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
}\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