int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
@Override
public boolean hasResults()
{
- if (subjobComplete
- && isFinished()
- && (alignment != null || (emptySeqs != null && emptySeqs
- .size() > 0)))
+ if (subjobComplete && isFinished() && (alignment != null
+ || (emptySeqs != null && emptySeqs.size() > 0)))
{
return true;
}
for (compbio.data.sequence.FastaSequence seq : alignment
.getSequences())
{
- alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
+ alseqs[alseq_l++] = new Sequence(seq.getId(),
+ seq.getSequence());
}
alseq_gapchar = alignment.getMetadata().getGapchar();
{
for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
}
// merge arguments with preset's own arguments.
for (Argument opt : arguments)
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
jobProgress.append("\nJob Output:\n");
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
else
{
do
{
j.setLastChunk(lastchunk);
- ChunkHolder chunk = server
- .pullExecStatistics(j.getJobId(), lastchunk);
+ ChunkHolder chunk = server.pullExecStatistics(j.getJobId(),
+ lastchunk);
if (chunk != null)
{
changed |= chunk.getChunk().length() > 0;
if (!(job instanceof MsaWSJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_msawbjob_called",
- new String[] { job.getClass().toString() }));
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Cache.log.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- new String[] { WsUrl }));
+ new String[]
+ { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
wsInfo.appendProgressText(MessageManager.formatMessage(
"info.job_couldnt_be_run_server_doesnt_support_program",
- new String[] { _lex.getMessage() }));
+ new String[]
+ { _lex.getMessage() }));
wsInfo.warnUser(_lex.getMessage(),
MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
{
lex = _lex;
wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_exceeded_hard_limit",
- new String[] { _lex.getMessage() }));
+ "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
+ { _lex.getMessage() }));
wsInfo.warnUser(_lex.getMessage(),
MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
MessageManager.getString("warn.invalid_job_param_set"));
wsInfo.appendProgressText(MessageManager.formatMessage(
"info.job_couldnt_be_run_incorrect_param_setting",
- new String[] { _lex.getMessage() }));
+ new String[]
+ { _lex.getMessage() }));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
} catch (Exception e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
// TODO: JBPNote catch timeout or other fault types explicitly
j.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(j.getJobnum(), MessageManager
- .getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString(
+ "info.failed_to_submit_sequences_for_alignment"));
}
}
}
} catch (Exception e)
{
- Cache.log
- .warn("Exception when retrieving remaining Job progress data for job "
+ Cache.log.warn(
+ "Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
nexcept--;
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log
- .debug("Results not available for finished job - marking as broken job.",
- e);
- msjob.jobProgress
- .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ Cache.log.debug(
+ "Results not available for finished job - marking as broken job.",
+ e);
+ msjob.jobProgress.append(
+ "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
// wsInfo.appendProgressText(jobs[j].getJobnum(),
// "\nAlignment Object Method Notes\n");
// wsInfo.appendProgressText(jobs[j].getJobnum(),
- // "Calculated with "+alignment.getMetadata().getProgram().toString());
+ // "Calculated with
+ // "+alignment.getMetadata().getProgram().toString());
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
// when clicked, pop up their corresponding data
} 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)
protected void displayInNewFrame(AlignmentI al,
List<AlignmentOrder> alorders, HiddenColumns hidden)
{
- AlignFrame af = new AlignFrame(al, hidden,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
* SplitFrame with the other pane similarly aligned.
*/
AlignFrame requestedBy = getRequestingAlignFrame();
- if (requestedBy != null
- && requestedBy.getSplitViewContainer() != null
- && requestedBy.getSplitViewContainer().getComplement(
- requestedBy) != null)
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
{
AlignmentI complement = requestedBy.getSplitViewContainer()
.getComplement(requestedBy);
af2.setTitle(complementTitle);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
- JInternalFrame splitFrame = new SplitFrame(al.isNucleotide() ? af
- : af2, al.isNucleotide() ? af2 : af);
+ JInternalFrame splitFrame = new SplitFrame(
+ al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return;
}
}
for (int i = 0, l = alorders.size(); i < l; i++)
{
- af.addSortByOrderMenuItem(WebServiceName + (names.get(i))
- + " Ordering", alorders.get(i));
+ af.addSortByOrderMenuItem(
+ WebServiceName + (names.get(i)) + " Ordering",
+ alorders.get(i));
}
}
}
git://source.jalview.org / jalview.git / blobdiff