JAL-1796 GeneLociI as distinguished DBRefEntry

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index f7837f7..98868ce 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -27,7 +27,20 @@ import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
 {
-  String source = "", version = "", accessionId = "";
+  /*
+   * the mapping to chromosome (genome) is held as an instance with
+   * source = speciesId
+   * version = assemblyId
+   * accessionId = "chromosome:" + chromosomeId
+   * map = mapping from sequence to reference assembly
+   */
+  public static final String CHROMOSOME = "chromosome";
+
+  String source = "";
+
+  String version = "";
+
+  String accessionId = "";
 
   /**
    * maps from associated sequence to the database sequence's coordinate system
@@ -331,4 +344,14 @@ public class DBRefEntry implements DBRefEntryI
     }
     return true;
   }
+
+  /**
+   * Mappings to chromosome are held with accessionId as "chromosome:id"
+   * 
+   * @return
+   */
+  public boolean isChromosome()
+  {
+    return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
+  }
 }