import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
for (SequenceI sq : seqs)
{
- char[] seq = sq.getSequence();
-
- int end_j = seq.length - 1;
+ int end_j = sq.getLength() - 1;
+ int length = sq.getLength();
for (int i = 0; i <= end_j; i++)
{
- if ((seq.length - 1) < i)
+ if (length - 1 < i)
{
res = 23;
}
else
{
- res = ResidueProperties.aaIndex[seq[i]];
+ res = ResidueProperties.aaIndex[sq.getCharAt(i)];
}
cons2[i][res]++;
}
}
@Override
- public Color findColour(char c, int j, SequenceI seq)
+ protected Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour;
-
- if (cons2.length <= j
- || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ // TODO why the test for includeGaps here?
+ 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 >85% conserved
+ */
if (conses[27].isConserved(cons2, j, size, includeGaps))
{
- currentColour = ClustalColour.PINK.colour;
+ colour = ClustalColour.PINK.colour;
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
/**
{
return JalviewColourScheme.Clustal.toString();
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}