From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 18 Jul 2016 08:31:06 +0000 (+0100)
Subject: JAL-2145 improvement: ensure conservation calculation performed between istart &... 
X-Git-Tag: Release_2_10_0~138^2~8
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=8cc3de5e7d587045f6d8e907ab9c630afb625d99

JAL-2145 improvement: ensure conservation calculation performed between istart & alwidth only!
---

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 7b3ce25..21d990c 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -693,7 +693,7 @@ public class Conservation
       qmax = qualityRange[1].floatValue();
     }
 
-    for (int i = 0; i < alWidth; i++)
+    for (int i = istart; i < alWidth; i++)
     {
       float value = 0;