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

[jalview.git] / src / jalview / workers / StrucConsensusThread.java

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index eda64b5..76b87a6 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -61,15 +61,23 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
       AlignmentAnnotation[] aa = alignViewport.getAlignment()
               .getAlignmentAnnotation();
       AlignmentAnnotation rnaStruc = null;
+      // 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;
         }
       }
-
+      // check to see if its valid
+      
+      if (rnaStruc==null || !rnaStruc.isValidStruc())
+      {
+        calcMan.workerComplete(this);
+        return;
+      }
+      
       jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
               alignment.getWidth(), hStrucConsensus, true, rnaStruc);
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);