X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;fp=src%2Fjalview%2Fws%2Fjws1%2FJPredThread.java;h=a239625f401fa20035072d4ce7bef46264c2192e;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=4e5cadc24e7647a01c25c6955fb0fc4b26a8427c;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java index 4e5cadc..a239625 100644 --- a/src/jalview/ws/jws1/JPredThread.java +++ b/src/jalview/ws/jws1/JPredThread.java @@ -27,7 +27,7 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.Desktop; @@ -114,7 +114,7 @@ class JPredThread extends JWS1Thread implements WSClientI return null; } AlignmentI al = null; - ColumnSelection alcsel = null; + HiddenColumns alhidden = null; int FirstSeq = -1; // the position of the query sequence in Alignment al JpredResult result = (JpredResult) this.result; @@ -122,8 +122,8 @@ class JPredThread extends JWS1Thread implements WSClientI Cache.log.debug("Parsing output from JNet job."); // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", // "File"); - JPredFile prediction = new JPredFile( - result.getPredfile(), DataSourceType.PASTE); + JPredFile prediction = new JPredFile(result.getPredfile(), + DataSourceType.PASTE); SequenceI[] preds = prediction.getSeqsAsArray(); Cache.log.debug("Got prediction profile."); @@ -132,8 +132,8 @@ class JPredThread extends JWS1Thread implements WSClientI Cache.log.debug("Getting associated alignment."); // we ignore the returned alignment if we only predicted on a single // sequence - FileFormatI format = new IdentifyFile().identify( - result.getAligfile(), DataSourceType.PASTE); + FileFormatI format = new IdentifyFile() + .identify(result.getAligfile(), DataSourceType.PASTE); if (format != null) { @@ -141,10 +141,10 @@ class JPredThread extends JWS1Thread implements WSClientI if (predMap != null) { Object[] alandcolsel = input - .getAlignmentAndColumnSelection(getGapChar()); + .getAlignmentAndHiddenColumns(getGapChar()); sqs = (SequenceI[]) alandcolsel[0]; al = new Alignment(sqs); - alcsel = (ColumnSelection) alandcolsel[1]; + alhidden = (HiddenColumns) alandcolsel[1]; } else { @@ -158,9 +158,8 @@ class JPredThread extends JWS1Thread implements WSClientI } if (!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; @@ -173,15 +172,15 @@ class JPredThread extends JWS1Thread implements WSClientI { al.setDataset(null); } - JnetAnnotationMaker.add_annotation(prediction, al, - FirstSeq, false, predMap); + JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, + false, predMap); } else { throw (new Exception(MessageManager.formatMessage( - "exception.unknown_format_for_file", new String[] { - format.toString(), result.getAligfile() }))); + "exception.unknown_format_for_file", new String[] + { "", result.getAligfile() }))); } } else @@ -192,12 +191,11 @@ class JPredThread extends JWS1Thread implements WSClientI { char gc = getGapChar(); SequenceI[] sqs = (SequenceI[]) input - .getAlignmentAndColumnSelection(gc)[0]; + .getAlignmentAndHiddenColumns(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")); } // /// @@ -205,7 +203,8 @@ class JPredThread extends JWS1Thread implements WSClientI // /// new jalview.commands.RemoveGapsCommand( MessageManager.getString("label.remove_gaps"), - new SequenceI[] { sqs[msaIndex] }, currentView); + new SequenceI[] + { sqs[msaIndex] }, currentView); SequenceI profileseq = al.getSequenceAt(FirstSeq); profileseq.setSequence(sqs[msaIndex].getSequenceAsString()); @@ -214,9 +213,8 @@ 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 { @@ -237,7 +235,7 @@ class JPredThread extends JWS1Thread implements WSClientI { // Adjust input view for gaps // propagate insertions into profile - alcsel = ColumnSelection.propagateInsertions(profileseq, al, + alhidden = HiddenColumns.propagateInsertions(profileseq, al, input); } } @@ -252,7 +250,7 @@ class JPredThread extends JWS1Thread implements WSClientI alant.sequenceRef); } } - return new Object[] { al, alcsel }; // , FirstSeq, noMsa}; + return new Object[] { al, alhidden }; // , FirstSeq, noMsa}; } /** @@ -273,8 +271,8 @@ class JPredThread extends JWS1Thread implements WSClientI dsseq = dsseq.getDatasetSequence(); } // look for same annotation on dataset and lift this one over - List dsan = dsseq.getAlignmentAnnotations( - calcId, typeName); + List dsan = dsseq.getAlignmentAnnotations(calcId, + typeName); if (dsan != null && dsan.size() > 0) { for (AlignmentAnnotation dssan : dsan) @@ -319,17 +317,15 @@ class JPredThread extends JWS1Thread implements WSClientI sq = sq + sb; while ((diff = gapMap[r] - sq.length()) > 0) { - sq = sq - + ((diff >= sb.length()) ? sb.toString() : sb - .substring(0, diff)); + sq = sq + ((diff >= sb.length()) ? sb.toString() + : sb.substring(0, diff)); } al.getSequenceAt(s).setSequence(sq); } else { - al.getSequenceAt(s).setSequence( - sq.substring(0, gapMap[r]) + sb.toString() - + sq.substring(gapMap[r])); + al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) + + sb.toString() + sq.substring(gapMap[r])); } } } @@ -435,8 +431,8 @@ 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() })); + "error.implementation_error_startjob_called", new String[] + { j.getClass().toString() })); } try { @@ -457,9 +453,9 @@ 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 @@ -471,9 +467,8 @@ 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) { @@ -483,12 +478,11 @@ class JPredThread extends JWS1Thread implements WSClientI { wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR); - wsInfo.setProgressText( - j.getJobnum(), + wsInfo.setProgressText(j.getJobnum(), "Failed to submit the prediction. (Just close the window)\n" + "It is most likely that there is a problem with the server.\n"); - System.err - .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" + System.err.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); @@ -497,14 +491,13 @@ 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); + jalview.bin.Cache.log + .debug("Failed Submission of job " + j.getJobnum(), e); } j.setAllowedServerExceptions(-1); @@ -531,8 +524,9 @@ class JPredThread extends JWS1Thread 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) @@ -594,20 +588,21 @@ 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) { - jalview.bin.Cache.log.error( - "JNet Client: JPred Annotation Parse Error", e); + jalview.bin.Cache.log + .error("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); } } @@ -618,14 +613,14 @@ class JPredThread extends JWS1Thread implements WSClientI if (newWindow) { AlignFrame af; - ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0]) - .getSequenceAt(0)); + ((AlignmentI) res[0]) + .setSeqrep(((AlignmentI) res[0]).getSequenceAt(0)); if (input == null) { if (res[1] != null) { af = new AlignFrame((Alignment) res[0], - (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH, + (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } else @@ -650,9 +645,8 @@ class JPredThread extends JWS1Thread implements WSClientI * alandcolsel[0])[0].gapMap())); } */ - af = new AlignFrame((Alignment) res[0], - (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + af = new AlignFrame((Alignment) res[0], (HiddenColumns) res[1], + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);