private boolean predefinedColours = false;
private boolean seqAssociated = false;
+
/**
* false if the scheme was constructed without a minColour and maxColour used
* to decide if existing colours should be taken from annotation elements when
* they exist
*/
private boolean noGradient = false;
+
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
bb = 0;
noGradient = true;
+ checkLimits();
}
/**
bb = maxColour.getBlue() - b1;
noGradient = false;
+ checkLimits();
+ }
+
+ private void checkLimits()
+ {
aamax = annotation.graphMax;
aamin = annotation.graphMin;
if (annotation.isRNA())
{
+ // reset colour palette
+ ColourSchemeProperty.resetRnaHelicesShading();
ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
}
}
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
: alignment.getContext();
- boolean f = true,rna=false;
+ boolean f = true, rna = false;
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
}
float aamin = 0f, aamax = 0f;
+
public String getAnnotation()
{
return annotation.label;
public Color findColour(char c, int j, SequenceI seq)
{
Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
- : this.annotation);
+ AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+ .get(seq) : this.annotation);
if (annotation == null)
{
return currentColour;
return new Color(dr, dg, db);
}
+
public boolean isPredefinedColours()
{
return predefinedColours;