(JAL-885 JAL-580) ignore invalid RNA structure lines

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index e8b2e72..47e2cb7 100644 (file)
--- 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 (file)
--- 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;