JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / io / vamsas / Sequencefeature.java

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 5d04c4c..0f9a664 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,23 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.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.Vector;
 
@@ -29,11 +37,6 @@ 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
@@ -197,15 +200,14 @@ 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())
         {
@@ -218,11 +220,10 @@ 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());
     }