From b207001ceedbf3b9d343ce1941226575da7974d2 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 22 Jul 2021 20:40:29 +0100 Subject: [PATCH] JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency/per sequence annotation score encoding --- src/jalview/schemes/AnnotationColourGradient.java | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index a84ea52..8526684 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -40,12 +40,12 @@ public class AnnotationColourGradient extends FollowerColourScheme /** * map positional scores to transparency rather than colour */ - boolean positionToTransparency = true; + boolean positionToTransparency = false; /** * compute shade based on annotation row score */ - boolean perLineScore = true; + boolean perLineScore = false; public static final int NO_THRESHOLD = -1; @@ -245,7 +245,7 @@ public class AnnotationColourGradient extends FollowerColourScheme } if (plcount > 0 && plcount == ancount) { - perLineScore = plcount == ancount; + perLineScore = plmax!=plmin; aamax=plmax; } else @@ -545,4 +545,14 @@ public class AnnotationColourGradient extends FollowerColourScheme { return false; } + + public boolean isPositionToTransparency() + { + return positionToTransparency; + } + + public void setPositionToTransparency(boolean positionToTransparency) + { + this.positionToTransparency = positionToTransparency; + } } -- 1.7.10.2