import java.io.Closeable;\r
import java.io.File;\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.List;\r
if (inputFile != null) {\r
System.out.println("Calculating conservation...");\r
result = analize(inputFile, msaws, preset, customOptions);\r
- OutputStream outStream = null;\r
+ Writer outStream = null;\r
if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
+ outStream = 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
+ outStream = new PrintWriter(System.out, true);\r
}\r
writeOut(outStream, result);\r
// stream is closed in the method no need to close it here\r
* @param result\r
* the AACon scores to output\r
*/\r
- static void writeOut(OutputStream outStream, ScoreManager result) {\r
+ static void writeOut(Writer writer, ScoreManager result) {\r
try {\r
- result.writeOut(outStream);\r
+ result.writeOut(writer);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\r
}\r