X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=c2afc14a672b2da9e37c545b6ef71e4cd603054b;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=2d28a9cb9a072116f2b843785c6930c74d2ef3bb;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 2d28a9c..c2afc14 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,20 +1,21 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- *
+ *  
  * 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/>.
- *******************************************************************************/
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.rest.params;
 
 import jalview.datamodel.AlignmentI;
@@ -24,19 +25,13 @@ import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.InputType.molType;
-import jalview.ws.rest.RestServiceDescription;
 
 import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
-import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -68,7 +63,7 @@ public class Alignment extends InputType
   /**
    * input data as a file upload rather than inline content
    */
-  public boolean writeAsFile=false;
+  public boolean writeAsFile = false;
 
   @Override
   public ContentBody formatForInput(RestJob rj)
@@ -186,20 +181,25 @@ public class Alignment extends InputType
     }
     return false;
   }
+
   @Override
   public List<OptionI> getOptions()
   {
     List<OptionI> lst = getBaseOptions();
-    lst.add(new BooleanOption("jvsuffix","Append jalview style /start-end suffix to ID", false, false, jvsuffix, null));
-    lst.add(new BooleanOption("writeasfile","Append jalview style /start-end suffix to ID", false, false, writeAsFile, null));
-    
-    lst.add(new Option("format",
-            "Alignment upload format", true, "FASTA",
-            format, Arrays.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS), null));
-    lst.add(createMolTypeOption("type", "Sequence type", false, type,
+    lst.add(new BooleanOption("jvsuffix",
+            "Append jalview style /start-end suffix to ID", false, false,
+            jvsuffix, null));
+    lst.add(new BooleanOption("writeasfile",
+            "Append jalview style /start-end suffix to ID", false, false,
+            writeAsFile, null));
+
+    lst.add(new Option("format", "Alignment upload format", true, "FASTA",
+            format, Arrays
+                    .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
             null));
-    
+    lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
+
     return lst;
   }
 
-}
\ No newline at end of file
+}