import java.io.ByteArrayInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.util.List;\r
\r
import compbio.data.msa.SequenceAnnotation;\r
// }\r
\r
/* Output the alignment to standard out */\r
- IOHelper.writeOut(System.out, result);\r
+ Writer writer = new PrintWriter(System.out, true);\r
+ IOHelper.writeOut(writer, result);\r
+ writer.close();\r
// Score.write(result, System.out);\r
\r
/* Alternatively, you can record retrieved alignment into the file */\r