnnotation(
+    // scr.getMethod(), typeName, new Annotation[]
+    // {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
+    // annotation.setCalcId(calcId);
+    AlignmentAnnotation annotation = alignViewport.getAlignment()
+            .findOrCreateAnnotation(typeName, calcId, false, dseq, null);
+    constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
+    annotation.createSequenceMapping(dseq, base, false);
+    annotation.adjustForAlignment();
+    dseq.addAlignmentAnnotation(annotation);
+    ourAnnot.add(annotation);
+    return annotation;
+  }
+
+  private void constructAnnotationFromScore(AlignmentAnnotation annotation, int base,
+          int alWidth, Score scr)
+  {
+    Annotation[] elm = new Annotation[alWidth];
+    Iterator<Float> vals = scr.getScores().iterator();
+    float m = 0f, x = 0f;
+    for (int i = 0; vals.hasNext(); i++)
+    {
+      float val = vals.next().floatValue();
+      if (i == 0)
+      {
+        m = val;
+        x = val;
+      }
+      else
+      {
+        if (m > val)
+        {
+          m = val;
+        }
+        ;
+        if (x < val)
+        {
+          x = val;
+        }
+      }
+      // if we're at a gapped column then skip to next ungapped position
+      if (gapMap != null && gapMap.length > 0)
+      {
+        while (!gapMap[i])
+        {
+          elm[i++] = new Annotation("", "", ' ', Float.NaN);
+        }
+      }
+      elm[i] = new Annotation("", "" + val, ' ', val);
+    }
+  
+    annotation.annotations = elm;
+    annotation.belowAlignment = true;
+    if (x < 0)
+    {
+      x = 0;
+    }
+    x += (x - m) * 0.1;
+    annotation.graphMax = x;
+    annotation.graphMin = m;
+    annotation.validateRangeAndDisplay();
+  }
+
+  protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
+  {
+    List<AlignmentAnnotation> our = ourAnnots;
+    ourAnnots = ourAnnot;
+    AlignmentI alignment = alignViewport.getAlignment();
+    if (our != null)
+    {
+      if (our.size() > 0)
+      {
+        for (AlignmentAnnotation an : our)
+        {
+          if (!ourAnnots.contains(an))
+          {
+            // remove the old annotation
+            alignment.deleteAnnotation(an);
+          }
+        }
+      }
+      our.clear();
+  
+      ap.adjustAnnotationHeight();
+    }
+  }
+
+}