X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=306c40d9ee50705b8ba7b3d0cbdf6c726a870d46;hb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;hp=dc6e6e8e1be0e015cde914855a2b1d02a2b173b5;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index dc6e6e8..306c40d 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,25 +1,42 @@
+/*
+ * 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.
+ *  
+ * 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;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
 import jalview.ws.params.OptionI;
 import jalview.ws.params.simple.BooleanOption;
 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;
@@ -38,11 +55,10 @@ public class Alignment extends InputType
 {
   public Alignment()
   {
-    super(new Class[]
-    { AlignmentI.class });
+    super(new Class[] { AlignmentI.class });
   }
 
-  String format = "FASTA";
+  FileFormatI format = FileFormat.Fasta;
 
   molType type;
 
@@ -51,7 +67,7 @@ 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)
@@ -66,7 +82,7 @@ public class Alignment extends InputType
         PrintWriter pw = new PrintWriter(
                 new OutputStreamWriter(new BufferedOutputStream(
                         new FileOutputStream(fa)), "UTF-8"));
-        pw.append(new jalview.io.FormatAdapter().formatSequences(format,
+        pw.append(new FormatAdapter().formatSequences(format,
                 alignment, jvsuffix));
         pw.close();
         return new FileBody(fa, "text/plain");
@@ -78,7 +94,7 @@ public class Alignment extends InputType
     }
     else
     {
-      jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
+      FormatAdapter fa = new FormatAdapter();
       fa.setNewlineString("\r\n");
       return new StringBody(
               (fa.formatSequences(format, alignment, jvsuffix)));
@@ -102,12 +118,10 @@ public class Alignment extends InputType
     {
       prms.add("jvsuffix");
     }
-    ;
     if (writeAsFile)
     {
       prms.add("writeasfile");
     }
-    ;
     return prms;
   }
 
@@ -169,20 +183,25 @@ 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
+}