From 86ca22920425001a99216f31f77909d8d48072b0 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 Dec 2014 10:44:16 +0000
Subject: [PATCH] JAL-1618 feature parsing bug (and formatting)

---
 src/jalview/datamodel/xdb/embl/EmblEntry.java |   16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 3c88083..47c732f 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -425,9 +425,13 @@ public class EmblEntry
       { 1, dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
+      {
         for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
                 .addDBRef((DBRefEntry) i.next()))
+        {
           ;
+        }
+      }
     }
     try
     {
@@ -440,7 +444,9 @@ public class EmblEntry
           {
             for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                     .addDBRef((DBRefEntry) dbr.next()))
+            {
               ;
+            }
           }
         }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -456,7 +462,9 @@ public class EmblEntry
             {
               for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                       .addDBRef((DBRefEntry) dbr.next()))
+              {
                 ;
+              }
             }
           }
         }
@@ -659,7 +667,9 @@ public class EmblEntry
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
           if (product != null)
+          {
             product.addDBRef(pcdnaref);
+          }
 
         }
       }
@@ -671,18 +681,20 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + (int) (xint / 2))
+        sf.setDescription("Exon " + (1 + xint / 2)
                 + " for protein '" + prname + "' EMBLCDS:" + prid);
         sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
         sf.setValue(FeatureProperties.EXONPRODUCT, prname);
         if (vals != null && vals.size() > 0)
         {
-          Enumeration kv = vals.elements();
+          Enumeration kv = vals.keys();
           while (kv.hasMoreElements())
           {
             Object key = kv.nextElement();
             if (key != null)
+            {
               sf.setValue(key.toString(), vals.get(key));
+            }
           }
         }
         dna.addSequenceFeature(sf);
-- 
1.7.10.2