Merge branch 'develop' into releases/Release_2_11_Branch

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index b22e48f..8dce31e 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
 import java.util.BitSet;
 import java.util.Iterator;
@@ -534,6 +535,25 @@ 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);
+
+
+  /**
    * Returns the sequence string constructed from the substrings of a sequence
    * defined by the int[] ranges provided by an iterator. E.g. the iterator
    * could iterate over all visible regions of the alignment