perLineScore = plcount == ancount;
aamax=plmax;
}
+ else
+ {
+ perLineScore = false;
+ }
if (rna)
{
ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
if (perLineScore)
{
trans = (int) ((1f - range) * midtr);
- range = (float) ((annotation.score - plmin) / (plmax - aamin));
+ range = (float) ((ann.score - plmin) / (plmax - aamin));
}
int dr = (int) (redRange * range + redMin),
dg = (int) (greenRange * range + greenMin),
db = (int) (blueRange * range + blueMin);
- if (annotation.score == annotation.score && positionToTransparency)
+ if (ann.score == ann.score && positionToTransparency)
{
return new Color(Math.min(dr + trans, midtr), Math.min(dg
+ trans, midtr), Math.min(db + trans, midtr));