X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;fp=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=220d3ab84f3ddcf6846ac6869f0305ae5287cb42;hb=667623e455de6756776d445c800d39d93fa060e2;hp=1a3e9efe49a8b0b105afc08aaefdb55f1c3b51d0;hpb=8f9537bd5d7f4455c6309569e2ca260463b7d2e4;p=jalview.git diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 1a3e9ef..220d3ab 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -27,6 +27,8 @@ import jalview.datamodel.Annotation; 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; @@ -40,15 +42,25 @@ public class AnnotationColourGradient extends FollowerColourScheme 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; @@ -61,7 +73,7 @@ public class AnnotationColourGradient extends FollowerColourScheme */ private boolean noGradient = false; - IdentityHashMap seqannot = null; + private IdentityHashMap seqannot = null; @Override public ColourSchemeI getInstance(AnnotatedCollectionI sg, @@ -72,12 +84,12 @@ public class AnnotationColourGradient extends FollowerColourScheme 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; @@ -109,12 +121,12 @@ public class AnnotationColourGradient extends FollowerColourScheme 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(); @@ -135,13 +147,13 @@ public class AnnotationColourGradient extends FollowerColourScheme 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(); @@ -211,9 +223,9 @@ public class AnnotationColourGradient extends FollowerColourScheme float aamin = 0f, aamax = 0f; - public String getAnnotation() + public AlignmentAnnotation getAnnotation() { - return annotation.label; + return annotation; } public int getAboveThreshold() @@ -235,12 +247,13 @@ public class AnnotationColourGradient extends FollowerColourScheme 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); } /** @@ -258,137 +271,157 @@ public class AnnotationColourGradient extends FollowerColourScheme } /** - * 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)) - // { - if (annotation.annotations != null && j < annotation.annotations.length - && annotation.annotations[j] != null - && !jalview.util.Comparison.isGap(c)) + + 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) { - 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 ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value) + || (aboveAnnotationThreshold == BELOW_THRESHOLD && 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) + 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 (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' - && aj.secondaryStructure != '-') - { - if (getColourScheme() != null) - { - currentColour = getColourScheme().findColour(c, j, seq, null, - 0f); - } - 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; - } + result = getColourScheme().findColour(c, j, seq, null, 0f); } - else if (noGradient) + else { - if (getColourScheme() != null) + if (ann.isRNA()) { - currentColour = getColourScheme().findColour(c, j, seq, null, - 0f); + result = ColourSchemeProperty.rnaHelices[(int) aj.value]; } else { - if (aj.colour != null) - { - currentColour = aj.colour; - } + result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR + : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR + : AnnotationRenderer.STEM_COLOUR; } } - else + } + else + { + return Color.white; + } + } + else if (noGradient) + { + if (getColourScheme() != null) + { + result = getColourScheme().findColour(c, j, seq, null, 0f); + } + else + { + if (aj.colour != null) { - currentColour = shadeCalculation(annotation, j); + result = aj.colour; } } - // if (conservationColouring) - // { - // currentColour = applyConservation(currentColour, j); - // } } - // } - 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 { @@ -396,11 +429,11 @@ public class AnnotationColourGradient extends FollowerColourScheme } } - 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() @@ -423,6 +456,16 @@ public class AnnotationColourGradient extends FollowerColourScheme seqAssociated = sassoc; } + public boolean isThresholdIsMinMax() + { + return thresholdIsMinMax; + } + + public void setThresholdIsMinMax(boolean minMax) + { + this.thresholdIsMinMax = minMax; + } + @Override public String getSchemeName() {