- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.ws.AWsJob;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
JpredResult result = (JpredResult) this.result;
ColumnSelection alcsel = null;
int FirstSeq = -1; // the position of the query sequence in Alignment al
JpredResult result = (JpredResult) this.result;
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(
- result.getPredfile(), "Paste");
+ JPredFile prediction = new JPredFile(
+ result.getPredfile(), DataSourceType.PASTE);
- String format = new jalview.io.IdentifyFile().Identify(
- result.getAligfile(), "Paste");
+ FileFormatI format = new IdentifyFile().identify(
+ result.getAligfile(), DataSourceType.PASTE);
sqs = new SequenceI[al.getHeight()];
for (int i = 0, j = al.getHeight(); i < j; i++)
{
sqs[i] = al.getSequenceAt(i);
}
sqs = new SequenceI[al.getHeight()];
for (int i = 0, j = al.getHeight(); i < j; i++)
{
sqs[i] = al.getSequenceAt(i);
}
- throw (new Exception(MessageManager.formatMessage("exception.unknown_format_for_file", new String[]{format,result.getAligfile()})));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.unknown_format_for_file", new String[] {
+ format.toString(), result.getAligfile() })));
- new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
- new SequenceI[]
- { sqs[msaIndex] }, currentView);
+ new jalview.commands.RemoveGapsCommand(
+ MessageManager.getString("label.remove_gaps"),
+ new SequenceI[] { sqs[msaIndex] }, currentView);
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), SequenceInfo))
{
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), SequenceInfo))
{
- return new Object[]
- { al, alcsel }; // , FirstSeq, noMsa};
+ return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
- jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
- msa.setMsf(pileup.print(msf));
+ PileUpfile pileup = new PileUpfile();
+ msa.setMsf(pileup.print(msf, true));
- throw new Error(MessageManager.formatMessage("error.implementation_error_startjob_called", new String[]{j.getClass().toString()}));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_startjob_called",
+ new String[] { j.getClass().toString() }));
- 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() }));
{
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
// JBPNote - this could be a popup informing the user of the problem.
{
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);
"JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_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() }));
public void pollJob(AWsJob job) throws Exception
{
((JPredJob) job).result = server.getresult(job.getJobId());
}
public void pollJob(AWsJob job) throws Exception
{
((JPredJob) job).result = server.getresult(job.getJobId());
}