+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
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 java.util.ArrayList;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import com.sun.xml.internal.ws.developer.ServerSideException;
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;
public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
{
+ Jws2Instance service;
@SuppressWarnings("unchecked")
protected SequenceAnnotation aaservice;
super(alignViewport, alignPanel);
}
+ IProgressIndicator guiProgress;
+
public JabawsAlignCalcWorker(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;
}
}
/**
- * reconfigure and restart the AAConsClient. This method will spawn a new
+ * 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.
*
public void updateParameters(final WsParamSetI newpreset,
final List<Argument> newarguments)
{
- if (calcMan.isWorking(this))
- {
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
-
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- updateParameters(newpreset, newarguments);
- }
- }).start();
- }
- else
- {
- preset = newpreset;
- arguments = newarguments;
- calcMan.startWorker(this);
- }
+ preset = newpreset;
+ arguments = newarguments;
+ calcMan.startWorker(this);
}
public List<Option> getJabaArguments()
{
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());
+ .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
if (seqs == null)
{
AlignmentAnnotation[] aa = alignViewport.getAlignment()
.getAlignmentAnnotation();
-
- String rslt;
- if (preset == null)
+ if (guiProgress != null)
+ {
+ guiProgress.setProgressBar("JABA " + getServiceActionText(),
+ progressId = System.currentTimeMillis());
+ }
+ if (preset == null && arguments == null)
{
rslt = aaservice.analize(seqs);
}
} catch (WrongParameterException x)
{
throw new JobSubmissionException(
- "Invalid paremeter set. Check Jalview implementation.", x);
+ "Invalid parameter set. Check Jalview implementation.", x);
}
}
{
finished = true;
}
- long cpos;
- ChunkHolder stats;
- do
+ if (calcMan.isPending(this) && this instanceof AAConClient)
{
- cpos = rpos;
+ finished = true;
+ // cancel this job and yield to the new job
try
{
- stats = aaservice.pullExecStatistics(rslt, rpos);
+ if (aaservice.cancelJob(rslt))
+ {
+ System.err.println("Cancelled AACon job: " + rslt);
+ }
+ else
+ {
+ System.err.println("FAILED TO CANCEL AACon job: " + rslt);
+ }
+
} catch (Exception x)
{
- if (x.getCause() instanceof ServerSideException)
+ }
+
+ 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!"))
+
+ 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
}
else
{
- throw x;
+ if (--serverErrorsLeft > 0)
+ {
+ retry = true;
+ try
+ {
+ Thread.sleep(200);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ }
+ else
+ {
+ throw x;
+ }
}
}
- else
- {
- throw x;
- }
- }
+ } while (retry);
if (stats != null)
{
System.out.print(stats.getChunk());
+ msg.append(stats);
rpos = stats.getNextPosition();
}
} while (stats != null && rpos > cpos);
}
;
}
-
} while (!finished);
- try
+ if (serverErrorsLeft > 0)
{
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- scoremanager = aaservice.getAnnotation(rslt);
- if (scoremanager != null)
- {
- updateResultAnnotation(true);
+ 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)
+ }
+
+ catch (JobSubmissionException x)
{
- System.err.println("submission error:");
+ System.err.println("submission error with " + getServiceActionText()
+ + " :");
x.printStackTrace();
calcMan.workerCannotRun(this);
} catch (ResultNotAvailableException x)
{
- System.err.println("collection error:");
+ System.err.println("collection error:\nJob ID: " + rslt);
x.printStackTrace();
calcMan.workerCannotRun(this);
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);
boolean nucleotidesAllowed = false;
boolean proteinAllowed = false;
-
+
/**
* record sequences for mapping result back to afterwards
*/
- protected boolean bySequence=false;
+ protected boolean bySequence = false;
- Map<String,SequenceI> seqNames;
- public List<FastaSequence> getInputSequences(AlignmentI alignment)
- {
+ Map<String, SequenceI> seqNames;
+
+ boolean[] gapMap;
+
+ int realw;
+
+ int start,end;
+ public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
+ {
if (alignment == null || alignment.getWidth() <= 0
|| alignment.getSequences() == null
- || (alignedSeqs && !alignment.isAligned())
+ // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
|| 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>();
+ seqNames = new HashMap<String, SequenceI>();
}
- for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+ gapMap = new boolean[0];
+ start=inputSeqs.getStartRes();
+ end=inputSeqs.getEndRes();
+
+ for (SequenceI sq : (List<SequenceI>) inputSeqs.getSequences())
{
-
- if (sq.getEnd() - sq.getStart() > minlen - 1)
+ if (sq.findPosition(end+1) -sq.findPosition(start+1) > 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);
+ 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();
}
- seqs.add(new compbio.data.sequence.FastaSequence(newname,
- (submitGaps) ? sq.getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString())));
}
}
- return seqs;
- }
-
- protected AlignmentAnnotation findOrCreate(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef)
- {
- for (AlignmentAnnotation annot : alignViewport.getAlignment()
- .getAlignmentAnnotation())
+ if (alignedSeqs && submitGaps)
{
- if (annot.autoCalculated == autoCalc
- && annot.getCalcId().equals(name)
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ realw = 0;
+ for (int i = 0; i < gapMap.length; i++)
{
- return annot;
+ 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)));
}
}
- AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
- new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
- annot.hasText = false;
- annot.setCalcId(new String(name));
- annot.autoCalculated = autoCalc;
- if (seqRef != null)
- {
- annot.setSequenceRef(seqRef);
- }
- annot.groupRef = groupRef;
- alignViewport.getAlignment().addAnnotation(annot);
-
- return annot;
+ return seqs;
}
/**
boolean checkDone()
{
calcMan.notifyStart(this);
- // ap.paintAlignment(false);
+ ap.paintAlignment(false);
while (!calcMan.notifyWorking(this))
{
if (calcMan.isWorking(this))
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