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;
public static final int ABOVE_THRESHOLD = 1;
- public AlignmentAnnotation annotation;
+ private final AlignmentAnnotation annotation;
- int aboveAnnotationThreshold = -1;
+ private final int aboveAnnotationThreshold;
public boolean thresholdIsMinMax = false;
- GraphLine annotationThreshold;
+ private GraphLine annotationThreshold;
- float r1, g1, b1, rr, gg, bb;
+ private int redMin;
+
+ private int greenMin;
+
+ private int blueMin;
+
+ private int redRange;
+
+ private int greenRange;
+
+ private int blueRange;
private boolean predefinedColours = false;
*/
private boolean noGradient = false;
- IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+ private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
- colourScheme, aboveAnnotationThreshold);
+ getColourScheme(), aboveAnnotationThreshold);
acg.thresholdIsMinMax = thresholdIsMinMax;
acg.annotationThreshold = (annotationThreshold == null) ? null
: new GraphLine(annotationThreshold);
- acg.r1 = r1;
- acg.g1 = g1;
- acg.b1 = b1;
- acg.rr = rr;
- acg.gg = gg;
- acg.bb = bb;
+ acg.redMin = redMin;
+ acg.greenMin = greenMin;
+ acg.blueMin = blueMin;
+ acg.redRange = redRange;
+ acg.greenRange = greenRange;
+ acg.blueRange = blueRange;
acg.predefinedColours = predefinedColours;
acg.seqAssociated = seqAssociated;
acg.noGradient = noGradient;
{
if (originalColour instanceof AnnotationColourGradient)
{
- colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+ setColourScheme(((AnnotationColourGradient) originalColour)
+ .getColourScheme());
}
else
{
- colourScheme = originalColour;
+ setColourScheme(originalColour);
}
this.annotation = annotation;
annotationThreshold = annotation.threshold;
}
// clear values so we don't get weird black bands...
- r1 = 254;
- g1 = 254;
- b1 = 254;
- rr = 0;
- gg = 0;
- bb = 0;
+ redMin = 254;
+ greenMin = 254;
+ blueMin = 254;
+ redRange = 0;
+ greenRange = 0;
+ blueRange = 0;
noGradient = true;
checkLimits();
annotationThreshold = annotation.threshold;
}
- r1 = minColour.getRed();
- g1 = minColour.getGreen();
- b1 = minColour.getBlue();
+ redMin = minColour.getRed();
+ greenMin = minColour.getGreen();
+ blueMin = minColour.getBlue();
- rr = maxColour.getRed() - r1;
- gg = maxColour.getGreen() - g1;
- bb = maxColour.getBlue() - b1;
+ redRange = maxColour.getRed() - redMin;
+ greenRange = maxColour.getGreen() - greenMin;
+ blueRange = maxColour.getBlue() - blueMin;
noGradient = false;
checkLimits();
float aamin = 0f, aamax = 0f;
- public String getAnnotation()
+ public AlignmentAnnotation getAnnotation()
{
- return annotation.label;
+ return annotation;
}
public int getAboveThreshold()
public Color getMinColour()
{
- return new Color((int) r1, (int) g1, (int) b1);
+ return new Color(redMin, greenMin, blueMin);
}
public Color getMaxColour()
{
- return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+ return new Color(redMin + redRange, greenMin + greenRange, blueMin
+ + blueRange);
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public Color findColour(char c)
{
return Color.red;
}
/**
- * 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 annotation = (seqAssociated && seqannot != null ? seqannot
+ /*
+ * locate the annotation we are configured to colour by
+ */
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
.get(seq) : this.annotation);
- if (annotation == null)
+
+ /*
+ * 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 currentColour;
+ return Color.white;
}
- if ((threshold == 0) || aboveThreshold(c, j))
+
+ 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 (annotation.annotations != null
- && j < annotation.annotations.length
- && annotation.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
{
- 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)))
+ 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 aj.colour;
+ }
+
+ Color result = Color.white;
+ if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ /*
+ * secondary structure symbol colouring
+ */
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-')
+ {
+ if (getColourScheme() != null)
{
- 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' ? 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)
+ 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(annotation, 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;
}
- private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ /**
+ * Returns a graduated colour for the annotation at the given column. If there
+ * is a threshold value, and it is used as the top/bottom of the colour range,
+ * and the value satisfies the threshold condition, then a colour
+ * proportionate to the range from the threshold is calculated. For all other
+ * cases, a colour proportionate to the annotation's min-max range is
+ * calulated. Note that thresholding is _not_ done here (a colour is computed
+ * even if threshold is not passed).
+ *
+ * @param ann
+ * @param col
+ * @return
+ */
+ Color shadeCalculation(AlignmentAnnotation ann, int col)
{
-
- // calculate a shade
float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
+ float value = ann.annotations[col].value;
+ if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
+ && value >= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
+ range = (value - ann.threshold.value)
+ / (ann.graphMax - ann.threshold.value);
}
- else if (thresholdIsMinMax && annotation.threshold != null
+ else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
+ && value <= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
+ range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
}
else
{
- if (annotation.graphMax != annotation.graphMin)
+ if (ann.graphMax != ann.graphMin)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
+ range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin);
}
else
{
}
}
- int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
- * range + b1);
+ int dr = (int) (redRange * range + redMin);
+ int dg = (int) (greenRange * range + greenMin);
+ int db = (int) (blueRange * range + blueMin);
return new Color(dr, dg, db);
-
}
public boolean isPredefinedColours()
{
seqAssociated = sassoc;
}
+
+ public boolean isThresholdIsMinMax()
+ {
+ return thresholdIsMinMax;
+ }
+
+ public void setThresholdIsMinMax(boolean minMax)
+ {
+ this.thresholdIsMinMax = minMax;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff