Merge branch 'Release_2_9_0b1_Branch'

[jalview.git] / src / jalview / ws / rest / params / AnnotationFile.java

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index 862023e..a8bf2d1 100644 (file)
--- 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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.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;
   }
 }