From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 10 Aug 2015 10:16:05 +0000 (+0100)
Subject: JAL-736 relocate group associated conservation symbols to alignment column position
X-Git-Tag: Release_2_10_0~538^2~7^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=22a19bd5a73225168170d2b48c91518c0a3fa294;p=jalview.git

JAL-736 relocate group associated conservation symbols to alignment column position
---

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 76323bc..b8f1d92 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -698,8 +698,11 @@ public class Conservation
 
       float vprop = value - min;
       vprop /= max;
+      int consp = i - start;
+      String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+              : "";
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              consSymbs[i-start], ' ', value, new Color(minR
+              conssym, ' ', value, new Color(minR
                       + (maxR * vprop), minG + (maxG * vprop), minB
                       + (maxB * vprop)));