/*
- * 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.
*
* 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);
+ }
}
@Override
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
: alignment.getContext();
+ boolean f = true, rna = false;
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
&& (alan.label != null && annotation != null && alan.label
.equals(annotation.label)))
{
+ if (!rna && alan.isRNA())
+ {
+ rna = true;
+ }
seqannot.put(alan.sequenceRef, alan);
+ if (f || alan.graphMax > aamax)
+ {
+ aamax = alan.graphMax;
+ }
+ if (f || alan.graphMin < aamin)
+ {
+ aamin = alan.graphMin;
+ }
+ f = false;
}
}
+ if (rna)
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
}
}
+ 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;
|| (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;
}
}
else
{
- currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ if (annotation.isRNA())
+ {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ }
+ else
+ {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+ : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ }
}
}
else
}
else
{
- // calculate a shade
- float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
- {
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
- }
- else if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
- {
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
- }
- else
- {
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
- }
-
- int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
- * range + b1);
-
- currentColour = new Color(dr, dg, db);
-
+ currentColour = shadeCalculation(annotation, j);
}
}
if (conservationColouring)
return currentColour;
}
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ {
+
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
+ {
+ range = (annotation.annotations[j].value - annotation.threshold.value)
+ / (annotation.graphMax - annotation.threshold.value);
+ }
+ else if (thresholdIsMinMax && annotation.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && annotation.annotations[j].value >= annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ if (annotation.graphMax != annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+ else
+ {
+ range = 0f;
+ }
+ }
+
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+
+ return new Color(dr, dg, db);
+
+ }
+
public boolean isPredefinedColours()
{
return predefinedColours;