import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.IProgressIndicator;
+import jalview.util.Comparison;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
{
if (getCalcId() != null)
{
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+ ((AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
(arguments != null) ? JabaParamStore
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Updating result annotation from Job " + rslt
+ " at " + service.getUri());
updateResultAnnotation(true);
start = inputSeqs.getStartRes();
end = inputSeqs.getEndRes();
- for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
+ for (SequenceI sq : (inputSeqs.getSequences()))
{
if (bySequence ? sq.findPosition(end + 1)
- sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
else
{
seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
- AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ AlignSeq.extractGaps(Comparison.GapChars,
sq.getSequenceAsString(start, end + 1))));
}
if (seq.getSequence().length() > ln)