+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 java.util.ArrayList;
-import java.util.HashMap;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
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.AnnotatedCollectionI;
-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
+public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
{
- 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);
- }
+ protected ScoreManager scoremanager;
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;
+ super(service, alignFrame, preset, paramset);
aaservice = (SequenceAnnotation) service.service;
-
}
- public WsParamSetI getPreset()
+ @Override
+ ChunkHolder pullExecStatistics(String rslt, long rpos)
{
- return preset;
+ return aaservice.pullExecStatistics(rslt, rpos);
}
- public List<Argument> getArguments()
+ @Override
+ boolean collectAnnotationResultsFor(String rslt)
+ throws ResultNotAvailableException
{
- return arguments;
+ scoremanager = aaservice.getAnnotation(rslt);
+ if (scoremanager != null)
+ {
+ return true;
+ }
+ return false;
}
- /**
- * 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)
+ @Override
+ boolean cancelJob(String rslt) throws Exception
{
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
+ return aaservice.cancelJob(rslt);
}
- public List<Option> getJabaArguments()
+ @Override
+ protected JobStatus getJobStatus(String rslt) throws Exception
{
- 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;
+ return aaservice.getJobStatus(rslt);
}
@Override
- public void run()
+ boolean hasService()
{
- 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(), bySequence ? alignViewport.getSelectionGroup() : null);
-
- 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);
- */
- }
- }
-
+ return aaservice != null;
}
@Override
- public void updateAnnotation()
+ protected boolean isInteractiveUpdate()
{
- updateResultAnnotation(false);
+ return this instanceof AAConClient;
}
- 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;
- int start,end;
-
- public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
+ @Override
+ protected String submitToService(
+ List<compbio.data.sequence.FastaSequence> seqs)
+ throws JobSubmissionException
{
- 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<compbio.data.sequence.FastaSequence>();
-
- int minlen = 10;
- int ln = -1;
- if (bySequence)
- {
- seqNames = new HashMap<String, SequenceI>();
- }
- gapMap = new boolean[0];
- start=inputSeqs.getStartRes();
- end=inputSeqs.getEndRes();
-
-
- for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
+ String rslt;
+ if (preset == null && arguments == null)
{
- 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())
- {
- gapMap[apos] = true; // aligned.
- }
- }
- 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();
- }
- }
+ rslt = aaservice.analize(seqs);
}
- if (alignedSeqs && submitGaps)
+ else
{
- 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)
+ rslt = aaservice.customAnalize(seqs, getJabaArguments());
+ } catch (WrongParameterException x)
{
- ex.printStackTrace();
+ throw new JobSubmissionException(
+ MessageManager
+ .getString("exception.jobsubmission_invalid_params_set"),
+ x);
+
}
}
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
+ return rslt;
}
- protected void createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String calcId,
- int alWidth, Score scr)
+ protected void createAnnotationRowsForScores(
+ List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
+ Score scr)
{
// simple annotation row
AlignmentAnnotation annotation = alignViewport.getAlignment()
}
}
- protected AlignmentAnnotation createAnnotationRowsForScores(List<AlignmentAnnotation> ourAnnot, String typeName,
+ 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()
return annotation;
}
- private void constructAnnotationFromScore(AlignmentAnnotation annotation, int base,
- int alWidth, Score scr)
+ protected void replaceAnnotationOnAlignmentWith(
+ AlignmentAnnotation newAnnot, String typeName, String calcId,
+ SequenceI aSeq)
+ {
+ SequenceI dsseq = aSeq.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
+ if (dsan != null && dsan.size() > 0)
+ {
+ for (AlignmentAnnotation dssan : dsan)
+ {
+ dsseq.removeAlignmentAnnotation(dssan);
+ }
+ }
+ AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+ dsseq.addAlignmentAnnotation(dssan);
+ dssan.adjustForAlignment();
+ }
+
+ private void constructAnnotationFromScore(AlignmentAnnotation annotation,
+ int base, int alWidth, Score scr)
{
Annotation[] elm = new Annotation[alWidth];
Iterator<Float> vals = scr.getScores().iterator();
}
elm[i] = new Annotation("", "" + val, ' ', val);
}
-
+
annotation.annotations = elm;
annotation.belowAlignment = true;
if (x < 0)
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