private boolean includeGaps = true;
+ /**
+ * Default constructor (required for Class.newInstance())
+ */
+ public ClustalxColourScheme()
+ {
+
+ }
+
public ClustalxColourScheme(AnnotatedCollectionI alignment,
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
}
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ protected Color findColour(char c, int j, SequenceI seq)
{
Color currentColour;
+ // TODO why the test for includeGaps here?
if (cons2.length <= j
- || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
}
if (i == 4)
{
+ /*
+ * override to colour C pink if 100% conserved
+ */
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
currentColour = ClustalColour.PINK.colour;
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
return currentColour;
}
}
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
ClustalxColourScheme css = new ClustalxColourScheme(sg,
{
return JalviewColourScheme.Clustal.toString();
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}