From 1b5c8f4a7296ae323fb886ebaa18c98110d34666 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 26 Feb 2018 15:59:53 +0000
Subject: [PATCH] JAL-2920 parse variation and original elements of the
 feature element, and include them in the returned
 description if they are present in the record

---
 resources/uniprot_mapping.xml                      |   16 ++++++---
 .../datamodel/xdb/uniprot/UniprotFeature.java      |   34 ++++++++++++++++++--
 2 files changed, 43 insertions(+), 7 deletions(-)

diff --git a/resources/uniprot_mapping.xml b/resources/uniprot_mapping.xml
index 6344d1e..832d3e5 100755
--- a/resources/uniprot_mapping.xml
+++ b/resources/uniprot_mapping.xml
@@ -62,13 +62,19 @@
 	 	</field>
 	 	<field name="position">
 	 	 <bind-xml name="position" node="attribute" location="location/position"/>
-	 	 </field>
+	 	</field>
 		<field name="begin">
 		 <bind-xml name="position" node="attribute" location="location/begin"/>
-	 	 </field>
-		<field name="end">
-		 <bind-xml name="position" node="attribute" location="location/end"/>
-	 	 </field>
+	 	</field>
+    <field name="end">
+      <bind-xml name="position" node="attribute" location="location/end"/>
+    </field>
+    <field name="variation">
+     <bind-xml name="variation"/>
+    </field>
+    <field name="original">
+     <bind-xml name="original"/>
+    </field>
 	 </class>
 	
           <class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
diff --git a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
index b1ed275..6102775 100644
--- a/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
+++ b/src/jalview/datamodel/xdb/uniprot/UniprotFeature.java
@@ -27,7 +27,11 @@ public class UniprotFeature
 {
   private String type;
 
-  private String description;
+  private String description = null;
+
+  private String original = null;
+
+  private String variation = null;
 
   private String status;
 
@@ -47,7 +51,13 @@ public class UniprotFeature
 
   public String getDescription()
   {
-    return description;
+    return (description == null && variation == null && original == null)
+            ? null
+            : (description == null ? "" : description)
+                    + ((variation != null)
+                            ? "Variation: '" + variation + "' "
+                    : "")
+            + ((original != null) ? "Original: '" + original + "'" : "");
   }
 
   public void setDescription(String d)
@@ -95,4 +105,24 @@ public class UniprotFeature
     this.begin = p;
     this.end = p;
   }
+
+  public String getOriginal()
+  {
+    return original;
+  }
+
+  public void setOriginal(String original)
+  {
+    this.original = original;
+  }
+
+  public String getVariation()
+  {
+    return variation;
+  }
+
+  public void setVariation(String variant)
+  {
+    this.variation = variant;
+  }
 }
-- 
1.7.10.2