Merge branch 'develop' into features/filetypeEnum

[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 28f2628..c78bced 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -21,6 +21,9 @@
 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;
@@ -52,11 +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;
 
@@ -80,7 +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");
@@ -92,7 +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)));
@@ -116,12 +118,10 @@ public class Alignment extends InputType
     {
       prms.add("jvsuffix");
     }
-    ;
     if (writeAsFile)
     {
       prms.add("writeasfile");
     }
-    ;
     return prms;
   }
 
@@ -148,9 +148,9 @@ public class Alignment extends InputType
 
     if (tok.startsWith("format"))
     {
-      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      for (FileFormatI fmt : FileFormat.values())
       {
-        if (val.equalsIgnoreCase(fmt))
+        if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString()))
         {
           format = fmt;
           return true;
@@ -158,9 +158,12 @@ public class Alignment extends InputType
       }
       warnings.append("Invalid alignment format '" + val
               + "'. Must be one of (");
-      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      for (FileFormatI fmt : FileFormat.values())
       {
-        warnings.append(" " + fmt);
+        if (fmt.isWritable())
+        {
+          warnings.append(" " + fmt).toString();
+        }
       }
       warnings.append(")\n");
     }
@@ -195,8 +198,9 @@ public class Alignment extends InputType
             "Append jalview style /start-end suffix to ID", false, false,
             writeAsFile, null));
 
-    lst.add(new Option("format", "Alignment upload format", true, "FASTA",
-            format, Arrays
+    lst.add(new Option("format", "Alignment upload format", true,
+            FileFormat.Fasta.toString(),
+ format.toString(), Arrays
                     .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
             null));
     lst.add(createMolTypeOption("type", "Sequence type", false, type, null));