X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencefeature.java;h=61491b2d9e019d9ad015ca33b1735e4c2025a7fd;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=3d598d29768487faa7b490eff673b908cb60314c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 3d598d2..61491b2 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -20,7 +20,14 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.UrlLink;
+
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.Vector;
 
 import uk.ac.vamsas.objects.core.DataSetAnnotations;
@@ -31,11 +38,6 @@ import uk.ac.vamsas.objects.core.RangeAnnotation;
 import uk.ac.vamsas.objects.core.Score;
 import uk.ac.vamsas.objects.core.Seg;
 import uk.ac.vamsas.objects.utils.Properties;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.UrlLink;
 
 /**
  * @author JimP
@@ -70,6 +72,7 @@ public class Sequencefeature extends Rangetype
     doJvUpdate();
   }
 
+  @Override
   public void addToDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -88,6 +91,7 @@ public class Sequencefeature extends Rangetype
     dataset.addDataSetAnnotations(dsa);
   }
 
+  @Override
   public void addFromDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -105,6 +109,7 @@ public class Sequencefeature extends Rangetype
     bindjvvobj(sf, dsa);
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Untested sequencefeature conflict code");
@@ -117,6 +122,7 @@ public class Sequencefeature extends Rangetype
     addToDocument(); // and create a new feature in the document
   }
 
+  @Override
   public void updateToDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -143,6 +149,7 @@ public class Sequencefeature extends Rangetype
 
   }
 
+  @Override
   public void updateFromDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -199,15 +206,14 @@ public class Sequencefeature extends Rangetype
               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
-    dsa.setSeg(new Seg[]
-    { vSeg });
+    dsa.setSeg(new Seg[] { vSeg });
     dsa.setDescription(feature.getDescription());
     dsa.setStatus(feature.getStatus());
     if (feature.links != null && feature.links.size() > 0)
     {
       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
       {
-        String link = (String) feature.links.elementAt(i);
+        String link = feature.links.elementAt(i);
         UrlLink ulink = new UrlLink(link);
         if (ulink.isValid())
         {
@@ -220,21 +226,20 @@ public class Sequencefeature extends Rangetype
       }
     }
     dsa.setGroup(feature.getFeatureGroup());
-    if (feature.getScore() != Float.NaN)
+    if (!Float.isNaN(feature.getScore()))
     {
       Score fscore = new Score();
-      dsa.setScore(new Score[]
-      { fscore });
+      dsa.setScore(new Score[] { fscore });
       fscore.setContent(feature.getScore());
       fscore.setName(feature.getType());
     }
     if (feature.otherDetails != null)
     {
-      Enumeration iter = feature.otherDetails.keys();
+      Iterator<String> iter = feature.otherDetails.keySet().iterator();
       Vector props = dsa.getPropertyAsReference();
-      while (iter.hasMoreElements())
+      while (iter.hasNext())
       {
-        String key = (String) iter.nextElement();
+        String key = iter.next();
         if (!key.equalsIgnoreCase("score")
                 && !key.equalsIgnoreCase("status"))
         {