JAL-2446 merged to spike branch

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

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index c78bced..b85073f 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -23,6 +23,7 @@ package jalview.ws.rest.params;
 import jalview.datamodel.AlignmentI;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.ws.params.OptionI;
 import jalview.ws.params.simple.BooleanOption;
@@ -38,7 +39,6 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -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() + "'");
@@ -148,9 +148,9 @@ public class Alignment extends InputType
 
     if (tok.startsWith("format"))
     {
-      for (FileFormatI fmt : FileFormat.values())
+      for (FileFormatI fmt : FileFormats.getInstance().getFormats())
       {
-        if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString()))
+        if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
         {
           format = fmt;
           return true;
@@ -158,12 +158,9 @@ public class Alignment extends InputType
       }
       warnings.append("Invalid alignment format '" + val
               + "'. Must be one of (");
-      for (FileFormatI fmt : FileFormat.values())
+      for (String fmt : FileFormats.getInstance().getWritableFormats(true))
       {
-        if (fmt.isWritable())
-        {
-          warnings.append(" " + fmt).toString();
-        }
+        warnings.append(" ").append(fmt);
       }
       warnings.append(")\n");
     }
@@ -198,10 +195,10 @@ public class Alignment extends InputType
             "Append jalview style /start-end suffix to ID", false, false,
             writeAsFile, null));
 
+    List<String> writable = FileFormats
+            .getInstance().getWritableFormats(true);
     lst.add(new Option("format", "Alignment upload format", true,
-            FileFormat.Fasta.toString(),
- format.toString(), Arrays
-                    .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+            FileFormat.Fasta.toString(), format.getName(), writable,
             null));
     lst.add(createMolTypeOption("type", "Sequence type", false, type, null));