JAL-2738 correct handling of reverse strand genes

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

diff --git a/src/jalview/datamodel/GeneLoci.java b/src/jalview/datamodel/GeneLoci.java
index 9f3520f..b4bd642 100644 (file)
--- a/src/jalview/datamodel/GeneLoci.java
+++ b/src/jalview/datamodel/GeneLoci.java
@@ -8,73 +8,39 @@ import jalview.util.MapList;
 public class GeneLoci
 {
   /*
-   * implemented as an adapter over DBRefEntry with
-   * source -> species id
-   * version -> reference
-   * accession -> chromosome
+   * an identifier for the species
    */
-  private DBRefEntry loci;
+  public final String species;
 
-  boolean forwardStrand;
-
-  /**
-   * Constructor
-   * 
-   * @param taxon
-   * @param ref
-   * @param chrId
-   * @param map
-   * @param forward
-   */
-  public GeneLoci(String taxon, String ref, String chrId, MapList map,
-          boolean forward)
-  {
-    loci = new DBRefEntry(taxon, ref, chrId, new Mapping(map));
-    forwardStrand = forward;
-  }
-
-  /**
-   * Answers the identifier for the species
-   * 
-   * @return
+  /*
+   * an identifier for a genome assembly, e.g. GRCh38
    */
-  public String getSpecies()
-  {
-    return loci.getSource();
-  }
+  public final String assembly;
 
-  /**
-   * Answers the identifier for the genomic reference assembly
+  /*
+   * a chromosome identifier, e.g. "5" or "X"
    */
-  public String getReference()
-  {
-    return loci.getVersion();
-  }
+  public final String chromosome;
 
-  /**
-   * Answers the chromosome identifier
-   * 
-   * @return
+  /*
+   * mapping from sequence positions to chromosome locations;
+   * any regions with start > end are on the reverse strand
    */
-  public String getChromosome()
-  {
-    return loci.getAccessionId();
-  }
+  public final MapList mapping;
 
   /**
-   * Answers the mapping from sequence positions (in sequence start..end
-   * coordinates) to the corresponding loci in the chromosome (in reference
-   * assembly coordinates, base 1)
+   * Constructor
    * 
-   * @return
+   * @param taxon
+   * @param ref
+   * @param chrId
+   * @param map
    */
-  public MapList getMapping()
-  {
-    return loci.getMap().getMap();
-  }
-
-  public boolean isForwardStrand()
+  public GeneLoci(String taxon, String ref, String chrId, MapList map)
   {
-    return forwardStrand;
+    species = taxon;
+    assembly = ref;
+    chromosome = chrId;
+    mapping = map;
   }
 }