From 92cccf420dbe7501fae76b9941fd701151bdf5ab Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Jan 2016 15:58:15 +0000
Subject: [PATCH] JAL-653 refactor / tidy

---
 src/jalview/io/gff/Gff3Helper.java |   61 ++++++++++++++++++++++++++----------
 1 file changed, 44 insertions(+), 17 deletions(-)

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 4c67caa..55a0f9a 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -61,19 +61,6 @@ public class Gff3Helper extends GffHelperBase
           AlignmentI align, List<SequenceI> newseqs,
           boolean relaxedIdMatching) throws IOException
   {
-    /*
-     * (For now) we don't process mappings from reverse complement ; to do
-     * this would require (a) creating a virtual sequence placeholder for
-     * the reverse complement (b) resolving the sequence by its id from some
-     * source (GFF ##FASTA or other) (c) creating the reverse complement
-     * sequence (d) updating the mapping to be to the reverse complement
-     */
-    if ("-".equals(gff[STRAND_COL]))
-    {
-      System.err
-              .println("Skipping mapping from reverse complement as not yet supported");
-      return null;
-    }
     SequenceFeature sf = null;
 
     if (gff.length == 9)
@@ -135,10 +122,18 @@ public class Gff3Helper extends GffHelperBase
           throws IOException
   {
     String strand = gffColumns[STRAND_COL];
-    if ("-1".equals(strand))
+
+    /*
+     * (For now) we don't process mappings from reverse complement ; to do
+     * this would require (a) creating a virtual sequence placeholder for
+     * the reverse complement (b) resolving the sequence by its id from some
+     * source (GFF ##FASTA or other) (c) creating the reverse complement
+     * sequence (d) updating the mapping to be to the reverse complement
+     */
+    if ("-".equals(strand))
     {
       System.err
-              .println("Currently ignoring mappings from reverse complement");
+              .println("Skipping mapping from reverse complement as not yet supported");
       return null;
     }
 
@@ -351,11 +346,43 @@ public class Gff3Helper extends GffHelperBase
           Map<String, List<String>> attributes)
   {
     SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    String desc = getDescription(sf, attributes);
+    if (desc != null)
+    {
+      sf.setDescription(desc);
+    }
+    return sf;
+  }
+
+  /**
+   * Apply heuristic rules to try to get the most useful feature description
+   * 
+   * @param sf
+   * @param attributes
+   * @return
+   */
+  protected String getDescription(SequenceFeature sf,
+          Map<String, List<String>> attributes)
+  {
+    String desc = null;
     String target = (String) sf.getValue(TARGET);
     if (target != null)
     {
-      sf.setDescription(target.split(" ")[0]);
+      desc = target.split(" ")[0];
     }
-    return sf;
+
+    if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
+    {
+      /*
+       * Ensembl returns alleles and consequence_type (amongst other details)
+       */
+      String alleles = StringUtils.listToDelimitedString(
+              attributes.get("alleles"), ",");
+      String consequence = StringUtils.listToDelimitedString(
+              attributes.get("consequence_type"), ",");
+      desc = String.format("alleles %s;  consequence %s", alleles,
+              consequence);
+    }
+    return desc;
   }
 }
-- 
1.7.10.2