// for
// any
// subjob
- SeqNames.put(newname, jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seqs[i]));
+ SeqNames.put(newname,
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
{
seqarray[n] = new vamsas.objects.simple.Sequence();
if (seqs[i].getEnd() >= seqs[i].getStart())
{
empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
- .getSequenceAsString());
+ .extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[]
{ newname, empty });
}
if (njobs > 0)
{
- wsinfo
- .setProgressName("region " + jobs[j].getJobnum(),
- jobs[j].getJobnum());
+ wsinfo.setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
}
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
}
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
Cache.log.warn(
- "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ "Exception whilst cancelling " + jobs[job].getJobId(),
+ exc);
}
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
{
if (!jobComplete)
{
- wsInfo
- .setProgressText(OutputHeader
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ wsInfo.setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
}
}
}
public void pollJob(AWsJob job) throws Exception
{
- ((SeqSearchWSJob) job).result = server
- .getResult(((SeqSearchWSJob) job).getJobId());
+ ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
+ .getJobId());
}
public void StartJob(AWsJob job)
}
try
{
- vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs
- .getSeqs()[0], dbArg);
+ vamsas.objects.simple.WsJobId jobsubmit = server.search(
+ j.seqs.getSeqs()[0], dbArg);
if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
{
+ e.toString() + "\n");
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .appendProgressText(
- j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.appendProgressText(
+ j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "It is most likely that there is a problem with the server.\n"
+ + "Just close the window\n");
// e.printStackTrace(); // TODO: JBPNote DEBUG
}
for (int i = 0, j = seqs.length; i < j; i++)
{
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
- .getSeq());
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+ seqs[i].getSeq());
}
return msa;
&& jobs[j].hasResults())
{
results++;
- vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result)
+ vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob) jobs[j]).result)
.getAlignment();
if (valign != null)
{
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n");
+ wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
+ + "\n");
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,