X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAnnotationFile.java;h=5962a9145bd8e55ca299bf3197cf4e6b4c508e8f;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=ed9383eceec22af2854f651795461b46d469dee5;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index ed9383e..5962a91 100644
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.rest.params;
@@ -43,8 +45,7 @@ public class AnnotationFile extends InputType
 {
   public AnnotationFile()
   {
-    super(new Class[]
-    { AlignmentI.class });
+    super(new Class[] { AlignmentI.class });
   }
 
   /**
@@ -71,9 +72,8 @@ public class AnnotationFile extends InputType
     if (format.equals(JVANNOT))
     {
       return new StringBody(
-              new jalview.io.AnnotationFile().printAnnotations(
-                      al.getAlignmentAnnotation(), al.getGroups(),
-                      al.getProperties()));
+              new jalview.io.AnnotationFile()
+                      .printAnnotationsForAlignment(al));
     }
     else
     {
@@ -111,8 +111,7 @@ public class AnnotationFile extends InputType
 
     if (tok.startsWith("format"))
     {
-      for (String fmt : new String[]
-      { CSVANNOT, JVANNOT })
+      for (String fmt : new String[] { CSVANNOT, JVANNOT })
       {
         if (val.equalsIgnoreCase(fmt))
         {
@@ -122,8 +121,7 @@ public class AnnotationFile extends InputType
       }
       warnings.append("Invalid annotation file format '" + val
               + "'. Must be one of (");
-      for (String fmt : new String[]
-      { CSVANNOT, JVANNOT })
+      for (String fmt : new String[] { CSVANNOT, JVANNOT })
       {
         warnings.append(" " + fmt);
       }
@@ -138,8 +136,8 @@ public class AnnotationFile extends InputType
     // TODO - consider disregarding base options here.
     List<OptionI> lst = getBaseOptions();
     lst.add(new Option("format", "Alignment annotation upload format",
-            true, JVANNOT, format, Arrays.asList(new String[]
-            { JVANNOT, CSVANNOT }), null));
+            true, JVANNOT, format, Arrays.asList(new String[] { JVANNOT,
+                CSVANNOT }), null));
     return lst;
   }
 }