JAL-1796 GeneLociI as distinguished DBRefEntry

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

diff --git a/src/jalview/datamodel/GeneLociI.java b/src/jalview/datamodel/GeneLociI.java
new file mode 100644 (file)
index 0000000..f8c7ec5
--- /dev/null
+++ b/src/jalview/datamodel/GeneLociI.java
@@ -0,0 +1,38 @@
+package jalview.datamodel;
+
+import jalview.util.MapList;
+
+/**
+ * An interface to model one or more contiguous regions on one chromosome
+ */
+public interface GeneLociI
+{
+  /**
+   * Answers the species identifier
+   * 
+   * @return
+   */
+  String getSpeciesId();
+
+  /**
+   * Answers the reference assembly identifier
+   * 
+   * @return
+   */
+  String getAssemblyId();
+
+  /**
+   * Answers the chromosome identifier e.g. "2", "Y", "II"
+   * 
+   * @return
+   */
+  String getChromosomeId();
+
+  /**
+   * Answers the mapping from sequence to chromosome loci. For a reverse strand
+   * mapping, the chromosomal ranges will have start > end.
+   * 
+   * @return
+   */
+  MapList getMap();
+}