import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
@Override
protected Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
-
// TODO why the test for includeGaps here?
- if (cons2.length <= j
+ if (cons2.length <= j || Comparison.isGap(c)
/*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
{
return Color.white;
int i = ResidueProperties.aaIndex[c];
- currentColour = Color.white;
+ Color colour = Color.white;
if (i > 19)
{
- return currentColour;
+ return colour;
}
for (int k = 0; k < residueColour[i].cons.length; k++)
if (residueColour[i].cons[k].isConserved(cons2, j, size,
includeGaps))
{
- currentColour = residueColour[i].c;
+ colour = residueColour[i].c;
}
}
if (i == 4)
{
/*
- * override to colour C pink if 100% conserved
+ * override to colour C pink if >85% conserved
*/
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = ClustalColour.PINK.colour;
+ colour = ClustalColour.PINK.colour;
}
}
- return currentColour;
+ return colour;
}
/**