Merge branch 'develop' into releases/Release_2_10_2_Branch

[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 b613aa1..31d64f5 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -27,6 +27,7 @@ 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;
@@ -71,6 +72,7 @@ public class Sequencefeature extends Rangetype
     doJvUpdate();
   }
 
+  @Override
   public void addToDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -89,15 +91,14 @@ public class Sequencefeature extends Rangetype
     dataset.addDataSetAnnotations(dsa);
   }
 
+  @Override
   public void addFromDocument()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
     if (dsa.getSeqRefCount() != 1)
     {
-      Cache.log
-              .warn("Not binding "
-                      + dsa.getVorbaId()
-                      + " to Sequence Feature - has multiple dataset sequence references.");
+      Cache.log.warn("Not binding " + dsa.getVorbaId()
+              + " to Sequence Feature - has multiple dataset sequence references.");
       return;
     }
     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
@@ -106,6 +107,7 @@ public class Sequencefeature extends Rangetype
     bindjvvobj(sf, dsa);
   }
 
+  @Override
   public void conflict()
   {
     log.warn("Untested sequencefeature conflict code");
@@ -118,6 +120,7 @@ public class Sequencefeature extends Rangetype
     addToDocument(); // and create a new feature in the document
   }
 
+  @Override
   public void updateToDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -125,8 +128,8 @@ public class Sequencefeature extends Rangetype
     if (dsa.getSeqRefCount() != 1)
     {
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+      Cache.log.warn(
+              "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
       doSync(); // re-verify bindings.
     }
     else
@@ -144,6 +147,7 @@ public class Sequencefeature extends Rangetype
 
   }
 
+  @Override
   public void updateFromDoc()
   {
     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
@@ -152,10 +156,8 @@ public class Sequencefeature extends Rangetype
     {
       // conflicting update from document - we cannot map this feature anymore.
       replaceJvObjMapping(feature, null);
-      Cache.log
-              .warn("annotation ("
-                      + dsa.getVorbaId()
-                      + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+      Cache.log.warn("annotation (" + dsa.getVorbaId()
+              + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
       // - consider deleting the feature ?
       dsSeq.deleteFeature(feature);
       // doSync();
@@ -196,8 +198,8 @@ public class Sequencefeature extends Rangetype
     vSeg.setInclusive(true);
     if (dsa.getSegCount() > 1)
     {
-      Cache.log
-              .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+      Cache.log.debug(
+              "About to destroy complex annotation in vamsas document mapped to sequence feature ("
                       + dsa.getVorbaId() + ")");
     }
     dsa.setSeg(new Seg[] { vSeg });
@@ -229,11 +231,11 @@ public class Sequencefeature extends Rangetype
     }
     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"))
         {
@@ -250,7 +252,8 @@ public class Sequencefeature extends Rangetype
           else if (vlu instanceof Integer)
           {
             valid = true;
-            nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+            nprop.setType(
+                    uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
           }
           else if (vlu instanceof Float)
           {