From 13f26fb9d1c8d6f27fcedbf5c760f8e3947fd145 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
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 17bc6df..1311405 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -416,8 +416,6 @@ public class AnnotationRenderer
     return null;
   }
 
-  boolean rna = false;
-
   /**
    * Render the annotation rows associated with an alignment.
    * 
@@ -470,10 +468,6 @@ 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
@@ -484,32 +478,29 @@ 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