X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=db6e03f2e511d9502a43a45df7c6c15b6821d185;hb=86b84a537a05d03a21ba115bffe3575cedf98be0;hp=0ab38c755ebabdd738d88b6f2190317062187b27;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index 0ab38c7..db6e03f 100644 --- a/src/jalview/ws/jws2/MsaWSThread.java +++ b/src/jalview/ws/jws2/MsaWSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -26,7 +26,7 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; @@ -125,9 +125,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI int nseqs = 0; if (minlen < 0) { - throw new Error( - MessageManager - .getString("error.implementation_error_minlen_must_be_greater_zero")); + throw new Error(MessageManager.getString( + "error.implementation_error_minlen_must_be_greater_zero")); } for (int i = 0; i < seqs.length; i++) { @@ -162,8 +161,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI String empty = null; if (seqs[i].getEnd() >= seqs[i].getStart()) { - empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq - .extractGaps(jalview.util.Comparison.GapChars, + empty = (submitGaps) ? seqs[i].getSequenceAsString() + : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, seqs[i].getSequenceAsString()); } emptySeqs.add(new String[] { newname, empty }); @@ -176,12 +175,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI * * @return true if getAlignment will return a valid alignment result. */ + @Override public boolean hasResults() { - if (subjobComplete - && isFinished() - && (alignment != null || (emptySeqs != null && emptySeqs - .size() > 0))) + if (subjobComplete && isFinished() && (alignment != null + || (emptySeqs != null && emptySeqs.size() > 0))) { return true; } @@ -210,7 +208,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI for (compbio.data.sequence.FastaSequence seq : alignment .getSequences()) { - alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence()); + alseqs[alseq_l++] = new Sequence(seq.getId(), + seq.getSequence()); } alseq_gapchar = alignment.getMetadata().getGapchar(); @@ -316,6 +315,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI * * @return boolean true if job can be submitted. */ + @Override public boolean hasValidInput() { // TODO: get attributes for this MsaWS instance to check if it can do two @@ -405,8 +405,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI { for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments()) { - jobProgress.append(opt.getName() + " " + opt.getDefaultValue() - + "\n"); + jobProgress.append( + opt.getName() + " " + opt.getDefaultValue() + "\n"); } } } @@ -416,8 +416,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI // merge arguments with preset's own arguments. for (Argument opt : arguments) { - jobProgress.append(opt.getName() + " " + opt.getDefaultValue() - + "\n"); + jobProgress.append( + opt.getName() + " " + opt.getDefaultValue() + "\n"); } } jobProgress.append("\nJob Output:\n"); @@ -436,7 +436,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI String alTitle; // name which will be used to form new alignment window. - Alignment dataset; // dataset to which the new alignment will be + AlignmentI dataset; // dataset to which the new alignment will be // associated. @@ -479,7 +479,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI String wsUrl, WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, String wsname, String title, AlignmentView _msa, boolean subgaps, boolean presorder, - Alignment seqset) + AlignmentI seqset) { this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder); OutputHeader = wsInfo.getProgressText(); @@ -530,11 +530,13 @@ class MsaWSThread extends AWS2Thread implements WSClientI return validInput; } + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -576,8 +578,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI "Exception whilst cancelling " + jobs[job].getJobId(), exc); } - wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader - + cancelledMessage + "\n"); + wsInfo.setProgressText(jobs[job].getJobnum(), + OutputHeader + cancelledMessage + "\n"); } else { @@ -605,6 +607,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI } } + @Override public void pollJob(AWsJob job) throws Exception { // TODO: investigate if we still need to cast here in J1.6 @@ -630,8 +633,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI do { j.setLastChunk(lastchunk); - ChunkHolder chunk = server - .pullExecStatistics(j.getJobId(), lastchunk); + ChunkHolder chunk = server.pullExecStatistics(j.getJobId(), + lastchunk); if (chunk != null) { changed |= chunk.getChunk().length() > 0; @@ -650,6 +653,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI return changed; } + @Override public void StartJob(AWsJob job) { Exception lex = null; @@ -657,16 +661,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI if (!(job instanceof MsaWSJob)) { throw new Error(MessageManager.formatMessage( - "error.implementation_error_msawbjob_called", - new String[] { job.getClass().toString() })); + "error.implementation_error_msawbjob_called", new String[] + { job.getClass().toString() })); } MsaWSJob j = (MsaWSJob) job; if (j.isSubmitted()) { if (Cache.log.isDebugEnabled()) { - Cache.log.debug("Tried to submit an already submitted job " - + j.getJobId()); + Cache.log.debug( + "Tried to submit an already submitted job " + j.getJobId()); } return; } @@ -706,14 +710,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI { throw new Exception(MessageManager.formatMessage( "exception.web_service_returned_null_try_later", - new String[] { WsUrl })); + new String[] + { WsUrl })); } } catch (compbio.metadata.UnsupportedRuntimeException _lex) { lex = _lex; wsInfo.appendProgressText(MessageManager.formatMessage( "info.job_couldnt_be_run_server_doesnt_support_program", - new String[] { _lex.getMessage() })); + new String[] + { _lex.getMessage() })); wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported")); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); @@ -723,8 +729,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI { lex = _lex; wsInfo.appendProgressText(MessageManager.formatMessage( - "info.job_couldnt_be_run_exceeded_hard_limit", - new String[] { _lex.getMessage() })); + "info.job_couldnt_be_run_exceeded_hard_limit", new String[] + { _lex.getMessage() })); wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big")); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); @@ -736,16 +742,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI MessageManager.getString("warn.invalid_job_param_set")); wsInfo.appendProgressText(MessageManager.formatMessage( "info.job_couldnt_be_run_incorrect_param_setting", - new String[] { _lex.getMessage() })); + new String[] + { _lex.getMessage() })); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR); } catch (Error e) { // 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"); + System.err.println(WebServiceName + + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" + + "When contacting Server:" + WsUrl + "\n"); e.printStackTrace(System.err); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); wsInfo.setStatus(j.getJobnum(), @@ -753,10 +759,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI } catch (Exception e) { // 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"); + System.err.println(WebServiceName + + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" + + "When contacting Server:" + WsUrl + "\n"); e.printStackTrace(System.err); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); wsInfo.setStatus(j.getJobnum(), @@ -769,12 +774,13 @@ class MsaWSThread extends AWS2Thread implements WSClientI // TODO: JBPNote catch timeout or other fault types explicitly j.setAllowedServerExceptions(0); - wsInfo.appendProgressText(j.getJobnum(), MessageManager - .getString("info.failed_to_submit_sequences_for_alignment")); + wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString( + "info.failed_to_submit_sequences_for_alignment")); } } } + @Override public void parseResult() { long progbar = System.currentTimeMillis(); @@ -805,8 +811,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI } catch (Exception e) { - Cache.log - .warn("Exception when retrieving remaining Job progress data for job " + Cache.log.warn( + "Exception when retrieving remaining Job progress data for job " + msjob.getJobId() + " on server " + WsUrl); e.printStackTrace(); nexcept--; @@ -844,11 +850,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI { // job has failed for some reason - probably due to invalid // parameters - Cache.log - .debug("Results not available for finished job - marking as broken job.", - e); - msjob.jobProgress - .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n" + Cache.log.debug( + "Results not available for finished job - marking as broken job.", + e); + msjob.jobProgress.append( + "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n" + e.getLocalizedMessage()); msjob.setjobStatus(JobStatus.FAILED); } catch (Exception e) @@ -870,7 +876,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI // wsInfo.appendProgressText(jobs[j].getJobnum(), // "\nAlignment Object Method Notes\n"); // wsInfo.appendProgressText(jobs[j].getJobnum(), - // "Calculated with "+alignment.getMetadata().getProgram().toString()); + // "Calculated with + // "+alignment.getMetadata().getProgram().toString()); // JBPNote The returned files from a webservice could be // hidden behind icons in the monitor window that, // when clicked, pop up their corresponding data @@ -880,8 +887,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI } catch (Exception ex) { - Cache.log.error("Unexpected exception when processing results for " - + alTitle, ex); + Cache.log.error( + "Unexpected exception when processing results for " + alTitle, + ex); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } if (results > 0) @@ -889,6 +897,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI wsInfo.showResultsNewFrame .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(true); @@ -897,6 +906,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI wsInfo.mergeResults .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(false); @@ -952,7 +962,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI orders[j] = null; } SequenceI[] alignment = (SequenceI[]) newview[0]; - ColumnSelection columnselection = (ColumnSelection) newview[1]; + HiddenColumns hidden = (HiddenColumns) newview[1]; Alignment al = new Alignment(alignment); // TODO: add 'provenance' property to alignment from the method notes if (lastProgram != null) @@ -970,7 +980,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI if (newFrame) { - displayInNewFrame(al, alorders, columnselection); + displayInNewFrame(al, alorders, hidden); } else @@ -991,10 +1001,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI * @param columnselection */ protected void displayInNewFrame(AlignmentI al, - List alorders, ColumnSelection columnselection) + List alorders, HiddenColumns hidden) { - AlignFrame af = new AlignFrame(al, columnselection, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); // initialise with same renderer settings as in parent alignframe. af.getFeatureRenderer().transferSettings(this.featureSettings); @@ -1011,10 +1021,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI * SplitFrame with the other pane similarly aligned. */ AlignFrame requestedBy = getRequestingAlignFrame(); - if (requestedBy != null - && requestedBy.getSplitViewContainer() != null - && requestedBy.getSplitViewContainer().getComplement( - requestedBy) != null) + if (requestedBy != null && requestedBy.getSplitViewContainer() != null + && requestedBy.getSplitViewContainer() + .getComplement(requestedBy) != null) { AlignmentI complement = requestedBy.getSplitViewContainer() .getComplement(requestedBy); @@ -1023,6 +1032,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI // becomes null if the alignment window was closed before the alignment // job finished. AlignmentI copyComplement = new Alignment(complement); + // todo should this be done by copy constructor? + copyComplement.setGapCharacter(complement.getGapCharacter()); + // share the same dataset (and the mappings it holds) + copyComplement.setDataset(complement.getDataset()); copyComplement.alignAs(al); if (copyComplement.getHeight() > 0) { @@ -1032,8 +1045,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI af2.setTitle(complementTitle); String linkedTitle = MessageManager .getString("label.linked_view_title"); - JInternalFrame splitFrame = new SplitFrame(al.isNucleotide() ? af - : af2, al.isNucleotide() ? af2 : af); + JInternalFrame splitFrame = new SplitFrame( + al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af); Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1); return; } @@ -1095,12 +1108,14 @@ class MsaWSThread extends AWS2Thread implements WSClientI } for (int i = 0, l = alorders.size(); i < l; i++) { - af.addSortByOrderMenuItem(WebServiceName + (names.get(i)) - + " Ordering", alorders.get(i)); + af.addSortByOrderMenuItem( + WebServiceName + (names.get(i)) + " Ordering", + alorders.get(i)); } } } + @Override public boolean canMergeResults() { return false;