*/
package jalview.schemes;
-import java.awt.Color;
-import java.util.IdentityHashMap;
-import java.util.Map;
-
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
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;
+import java.util.Map;
public class AnnotationColourGradient extends FollowerColourScheme
{
+ /**
+ * map positional scores to transparency rather than colour
+ */
+ boolean positionToTransparency = false;
+
+ /**
+ * compute shade based on annotation row score
+ */
+ boolean perLineScore = false;
+
public static final int NO_THRESHOLD = -1;
public static final int BELOW_THRESHOLD = 0;
private final int aboveAnnotationThreshold;
- private boolean thresholdIsMinMax = false;
+ public boolean thresholdIsMinMax = false;
private GraphLine annotationThreshold;
private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
- colourScheme, aboveAnnotationThreshold);
+ getColourScheme(), aboveAnnotationThreshold);
acg.thresholdIsMinMax = thresholdIsMinMax;
acg.annotationThreshold = (annotationThreshold == null) ? null
: new GraphLine(annotationThreshold);
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
acg.noGradient = noGradient;
+ acg.positionToTransparency = positionToTransparency;
+ acg.perLineScore = perLineScore;
return acg;
}
{
if (originalColour instanceof AnnotationColourGradient)
{
- colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+ setColourScheme(((AnnotationColourGradient) originalColour)
+ .getColourScheme());
}
else
{
- colourScheme = originalColour;
+ setColourScheme(originalColour);
}
this.annotation = annotation;
}
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 = plmax!=plmin;
+ 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);
}
/**
}
/**
- * DOCUMENT ME!
+ * Returns the colour for a given character and position in a sequence
*
- * @param n
- * DOCUMENT ME!
+ * @param c
+ * the residue character
* @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * the aligned position
+ * @param seq
+ * the sequence
+ * @return
*/
@Override
public Color findColour(char c, int j, SequenceI seq)
{
- Color currentColour = Color.white;
- AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
- .get(seq) : this.annotation);
- if (ann == null)
+ /*
+ * locate the annotation we are configured to colour by
+ */
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null
+ ? seqannot.get(seq)
+ : this.annotation);
+
+ /*
+ * if gap or no annotation at position, no colour (White)
+ */
+ if (ann == null || ann.annotations == null
+ || j >= ann.annotations.length || ann.annotations[j] == null
+ || Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Annotation aj = ann.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 threshold applies, and annotation fails the test - no colour (white)
+ */
+ if (annotationThreshold != null)
+ {
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && aj.value <= annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD
+ && aj.value >= annotationThreshold.value))
+ {
+ return Color.white;
+ }
+ }
+
+ /*
+ * If 'use original colours' then return the colour of the annotation
+ * at the aligned position - computed using the background colour scheme
+ */
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black))
{
- return currentColour;
+ return aj.colour;
}
- if ((threshold == 0) || aboveThreshold(c, j))
+
+ Color result = Color.white;
+ if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
{
- if (ann.annotations != null && j < ann.annotations.length
- && ann.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
+ /*
+ * secondary structure symbol colouring
+ */
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
{
- Annotation aj = ann.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 (getColourScheme() != null)
{
- if (predefinedColours && aj.colour != null
- && !aj.colour.equals(Color.black))
- {
- currentColour = aj.colour;
- }
- else if (ann.hasIcons
- && ann.graph == AlignmentAnnotation.NO_GRAPH)
- {
- if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
- && aj.secondaryStructure != '-')
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (ann.isRNA())
- {
- currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
- }
- else
- {
- currentColour = ann.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : ann.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
- }
- }
- }
- else
- {
- //
- return Color.white;
- }
- }
- else if (noGradient)
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (ann.isRNA())
{
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (aj.colour != null)
- {
- currentColour = aj.colour;
- }
- }
+ result = ColourSchemeProperty.rnaHelices[(int) aj.value];
}
else
{
- currentColour = shadeCalculation(ann, j);
+ result = ann.annotations[j].secondaryStructure == 'H'
+ ? AnnotationRenderer.HELIX_COLOUR
+ : ann.annotations[j].secondaryStructure == 'E'
+ ? AnnotationRenderer.SHEET_COLOUR
+ : AnnotationRenderer.STEM_COLOUR;
}
}
- if (conservationColouring)
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+ else if (noGradient)
+ {
+ if (getColourScheme() != null)
+ {
+ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
+ else
+ {
+ if (aj.colour != null)
{
- currentColour = applyConservation(currentColour, j);
+ result = aj.colour;
}
}
}
- return currentColour;
+ else
+ {
+ result = shadeCalculation(ann, j);
+ }
+
+ return result;
}
/**
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
&& value >= ann.threshold.value)
{
- range = (value - ann.threshold.value)
+ range = ann.graphMax == ann.threshold.value ? 1f
+ : (value - ann.threshold.value)
/ (ann.graphMax - ann.threshold.value);
}
else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
&& value <= ann.threshold.value)
{
- range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+ range = ann.graphMin == ann.threshold.value ? 0f
+ : (value - ann.graphMin)
+ / (ann.threshold.value - ann.graphMin);
}
else
{
}
}
- 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()
return thresholdIsMinMax;
}
- public void setThresholdIsMinMax(boolean thresholdIsMinMax)
+ public void setThresholdIsMinMax(boolean minMax)
+ {
+ this.thresholdIsMinMax = minMax;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return ANNOTATION_COLOUR;
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+
+ public boolean isPositionToTransparency()
+ {
+ return positionToTransparency;
+ }
+
+ public void setPositionToTransparency(boolean positionToTransparency)
{
- this.thresholdIsMinMax = thresholdIsMinMax;
+ this.positionToTransparency = positionToTransparency;
}
}
git://source.jalview.org / jalview.git / blobdiff