public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRendererI sr,
- AlignmentViewPanel viewPanel)
+ AlignmentViewPanel viewPanel, boolean showFeatures)
{
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, viewPanel);
+ sequence, sr, viewPanel, showFeatures);
List<String> colourCommands = buildColourCommands(colourMap);
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRendererI sr,
- AlignmentViewPanel viewPanel)
+ AlignmentViewPanel viewPanel, boolean showFeatures)
{
FeatureRenderer fr = viewPanel.getFeatureRenderer();
- FeatureColourFinder finder = new FeatureColourFinder(fr);
+ FeatureColourFinder finder = showFeatures ? new FeatureColourFinder(fr) : null;
AlignViewportI viewport = viewPanel.getAlignViewport();
HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();