JAL-3567 adjust layout of linked feature report, unit test

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

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index a42f34a..520ff92 100644 (file)
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -119,11 +119,14 @@ public class MappedFeatures
   /**
    * Computes and returns comma-delimited HGVS notation peptide variants derived
    * from codon allele variants. If no variants are found, answers an empty
-   * string.
+   * string. The peptide variant is either simply read from the "CSQ:HGVSp"
+   * attribute if present, else computed based on the "alleles" attribute if
+   * present. If neither attribute is found, no variant (empty string) is
+   * returned.
    * 
    * @param sf
-   *             a sequence feature (which must be one of those held in this
-   *             object)
+   *          a sequence feature (which must be one of those held in this
+   *          object)
    * @return
    */
   public String findProteinVariants(SequenceFeature sf)