X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=4426c5f7e79d041e6e0589bdce37b77d21fe5f30;hb=353511c16c62e2f5a0bef407646b3f47dbb9e68c;hp=a8258e2e63fd0527725735b14f79f896f6e1e2e5;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index a8258e2..4426c5f 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -79,11 +79,11 @@ public class Alignment extends InputType
       try
       {
         File fa = File.createTempFile("jvmime", ".fa");
-        PrintWriter pw = new PrintWriter(
-                new OutputStreamWriter(new BufferedOutputStream(
-                        new FileOutputStream(fa)), "UTF-8"));
-        pw.append(new FormatAdapter().formatSequences(format,
-                alignment, jvsuffix));
+        PrintWriter pw = new PrintWriter(new OutputStreamWriter(
+                new BufferedOutputStream(new FileOutputStream(fa)),
+                "UTF-8"));
+        pw.append(new FormatAdapter().formatSequences(format, alignment,
+                jvsuffix));
         pw.close();
         return new FileBody(fa, "text/plain");
       } catch (Exception ex)
@@ -108,8 +108,8 @@ public class Alignment extends InputType
   @Override
   public List<String> getURLEncodedParameter()
   {
-    ArrayList<String> prms = new ArrayList<String>();
-    prms.add("format='" + format + "'");
+    List<String> prms = new ArrayList<String>();
+    prms.add("format='" + format.getName() + "'");
     if (type != null)
     {
       prms.add("type='" + type.toString() + "'");
@@ -156,8 +156,8 @@ public class Alignment extends InputType
           return true;
         }
       }
-      warnings.append("Invalid alignment format '" + val
-              + "'. Must be one of (");
+      warnings.append(
+              "Invalid alignment format '" + val + "'. Must be one of (");
       for (String fmt : FileFormats.getInstance().getWritableFormats(true))
       {
         warnings.append(" ").append(fmt);
@@ -172,8 +172,8 @@ public class Alignment extends InputType
         return true;
       } catch (Exception x)
       {
-        warnings.append("Invalid molecule type '" + val
-                + "'. Must be one of (");
+        warnings.append(
+                "Invalid molecule type '" + val + "'. Must be one of (");
         for (molType v : molType.values())
         {
           warnings.append(" " + v);
@@ -195,12 +195,12 @@ public class Alignment extends InputType
             "Append jalview style /start-end suffix to ID", false, false,
             writeAsFile, null));
 
-    List<String> writable = FileFormats
-            .getInstance().getWritableFormats(true);
+    List<String> writable = FileFormats.getInstance()
+            .getWritableFormats(true);
     lst.add(new Option("format", "Alignment upload format", true,
-            FileFormat.Fasta.toString(), format.getName(), writable,
+            FileFormat.Fasta.toString(), format.getName(), writable, null));
+    lst.add(createMolTypeOption("type", "Sequence type", false, type,
             null));
-    lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
 
     return lst;
   }