From 55eef00ac2435b5cc0ee64b92ad87a915375a709 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 25 Sep 2017 10:07:32 +0100
Subject: [PATCH] JAL-2738 one constant in codebase for "alleles" attribute of
 GFF/SequenceFeature

---
 src/jalview/analysis/AlignmentUtils.java     |    9 +++++----
 src/jalview/ext/ensembl/EnsemblSeqProxy.java |   10 +++++-----
 src/jalview/io/gff/Gff3Helper.java           |    4 +++-
 src/jalview/io/vcf/VCFLoader.java            |    3 ++-
 4 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 41fe77e..6acac01 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -36,6 +36,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
@@ -2374,7 +2375,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2396,7 +2397,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2418,7 +2419,7 @@ public class AlignmentUtils
     {
       if (var.variant != null)
       {
-        String alleles = (String) var.variant.getValue("alleles");
+        String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES);
         if (alleles != null)
         {
           for (String base : alleles.split(","))
@@ -2555,7 +2556,7 @@ public class AlignmentUtils
       /*
        * extract dna variants to a string array
        */
-      String alls = (String) sf.getValue("alleles");
+      String alls = (String) sf.getValue(Gff3Helper.ALLELES);
       if (alls == null)
       {
         continue; // non-SNP VCF variant perhaps - can't process this
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 577111e..35ceea3 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -34,6 +34,7 @@ import jalview.datamodel.features.SequenceFeatures;
 import jalview.exceptions.JalviewException;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
@@ -59,8 +60,6 @@ import java.util.Map.Entry;
  */
 public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
-  private static final String ALLELES = "alleles";
-
   protected static final String PARENT = "Parent";
 
   protected static final String ID = "ID";
@@ -717,7 +716,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   static void reverseComplementAlleles(SequenceFeature sf)
   {
-    final String alleles = (String) sf.getValue(ALLELES);
+    final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
     if (alleles == null)
     {
       return;
@@ -728,7 +727,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       reverseComplementAllele(complement, allele);
     }
     String comp = complement.toString();
-    sf.setValue(ALLELES, comp);
+    sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
 
     /*
@@ -738,7 +737,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String atts = sf.getAttributes();
     if (atts != null)
     {
-      atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+              Gff3Helper.ALLELES + "=" + comp);
       sf.setAttributes(atts);
     }
   }
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index c7e1d7a..a25a014 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -39,6 +39,8 @@ import java.util.Map;
  */
 public class Gff3Helper extends GffHelperBase
 {
+  public static final String ALLELES = "alleles";
+
   protected static final String TARGET = "Target";
 
   protected static final String ID = "ID";
@@ -399,7 +401,7 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+      desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
               ",");
     }
 
diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index e725a22..13966f4 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -17,6 +17,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.ext.ensembl.EnsemblMap;
 import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -361,7 +362,7 @@ public class VCFLoader
     SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
             featureEnd, score, "VCF");
 
-    sf.setValue("alleles", alleles);
+    sf.setValue(Gff3Helper.ALLELES, alleles);
 
     Map<String, Object> atts = variant.getAttributes();
     for (Entry<String, Object> att : atts.entrySet())
-- 
1.7.10.2