X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=1905f421569d5d1b046812c31653d4aa57f64001;hb=5b0949ce83f4ae4f1327fe386340064c83d88178;hp=1b91ee5309843bdc1adc03932a27148079b68674;hpb=f5e0f36fc8da4fd18f255bf3cc82005a2b94e245;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 1b91ee5..1905f42 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -82,7 +82,7 @@ public class Sequence extends ASequence implements SequenceI
    */
   int index = -1;
 
-  private SequenceFeatures sequenceFeatureStore;
+  private SequenceFeaturesI sequenceFeatureStore;
 
   /*
    * A cursor holding the approximate current view position to the sequence,
@@ -662,10 +662,10 @@ 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 +673,67 @@ 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()
@@ -1844,7 +1901,9 @@ public class Sequence extends ASequence implements SequenceI
      * and we may have included adjacent or enclosing features;
      * remove any that are not enclosing, non-contact features
      */
-    if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
+    boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+            && Comparison.isGap(sequence[toColumn - 1]);
+    if (endPos > this.end || endColumnIsGapped)
     {
       ListIterator<SequenceFeature> it = result.listIterator();
       while (it.hasNext())