Further structure accessing feature

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 9037008..ad07680 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -37,7 +37,7 @@ public class AlignmentAnnotation
   public boolean autoCalculated = false;
 
   public String annotationId;
-
+  
   public SequenceI sequenceRef;
 
   /** DOCUMENT ME!! */
@@ -53,6 +53,8 @@ public class AlignmentAnnotation
    * RNA secondary structure contact positions
    */
   public SequenceFeature[] _rnasecstr = null;
+  
+  public String rnaStructure;
 
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
@@ -64,6 +66,8 @@ public class AlignmentAnnotation
   {
     _rnasecstr = Rna.GetBasePairs(RNAannot);
     Rna.HelixMap(_rnasecstr);
+    
+    setRNAStruc(RNAannot);
 
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
@@ -73,7 +77,7 @@ public class AlignmentAnnotation
     }
     // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
   }
-
+  
   public java.util.Hashtable sequenceMapping;
 
   /** DOCUMENT ME!! */
@@ -304,7 +308,15 @@ public class AlignmentAnnotation
     annotationId = this.hashCode() + "";
   }
 
-  /**
+  public void setRNAStruc(String string) {
+       rnaStructure=string;    
+}
+  
+  public String getRNAStruc(){
+         return rnaStructure;
+  }
+
+/**
    * Creates a new AlignmentAnnotation object.
    * 
    * @param label