Merge branch 'develop' into features/JAL-1793VCF

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96b0757..9e81d81 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -77,11 +77,6 @@ public class Sequence extends ASequence implements SequenceI
    */
   Vector<AlignmentAnnotation> annotation;
 
-  /**
-   * The index of the sequence in a MSA
-   */
-  int index = -1;
-
   private SequenceFeaturesI sequenceFeatureStore;
 
   /*
@@ -662,10 +657,10 @@ 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)
@@ -673,10 +668,67 @@ public class Sequence extends ASequence implements SequenceI
     this.description = desc;
   }
 
+  @Override
+  public void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map)
+  {
+    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
+            + ":" + chromosomeId, new Mapping(map)));
+  }
+
   /**
-   * DOCUMENT ME!
+   * Returns the gene loci mapping for the sequence (may be null)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   */
+  @Override
+  public GeneLociI getGeneLoci()
+  {
+    DBRefEntry[] refs = getDBRefs();
+    if (refs != null)
+    {
+      for (final DBRefEntry ref : refs)
+      {
+        if (ref.isChromosome())
+        {
+          return new GeneLociI()
+          {
+            @Override
+            public String getSpeciesId()
+            {
+              return ref.getSource();
+            }
+
+            @Override
+            public String getAssemblyId()
+            {
+              return ref.getVersion();
+            }
+
+            @Override
+            public String getChromosomeId()
+            {
+              // strip off "chromosome:" prefix to chrId
+              return ref.getAccessionId().substring(
+                      DBRefEntry.CHROMOSOME.length() + 1);
+            }
+
+            @Override
+            public MapList getMap()
+            {
+              return ref.getMap().getMap();
+            }
+          };
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Answers the description
+   * 
+   * @return
    */
   @Override
   public String getDescription()
@@ -1682,30 +1734,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-  /**
-   * @return The index (zero-based) on this sequence in the MSA. It returns
-   *         {@code -1} if this information is not available.
-   */
-  @Override
-  public int getIndex()
-  {
-    return index;
-  }
-
-  /**
-   * Defines the position of this sequence in the MSA. Use the value {@code -1}
-   * if this information is undefined.
-   * 
-   * @param The
-   *          position for this sequence. This value is zero-based (zero for
-   *          this first sequence)
-   */
-  @Override
-  public void setIndex(int value)
-  {
-    index = value;
-  }
-
   @Override
   public void setRNA(RNA r)
   {