+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
}
/**
- * reconfigure and restart the AAConsClient. This method will spawn a new
+ * reconfigure and restart the AAConClient. This method will spawn a new
* thread that will wait until any current jobs are finished, modify the
* parameters and restart the conservation calculation with the new values.
*
} catch (WrongParameterException x)
{
throw new JobSubmissionException(
- "Invalid paremeter set. Check Jalview implementation.", x);
+ "Invalid parameter set. Check Jalview implementation.", x);
}
}
{
finished = true;
}
- if (calcMan.isPending(this) && this instanceof AAConsClient)
+ if (calcMan.isPending(this) && this instanceof AAConClient)
{
finished = true;
// cancel this job and yield to the new job
}
else
{
- System.err.println("FAILED TO CANCELL AACon job: " + rslt);
+ System.err.println("FAILED TO CANCEL AACon job: " + rslt);
}
} catch (Exception x)
try
{
stats = aaservice.pullExecStatistics(rslt, rpos);
- } catch (Exception x)
+ } catch (Exception x)
{
if (x.getMessage().contains(
if (--serverErrorsLeft > 0)
{
retry = true;
- try {
+ try
+ {
Thread.sleep(200);
- } catch (InterruptedException q) {};
- } else {
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ }
+ else
+ {
throw x;
}
}
;
}
} while (!finished);
- if (serverErrorsLeft>0)
+ if (serverErrorsLeft > 0)
{
try
{
.debug("Updating result annotation from Job " + rslt
+ " at " + service.getUri());
updateResultAnnotation(true);
+ ap.adjustAnnotationHeight();
}
}
}
}
}
// try real hard to return something submittable
- // TODO: some of AAcons measures need a minimum of two or three amino
- // acids at each position, and aacons doesn't gracefully degrade.
+ // TODO: some of AAcon measures need a minimum of two or three amino
+ // acids at each position, and AAcon doesn't gracefully degrade.
for (int p = 0; p < seqs.size(); p++)
{
FastaSequence sq = seqs.get(p);
// annotation.setCalcId(calcId);
AlignmentAnnotation annotation = alignViewport.getAlignment()
.findOrCreateAnnotation(typeName, calcId, false, dseq, null);
- constructAnnotationFromScore(annotation, base, dseq.getLength(), scr);
- annotation.createSequenceMapping(dseq, dseq.findPosition(base), false);
+ constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
+ annotation.createSequenceMapping(dseq, base, false);
annotation.adjustForAlignment();
dseq.addAlignmentAnnotation(annotation);
ourAnnot.add(annotation);
Annotation[] elm = new Annotation[alWidth];
Iterator<Float> vals = scr.getScores().iterator();
float m = 0f, x = 0f;
- for (int i = base; vals.hasNext(); i++)
+ for (int i = 0; vals.hasNext(); i++)
{
float val = vals.next().floatValue();
if (i == 0)