Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge' into develop (JAL-826)

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 707eee8..697920e 100755 (executable)
--- 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)
   {