public class AnnotationColourGradient extends FollowerColourScheme
{
+ /**
+ * map positional scores to transparency rather than colour
+ */
+ boolean positionToTransparency = true;
+
+ /**
+ * compute shade based on annotation row score
+ */
+ boolean perLineScore = true;
+
public static final int NO_THRESHOLD = -1;
public static final int BELOW_THRESHOLD = 0;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
acg.noGradient = noGradient;
+ acg.positionToTransparency = positionToTransparency;
+ acg.perLineScore = perLineScore;
return acg;
}
}
else
{
- seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ seqannot = new IdentityHashMap<>();
}
// resolve the context containing all the annotation for the sequence
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
: alignment.getContext();
- boolean f = true, rna = false;
+ boolean f = true, sf = true, rna = false;
+ long plcount = 0, ancount = 0;
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
if (alan.sequenceRef != null
- && (alan.label != null && annotation != null && alan.label
- .equals(annotation.label)))
+ && (alan.label != null && annotation != null
+ && alan.label.equals(annotation.label)))
{
+ ancount++;
if (!rna && alan.isRNA())
{
rna = true;
aamin = alan.graphMin;
}
f = false;
+ if (alan.score == alan.score)
+ {
+ if (sf || alan.score < plmin)
+ {
+ plmin = alan.score;
+ }
+ if (sf || alan.score > plmax)
+ {
+ plmax = alan.score;
+ }
+ sf = false;
+ plcount++;
+ }
}
}
+ if (plcount > 0 && plcount == ancount)
+ {
+ perLineScore = plcount == ancount;
+ aamax=plmax;
+ }
+ else
+ {
+ perLineScore = false;
+ }
if (rna)
{
ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
}
}
- float aamin = 0f, aamax = 0f;
+ /**
+ * positional annotation max/min
+ */
+ double aamin = 0.0, aamax = 0.0;
+
+ /**
+ * per line score max/min
+ */
+ double plmin = Double.NaN, plmax = Double.NaN;
public AlignmentAnnotation getAnnotation()
{
public Color getMaxColour()
{
- return new Color(redMin + redRange, greenMin + greenRange, blueMin
- + blueRange);
+ return new Color(redMin + redRange, greenMin + greenRange,
+ blueMin + blueRange);
}
/**
/*
* locate the annotation we are configured to colour by
*/
- AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
- .get(seq) : this.annotation);
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null
+ ? seqannot.get(seq)
+ : this.annotation);
/*
* if gap or no annotation at position, no colour (White)
*/
if (annotationThreshold != null)
{
- if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value >= annotationThreshold.value)
- || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && aj.value < annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD
+ && aj.value > annotationThreshold.value))
{
return Color.white;
}
}
else
{
- result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
- : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+ result = ann.annotations[j].secondaryStructure == 'H'
+ ? AnnotationRenderer.HELIX_COLOUR
+ : ann.annotations[j].secondaryStructure == 'E'
+ ? AnnotationRenderer.SHEET_COLOUR
: AnnotationRenderer.STEM_COLOUR;
}
}
}
}
- int dr = (int) (redRange * range + redMin);
- int dg = (int) (greenRange * range + greenMin);
- int db = (int) (blueRange * range + blueMin);
-
- return new Color(dr, dg, db);
+ // midtr sets the ceiling for bleaching out the shading
+ int trans = 0, midtr = 239;
+ if (perLineScore)
+ {
+ trans = (int) ((1f - range) * midtr);
+ range = (float) ((ann.score - plmin) / (plmax - aamin));
+ }
+ int dr = (int) (redRange * range + redMin),
+ dg = (int) (greenRange * range + greenMin),
+ db = (int) (blueRange * range + blueMin);
+ if (ann.score == ann.score && positionToTransparency)
+ {
+ return new Color(Math.min(dr + trans, midtr), Math.min(dg
+ + trans, midtr), Math.min(db + trans, midtr));
+ }
+ else
+ {
+ return new Color(dr, dg, db);
+ }
}
public boolean isPredefinedColours()