From cd578c5f56a88269077e547ed22f3b5f4bd033cb Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 27 Feb 2019 15:33:49 +0000 Subject: [PATCH] JAL-3202 reduced scope of rendering flags --- src/jalview/renderer/AnnotationRenderer.java | 51 +++++++++++--------------- 1 file changed, 21 insertions(+), 30 deletions(-) diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index c849e8c..aeb17ba 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -417,8 +417,6 @@ public class AnnotationRenderer return null; } - boolean rna = false; - /** * Render the annotation rows associated with an alignment. * @@ -471,10 +469,6 @@ public class AnnotationRenderer .getAlignmentStrucConsensusAnnotation(); final AlignmentAnnotation complementConsensusAnnot = av .getComplementConsensusAnnotation(); - boolean renderHistogram = true; - boolean renderProfile = false; - boolean normaliseProfile = false; - boolean isRNA = rna; BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label @@ -488,32 +482,29 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - isRNA = row.isRNA(); + boolean renderHistogram = true; + boolean renderProfile = false; + boolean normaliseProfile = false; + boolean isRNA = row.isRNA(); + + // check if this is a consensus annotation row and set the display + // settings appropriately + // TODO: generalise this to have render styles for consensus/profile + // data + if (row.groupRef != null && row == row.groupRef.getConsensus()) { - // check if this is a consensus annotation row and set the display - // settings appropriately - // TODO: generalise this to have render styles for consensus/profile - // data - if (row.groupRef != null && row == row.groupRef.getConsensus()) - { - renderHistogram = row.groupRef.isShowConsensusHistogram(); - renderProfile = row.groupRef.isShowSequenceLogo(); - normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); - } - else if (row == consensusAnnot || row == structConsensusAnnot - || row == complementConsensusAnnot) - { - renderHistogram = av_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - else - { - renderHistogram = true; - // don't need to set render/normaliseProfile since they are not - // currently used in any other annotation track renderer - } + renderHistogram = row.groupRef.isShowConsensusHistogram(); + renderProfile = row.groupRef.isShowSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); } + else if (row == consensusAnnot || row == structConsensusAnnot + || row == complementConsensusAnnot) + { + renderHistogram = av_renderHistogram; + renderProfile = av_renderProfile; + normaliseProfile = av_normaliseProfile; + } + Annotation[] row_annotations = row.annotations; if (!row.visible) { -- 1.7.10.2