X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=69d0ae48e023ea9c7fe3a9773dbf02e3d1957f40;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=6531bbf122e465d1f9bb3989ae7d564f36f854ab;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 6531bbf..69d0ae4 100644 --- a/src/jalview/ws/jws1/JPredThread.java +++ b/src/jalview/ws/jws1/JPredThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * @@ -20,17 +20,26 @@ */ package jalview.ws.jws1; -import java.util.*; - -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.io.*; -import jalview.util.*; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; +import jalview.io.FormatAdapter; +import jalview.util.Comparison; +import jalview.util.MessageManager; import jalview.ws.AWsJob; import jalview.ws.JobStateSummary; import jalview.ws.WSClientI; + +import java.util.Hashtable; +import java.util.List; + import vamsas.objects.simple.JpredResult; class JPredThread extends JWS1Thread implements WSClientI @@ -138,23 +147,28 @@ class JPredThread extends JWS1Thread implements WSClientI sqs[i] = al.getSequenceAt(i); } if (!jalview.analysis.SeqsetUtils.deuniquify( - (Hashtable) SequenceInfo, sqs)) + SequenceInfo, sqs)) { - throw (new Exception( - "Couldn't recover sequence properties for alignment.")); + throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment"))); } } FirstSeq = 0; - al.setDataset(null); + if (currentView.getDataset() != null) + { + al.setDataset(currentView.getDataset()); + } + else + { + al.setDataset(null); + } jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, false, predMap); } else { - throw (new Exception("Unknown format " + format - + " for file : \n" + result.getAligfile())); + throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()}))); } } else @@ -164,18 +178,17 @@ class JPredThread extends JWS1Thread implements WSClientI if (predMap != null) { char gc = getGapChar(); - SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input - .getAlignmentAndColumnSelection(gc))[0]; + SequenceI[] sqs = (SequenceI[]) input + .getAlignmentAndColumnSelection(gc)[0]; if (this.msaIndex >= sqs.length) { - throw new Error( - "Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!"); + throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job")); } // /// // Uses RemoveGapsCommand // /// - new jalview.commands.RemoveGapsCommand("Remove Gaps", + new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"), new SequenceI[] { sqs[msaIndex] }, currentView); @@ -186,12 +199,19 @@ class JPredThread extends JWS1Thread implements WSClientI if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( al.getSequenceAt(FirstSeq), SequenceInfo)) { - throw (new Exception( - "Couldn't recover sequence properties for JNet Query sequence!")); + throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query"))); } else { - al.setDataset(null); + if (currentView.getDataset() != null) + { + al.setDataset(currentView.getDataset()); + + } + else + { + al.setDataset(null); + } jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, true, predMap); SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps. @@ -205,11 +225,53 @@ class JPredThread extends JWS1Thread implements WSClientI } } } + // transfer to dataset + for (AlignmentAnnotation alant : al.getAlignmentAnnotation()) + { + if (alant.sequenceRef != null) + { + replaceAnnotationOnAlignmentWith(alant, alant.label, + "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"), + alant.sequenceRef); + } + } return new Object[] { al, alcsel }; // , FirstSeq, noMsa}; } /** + * copied from JabawsCalcWorker + * + * @param newAnnot + * @param typeName + * @param calcId + * @param aSeq + */ + protected void replaceAnnotationOnAlignmentWith( + AlignmentAnnotation newAnnot, String typeName, String calcId, + SequenceI aSeq) + { + SequenceI dsseq = aSeq.getDatasetSequence(); + while (dsseq.getDatasetSequence() != null) + { + dsseq = dsseq.getDatasetSequence(); + } + // look for same annotation on dataset and lift this one over + List dsan = dsseq.getAlignmentAnnotations( + calcId, typeName); + if (dsan != null && dsan.size() > 0) + { + for (AlignmentAnnotation dssan : dsan) + { + dsseq.removeAlignmentAnnotation(dssan); + } + } + AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot); + dsseq.addAlignmentAnnotation(dssan); + dssan.adjustForAlignment(); + } + + /** * Given an alignment where all other sequences except profileseq are * aligned to the ungapped profileseq, insert gaps in the other sequences to * realign them with the residues in profileseq @@ -357,9 +419,7 @@ class JPredThread extends JWS1Thread implements WSClientI { if (!(j instanceof JPredJob)) { - throw new Error( - "Implementation error - StartJob(JpredJob) called on " - + j.getClass()); + throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()})); } try { @@ -378,9 +438,9 @@ class JPredThread extends JWS1Thread implements WSClientI { if (job.getJobId().startsWith("Broken")) { - job.result = (vamsas.objects.simple.Result) new JpredResult(); + job.result = new JpredResult(); job.result.setInvalid(true); - job.result.setStatus("Submission " + job.getJobId()); + job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()})); throw new Exception(job.getJobId()); } else @@ -392,7 +452,7 @@ class JPredThread extends JWS1Thread implements WSClientI } else { - throw new Exception("Server timed out - try again later\n"); + throw new Exception(MessageManager.getString("exception.server_timeout_try_later")); } } catch (Exception e) { @@ -416,9 +476,7 @@ class JPredThread extends JWS1Thread implements WSClientI { wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR); // JBPNote - this could be a popup informing the user of the problem. - wsInfo.appendProgressText(j.getJobnum(), - "Failed to submit the prediction:\n" + e.getMessage() - + wsInfo.getProgressText()); + wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()})); jalview.bin.Cache.log.debug( "Failed Submission of job " + j.getJobnum(), e); @@ -508,8 +566,7 @@ class JPredThread extends JWS1Thread implements WSClientI else { // do merge with other job results - throw new Error( - "Multiple JNet subjob merging not yet implemented."); + throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented")); } } catch (Exception e) { @@ -517,9 +574,7 @@ class JPredThread extends JWS1Thread implements WSClientI "JNet Client: JPred Annotation Parse Error", e); wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR); - wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n" - + j.result.getStatus() - + "\nInvalid JNet job result data!\n" + e.getMessage()); + wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), e.getMessage() })); j.result.setBroken(true); } } @@ -587,7 +642,7 @@ class JPredThread extends JWS1Thread implements WSClientI public void cancelJob() { - throw new Error("Implementation error!"); + throw new Error(MessageManager.getString("error.implementation_error")); } public boolean canMergeResults()