+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws.jws2;
-
-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.AnnotatedCollectionI;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.IProgressIndicator;
-import jalview.gui.IProgressIndicatorHandler;
-import jalview.schemes.ResidueProperties;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.dm.JabaWsParamSet;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-
-public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
-{
-
- protected Jws2Instance service;
-
- protected WsParamSetI preset;
-
- protected List<Argument> arguments;
-
- protected IProgressIndicator guiProgress;
-
- protected boolean submitGaps = true;
-
- /**
- * by default, we filter out non-standard residues before submission
- */
- protected boolean filterNonStandardResidues = true;
-
- /**
- * Recover any existing parameters for this service
- */
- protected void initViewportParams()
- {
- if (getCalcId() != null)
- {
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null)
- ? JabaParamStore.getJwsArgsfromJaba(arguments)
- : null),
- true);
- }
- }
-
- /**
- *
- * @return null or a string used to recover all annotation generated by this
- * worker
- */
- public abstract String getCalcId();
-
- 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);
- initViewportParams();
- }
-
- public List<Option> getJabaArguments()
- {
- List<Option> newargs = new ArrayList<>();
- 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;
- }
-
- 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;
-
- protected int start;
-
- int end;
-
- public AbstractJabaCalcWorker(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
- public AbstractJabaCalcWorker(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;
- }
-
- /**
- *
- * @return true if the submission thread should attempt to submit data
- */
- abstract boolean hasService();
-
- volatile String rslt = "JOB NOT DEFINED";
-
- @Override
- public void run()
- {
- if (!hasService())
- {
- return;
- }
- long progressId = -1;
-
- int serverErrorsLeft = 3;
-
- StringBuffer msg = new StringBuffer();
- try
- {
- if (checkDone())
- {
- return;
- }
- List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(
- alignViewport.getAlignment(),
- bySequence ? alignViewport.getSelectionGroup() : null);
-
- if (seqs == null || !checkValidInputSeqs(true, seqs))
- {
- calcMan.workerComplete(this);
- return;
- }
-
- AlignmentAnnotation[] aa = alignViewport.getAlignment()
- .getAlignmentAnnotation();
- if (guiProgress != null)
- {
- guiProgress.setProgressBar("JABA " + getServiceActionText(),
- progressId = System.currentTimeMillis());
- }
- rslt = submitToService(seqs);
- if (guiProgress != null)
- {
- guiProgress.registerHandler(progressId,
- new IProgressIndicatorHandler()
- {
-
- @Override
- public boolean cancelActivity(long id)
- {
- cancelCurrentJob();
- return true;
- }
-
- @Override
- public boolean canCancel()
- {
- return true;
- }
- });
- }
- boolean finished = false;
- long rpos = 0;
- do
- {
- JobStatus status = getJobStatus(rslt);
- if (status.equals(JobStatus.FINISHED))
- {
- finished = true;
- }
- if (calcMan.isPending(this) && isInteractiveUpdate())
- {
- finished = true;
- // cancel this job and yield to the new job
- try
- {
- if (cancelJob(rslt))
- {
- System.err.println("Cancelled AACon job: " + rslt);
- }
- else
- {
- System.err.println("FAILED TO CANCEL AACon job: " + rslt);
- }
-
- } catch (Exception x)
- {
-
- }
- rslt = "CANCELLED JOB";
- return;
- }
- long cpos;
- ChunkHolder stats = null;
- do
- {
- cpos = rpos;
- boolean retry = false;
- do
- {
- try
- {
- stats = 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)
- {
- }
- if (collectAnnotationResultsFor(rslt))
- {
- 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.disableWorker(this);
- } catch (ResultNotAvailableException x)
- {
- System.err.println("collection error:\nJob ID: " + rslt);
- x.printStackTrace();
- calcMan.disableWorker(this);
-
- } catch (OutOfMemoryError error)
- {
- calcMan.disableWorker(this);
-
- // consensus = null;
- // hconsensus = null;
- ap.raiseOOMWarning(getServiceActionText(), error);
- } catch (Exception x)
- {
- calcMan.disableWorker(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);
- }
- // TODO: may not need to paintAlignment again !
- ap.paintAlignment(false, false);
- }
- 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);
- */
- }
- }
-
- }
-
- /**
- * validate input for dynamic/non-dynamic update context
- *
- * @param dynamic
- * @param seqs
- * @return true if input is valid
- */
- abstract boolean checkValidInputSeqs(boolean dynamic,
- List<FastaSequence> seqs);
-
- abstract String submitToService(
- List<compbio.data.sequence.FastaSequence> seqs)
- throws JobSubmissionException;
-
- abstract boolean cancelJob(String rslt) throws Exception;
-
- abstract JobStatus getJobStatus(String rslt) throws Exception;
-
- abstract ChunkHolder pullExecStatistics(String rslt, long rpos);
-
- abstract boolean collectAnnotationResultsFor(String rslt)
- throws ResultNotAvailableException;
-
- public void cancelCurrentJob()
- {
- try
- {
- String id = rslt;
- if (cancelJob(rslt))
- {
- System.err.println("Cancelled job " + id);
- }
- else
- {
- System.err.println("Job " + id + " couldn't be cancelled.");
- }
- } catch (Exception q)
- {
- q.printStackTrace();
- }
- }
-
- /**
- * Interactive updating. Analysis calculations that work on the currently
- * displayed alignment data should cancel existing jobs when the input data
- * has changed.
- *
- * @return true if a running job should be cancelled because new input data is
- * available for analysis
- */
- abstract boolean isInteractiveUpdate();
-
- public List<FastaSequence> getInputSequences(AlignmentI alignment,
- AnnotatedCollectionI inputSeqs)
- {
- if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null || alignment.isNucleotide()
- ? !nucleotidesAllowed
- : !proteinAllowed)
- {
- return null;
- }
- if (inputSeqs == null || inputSeqs.getWidth() <= 0
- || inputSeqs.getSequences() == null
- || inputSeqs.getSequences().size() < 1)
- {
- inputSeqs = alignment;
- }
-
- List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
-
- int minlen = 10;
- int ln = -1;
- if (bySequence)
- {
- seqNames = new HashMap<>();
- }
- gapMap = new boolean[0];
- start = inputSeqs.getStartRes();
- end = inputSeqs.getEndRes();
-
- for (SequenceI sq : (inputSeqs.getSequences()))
- {
- if (bySequence
- ? sq.findPosition(end + 1)
- - sq.findPosition(start + 1) > minlen - 1
- : 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())
- {
- char sqc = sq.getCharAt(apos);
- if (!filterNonStandardResidues
- || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
- : ResidueProperties.nucleotideIndex[sqc] < 5))
- {
- gapMap[apos] = true; // aligned and real amino acid residue
- }
- ;
- }
- }
- else
- {
- seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString(start, end + 1))));
- }
- 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;
- }
-
- @Override
- public void updateAnnotation()
- {
- updateResultAnnotation(false);
- }
-
- public abstract void updateResultAnnotation(boolean immediate);
-
- public abstract String getServiceActionText();
-
- /**
- * 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.
- */
- protected boolean checkDone()
- {
- calcMan.notifyStart(this);
- ap.paintAlignment(false, false);
- while (!calcMan.notifyWorking(this))
- {
- if (calcMan.isWorking(this))
- {
- return true;
- }
- try
- {
- if (ap != null)
- {
- ap.paintAlignment(false, false);
- }
-
- Thread.sleep(200);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
- }
-
- 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