/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
jalview.bin.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");
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(
+ result.getPredfile(), "Paste");
SequenceI[] preds = prediction.getSeqsAsArray();
jalview.bin.Cache.log.debug("Got prediction profile.");
jalview.bin.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 jalview.io.IdentifyFile().Identify(
+ result.getAligfile(), "Paste");
if (jalview.io.FormatAdapter.isValidFormat(format))
{
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
}
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al
- .getSequenceAt(FirstSeq), SequenceInfo))
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+ al.getSequenceAt(FirstSeq), SequenceInfo))
{
throw (new Exception(
"Couldn't recover sequence properties for JNet Query sequence!"));
{
super();
this.predMap = delMap;
- String sq = AlignSeq.extractGaps(Comparison.GapChars, seq
- .getSequenceAsString());
+ String sq = AlignSeq.extractGaps(Comparison.GapChars,
+ seq.getSequenceAsString());
if (sq.length() >= 20)
{
this.SequenceInfo = SequenceInfo;
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
if (e.getMessage().indexOf("Exception") > -1)
{
- wsInfo
- .setStatus(j.getJobnum(),
- WebserviceInfo.STATE_STOPPED_SERVERERROR);
- 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");
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ 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"
+ e.getMessage() + "\n");
"Failed to submit the prediction:\n" + 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);
{
jalview.bin.Cache.log.error(
"JNet Client: JPred Annotation Parse Error", e);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(j.getJobnum(), OutputHeader + "\n"
+ j.result.getStatus()
+ "\nInvalid JNet job result data!\n" + e.getMessage());
public void pollJob(AWsJob job) throws Exception
{
- ((JPredJob)job).result = server.getresult(job.getJobId());
+ ((JPredJob) job).result = server.getresult(job.getJobId());
}
public boolean isCancellable()