From 4e54a7c4a842b186926de0b7b8b5c4bd9c522413 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 16 Nov 2015 14:35:03 +0000 Subject: [PATCH] JAL-1958 modulate per-sequence shading with local score - low scores tend to grey. --- src/jalview/schemes/AnnotationColourGradient.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index 8511d86..b580be2 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -433,18 +433,19 @@ public class AnnotationColourGradient extends FollowerColourScheme range = 0f; } } - int trans = 0; + // midtr sets the ceiling for bleaching out the shading + int trans = 0, midtr = 239; if (perLineScore) { - trans = (int) ((1f - range) * 255.0); + trans = (int) ((1f - range) * midtr); range = (float) ((annotation.score - plmin) / (plmax - aamin)); } int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb * range + b1); if (annotation.score == annotation.score && positionToTransparency) { - return new Color(Integer.min(dr + trans, 255), Integer.min( - dg + trans, 255), Integer.min(db + trans, 255)); + return new Color(Integer.min(dr + trans, midtr), Integer.min(dg + + trans, midtr), Integer.min(db + trans, midtr)); } else { -- 1.7.10.2