import java.util.Set;
import java.util.TreeSet;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
-public class AAConClient extends JabawsAlignCalcWorker
+public class AAConClient extends JabawsCalcWorker
{
public AAConClient(Jws2Instance service, AlignFrame alignFrame,
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public String getCalcId()
{
return CALC_ID;
import java.util.List;
import java.util.Map;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
return "Submitting amino acid sequences for disorder prediction.";
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
private static Map<String, Map<String, String[]>> featureMap;
private static Map<String, Map<String, Map<String, Object>>> annotMap;
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}
--- /dev/null
+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.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;
+
+ /**
+ * 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<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;
+ }
+
+ 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);
+
+ 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.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);
+ */
+ }
+ }
+
+ }
+
+ /**
+ * 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<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()))
+ {
+ 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();
+ }
+ }
+ }
+ 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);
+ 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 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();
+ }
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.api.AlignCalcWorkerI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.gui.AlignFrame;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.JpredAlignment;
+import compbio.metadata.Argument;
+
+public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
+ implements AlignCalcWorkerI
+{
+
+ /**
+ *
+ * @return default args for this service when run as dynamic web service
+ */
+ public List<Argument> selectDefaultArgs()
+ {
+ List<ArgumentI> rgs = new ArrayList<ArgumentI>();
+ for (ArgumentI argi: service.getParamStore().getServiceParameters())
+ {
+ if (argi instanceof OptionI)
+ {
+ List<String> o = ((OptionI) argi).getPossibleValues();
+ if (o.contains("-pred-nohits"))
+ {
+ OptionI cpy = ((OptionI)argi).copy();
+ cpy.setValue("-pred-nohits");
+ rgs.add(cpy);
+ }
+ }
+ }
+ return JabaParamStore.getJabafromJwsArgs(rgs);
+ }
+
+ public JPred301Client(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
+ {
+ super(service, alignFrame, preset, paramset);
+ submitGaps = true;
+ alignedSeqs = true;
+ nucleotidesAllowed = false;
+ proteinAllowed = true;
+ gapMap = new boolean[0];
+ updateParameters(null, selectDefaultArgs());
+ }
+
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ public String getServiceActionText()
+ {
+ return "calculating consensus secondary structure prediction using JPred service";
+ }
+ private static HashMap<String, String[]> jpredRowLabels = new HashMap<String,String[]>();
+ private static HashSet<String>jpredRes_graph,jpredRes_ssonly;
+ {
+ jpredRes_ssonly=new HashSet();
+ jpredRes_ssonly.add("jnetpred".toLowerCase());
+ jpredRes_graph=new HashSet();
+ jpredRes_graph.add("jnetconf".toLowerCase());
+
+ }
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateResultAnnotation(boolean immediate)
+ {
+ if (immediate || !calcMan.isWorking(this) && msascoreset != null)
+ {
+ if (msascoreset instanceof compbio.data.sequence.JpredAlignment)
+ {
+ JpredAlignment jpres = (JpredAlignment) msascoreset;
+ int alWidth = alignViewport.getAlignment().getWidth();
+ ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ for (FastaSequence fsq:jpres.getJpredSequences())
+ {
+ String[] k = jpredRowLabels.get(fsq.getId());
+ if (k==null)
+ {
+ k = new String[] { fsq.getId(), "JNet Output"};
+ }
+ createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
+ k[0],k[1],
+ jpredRes_graph.contains(fsq.getId()) ? AlignmentAnnotation.BAR_GRAPH : AlignmentAnnotation.NO_GRAPH, 0f, 0f,
+ fsq.getSequence());
+
+ }
+ for (FastaSequence fsq: jpres.getSequences())
+ {
+ if (fsq.getId().equalsIgnoreCase("QUERY"))
+ {
+ createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
+ "Query", "JPred Reference Sequence",
+ AlignmentAnnotation.NO_GRAPH, 0f, 0f,
+ fsq.getSequence());
+ }
+ }
+ if (ourAnnot.size() > 0)
+ {
+ updateOurAnnots(ourAnnot);
+ }
+ }
+ }
+ }
+
+ private void createAnnotationRowFromString(
+ ArrayList<AlignmentAnnotation> ourAnnot, String calcId,
+ int alWidth, String label, String descr, int rowType, float min,
+ float max, String jpredPrediction)
+ {
+ // simple annotation row
+ AlignmentAnnotation annotation = alignViewport.getAlignment()
+ .findOrCreateAnnotation(label, calcId, true, null, null);
+ if (alWidth == gapMap.length) // scr.getScores().size())
+ {
+ annotation.label = new String(label);
+ annotation.description = new String(descr);
+ annotation.graph = rowType;
+ annotation.graphMin = min;
+ annotation.graphMax = max;
+ if (constructAnnotationFromString(annotation, jpredPrediction,
+ alWidth, rowType))
+ {
+ // created a valid annotation from the data
+ ourAnnot.add(annotation);
+ }
+ }
+ }
+
+ private boolean constructAnnotationFromString(
+ AlignmentAnnotation annotation, String sourceData, int alWidth,
+ int rowType)
+ {
+ if (sourceData.length()==0 && alWidth>0)
+ {
+ return false;
+ }
+ Annotation[] elm = new Annotation[alWidth];
+
+ for (int i = 0, iSize = sourceData.length(); i < iSize; i++)
+ {
+ char annot = sourceData.charAt(i);
+ // 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);
+ }
+ }
+ switch (rowType)
+ {
+ case AlignmentAnnotation.NO_GRAPH:
+ elm[i] = new Annotation("" + annot, "" + annot, annot, Float.NaN);
+ break;
+ default:
+ try
+ {
+ elm[i] = new Annotation("" + annot, "" + annot, annot,
+ Integer.valueOf(annot));
+ } catch (Exception x)
+ {
+ System.err.println("Expected numeric value in character '"
+ + annot + "'");
+ }
+ }
+ }
+
+ annotation.annotations = elm;
+ annotation.belowAlignment = true;
+ annotation.validateRangeAndDisplay();
+ return true;
+ }
+
+ @Override
+ public String getCalcId()
+ {
+ return CALC_ID;
+ }
+
+ private static String CALC_ID = "jabaws21.JPred3Cons";
+
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
+ {
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.JpredWS.toString(),
+ jalview.ws.jws2.JPred301Client.class, CALC_ID, false, true,
+ true, "JPred Consensus",
+ "When checked, JPred consensus is updated automatically.",
+ "Change JPred Settings...",
+ "Modify settings for JPred calculations.");
+ }
+}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.gui.AlignFrame;
-import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
-
-import java.util.List;
-
-import compbio.metadata.Argument;
-
-public abstract class JabawsAlignCalcWorker extends JabawsCalcWorker
-{
-
- public JabawsAlignCalcWorker(AlignViewportI alignViewport,
- AlignmentViewPanel alignPanel)
- {
- super(alignViewport, alignPanel);
- }
-
- public JabawsAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
- {
- super(service, alignFrame, preset, paramset);
- }
-
- /**
- * Recover any existing parameters for this service
- */
- protected void initViewportParams()
- {
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
- }
-
- /**
- *
- * @return
- */
- public abstract String getCalcId();
-
- @Override
- public void updateParameters(WsParamSetI newpreset,
- java.util.List<Argument> newarguments)
- {
- super.updateParameters(newpreset, newarguments);
- initViewportParams();
- }
-}
*/
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.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);
- }
-
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()))
- {
- 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();
- }
- }
- }
- if (alignedSeqs && submitGaps)
+ String rslt;
+ if (preset == null && arguments == null)
{
- 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)));
- }
+ rslt = aaservice.analize(seqs);
}
- 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))
+ else
{
- 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(
+ "Invalid parameter set. Check Jalview implementation.", x);
+
}
}
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return true;
- }
- return false;
+ return rslt;
}
protected void createAnnotationRowsForScores(
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();
- }
- }
-
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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 java.util.Iterator;
+import java.util.List;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.Alignment;
+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.ResultNotAvailableException;
+import compbio.metadata.WrongParameterException;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.workers.AlignCalcWorker;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
+public abstract class JabawsMsaInterfaceAlignCalcWorker extends AbstractJabaCalcWorker
+{
+
+ @SuppressWarnings("unchecked")
+ protected MsaWS msaservice;
+
+ protected Alignment msascoreset;
+
+ public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ public JabawsMsaInterfaceAlignCalcWorker(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;
+ msaservice = (MsaWS) service.service;
+
+ }
+
+ @Override
+ ChunkHolder pullExecStatistics(String rslt, long rpos)
+ {
+ return msaservice.pullExecStatistics(rslt, rpos);
+ }
+
+ @Override
+ boolean collectAnnotationResultsFor(String rslt)
+ throws ResultNotAvailableException
+ {
+ msascoreset = msaservice.getResult(rslt);
+ if (msascoreset != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ boolean cancelJob(String rslt) throws Exception
+ {
+ return msaservice.cancelJob(rslt);
+ }
+
+ @Override
+ protected JobStatus getJobStatus(String rslt) throws Exception
+ {
+ return msaservice.getJobStatus(rslt);
+ }
+
+ @Override
+ boolean hasService()
+ {
+ return msaservice != null;
+ }
+
+ @Override
+ protected boolean isInteractiveUpdate()
+ {
+ return false; // this instanceof AAConClient;
+ }
+
+ @Override
+ protected String submitToService(
+ List<compbio.data.sequence.FastaSequence> seqs)
+ throws JobSubmissionException
+ {
+ String rslt;
+ if (preset == null && arguments == null)
+ {
+ rslt = msaservice.align(seqs);
+ }
+ else
+ {
+ try
+ {
+ rslt = msaservice.customAlign(seqs, getJabaArguments());
+ } catch (WrongParameterException x)
+ {
+ throw new JobSubmissionException(
+ "Invalid parameter set. Check Jalview implementation.", x);
+
+ }
+ }
+ return rslt;
+ }
+
+ 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();
+ }
+
+}
*/
package jalview.ws.jws2;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.util.List;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
import compbio.metadata.Argument;
-
+import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.gui.WebserviceInfo;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
+import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
/**
* provides metadata for a jabaws2 service instance - resolves names, etc.
*/
abstract void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
final AlignFrame alignFrame);
+
+
+ protected boolean registerAAConWSInstance(final JMenu wsmenu,
+ final Jws2Instance service, final AlignFrame alignFrame)
+ {
+ final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; //
+ // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
+ if (aaui == null)
+ {
+ // not an instantaneous calculation GUI type service
+ return false;
+ }
+ // create the instaneous calculation GUI bits and update state if existing
+ // GUI elements already present
+
+ JCheckBoxMenuItem _aaConEnabled = null;
+ for (int i = 0; i < wsmenu.getItemCount(); i++)
+ {
+ JMenuItem item = wsmenu.getItem(i);
+ if (item instanceof JCheckBoxMenuItem
+ && item.getText().equals(aaui.getAAconToggle()))
+ {
+ _aaConEnabled = (JCheckBoxMenuItem) item;
+ }
+ }
+ // is there an aaCon worker already present - if so, set it to use the
+ // given service handle
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ AbstractJabaCalcWorker worker = (AbstractJabaCalcWorker) aaconClient
+ .get(0);
+ if (!worker.service.hosturl.equals(service.hosturl))
+ {
+ // javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ // @Override
+ // public void run()
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ buildCurrentAAConWorkerFor(aaui, alignFrame, service);
+ }
+ }// );
+ }
+ }
+ }
+
+ // is there a service already registered ? there shouldn't be if we are
+ // being called correctly
+ if (_aaConEnabled == null)
+ {
+ final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
+ aaui.getAAconToggle());
+
+ aaConEnabled.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip()
+ + "</p>") + "</html>");
+ aaConEnabled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ removeCurrentAAConWorkerFor(aaui, alignFrame);
+ }
+ else
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame);
+
+ }
+ }
+
+ });
+ wsmenu.add(aaConEnabled);
+ final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
+ modifyParams.setToolTipText("<html><p>"
+ + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip()
+ + "</p>") + "</html>");
+ modifyParams.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ showAAConAnnotationSettingsFor(aaui, alignFrame);
+ }
+ });
+ wsmenu.add(modifyParams);
+ wsmenu.addMenuListener(new MenuListener()
+ {
+
+ @Override
+ public void menuSelected(MenuEvent arg0)
+ {
+ // TODO: refactor to the implementing class.
+ if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
+ .isNa() : aaui.isPr())
+ {
+ aaConEnabled.setEnabled(true);
+ modifyParams.setEnabled(true);
+ }
+ else
+ {
+ aaConEnabled.setEnabled(false);
+ modifyParams.setEnabled(false);
+ }
+ List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
+ .getCalcManager()
+ .getRegisteredWorkersOfClass(aaui.getClient());
+ if (aaconClient != null && aaconClient.size() > 0)
+ {
+ aaConEnabled.setSelected(true);
+ }
+ else
+ {
+ aaConEnabled.setSelected(false);
+ }
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
+
+ }
+ return true;
+ }
+
+ private static void showAAConAnnotationSettingsFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ // could actually do a class search for this too
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui);
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, true);
+
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame)
+ {
+ buildCurrentAAConWorkerFor(aaui, alignFrame, null);
+ }
+
+ private static void buildCurrentAAConWorkerFor(
+ final AlignAnalysisUIText aaui, AlignFrame alignFrame,
+ Jws2Instance service)
+ {
+ /*
+ * preferred settings Whether AACon is automatically recalculated Which
+ * AACon server to use What parameters to use
+ */
+ AAConSettings fave = (AAConSettings) alignFrame.getViewport()
+ .getCalcIdSettingsFor(aaui.getCalcId());
+ if (fave == null)
+ {
+ fave = createDefaultAAConSettings(aaui, service);
+ }
+ else
+ {
+ if (service != null
+ && !fave.getService().hosturl.equals(service.hosturl))
+ {
+ Cache.log.debug("Changing AACon service to " + service.hosturl
+ + " from " + fave.getService().hosturl);
+ fave.setService(service);
+ }
+ }
+ new SequenceAnnotationWSClient(fave, alignFrame, false);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui)
+ {
+ return createDefaultAAConSettings(aaui, null);
+ }
+
+ private static AAConSettings createDefaultAAConSettings(
+ AlignAnalysisUIText aaui, Jws2Instance service)
+ {
+ if (service != null)
+ {
+ if (!service.serviceType.toString().equals(
+ compbio.ws.client.Services.AAConWS.toString()))
+ {
+ Cache.log
+ .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ + service.serviceType + ")");
+ service = null;
+ }
+ else
+ {
+ // check service is actually in the list of currently avaialable
+ // services
+ if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
+ {
+ // it isn't ..
+ service = null;
+ }
+ }
+ }
+ if (service == null)
+ {
+ // get the default service for AACon
+ service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
+ aaui.getServiceType());
+ }
+ if (service == null)
+ {
+ // TODO raise dialog box explaining error, and/or open the JABA
+ // preferences menu.
+ throw new Error("No AACon service found.");
+ }
+ return new AAConSettings(true, service, null, null);
+ }
+
+ private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui,
+ AlignFrame alignFrame)
+ {
+ alignFrame.getViewport().getCalcManager()
+ .removeRegisteredWorkersOfClass(aaui.getClient());
+ }
}
// first set up exclusion list if needed
final Set<String> ignoredServices = new HashSet<String>();
for (String ignored : jalview.bin.Cache.getDefault(
- "IGNORED_JABAWS_SERVICETYPES", Services.JpredWS.toString())
+ "IGNORED_JABAWS_SERVICETYPES", "")
.split("\\|"))
{
ignoredServices.add(ignored);
public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
+ if (registerAAConWSInstance(rmsawsmenu, service, alignFrame))
+ {
+ // Alignment dependent analysis calculation WS gui
+ return;
+ }
setWebService(service, true); // headless
boolean finished = true, submitGaps = false;
JMenu msawsmenu = rmsawsmenu;
import java.util.regex.Pattern;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
*
*/
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+public class RNAalifoldClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
WsParamSetI preset, List<Argument> paramset)
{
super(sh, alignFrame, preset, paramset);
-
- // if (arguments == null)
- // arguments = new ArrayList<Argument>();
-
af = alignFrame;
methodName = sh.serviceType;
alignedSeqs = true;
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public void updateResultAnnotation(boolean immediate)
{
List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
.getCalcManager().getRegisteredWorkersOfClass(clientClass);
- JabawsAlignCalcWorker worker;
+ AbstractJabaCalcWorker worker;
if (clnts == null || clnts.size() == 0)
{
if (!processParams(sh, editParams))
}
try
{
- worker = (JabawsAlignCalcWorker) (clientClass
+ worker = (AbstractJabaCalcWorker) (clientClass
.getConstructor(new Class[]
{ Jws2Instance.class, AlignFrame.class,
WsParamSetI.class, List.class })
}
else
{
- worker = (JabawsAlignCalcWorker) clnts.get(0);
+ worker = (AbstractJabaCalcWorker) clnts.get(0);
if (editParams)
{
paramset = worker.getArguments();
}
}
}
-
- private boolean registerAAConWSInstance(final JMenu wsmenu,
- final Jws2Instance service, final AlignFrame alignFrame)
- {
- final AlignAnalysisUIText aaui = service.getAlignAnalysisUI(); // null ; //
- // AlignAnalysisUIText.aaConGUI.get(service.serviceType.toString());
- if (aaui == null)
- {
- // not an instantaneous calculation GUI type service
- return false;
- }
- // create the instaneous calculation GUI bits and update state if existing
- // GUI elements already present
-
- JCheckBoxMenuItem _aaConEnabled = null;
- for (int i = 0; i < wsmenu.getItemCount(); i++)
- {
- JMenuItem item = wsmenu.getItem(i);
- if (item instanceof JCheckBoxMenuItem
- && item.getText().equals(aaui.getAAconToggle()))
- {
- _aaConEnabled = (JCheckBoxMenuItem) item;
- }
- }
- // is there an aaCon worker already present - if so, set it to use the
- // given service handle
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- JabawsAlignCalcWorker worker = (JabawsAlignCalcWorker) aaconClient
- .get(0);
- if (!worker.service.hosturl.equals(service.hosturl))
- {
- // javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- // @Override
- // public void run()
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- buildCurrentAAConWorkerFor(aaui, alignFrame, service);
- }
- }// );
- }
- }
- }
-
- // is there a service already registered ? there shouldn't be if we are
- // being called correctly
- if (_aaConEnabled == null)
- {
- final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
- aaui.getAAconToggle());
-
- aaConEnabled.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAconToggleTooltip()
- + "</p>") + "</html>");
- aaConEnabled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- removeCurrentAAConWorkerFor(aaui, alignFrame);
- }
- else
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame);
-
- }
- }
-
- });
- wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
- modifyParams.setToolTipText("<html><p>"
- + JvSwingUtils.wrapTooltip(aaui.getAAeditSettingsTooltip()
- + "</p>") + "</html>");
- modifyParams.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- showAAConAnnotationSettingsFor(aaui, alignFrame);
- }
- });
- wsmenu.add(modifyParams);
- wsmenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
- // TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
- .isNa() : aaui.isPr())
- {
- aaConEnabled.setEnabled(true);
- modifyParams.setEnabled(true);
- }
- else
- {
- aaConEnabled.setEnabled(false);
- modifyParams.setEnabled(false);
- }
- List<AlignCalcWorkerI> aaconClient = alignFrame.getViewport()
- .getCalcManager()
- .getRegisteredWorkersOfClass(aaui.getClient());
- if (aaconClient != null && aaconClient.size() > 0)
- {
- aaConEnabled.setSelected(true);
- }
- else
- {
- aaConEnabled.setSelected(false);
- }
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- // TODO Auto-generated method stub
-
- }
- });
-
- }
- return true;
- }
-
- private static void showAAConAnnotationSettingsFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- // could actually do a class search for this too
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui);
- }
- new SequenceAnnotationWSClient(fave, alignFrame, true);
-
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame)
- {
- buildCurrentAAConWorkerFor(aaui, alignFrame, null);
- }
-
- private static void buildCurrentAAConWorkerFor(
- final AlignAnalysisUIText aaui, AlignFrame alignFrame,
- Jws2Instance service)
- {
- /*
- * preferred settings Whether AACon is automatically recalculated Which
- * AACon server to use What parameters to use
- */
- AAConSettings fave = (AAConSettings) alignFrame.getViewport()
- .getCalcIdSettingsFor(aaui.getCalcId());
- if (fave == null)
- {
- fave = createDefaultAAConSettings(aaui, service);
- }
- else
- {
- if (service != null
- && !fave.getService().hosturl.equals(service.hosturl))
- {
- Cache.log.debug("Changing AACon service to " + service.hosturl
- + " from " + fave.getService().hosturl);
- fave.setService(service);
- }
- }
- new SequenceAnnotationWSClient(fave, alignFrame, false);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- AlignAnalysisUIText aaui)
- {
- return createDefaultAAConSettings(aaui, null);
- }
-
- private static AAConSettings createDefaultAAConSettings(
- AlignAnalysisUIText aaui, Jws2Instance service)
- {
- if (service != null)
- {
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
- {
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
- + service.serviceType + ")");
- service = null;
- }
- else
- {
- // check service is actually in the list of currently avaialable
- // services
- if (!Jws2Discoverer.getDiscoverer().getServices().contains(service))
- {
- // it isn't ..
- service = null;
- }
- }
- }
- if (service == null)
- {
- // get the default service for AACon
- service = Jws2Discoverer.getDiscoverer().getPreferredServiceFor(null,
- aaui.getServiceType());
- }
- if (service == null)
- {
- // TODO raise dialog box explaining error, and/or open the JABA
- // preferences menu.
- throw new Error("No AACon service found.");
- }
- return new AAConSettings(true, service, null, null);
- }
-
- private static void removeCurrentAAConWorkerFor(AlignAnalysisUIText aaui,
- AlignFrame alignFrame)
- {
- alignFrame.getViewport().getCalcManager()
- .removeRegisteredWorkersOfClass(aaui.getClient());
- }
}
import java.util.HashMap;
import compbio.data.msa.JABAService;
-
import jalview.ws.jws2.AAConClient;
+import jalview.ws.jws2.JPred301Client;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.uimodel.AlignAnalysisUIText;
AAConClient.getAlignAnalysisUITest());
aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
RNAalifoldClient.getAlignAnalysisUITest());
+ aaConGUI.put(compbio.ws.client.Services.JpredWS.toString(),
+ JPred301Client.getAlignAnalysisUITest());
}
}
public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer()
{
+ return getJabawsDiscoverer(true);
+ }
+ public static Jws2Discoverer getJabawsDiscoverer(boolean localhost)
+ {
jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
.getDiscoverer();
- int p = 0;
String svcurls = "";
- Vector<String> services = new Vector<String>();
- for (String url : JalviewJabawsTestUtils.serviceUrls)
+ if (localhost)
{
- svcurls += url + "; ";
- services.add(url);
+ int p = 0;
+ Vector<String> services = new Vector<String>();
+ for (String url : JalviewJabawsTestUtils.serviceUrls)
+ {
+ svcurls += url + "; ";
+ services.add(url);
+ }
+ ;
+ Jws2Discoverer.setServiceUrls(services);
}
- ;
- Jws2Discoverer.setServiceUrls(services);
-
try
{
disc.run();
return disc;
}
+
}
{
jalview.bin.Cache.initLogger();
- disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
for (Jws2Instance svc : disc.getServices())
{
git://source.jalview.org / jalview.git / commitdiff