From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 11 Jul 2013 12:57:03 +0000 (+0100)
Subject: JAL-1347 identify and set rendering settings for consensus annotation rows
X-Git-Tag: Jalview_2_9~226^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e66bdc1c0086ab56c56979d9dc6635e81503eb84;p=jalview.git

JAL-1347 identify and set rendering settings for consensus annotation rows
JAL-966 Note  - should abstract this logic even further away in Jalview v3
---

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index f492d9c..8f25e77 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -333,6 +333,26 @@ public class AnnotationRenderer
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
+      {
+        // 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)
+        {
+          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
+        }
+      }
       Annotation[] row_annotations = row.annotations;
       if (!row.visible)
       {