- * Title: - *
- * - *- * Description: - *
- * - *- * Copyright: Copyright (c) 2004 - *
- * - *- * Company: Dundee University - *
- * - * @author not attributable - * @version 1.0 - */ -class MsaWSThread extends Thread implements WSClientI { - jalview.gui.AlignFrame alignFrame; - - WebserviceInfo wsInfo = null; - - String WebServiceName = null; - - String OutputHeader; - AlignmentView input; - boolean submitGaps = false; // pass sequences including gaps to alignment - - // service - - boolean preserveOrder = true; // and always store and recover sequence - - // order - - class MsaWSJob { - int jobnum = 0; // WebServiceInfo pane for this job - - String jobId; // ws job ticket - - vamsas.objects.simple.MsaResult result = null; - - vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet(); - - /** - * MsaWSJob - * - * @param jobNum - * int - * @param jobId - * String - */ - public MsaWSJob(int jobNum, SequenceI[] inSeqs) { - this.jobnum = jobNum; - prepareInput(inSeqs); - } - - int allowedServerExceptions = 3; // thread dies if too many - - // exceptions. - boolean submitted=false; - boolean subjobComplete = false; - - Hashtable SeqNames = new Hashtable(); - Vector emptySeqs = new Vector(); - private void prepareInput(SequenceI[] seqs) { - int nseqs = 0; - for (int i = 0; i < seqs.length; i++) { - if (seqs[i].getStart() < seqs[i].getEnd()) { - nseqs++; - } - } - vamsas.objects.simple.Sequence[] seqarray = - (nseqs>0) - ? new vamsas.objects.simple.Sequence[nseqs] - :null; - for (int i = 0, n = 0; i < seqs.length; i++) { - - String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same - // for - // any - // subjob - SeqNames.put(newname, jalview.analysis.SeqsetUtils - .SeqCharacterHash(seqs[i])); - if (seqs[i].getStart() < seqs[i].getEnd()) { - seqarray[n] = new vamsas.objects.simple.Sequence(); - seqarray[n].setId(newname); - seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequence() - : AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, seqs[i] - .getSequence())); - } else { - emptySeqs.add(newname); - } - } - this.seqs = new vamsas.objects.simple.SequenceSet(); - this.seqs.setSeqs(seqarray); - } - /** - * - * @return true if getAlignment will return a valid alignment result. - */ - public boolean hasResults() { - if (subjobComplete && result!=null && jobs[0].result.isFinished()) - return true; - return false; - } - public Object[] getAlignment() { - - if (result!=null && result.isFinished()) { - SequenceI[] alseqs=null; - char alseq_gapchar='-'; - int alseq_l=0; - if (result.getMsa() != null) { - alseqs = getVamsasAlignment(result.getMsa()); - alseq_gapchar=result.getMsa().getGapchar().charAt(0); - alseq_l = alseqs.length; - } - if (emptySeqs.size()>0) { - SequenceI[] t_alseqs = new SequenceI[alseq_l+emptySeqs.size()]; - // get width - int i,w=0; - if (alseq_l>0) { - for (i=0,w=alseqs[0].getLength(); i+ * Description: + *
+ * + *+ * Copyright: Copyright (c) 2004 + *
+ * + *+ * Company: Dundee University + *
+ * + * @author not attributable + * @version 1.0 + */ +class MsaWSThread extends WSThread implements WSClientI +{ + boolean submitGaps = false; // pass sequences including gaps to alignment + + // service + + boolean preserveOrder = true; // and always store and recover sequence + + // order + + class MsaWSJob extends WSThread.WSJob + { + // hold special input for this + vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet(); + + /** + * MsaWSJob + * + * @param jobNum + * int + * @param jobId + * String + */ + public MsaWSJob(int jobNum, SequenceI[] inSeqs) + { + this.jobnum = jobNum; + if (!prepareInput(inSeqs, 2)) + { + submitted = true; + subjobComplete = true; + result = new MsaResult(); + result.setFinished(true); + result.setStatus("Job never ran - input returned to user."); + } + + } + + Hashtable SeqNames = new Hashtable(); + + Vector emptySeqs = new Vector(); + + /** + * prepare input sequences for MsaWS service + * + * @param seqs + * jalview sequences to be prepared + * @param minlen + * minimum number of residues required for this MsaWS service + * @return true if seqs contains sequences to be submitted to service. + */ + private boolean prepareInput(SequenceI[] seqs, int minlen) + { + int nseqs = 0; + if (minlen < 0) + { + throw new Error( + "Implementation error: minlen must be zero or more."); + } + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1) + { + nseqs++; + } + } + boolean valid = nseqs > 1; // need at least two seqs + vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs] + : null; + for (int i = 0, n = 0; i < seqs.length; i++) + { + + String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same + // for + // any + // subjob + SeqNames.put(newname, jalview.analysis.SeqsetUtils + .SeqCharacterHash(seqs[i])); + if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1) + { + seqarray[n] = new vamsas.objects.simple.Sequence(); + seqarray[n].setId(newname); + seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString() + : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, + seqs[i].getSequenceAsString())); + } + else + { + String empty = null; + if (seqs[i].getEnd() >= seqs[i].getStart()) + { + empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq + .extractGaps(jalview.util.Comparison.GapChars, seqs[i] + .getSequenceAsString()); + } + emptySeqs.add(new String[] + { newname, empty }); + } + } + this.seqs = new vamsas.objects.simple.SequenceSet(); + this.seqs.setSeqs(seqarray); + return valid; + } + + /** + * + * @return true if getAlignment will return a valid alignment result. + */ + public boolean hasResults() + { + if (subjobComplete && result != null && result.isFinished() + && ((MsaResult) result).getMsa() != null + && ((MsaResult) result).getMsa().getSeqs() != null) + { + return true; + } + return false; + } + + public Object[] getAlignment() + { + + if (result != null && result.isFinished()) + { + SequenceI[] alseqs = null; + char alseq_gapchar = '-'; + int alseq_l = 0; + if (((MsaResult) result).getMsa() != null) + { + alseqs = getVamsasAlignment(((MsaResult) result).getMsa()); + alseq_gapchar = ((MsaResult) result).getMsa().getGapchar() + .charAt(0); + alseq_l = alseqs.length; + } + if (emptySeqs.size() > 0) + { + SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()]; + // get width + int i, w = 0; + if (alseq_l > 0) + { + for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++) + { + if (w < alseqs[i].getLength()) + { + w = alseqs[i].getLength(); + } + t_alseqs[i] = alseqs[i]; + alseqs[i] = null; + } + } + // check that aligned width is at least as wide as emptySeqs width. + int ow = w, nw = w; + for (i = 0, w = emptySeqs.size(); i < w; i++) + { + String[] es = (String[]) emptySeqs.get(i); + if (es != null && es[1] != null) + { + int sw = es[1].length(); + if (nw < sw) + { + nw = sw; + } + } + } + // make a gapped string. + StringBuffer insbuff = new StringBuffer(w); + for (i = 0; i < nw; i++) + { + insbuff.append(alseq_gapchar); + } + if (ow < nw) + { + for (i = 0; i < alseq_l; i++) + { + int sw = t_alseqs[i].getLength(); + if (nw > sw) + { + // pad at end + alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() + + insbuff.substring(0, sw - nw)); + } + } + } + for (i = 0, w = emptySeqs.size(); i < w; i++) + { + String[] es = (String[]) emptySeqs.get(i); + if (es[1] == null) + { + t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0], + insbuff.toString(), 1, 0); + } + else + { + if (es[1].length() < nw) + { + t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence( + es[0], + es[1] + insbuff.substring(0, nw - es[1].length()), + 1, 1 + es[1].length()); + } + else + { + t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence( + es[0], es[1]); + } + } + } + alseqs = t_alseqs; + } + AlignmentOrder msaorder = new AlignmentOrder(alseqs); + // always recover the order - makes parseResult()'s life easier. + jalview.analysis.AlignmentSorter.recoverOrder(alseqs); + // account for any missing sequences + jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs); + return new Object[] + { alseqs, msaorder }; + } + return null; + } + + /** + * mark subjob as cancelled and set result object appropriatly + */ + void cancel() + { + cancelled = true; + subjobComplete = true; + result = null; + } + + /** + * + * @return boolean true if job can be submitted. + */ + boolean hasValidInput() + { + if (seqs.getSeqs() != null) + { + return true; + } + return false; + } + } + + String alTitle; // name which will be used to form new alignment window. + + Alignment dataset; // dataset to which the new alignment will be + + // associated. + + ext.vamsas.MuscleWS server = null; + + /** + * set basic options for this (group) of Msa jobs + * + * @param subgaps + * boolean + * @param presorder + * boolean + */ + MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl, + WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, + AlignmentView alview, String wsname, boolean subgaps, + boolean presorder) + { + super(alFrame, wsinfo, alview, wsname, wsUrl); + this.server = server; + this.submitGaps = subgaps; + this.preserveOrder = presorder; + } + + /** + * create one or more Msa jobs to align visible seuqences in _msa + * + * @param title + * String + * @param _msa + * AlignmentView + * @param subgaps + * boolean + * @param presorder + * boolean + * @param seqset + * Alignment + */ + MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl, + WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, + String wsname, String title, AlignmentView _msa, boolean subgaps, + boolean presorder, Alignment seqset) + { + this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder); + OutputHeader = wsInfo.getProgressText(); + alTitle = title; + dataset = seqset; + + SequenceI[][] conmsa = _msa.getVisibleContigs('-'); + if (conmsa != null) + { + int njobs = conmsa.length; + jobs = new MsaWSJob[njobs]; + for (int j = 0; j < njobs; j++) + { + if (j != 0) + { + jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]); + } + else + { + jobs[j] = new MsaWSJob(0, conmsa[j]); + } + if (njobs > 0) + { + wsinfo + .setProgressName("region " + jobs[j].jobnum, + jobs[j].jobnum); + } + wsinfo.setProgressText(jobs[j].jobnum, OutputHeader); + } + } + } + + public boolean isCancellable() + { + return true; + } + + public void cancelJob() + { + if (!jobComplete && jobs != null) + { + boolean cancelled = true; + for (int job = 0; job < jobs.length; job++) + { + if (jobs[job].submitted && !jobs[job].subjobComplete) + { + String cancelledMessage = ""; + try + { + vamsas.objects.simple.WsJobId cancelledJob = server + .cancel(jobs[job].jobId); + if (cancelledJob.getStatus() == 2) + { + // CANCELLED_JOB + cancelledMessage = "Job cancelled."; + ((MsaWSJob) jobs[job]).cancel(); + wsInfo.setStatus(jobs[job].jobnum, + WebserviceInfo.STATE_CANCELLED_OK); + } + else if (cancelledJob.getStatus() == 3) + { + // VALID UNSTOPPABLE JOB + cancelledMessage += "Server cannot cancel this job. just close the window.\n"; + cancelled = false; + // wsInfo.setStatus(jobs[job].jobnum, + // WebserviceInfo.STATE_RUNNING); + } + + if (cancelledJob.getJobId() != null) + { + cancelledMessage += ("[" + cancelledJob.getJobId() + "]"); + } + + cancelledMessage += "\n"; + } catch (Exception exc) + { + cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" + + exc + "\n"); + Cache.log.warn( + "Exception whilst cancelling " + jobs[job].jobId, exc); + } + wsInfo.setProgressText(jobs[job].jobnum, OutputHeader + + cancelledMessage + "\n"); + } + } + if (cancelled) + { + wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK); + jobComplete = true; + } + this.interrupt(); // kick thread to update job states. + } + else + { + if (!jobComplete) + { + wsInfo + .setProgressText(OutputHeader + + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n"); + } + } + } + + void pollJob(WSJob job) throws Exception + { + ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId); + } + + void StartJob(WSJob job) + { + if (!(job instanceof MsaWSJob)) + { + throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " + + job.getClass()); + } + MsaWSJob j = (MsaWSJob) job; + if (j.submitted) + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.debug("Tried to submit an already submitted job " + + j.jobId); + } + return; + } + if (j.seqs.getSeqs() == null) + { + // special case - selection consisted entirely of empty sequences... + j.submitted = true; + j.result = new MsaResult(); + j.result.setFinished(true); + j.result.setStatus("Empty Alignment Job"); + ((MsaResult) j.result).setMsa(null); + } + try + { + vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs); + + if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) + { + j.jobId = jobsubmit.getJobId(); + j.submitted = true; + j.subjobComplete = false; + // System.out.println(WsURL + " Job Id '" + jobId + "'"); + } + else + { + if (jobsubmit == null) + { + throw new Exception( + "Server at " + + WsUrl + + " returned null object, it probably cannot be contacted. Try again later ?"); + } + + throw new Exception(jobsubmit.getJobId()); + } + } catch (Exception e) + { + // TODO: JBPNote catch timeout or other fault types explicitly + // For unexpected errors + System.err + .println(WebServiceName + + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" + + "When contacting Server:" + WsUrl + "\n" + + e.toString() + "\n"); + j.allowedServerExceptions = 0; + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); + wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR); + wsInfo + .appendProgressText( + j.jobnum, + "Failed to submit sequences for alignment.\n" + + "It is most likely that there is a problem with the server.\n" + + "Just close the window\n"); + + // e.printStackTrace(); // TODO: JBPNote DEBUG + } + } + + private jalview.datamodel.Sequence[] getVamsasAlignment( + vamsas.objects.simple.Alignment valign) + { + // TODO: refactor to helper class for vamsas.objects.simple objects + vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs(); + jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length]; + + for (int i = 0, j = seqs.length; i < j; i++) + { + msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i] + .getSeq()); + } + + return msa; + } + + void parseResult() + { + int results = 0; // number of result sets received + JobStateSummary finalState = new JobStateSummary(); + try + { + for (int j = 0; j < jobs.length; j++) + { + finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]); + if (jobs[j].submitted && jobs[j].subjobComplete + && jobs[j].hasResults()) + { + results++; + vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result) + .getMsa(); + if (valign != null) + { + wsInfo.appendProgressText(jobs[j].jobnum, + "\nAlignment Object Method Notes\n"); + String[] lines = valign.getMethod(); + for (int line = 0; line < lines.length; line++) + { + wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n"); + } + // JBPNote The returned files from a webservice could be + // hidden behind icons in the monitor window that, + // when clicked, pop up their corresponding data + } + } + } + } catch (Exception ex) + { + + Cache.log.error("Unexpected exception when processing results for " + + alTitle, ex); + wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); + } + if (results > 0) + { + wsInfo.showResultsNewFrame + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(java.awt.event.ActionEvent evt) + { + displayResults(true); + } + }); + wsInfo.mergeResults + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(java.awt.event.ActionEvent evt) + { + displayResults(false); + } + }); + wsInfo.setResultsReady(); + } + else + { + wsInfo.setFinishedNoResults(); + } + } + + void displayResults(boolean newFrame) + { + // view input or result data for each block + Vector alorders = new Vector(); + SequenceI[][] results = new SequenceI[jobs.length][]; + AlignmentOrder[] orders = new AlignmentOrder[jobs.length]; + for (int j = 0; j < jobs.length; j++) + { + if (jobs[j].hasResults()) + { + Object[] res = ((MsaWSJob) jobs[j]).getAlignment(); + alorders.add(res[1]); + results[j] = (SequenceI[]) res[0]; + orders[j] = (AlignmentOrder) res[1]; + + // SequenceI[] alignment = input.getUpdated + } + else + { + results[j] = null; + } + } + Object[] newview = input.getUpdatedView(results, orders, getGapChar()); + // trash references to original result data + for (int j = 0; j < jobs.length; j++) + { + results[j] = null; + orders[j] = null; + } + SequenceI[] alignment = (SequenceI[]) newview[0]; + ColumnSelection columnselection = (ColumnSelection) newview[1]; + Alignment al = new Alignment(alignment); + // TODO: add 'provenance' property to alignment from the method notes + // accompanying each subjob + if (dataset != null) + { + al.setDataset(dataset); + } + + propagateDatasetMappings(al); + // JBNote- TODO: warn user if a block is input rather than aligned data ? + + if (newFrame) + { + AlignFrame af = new AlignFrame(al, columnselection, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + // initialise with same renderer settings as in parent alignframe. + af.getFeatureRenderer().transferSettings(this.featureSettings); + // update orders + if (alorders.size() > 0) + { + if (alorders.size() == 1) + { + af.addSortByOrderMenuItem(WebServiceName + " Ordering", + (AlignmentOrder) alorders.get(0)); + } + else + { + // construct a non-redundant ordering set + Vector names = new Vector(); + for (int i = 0, l = alorders.size(); i < l; i++) + { + String orderName = new String(" Region " + i); + int j = i + 1; + + while (j < l) + { + if (((AlignmentOrder) alorders.get(i)) + .equals(((AlignmentOrder) alorders.get(j)))) + { + alorders.remove(j); + l--; + orderName += "," + j; + } + else + { + j++; + } + } + + if (i == 0 && j == 1) + { + names.add(new String("")); + } + else + { + names.add(orderName); + } + } + for (int i = 0, l = alorders.size(); i < l; i++) + { + af.addSortByOrderMenuItem(WebServiceName + + ((String) names.get(i)) + " Ordering", + (AlignmentOrder) alorders.get(i)); + } + } + } + + Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + } + else + { + System.out.println("MERGE WITH OLD FRAME"); + // TODO: modify alignment in original frame, replacing old for new + // alignment using the commands.EditCommand model to ensure the update can + // be undone + } + } + + public boolean canMergeResults() + { + return false; + } +}