--- /dev/null
+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();
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff