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.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
import java.util.Map;
import java.util.TreeSet;
-import compbio.data.msa.SequenceAnnotation;
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;
-public class AAConsClient extends AlignCalcWorker
+public class AAConsClient extends JabawsAlignCalcWorker
{
- public AAConsClient(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
- @SuppressWarnings("unchecked")
- SequenceAnnotation aaservice;
-
- private ScoreManager scoremanager;
-
- private WsParamSetI preset;
-
- private List<Argument> arguments;
-
- public WsParamSetI getPreset()
- {
- return preset;
- }
- public List<Argument> getArguments()
- {
- return arguments;
- }
- /**
- * reconfigure and restart the AAConsClient. 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)
- {
- 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);
- }
- }
-
-
public AAConsClient(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List<Argument> paramset)
{
- this(alignFrame.getCurrentView(), alignFrame.alignPanel);
- this.preset = preset;
- this.arguments = paramset;
- aaservice = (SequenceAnnotation) service.service;
-
- }
-
- 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;
- }
-
- try
- {
- if (checkDone())
- {
- return;
- }
- AlignmentI alignment = alignViewport.getAlignment();
-
- int aWidth = -1;
-
- if (alignment == null || (aWidth = alignment.getWidth()) < 0)
- {
- calcMan.workerComplete(this);
- return;
- }
-
- /*
- * AlignmentAnnotation
- * strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
- * Hashtable[]
- * hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
- * strucConsensus.annotations = null; strucConsensus.annotations = new
- * Annotation[aWidth];
- *
- * hStrucConsensus = new Hashtable[aWidth];
- */
- AlignmentAnnotation[] aa = alignViewport.getAlignment()
- .getAlignmentAnnotation();
- /*
- * AlignmentAnnotation rnaStruc = null; // select rna struct to use for
- * calculation for (int i = 0; i < aa.length; i++) { if
- * (aa[i].getRNAStruc() != null && aa[i].isValidStruc()) { rnaStruc =
- * aa[i]; break; } } // check to see if its valid
- *
- * if (rnaStruc==null || !rnaStruc.isValidStruc()) {
- * calcMan.workerComplete(this); return; }
- */
- List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
-
- boolean submitGaps = true;
- int minlen = 10;
- 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
- seqs.add(new compbio.data.sequence.FastaSequence(newname,
- (submitGaps) ? sq.getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString())));
- }
- }
-
- String rslt;
- if (preset == null)
- {
- rslt=aaservice.analize(seqs);
- }
- else
- {
- try {
- rslt=aaservice.customAnalize(seqs, getJabaArguments());
- } catch (WrongParameterException x)
- {
- throw new JobSubmissionException("Invalid paremeter set. Check Jalview implementation.",x);
-
- }
- }
- boolean finished = false;
- long rpos = 0;
- do
- {
- JobStatus status = aaservice.getJobStatus(rslt);
- if (status.equals(JobStatus.FINISHED))
- {
- finished = true;
- }
- long cpos;
- do
- {
- cpos = rpos;
- ChunkHolder stats = aaservice.pullExecStatistics(rslt, rpos);
- if (stats != null)
- {
- System.out.print(stats.getChunk());
- rpos = stats.getNextPosition();
- }
- } while (rpos > cpos);
-
- if (!finished && status.equals(JobStatus.FAILED))
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- }
-
- } while (!finished);
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
- }
- ;
- scoremanager = aaservice.getAnnotation(rslt);
- if (scoremanager != null)
- {
- updateResultAnnotation(true);
- }
- } catch (JobSubmissionException x)
- {
-
- System.err.println("submission error:");
- x.printStackTrace();
- calcMan.workerCannotRun(this);
- } catch (ResultNotAvailableException x)
- {
- System.err.println("collection error:");
- x.printStackTrace();
- calcMan.workerCannotRun(this);
-
- } catch (OutOfMemoryError error)
- {
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
- ap.raiseOOMWarning("calculating Amino acid consensus using AACons service", 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)
- {
- ap.paintAlignment(true);
- }
- }
-
+ super(service, alignFrame, preset, paramset);
+ submitGaps = true;
+ alignedSeqs = true;
+ nucleotidesAllowed = false;
+ proteinAllowed = true;
+ gapMap=new boolean[0];
}
- /**
- * 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.
- */
- private boolean checkDone()
+ public String getServiceActionText()
{
- 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;
+ return "calculating Amino acid consensus using AACons service";
}
/**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
- public void updateAnnotation()
- {
- updateResultAnnotation(false);
- }
-
- private AlignmentAnnotation findOrCreate(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef)
- {
- for (AlignmentAnnotation annot : alignViewport.getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot.autoCalculated == autoCalc
- && annot.getCalcId().equals(name)
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
- {
- return annot;
- }
- }
- 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;
- }
public void updateResultAnnotation(boolean immediate)
{
Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
int alWidth = alignViewport.getAlignment().getWidth();
AlignmentI alignment;
- int ann = (alignment=alignViewport.getAlignment()).getAlignmentAnnotation().length;
- ArrayList<AlignmentAnnotation> ourAnnot=new ArrayList<AlignmentAnnotation>();
+ int ann = (alignment = alignViewport.getAlignment())
+ .getAlignmentAnnotation().length;
+ ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
for (String score : scoremap.keySet())
{
TreeSet<Score> scores = scoremap.get(score);
else
{
// simple annotation row
- annotation = findOrCreate(scr.getMethod(), true, null, null);
+ annotation = alignViewport.getAlignment().findOrCreateAnnotation(scr.getMethod(), true, null, null);
Annotation[] elm = new Annotation[alWidth];
- if (alWidth==scr.getScores().size())
- {
- Iterator<Float> vals = scr.getScores().iterator();
- float m=0f,x=0f;
- for (int i = 0; vals.hasNext(); i++)
+ if (alWidth == scr.getScores().size())
{
- float val = vals.next().floatValue();
- if (i==0) { m=val;x=val;} else { if (m>val) { m=val; }; if (x<val) { x=val;}}
- 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();
- ourAnnot.add(annotation);
+ 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();
+ ourAnnot.add(annotation);
}
}
}
}
- if (ourAnnot.size()>0)
+ if (ourAnnot.size() > 0)
{
- List<AlignmentAnnotation> our=ourAnnots;
+ List<AlignmentAnnotation> our = ourAnnots;
ourAnnots = ourAnnot;
- if (our!=null) {
- if (our.size()>0)
+ if (our != null)
+ {
+ if (our.size() > 0)
{
- for (AlignmentAnnotation an:our)
+ for (AlignmentAnnotation an : our)
{
if (!ourAnnots.contains(an))
{
our.clear();
}
}
- //if (ann != alignViewport.getAlignment().getAlignmentAnnotation().length)
+ // if (ann !=
+ // alignViewport.getAlignment().getAlignmentAnnotation().length)
{
ap.adjustAnnotationHeight();
}
- /* else
- {
- ap.paintAlignment(true);
- }*/
+ /*
+ * else { ap.paintAlignment(true); }
+ */
}
}
git://source.jalview.org / jalview.git / blobdiff