X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FAAConClient.java;h=f7f26038eb03001fe9da7605d7fb9e4964b229df;hb=4c022b67a736b6f79dbe212d73016607cf298422;hp=4619c602dd08b91d1f216bf9c5cd95d6f03f859a;hpb=9d860c3793c6812f643caa01fc80a0036fa3fe2b;p=jabaws.git

diff --git a/webservices/compbio/ws/client/AAConClient.java b/webservices/compbio/ws/client/AAConClient.java
index 4619c60..f7f2603 100644
--- a/webservices/compbio/ws/client/AAConClient.java
+++ b/webservices/compbio/ws/client/AAConClient.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2010 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  Amino Acid Conservation Web Service client @version: 1.0     
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -30,7 +30,8 @@ import static compbio.ws.client.Constraints.pseparator;
 import java.io.Closeable;
 import java.io.File;
 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.List;
@@ -116,13 +117,13 @@ public class AAConClient {
 		if (inputFile != null) {
 			System.out.println("Calculating conservation...");
 			result = analize(inputFile, msaws, preset, customOptions);
-			OutputStream outStream = null;
+			Writer outStream = null;
 			if (outFile != null) {
-				outStream = IOHelper.getOutStream(outFile);
+				outStream = IOHelper.getWriter(outFile);
 			} else {
 				// this stream is going to be closed later which is fine as
 				// std.out will not be
-				outStream = System.out;
+				outStream = new PrintWriter(System.out, true);
 			}
 			writeOut(outStream, result);
 			// stream is closed in the method no need to close it here
@@ -152,17 +153,17 @@ public class AAConClient {
 	 * @param result
 	 *            the AACon scores to output
 	 */
-	static void writeOut(OutputStream outStream, ScoreManager result) {
+	static void writeOut(Writer writer, ScoreManager result) {
 		try {
-			result.writeOut(outStream);
+			result.writeOut(writer);
 		} catch (IOException e) {
 			System.err
 					.println("Problems writing output file! Stack trace is below: ");
 			e.printStackTrace();
 		} finally {
-			if (outStream != null) {
+			if (writer != null) {
 				try {
-					outStream.close();
+					writer.close();
 				} catch (IOException ignored) {
 					// e.printStackTrace();
 				}