setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
- showSeqFeatures.setSelected(av.showSequenceFeatures);
+ showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
// new HTMLOutput(alignPanel,
// alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
// alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
- new HtmlSvgOutput(alignPanel);
+ new HtmlSvgOutput(null, alignPanel);
}
@Override
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
.isSelected());
- if (viewport.getShowSequenceFeaturesHeight())
+ if (viewport.isShowSequenceFeaturesHeight())
{
// ensure we're actually displaying features
viewport.setShowSequenceFeatures(true);
{
featuresFile = new FeaturesFile(file, type).parse(viewport
.getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().featureColours, false,
+ .getFeatureRenderer().getFeatureColours(), false,
jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
if (featuresFile)
{
- viewport.showSequenceFeatures = true;
+ viewport.setShowSequenceFeatures(true);
showSeqFeatures.setSelected(true);
if (alignPanel.getSeqPanel().seqCanvas.fr != null)
{
// try to parse as annotation.
boolean isAnnotation = (format == null || format
.equalsIgnoreCase("PFAM")) ? new AnnotationFile()
- .readAnnotationFile(viewport.getAlignment(), file, protocol)
+ .annotateAlignmentView(viewport, file, protocol)
: false;
if (!isAnnotation)
alignPanel.paintAlignment(true);
}
}
+ public void clearAlignmentSeqRep()
+ {
+ // TODO refactor alignmentseqrep to controller
+ if (viewport.getAlignment().hasSeqrep()) {
+ viewport.getAlignment().setSeqrep(null);
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
@Override
protected void createGroup_actionPerformed(ActionEvent e)