X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;fp=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=a71c7b1d67dc43d66b17ec7df382658828e90667;hb=0031ee4b6a42ad328e417cb65c7a840183e62e87;hp=bf2408c79e2ec7d4ff1ff9888861bbe86019a582;hpb=e6b6f08502b7a31b22ae18e31c4ada1dba58be54;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index bf2408c..a71c7b1 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -35,6 +35,8 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
+import intervalstore.api.IntervalI;
+
 /**
  * A class that models a single contiguous feature on a sequence. If flag
  * 'contactFeature' is true, the start and end positions are interpreted instead
@@ -99,9 +101,14 @@ public class SequenceFeature implements FeatureLocationI
    */
   private String source;
 
-  // for Overview sort:
-  public int index;
+  /**
+   * 1-based index into the featureList used by FeatureStoreJS
+   */
+  public int index1;
 
+  /**
+   * containment nesting link used by FeatureStoreJS to track starting points
+   */
   public SequenceFeature containedBy;
 
   /**
@@ -741,6 +748,20 @@ public class SequenceFeature implements FeatureLocationI
   {
     source = theSource;
   }
+
+  @Override
+  public IntervalI getContainedBy()
+  {
+    return containedBy;
+  }
+
+  @Override
+  public void setContainedBy(IntervalI containedBy)
+  {
+    this.containedBy = (SequenceFeature) containedBy;
+
+  }
+
 }
 
 class SFSortByEnd implements Comparator<SequenceFeature>