hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
hiddenMarkers.setState(av.showHiddenMarkers);
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
// new HTMLOutput(alignPanel,
// alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
// alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
// new HTMLOutput(alignPanel,
// alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
// alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
{
featuresFile = new FeaturesFile(file, type).parse(viewport
.getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
{
featuresFile = new FeaturesFile(file, type).parse(viewport
.getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas