From f27e64795343e9e4bdf79dab4dacd037e0cb04a6 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 14 Mar 2017 12:25:09 +0000 Subject: [PATCH] JAL-2438 Javadoc updates --- src/jalview/renderer/seqfeatures/FeatureColourFinder.java | 10 ++++++---- src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java | 7 ++++--- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java index 6f4d4de..761f418 100644 --- a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java +++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java @@ -41,14 +41,16 @@ public class FeatureColourFinder /** * Answers the feature colour to show for the given sequence and column * position. This delegates to the FeatureRenderer to find the colour, which - * will depend on feature location, visibility, ordering, and whether or not - * transparency is applied. For feature rendering with transparency, this - * class provides a dummy 'offscreen' graphics context where multiple feature - * colours can be overlaid and the combined colour read back. + * will depend on feature location, visibility, ordering, colour scheme, and + * whether or not transparency is applied. For feature rendering with + * transparency, this class provides a dummy 'offscreen' graphics context + * where multiple feature colours can be overlaid and the combined colour read + * back. * * @param defaultColour * @param seq * @param column + * alignment column position (base zero) * @return */ public Color findFeatureColour(Color defaultColour, SequenceI seq, diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 100b58f..84c9477 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -550,9 +550,10 @@ public abstract class FeatureRendererModel implements } /** - * Returns the configured colour for a specific feature using current feature - * settings. This does not include any consideration of feature visibility, - * colour transparency, graduated colour shading etc. + * Returns the configured colour for a particular feature instance. This + * includes calculation of 'colour by label', or of a graduated score colour, + * if applicable. It does not take into account feature visibility or colour + * transparency. * * @param feature * @return -- 1.7.10.2