From 9a8cd338482d62f30297119ac6273da5f5b6ea6c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 23 Nov 2014 16:42:01 +0000 Subject: [PATCH] JAL-1593 allow per-sequence shading of RNA helix (stored in each annotation element's value field for a paired base) --- src/jalview/schemes/AnnotationColourGradient.java | 135 ++++++++++++++++----- 1 file changed, 102 insertions(+), 33 deletions(-) diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 713e55d..ef77e4d 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -53,7 +53,33 @@ public class AnnotationColourGradient extends FollowerColourScheme private boolean predefinedColours = false; private boolean seqAssociated = false; - + Color rnaHelices[] = null; + private void initRnaHelicesShading(int n) + { + int j = 0; + if (rnaHelices==null) + { + rnaHelices = new Color[n + 1]; + } + else + if (rnaHelices != null && rnaHelices.length <= n) + { + Color[] t = new Color[n + 1]; + System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length); + j = rnaHelices.length; + rnaHelices = t; + } + else + { + return; + } + // Generate random colors and store + for (; j <= n; j++) + { + rnaHelices[j] = jalview.util.ColorUtils + .generateRandomColor(Color.white); + } + } /** * false if the scheme was constructed without a minColour and maxColour used * to decide if existing colours should be taken from annotation elements when @@ -141,6 +167,12 @@ public class AnnotationColourGradient extends FollowerColourScheme bb = maxColour.getBlue() - b1; noGradient = false; + aamax = annotation.graphMax; + aamin = annotation.graphMin; + if (annotation.isRNA()) + { + initRnaHelicesShading(1 + (int) aamax); + } } @Override @@ -162,6 +194,7 @@ public class AnnotationColourGradient extends FollowerColourScheme // 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())) { @@ -169,12 +202,30 @@ public class AnnotationColourGradient extends FollowerColourScheme && (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) + { + initRnaHelicesShading(1 + (int) aamax); + } } } + float aamin = 0f, aamax = 0f; public String getAnnotation() { return annotation.label; @@ -278,9 +329,16 @@ public class AnnotationColourGradient extends FollowerColourScheme } 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 = 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 @@ -305,35 +363,7 @@ public class AnnotationColourGradient extends FollowerColourScheme } 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) @@ -345,6 +375,45 @@ public class AnnotationColourGradient extends FollowerColourScheme 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; -- 1.7.10.2