From 82a1660cd4ac60d30f947e2c57c66f7fb2a40996 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 11 Jul 2013 13:54:25 +0100
Subject: [PATCH] JAL-1347 refactor logic for setting display flags for
 histogram and profile to main control loop

---
 src/jalview/renderer/AnnotationRenderer.java |   23 ++++-------------------
 1 file changed, 4 insertions(+), 19 deletions(-)

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 6ed2b9f..f492d9c 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -318,6 +318,8 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
+    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation();
+    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
 
     BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
@@ -674,7 +676,7 @@ public class AnnotationRenderer
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
           drawBarGraph(g, row, row_annotations, startRes, endRes,
-                  row.graphMin, row.graphMax, y);
+                  row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
         }
       }
     } else {
@@ -910,7 +912,7 @@ public class AnnotationRenderer
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
-          float max, int y)
+          float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
   {
     if (sRes > aa_annotations.length)
     {
@@ -934,23 +936,6 @@ public class AnnotationRenderer
 
     int column;
     int aaMax = aa_annotations.length - 1;
-    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
-    // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
-    {
-      // TODO: generalise this to have render styles for consensus/profile data
-      if (_aa.groupRef != null)
-      {
-        renderHistogram = _aa.groupRef.isShowConsensusHistogram();
-        renderProfile = _aa.groupRef.isShowSequenceLogo();
-        normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
-      }
-      else
-      {
-        renderHistogram = av_renderHistogram;
-        renderProfile = av_renderProfile;
-        normaliseProfile = av_normaliseProfile;
-      }
-    }
     while (x < eRes - sRes)
     {
       column = sRes + x;
-- 
1.7.10.2