X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=f9655721b62819b2eb435871957254bc82e8ac80;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=72274de5071effd17232818cd38e854358e8bfce;hpb=9967bbf3d9c8e015662f09f5ec1b363333f0b117;p=jalview.git diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 72274de..f965572 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. * @@ -21,9 +21,12 @@ package jalview.ws.jws1; import jalview.analysis.AlignSeq; +import jalview.analysis.SeqsetUtils; import jalview.bin.Cache; +import jalview.commands.RemoveGapsCommand; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; import jalview.datamodel.SequenceI; @@ -31,6 +34,10 @@ import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.WebserviceInfo; import jalview.io.FormatAdapter; +import jalview.io.IdentifyFile; +import jalview.io.JPredFile; +import jalview.io.JnetAnnotationMaker; +import jalview.io.PileUpfile; import jalview.util.Comparison; import jalview.util.MessageManager; import jalview.ws.AWsJob; @@ -41,6 +48,7 @@ import java.util.Hashtable; import java.util.List; import vamsas.objects.simple.JpredResult; +import vamsas.objects.simple.Msfalignment; class JPredThread extends JWS1Thread implements WSClientI { @@ -103,29 +111,28 @@ class JPredThread extends JWS1Thread implements WSClientI { return null; } - Alignment al = null; + AlignmentI al = null; ColumnSelection alcsel = null; int FirstSeq = -1; // the position of the query sequence in Alignment al JpredResult result = (JpredResult) this.result; - jalview.bin.Cache.log.debug("Parsing output from JNet job."); + Cache.log.debug("Parsing output from JNet job."); // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", // "File"); - jalview.io.JPredFile prediction = new jalview.io.JPredFile( - result.getPredfile(), "Paste"); + JPredFile prediction = new JPredFile(result.getPredfile(), "Paste"); SequenceI[] preds = prediction.getSeqsAsArray(); - jalview.bin.Cache.log.debug("Got prediction profile."); + Cache.log.debug("Got prediction profile."); if ((this.msa != null) && (result.getAligfile() != null)) { - jalview.bin.Cache.log.debug("Getting associated alignment."); + Cache.log.debug("Getting associated alignment."); // we ignore the returned alignment if we only predicted on a single // sequence - String format = new jalview.io.IdentifyFile().Identify( - result.getAligfile(), "Paste"); + String format = new IdentifyFile().Identify(result.getAligfile(), + "Paste"); - if (jalview.io.FormatAdapter.isValidFormat(format)) + if (FormatAdapter.isValidFormat(format)) { SequenceI sqs[]; if (predMap != null) @@ -146,8 +153,7 @@ class JPredThread extends JWS1Thread implements WSClientI { sqs[i] = al.getSequenceAt(i); } - if (!jalview.analysis.SeqsetUtils.deuniquify( - SequenceInfo, sqs)) + if (!SeqsetUtils.deuniquify(SequenceInfo, sqs)) { throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment"))); } @@ -162,8 +168,8 @@ class JPredThread extends JWS1Thread implements WSClientI { al.setDataset(null); } - jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, - FirstSeq, false, predMap); + JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, + false, predMap); } else @@ -188,7 +194,8 @@ class JPredThread extends JWS1Thread implements WSClientI // /// // Uses RemoveGapsCommand // /// - new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"), + new RemoveGapsCommand( + MessageManager.getString("label.remove_gaps"), new SequenceI[] { sqs[msaIndex] }, currentView); @@ -196,7 +203,7 @@ class JPredThread extends JWS1Thread implements WSClientI profileseq.setSequence(sqs[msaIndex].getSequenceAsString()); } - if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( + if (!SeqsetUtils.SeqCharacterUnhash( al.getSequenceAt(FirstSeq), SequenceInfo)) { throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query"))); @@ -212,7 +219,7 @@ class JPredThread extends JWS1Thread implements WSClientI { al.setDataset(null); } - jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, + JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, true, predMap); SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps. alignToProfileSeq(al, profileseq); @@ -231,7 +238,8 @@ class JPredThread extends JWS1Thread implements WSClientI if (alant.sequenceRef != null) { replaceAnnotationOnAlignmentWith(alant, alant.label, - "jalview.jws1.Jpred", alant.sequenceRef); + "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"), + alant.sequenceRef); } } return new Object[] @@ -278,7 +286,7 @@ class JPredThread extends JWS1Thread implements WSClientI * @param al * @param profileseq */ - private void alignToProfileSeq(Alignment al, SequenceI profileseq) + private void alignToProfileSeq(AlignmentI al, SequenceI profileseq) { char gc = al.getGapCharacter(); int[] gapMap = profileseq.gapMap(); @@ -346,8 +354,8 @@ class JPredThread extends JWS1Thread implements WSClientI { if (msf.length > 1) { - msa = new vamsas.objects.simple.Msfalignment(); - jalview.io.PileUpfile pileup = new jalview.io.PileUpfile(); + msa = new Msfalignment(); + PileUpfile pileup = new PileUpfile(); msa.setMsf(pileup.print(msf)); } } @@ -469,7 +477,7 @@ class JPredThread extends JWS1Thread implements WSClientI .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" + e.getMessage() + "\n"); - jalview.bin.Cache.log.warn("Server Exception", e); + Cache.log.warn("Server Exception", e); } else { @@ -477,7 +485,7 @@ class JPredThread extends JWS1Thread implements WSClientI // JBPNote - this could be a popup informing the user of the problem. wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()})); - jalview.bin.Cache.log.debug( + Cache.log.debug( "Failed Submission of job " + j.getJobnum(), e); } @@ -555,9 +563,9 @@ class JPredThread extends JWS1Thread implements WSClientI msa = (j.msa != null) ? true : msa; try { - jalview.bin.Cache.log.debug("Parsing output of job " + jn); + Cache.log.debug("Parsing output of job " + jn); jobres = j.getResultSet(); - jalview.bin.Cache.log.debug("Finished parsing output."); + Cache.log.debug("Finished parsing output."); if (jobs.length == 1) { res = jobres; @@ -569,7 +577,7 @@ class JPredThread extends JWS1Thread implements WSClientI } } catch (Exception e) { - jalview.bin.Cache.log.error( + Cache.log.error( "JNet Client: JPred Annotation Parse Error", e); wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);