From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 5 Sep 2015 09:13:54 +0000 (+0100)
Subject: JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structur... 
X-Git-Tag: Release_2_10_0~492^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=691a5b054954b834fb25a357320e47d89543a4cd;p=jalview.git

JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structure annotation employed for structure consensus and colour by helices
---

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 76592ba..5518f8f 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -99,7 +99,8 @@ public class RNAHelicesColour extends ResidueColourScheme
     {
 
       // is this a sensible way of determining type of annotation?
-      if (annotations[i].getRNAStruc() != null)
+      if (annotations[i].visible && annotations[i].isRNA()
+              && annotations[i].isValidStruc())
       {
         annotation = annotations[i];
         break;
diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 4471b6e..3113806 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -98,7 +98,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       // select rna struct to use for calculation
       for (int i = 0; i < aa.length; i++)
       {
-        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+        if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
         {
           rnaStruc = aa[i];
           break;