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.");
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)
{
}
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;
{
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[] { "",
- result.getAligfile() })));
+ "exception.unknown_format_for_file", new String[]
+ { "", result.getAligfile() })));
}
}
else
.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"));
}
// ///
// ///
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());
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
{
dsseq = dsseq.getDatasetSequence();
}
// look for same annotation on dataset and lift this one over
- List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
- calcId, typeName);
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
if (dsan != null && dsan.size() > 0)
{
for (AlignmentAnnotation dssan : dsan)
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]));
}
}
}
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
{
{
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
}
else
{
- throw new Exception(
- MessageManager
- .getString("exception.server_timeout_try_later"));
+ throw new Exception(MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
{
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);
{
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);
} 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)
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);
}
}
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)
* alandcolsel[0])[0].gapMap())); }
*/
- af = new AlignFrame((Alignment) res[0],
- (HiddenColumns) 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);
git://source.jalview.org / jalview.git / blobdiff