JAL-2738 getGeneLoci promoted to SequenceI

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 2f1da7f..5d8a3ef 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -106,6 +106,8 @@ public class Sequence extends ASequence implements SequenceI
    */
   private int changeCount;
 
+  private GeneLoci geneLoci;
+
   /**
    * Creates a new Sequence object.
    * 
@@ -645,21 +647,70 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the sequence description, and also parses out any special formats of
+   * interest
    * 
    * @param desc
-   *          DOCUMENT ME!
    */
   @Override
   public void setDescription(String desc)
   {
     this.description = desc;
+    parseDescription();
   }
 
   /**
-   * DOCUMENT ME!
+   * Parses and saves fields of an Ensembl-style description e.g.
+   * chromosome:GRCh38:17:45051610:45109016:1
+   */
+  protected void parseDescription()
+  {
+    if (description == null)
+    {
+      return;
+    }
+    String[] tokens = description.split(":");
+    if (tokens.length == 6 && "chromosome".equals(tokens[0])) {
+      String ref = tokens[1];
+      String chrom = tokens[2];
+      try {
+        int chStart = Integer.parseInt(tokens[3]);
+        int chEnd = Integer.parseInt(tokens[4]);
+        boolean forwardStrand = "1".equals(tokens[5]);
+        String species = ""; // dunno yet!
+        int[] from = new int[] { start, end };
+        int[] to = new int[] { forwardStrand ? chStart : chEnd,
+            forwardStrand ? chEnd : chStart };
+        MapList map = new MapList(from, to, 1, 1);
+        GeneLoci gl = new GeneLoci(species, ref, chrom, map);
+        setGeneLoci(gl);
+      } catch (NumberFormatException e)
+      {
+        System.err.println("Bad integers in description " + description);
+      }
+    }
+  }
+
+  public void setGeneLoci(GeneLoci gl)
+  {
+    geneLoci = gl;
+  }
+
+  /**
+   * Returns the gene loci mapping for the sequence (may be null)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   */
+  @Override
+  public GeneLoci getGeneLoci()
+  {
+    return geneLoci;
+  }
+
+  /**
+   * Answers the description
+   * 
+   * @return
    */
   @Override
   public String getDescription()