/*
- * 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.
*
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.IdentityHashMap;
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
bb = maxColour.getBlue() - b1;
noGradient = false;
+ aamax = annotation.graphMax;
+ aamin = annotation.graphMin;
+ if (annotation.isRNA())
+ {
+ 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;
return Color.red;
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c, int j, SequenceI seq)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq) {
+ Color currentColour = Color.white;
+ AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+ .get(seq) : this.annotation);
+ if (annotation == null) {
+ return currentColour;
+ }
+ if ((threshold == 0) || aboveThreshold(c, j)) {
+ if (annotation.annotations != null && j < annotation.annotations.length
+ && annotation.annotations[j] != null && !Comparison.isGap(c)) {
+ Annotation aj = annotation.annotations[j];
+ // 'use original colours' => colourScheme != null
+ // -> look up colour to be used
+ // predefined colours => preconfigured shading
+ // -> only use original colours reference if thresholding enabled &
+ // minmax exists
+ // annotation.hasIcons => null or black colours replaced with glyph
+ // colours
+ // -> reuse original colours if present
+ // -> if thresholding enabled then return colour on non-whitespace glyph
+
+ if (aboveAnnotationThreshold == NO_THRESHOLD
+ || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+ : aj.value <= annotationThreshold.value))) {
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black)) {
+ currentColour = aj.colour;
+ } else if (annotation.hasIcons
+ && annotation.graph == AlignmentAnnotation.NO_GRAPH) {
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-') {
+ if (colourScheme != null) {
+ currentColour = colourScheme.findColour(c, j, seq);
+ } else {
+ if (annotation.isRNA()) {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ } else {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+ : AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ } else {
+ //
+ return Color.white;
+ }
+ } else if (noGradient) {
+ if (colourScheme != null) {
+ currentColour = colourScheme.findColour(c, j, seq);
+ } else {
+ if (aj.colour != null) {
+ currentColour = aj.colour;
+ }
+ }
+ } else {
+ currentColour = shadeCalculation(annotation, j);
+ }
+ }
+ if (conservationColouring) {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ }
+ return currentColour;
+ }
+
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
{
- Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
- : this.annotation);
- if (annotation == null)
+
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
{
- return currentColour;
+ range = (annotation.annotations[j].value - annotation.threshold.value)
+ / (annotation.graphMax - annotation.threshold.value);
}
- if ((threshold == 0) || aboveThreshold(c, j))
+ else if (thresholdIsMinMax && annotation.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && annotation.annotations[j].value >= annotation.graphMin)
{
- if (annotation.annotations != null
- && j < annotation.annotations.length
- && annotation.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ if (annotation.graphMax != annotation.graphMin)
{
- Annotation aj = annotation.annotations[j];
- // 'use original colours' => colourScheme != null
- // -> look up colour to be used
- // predefined colours => preconfigured shading
- // -> only use original colours reference if thresholding enabled &
- // minmax exists
- // annotation.hasIcons => null or black colours replaced with glyph
- // colours
- // -> reuse original colours if present
- // -> if thresholding enabled then return colour on non-whitespace glyph
-
- if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
- : aj.value <= annotationThreshold.value)))
- {
- if (predefinedColours && aj.colour != null)
- {
- currentColour = aj.colour;
- }
- else if (annotation.hasIcons
- && annotation.graph == AlignmentAnnotation.NO_GRAPH)
- {
- if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
- && aj.secondaryStructure != '-')
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- 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
- {
- //
- return Color.white;
- }
- }
- else if (noGradient)
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (aj.colour != null)
- {
- currentColour = aj.colour;
- }
- }
- }
- 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);
-
- }
- }
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+ else
+ {
+ range = 0f;
}
}
- return currentColour;
- }
+ 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;
git://source.jalview.org / jalview.git / blobdiff