X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=30f927221a294ccb348e8a291e2e31038f7d18aa;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=dc245ae6c7559fa0d0f11ca1cbc94ac08ebdcbb7;hpb=5c3e1272c6bf1e145a65050c0cc73737eee788b5;p=jalview.git diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index dc245ae..30f9272 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 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,27 @@ */ 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.AlignmentI; +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 @@ -94,7 +104,7 @@ 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 @@ -137,10 +147,11 @@ class JPredThread extends JWS1Thread implements WSClientI { sqs[i] = al.getSequenceAt(i); } - if (!jalview.analysis.SeqsetUtils.deuniquify( - (Hashtable) SequenceInfo, sqs)) + if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs)) { - throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment"))); + throw (new Exception( + MessageManager + .getString("exception.couldnt_recover_sequence_properties_for_alignment"))); } } FirstSeq = 0; @@ -159,7 +170,9 @@ class JPredThread extends JWS1Thread implements WSClientI } else { - throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()}))); + throw (new Exception(MessageManager.formatMessage( + "exception.unknown_format_for_file", new String[] { + format, result.getAligfile() }))); } } else @@ -169,19 +182,21 @@ 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(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job")); + throw new Error( + MessageManager + .getString("error.implementation_error_invalid_msa_index_for_job")); } // /// // Uses RemoveGapsCommand // /// - new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"), - new SequenceI[] - { sqs[msaIndex] }, currentView); + new jalview.commands.RemoveGapsCommand( + MessageManager.getString("label.remove_gaps"), + new SequenceI[] { sqs[msaIndex] }, currentView); SequenceI profileseq = al.getSequenceAt(FirstSeq); profileseq.setSequence(sqs[msaIndex].getSequenceAsString()); @@ -190,7 +205,9 @@ class JPredThread extends JWS1Thread implements WSClientI if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( al.getSequenceAt(FirstSeq), SequenceInfo)) { - throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query"))); + throw (new Exception( + MessageManager + .getString("exception.couldnt_recover_sequence_props_for_jnet_query"))); } else { @@ -222,11 +239,11 @@ 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[] - { al, alcsel }; // , FirstSeq, noMsa}; + return new Object[] { al, alcsel }; // , FirstSeq, noMsa}; } /** @@ -269,7 +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(); @@ -375,8 +392,7 @@ class JPredThread extends JWS1Thread implements WSClientI if (job.hasValidInput()) { OutputHeader = wsInfo.getProgressText(); - jobs = new WSJob[] - { job }; + jobs = new WSJob[] { job }; job.setJobnum(0); } else @@ -394,8 +410,7 @@ class JPredThread extends JWS1Thread implements WSClientI JPredJob job = new JPredJob(SequenceInfo, msf, delMap); if (job.hasValidInput()) { - jobs = new WSJob[] - { job }; + jobs = new WSJob[] { job }; OutputHeader = wsInfo.getProgressText(); job.setJobnum(0); } @@ -409,7 +424,9 @@ class JPredThread extends JWS1Thread implements WSClientI { if (!(j instanceof JPredJob)) { - throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()})); + throw new Error(MessageManager.formatMessage( + "error.implementation_error_startjob_called", + new String[] { j.getClass().toString() })); } try { @@ -428,9 +445,11 @@ 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(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()})); + job.result.setStatus(MessageManager.formatMessage( + "label.submission_params", new String[] { job.getJobId() + .toString() })); throw new Exception(job.getJobId()); } else @@ -442,7 +461,9 @@ class JPredThread extends JWS1Thread implements WSClientI } else { - throw new Exception(MessageManager.getString("exception.server_timeout_try_later")); + throw new Exception( + MessageManager + .getString("exception.server_timeout_try_later")); } } catch (Exception e) { @@ -466,7 +487,11 @@ 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(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{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); @@ -556,7 +581,9 @@ class JPredThread extends JWS1Thread implements WSClientI else { // do merge with other job results - throw new Error(MessageManager.getString("error.multiple_jnet_subjob_merge_not_implemented")); + throw new Error( + MessageManager + .getString("error.multiple_jnet_subjob_merge_not_implemented")); } } catch (Exception e) { @@ -564,7 +591,10 @@ 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(), MessageManager.formatMessage("info.invalid_jnet_job_result_data", new String[]{OutputHeader.toString(),j.result.getStatus(), 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); } } @@ -575,6 +605,8 @@ class JPredThread extends JWS1Thread implements WSClientI if (newWindow) { AlignFrame af; + ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0]) + .getSequenceAt(0)); if (input == null) { if (res[1] != null)