ColourSchemeI cs = null;
+ SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+ false, 0, av.getAlignment().getWidth() - 1);
+
if (av.getGlobalColourScheme() != null)
{
if (av.getGlobalColourScheme() instanceof UserColourScheme)
}
else
{
- cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
- .getWidth(), ColourSchemeProperty.getColourName(av
+ cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
av.getIgnoreGapsConsensus());
}
}
-
- SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
- false, 0, av.getAlignment().getWidth() - 1);
+ // TODO: cs used to be initialized with a sequence collection and recalcConservation called automatically
+ // instead we set it manually - recalc called after updateAnnotation
+ sg.cs=cs;
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);