X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=6b143ce32258902bf40a77d078a5ee6f37da88d5;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=580c85021a8850e8f4b423bf954677e9154c785d;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 580c850..6b143ce 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,6 +22,8 @@ import jalview.analysis.AlignSeq;
 import java.util.Enumeration;
 import java.util.Vector;
 
+import fr.orsay.lri.varna.models.rna.RNA;
+
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -48,6 +50,8 @@ public class Sequence implements SequenceI
   String vamsasId;
 
   DBRefEntry[] dbrefs;
+  
+  RNA rna;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
@@ -60,7 +64,7 @@ public class Sequence implements SequenceI
    */
   int index = -1;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
+  /** array of sequence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
   /**
@@ -707,6 +711,7 @@ public class Sequence implements SequenceI
     {
       tmp = new char[i];
       System.arraycopy(sequence, 0, tmp, 0, i);
+      j=sequence.length;
     }
     else
     {
@@ -715,6 +720,9 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence, j, tmp, i, sequence.length - j);
     }
     boolean createNewDs = false;
+    // TODO: take a look at the new dataset creation validation method below -
+    // this could become time comsuming for large sequences - consider making it
+    // more efficient
     for (int s = i; s < j; s++)
     {
       if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@ -1200,4 +1208,9 @@ public class Sequence implements SequenceI
   {
     index = value;
   }
+  
+  public void setRNA(RNA r){rna=r;}
+  
+  public RNA getRNA() { return rna; }
+  
 }