Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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 18c1ad0..b85073f 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -21,6 +21,10 @@
 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;
 import jalview.ws.params.simple.Option;
@@ -35,7 +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;
@@ -55,7 +58,7 @@ public class Alignment extends InputType
     super(new Class[] { AlignmentI.class });
   }
 
-  String format = "FASTA";
+  FileFormatI format = FileFormat.Fasta;
 
   molType type;
 
@@ -79,7 +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");
@@ -91,7 +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)));
@@ -105,8 +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() + "'");
@@ -115,12 +118,10 @@ public class Alignment extends InputType
     {
       prms.add("jvsuffix");
     }
-    ;
     if (writeAsFile)
     {
       prms.add("writeasfile");
     }
-    ;
     return prms;
   }
 
@@ -147,9 +148,9 @@ public class Alignment extends InputType
 
     if (tok.startsWith("format"))
     {
-      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      for (FileFormatI fmt : FileFormats.getInstance().getFormats())
       {
-        if (val.equalsIgnoreCase(fmt))
+        if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
         {
           format = fmt;
           return true;
@@ -157,9 +158,9 @@ public class Alignment extends InputType
       }
       warnings.append("Invalid alignment format '" + val
               + "'. Must be one of (");
-      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      for (String fmt : FileFormats.getInstance().getWritableFormats(true))
       {
-        warnings.append(" " + fmt);
+        warnings.append(" ").append(fmt);
       }
       warnings.append(")\n");
     }
@@ -194,9 +195,10 @@ 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
-                    .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+    List<String> writable = FileFormats
+            .getInstance().getWritableFormats(true);
+    lst.add(new Option("format", "Alignment upload format", true,
+            FileFormat.Fasta.toString(), format.getName(), writable,
             null));
     lst.add(createMolTypeOption("type", "Sequence type", false, type, null));