More work to disorder prediction client & services.

[jabaws.git] / webservices / compbio / ws / client / Jws2Client.java

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