X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=697920e90cabccf7f06accf20cee98407ef636ca;hb=2026a420963f094072607c0495b6369ba96e60c0;hp=707eee83868e58ec7c0a99329848dc9761f1248a;hpb=a831db70f876aaeeb5b36624c9d10816fd8bb7c7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 707eee8..697920e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -43,6 +43,8 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -732,6 +734,10 @@ public class Alignment implements AlignmentI
    */
   public void addAnnotation(AlignmentAnnotation aa, int pos)
   {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -832,6 +838,11 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    //TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {