- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
- public AbstractJabaCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
+ if (guiProgress != null)
+ {
+ guiProgress.registerHandler(progressId,
+ new IProgressIndicatorHandler()
+ {
+
+ @Override
+ public boolean cancelActivity(long id)
+ {
+ cancelCurrentJob();
+ return true;
+ }
- if (bySequence ? sq.findPosition(end + 1)
- - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
- - sq.getStart() > minlen - 1)
+ if (bySequence
+ ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1
+ : sq.getEnd() - sq.getStart() > minlen - 1)
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
- gapMap[apos] = true; // aligned.
+ char sqc = sq.getCharAt(apos);
+ if (!filterNonStandardResidues
+ || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
+ : ResidueProperties.nucleotideIndex[sqc] < 5))
+ {
+ gapMap[apos] = true; // aligned and real amino acid residue
+ }
+ ;