import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
import jalview.analysis.SeqsetUtils.SequenceInfo;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
JpredResult result = (JpredResult) this.result;
- Cache.log.debug("Parsing output from JNet job.");
+ Console.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
JPredFile prediction = new JPredFile(result.getPredfile(),
DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
- Cache.log.debug("Got prediction profile.");
+ Console.debug("Got prediction profile.");
if ((this.msa != null) && (result.getAligfile() != null))
{
- Cache.log.debug("Getting associated alignment.");
+ Console.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
FileFormatI format = new IdentifyFile()
{
job.setSubmitted(true);
job.setSubjobComplete(false);
- Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
+ Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
}
}
else
"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);
+ Console.warn("Server Exception", e);
}
else
{
"info.failed_to_submit_prediction", new String[]
{ e.getMessage(), wsInfo.getProgressText() }));
- jalview.bin.Cache.log
- .debug("Failed Submission of job " + j.getJobnum(), e);
+ Console.debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + altitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
msa = (j.msa != null) ? true : msa;
try
{
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ Console.debug("Parsing output of job " + jn);
jobres = j.getResultSet();
- jalview.bin.Cache.log.debug("Finished parsing output.");
+ Console.debug("Finished parsing output.");
if (jobs.length == 1)
{
res = jobres;
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("JNet Client: JPred Annotation Parse Error", e);
+ Console.error("JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.appendProgressText(j.getJobnum(),
}
else
{
- Cache.log.info("Append results onto existing alignment.");
+ Console.info("Append results onto existing alignment.");
}
}
}