From cf2e3cf08db12cd9b1ad97d2c2b7e97d9c126ce7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 28 Oct 2011 17:17:27 +0100 Subject: [PATCH] (JAL-885 JAL-580) ignore invalid RNA structure lines --- src/jalview/renderer/AnnotationRenderer.java | 4 +++- src/jalview/workers/StrucConsensusThread.java | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index e8b2e72..47e2cb7 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -163,7 +163,8 @@ public class AnnotationRenderer { if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) { - if (aa.groupRef != null && aa.groupRef.consensusData != null + // TODO implement group structure consensus + /* if (aa.groupRef != null && aa.groupRef.consensusData != null && aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for group selections @@ -171,6 +172,7 @@ public class AnnotationRenderer aa.groupRef.consensusData[column], aa.groupRef .getIgnoreGapsConsensus()); } + */ // TODO extend annotation row to enable dynamic and static profile data // to // be stored diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java index 9143ad7..76b87a6 100644 --- a/src/jalview/workers/StrucConsensusThread.java +++ b/src/jalview/workers/StrucConsensusThread.java @@ -64,7 +64,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo // select rna struct to use for calculation for (int i = 0; i < aa.length; i++) { - if (aa[i].getRNAStruc() != null) + if (aa[i].getRNAStruc() != null && aa[i].isValidStruc()) { rnaStruc = aa[i]; break; -- 1.7.10.2