/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+ AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
: this.annotation);
if (annotation == null)
{
|| (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
: aj.value <= annotationThreshold.value)))
{
- if (predefinedColours && aj.colour != null)
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
currentColour = aj.colour;
}