Merge branch 'develop' into features/JAL-1793VCF

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 03fc545..c064373 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -450,17 +450,6 @@ public interface SequenceI extends ASequenceI
   public void transferAnnotation(SequenceI entry, Mapping mp);
 
   /**
-   * @param index
-   *          The sequence index in the MSA
-   */
-  public void setIndex(int index);
-
-  /**
-   * @return The index of the sequence in the alignment
-   */
-  public int getIndex();
-
-  /**
    * @return The RNA of the sequence in the alignment
    */
 
@@ -536,8 +525,21 @@ public interface SequenceI extends ASequenceI
    */
   public int replace(char c1, char c2);
 
+  /**
+   * Answers the GeneLociI, or null if not known
+   * 
+   * @return
+   */
   GeneLociI getGeneLoci();
 
+  /**
+   * Sets the mapping to gene loci for the sequence
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   * @param map
+   */
   void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map);
 }