JAL-1618 feature parsing bug (and formatting)

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index a1b8509..47c732f 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel.xdb.embl;
 
@@ -422,9 +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
     {
@@ -437,7 +444,9 @@ public class EmblEntry
           {
             for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                     .addDBRef((DBRefEntry) dbr.next()))
+            {
               ;
+            }
           }
         }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -453,7 +462,9 @@ public class EmblEntry
             {
               for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
                       .addDBRef((DBRefEntry) dbr.next()))
+              {
                 ;
+              }
             }
           }
         }
@@ -585,10 +596,9 @@ public class EmblEntry
     {
       // extract proteins.
       product = new Sequence(prid, prseq, 1, prseq.length());
-      product
-              .setDescription(((prname.length() == 0) ? "Protein Product from "
-                      + sourceDb
-                      : prname));
+      product.setDescription(((prname.length() == 0) ? "Protein Product from "
+              + sourceDb
+              : prname));
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -657,7 +667,9 @@ public class EmblEntry
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
           if (product != null)
+          {
             product.addDBRef(pcdnaref);
+          }
 
         }
       }
@@ -669,18 +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);
@@ -713,16 +727,16 @@ public class EmblEntry
         }
         if (product != null)
         {
-          DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                  .getVersion(), ref.getAccessionId());
+          DBRefEntry pref = new DBRefEntry(ref.getSource(),
+                  ref.getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
           if (map != null)
           {
             Mapping pmap = new Mapping(dna, map.getMap().getInverse());
-            pref = new DBRefEntry(sourceDb, getVersion(), this
-                    .getAccession());
+            pref = new DBRefEntry(sourceDb, getVersion(),
+                    this.getAccession());
             pref.setMap(pmap);
             if (map.getTo() != null)
             {