From 691a5b054954b834fb25a357320e47d89543a4cd Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sat, 5 Sep 2015 10:13:54 +0100 Subject: [PATCH] JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structure annotation employed for structure consensus and colour by helices --- src/jalview/schemes/RNAHelicesColour.java | 3 ++- src/jalview/workers/StrucConsensusThread.java | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) 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; -- 1.7.10.2