X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=1e48c06b51e38cf8b7b59107ac233eb953e1b09c;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=69d0ae48e023ea9c7fe3a9773dbf02e3d1957f40;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 69d0ae4..1e48c06 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 ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -24,6 +24,7 @@ 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; @@ -103,7 +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 @@ -146,10 +147,11 @@ class JPredThread extends JWS1Thread implements WSClientI { sqs[i] = al.getSequenceAt(i); } - if (!jalview.analysis.SeqsetUtils.deuniquify( - 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; @@ -168,7 +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 @@ -182,15 +186,17 @@ class JPredThread extends JWS1Thread implements WSClientI .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()); @@ -199,7 +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 { @@ -235,8 +243,7 @@ class JPredThread extends JWS1Thread implements WSClientI alant.sequenceRef); } } - return new Object[] - { al, alcsel }; // , FirstSeq, noMsa}; + return new Object[] { al, alcsel }; // , FirstSeq, noMsa}; } /** @@ -279,7 +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(); @@ -385,8 +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 @@ -404,8 +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); } @@ -419,7 +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 { @@ -440,7 +447,9 @@ class JPredThread extends JWS1Thread implements WSClientI { 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 @@ -452,7 +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) { @@ -476,7 +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); @@ -566,7 +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) { @@ -574,7 +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); } } @@ -585,6 +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)