X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;fp=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=f3ca47160c8fda0f3823dab0b7647d047dfc0652;hb=99ab39d360a99ec101152070146b63773a1d6453;hp=ceb9501cea191653179d4f10a6d3bd351f3d1224;hpb=175c6382f4b2838916a98a2d87f1a4fff0103ea6;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index ceb9501..f3ca471 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -33,7 +33,8 @@ import java.io.Closeable;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.Writer;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
@@ -151,25 +152,25 @@ public class Jws2Client {
 		}
 		Alignment alignment = null;
 		if (inputFile != null) {
-			OutputStream outStream = null;
+			Writer writer = null;
 			if (outFile != null) {
-				outStream = IOHelper.getOutStream(outFile);
+				writer = IOHelper.getWriter(outFile);
 			} else {
 				// this stream is going to be closed later which is fine as
 				// std.out will not be
-				outStream = System.out;
+				writer = new PrintWriter(System.out, true);
 			}
 			if (service.getServiceType() == SequenceAnnotation.class) {
 				ScoreManager result = analize(inputFile,
 						((SequenceAnnotation<T>) msaws), preset, customOptions);
 
-				IOHelper.writeOut(outStream, result);
+				IOHelper.writeOut(writer, result);
 			} else {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
 						customOptions);
-				IOHelper.writeOut(outStream, alignment);
+				IOHelper.writeOut(writer, alignment);
 			}
-			outStream.close();
+			writer.close();
 		}
 
 		boolean listParameters = CmdHelper.listParameters(cmd);