X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=0027057390c4fde89434f92b8afbb2340eefb4f9;hb=ccd341fe829d12e0ec54be126ad561a7ce1a2987;hp=922f933a0146f22707860339c77b8faaae7562a3;hpb=f5d48464f668eb2ffd8f6cdcd0d04ff5658c54fc;p=jalview.git

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 922f933..0027057 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -7,11 +7,14 @@ import jalview.ws.rest.RestJob;
 import jalview.ws.rest.InputType.molType;
 
 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 org.apache.http.entity.mime.content.ContentBody;
@@ -53,9 +56,13 @@ public class Alignment extends InputType {
       throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
     }
     } else {
-    StringBody sb = new StringBody(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix)); // , "text/plain", Charset.forName("UTF-8"));
+      jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
+      fa.setNewlineString("\r\n");
+      return new StringBody((fa.formatSequences(format, alignment, jvsuffix)));
+      //,
+      //"text/plain",Charset.forName("UTF-8"));
+      // , "text/plain", Charset.forName("UTF-8"));
     // sb.getContentTypeParameters().put("filename", "alignment.fa");
-    return sb; 
     }
   }
 }
\ No newline at end of file