JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structur...

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 76592ba..5518f8f 100644 (file)
--- 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 (file)
--- 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;