@@ -0,0 +1,1397 @@
+import java.io.FileNotFoundException;%0Aimport java.io.PrintWriter;%0Aimport java.io.UnsupportedEncodingException;%0A%0A%0Apublic class Runner %7B%0A%09%0A%09public static String usageInfo = %22usage: java Runner %3Cfilepath%3E%22;%0A%0A%09public static void main(String%5B%5D args) %7B%0A%09%09if (args.length != 1) %7B%0A%09%09%09System.out.println(%22Number of arguments is not valid.%5Cn%22%0A%09%09%09%09%09+ usageInfo);%0A%09%09%09System.exit(1);%0A%09%09%7D%0A%09%09%0A%09%09PrintWriter writer_read = null;%0A%09%09PrintWriter writer_build = null;%0A%09%09try %7B%0A%09%09%09writer_read = new PrintWriter(%22read.out%22, %22UTF-8%22);%0A%09%09%09writer_build = new PrintWriter(%22build.out%22, %22UTF-8%22);%0A%09%09%7D catch (FileNotFoundException e) %7B%0A%09%09%09System.out.println(%22Result filepath is not valid.%22);%0A%09%09%09System.exit(1);%0A%09%09%7D catch (UnsupportedEncodingException e) %7B%0A%09%09%09System.out.println(%22Result file encoding is unsupported.%22);%0A%09%09%09System.exit(1);%0A%09%09%7D%0A%0A%09%09String filepath = args%5B0%5D;%0A%0A%09%09long readElapsedTime = System.currentTimeMillis();%0A%09%09// parse FASTA file%0A%09%09String fileData = Parser.parseFASTA(filepath);%0A%09%09readElapsedTime = System.currentTimeMillis() - readElapsedTime;%0A%09%09%0A%09%09writer_read.write(Long.toString(readElapsedTime));%0A%09%09writer_read.close();%0A%09%09%0A%09%09long buildElapsedTime = System.currentTimeMillis();%0A%09%09// build tree%0A%09%09WaveletTree wt = new WaveletTree(fileData.getBytes());%0A%09%09buildElapsedTime = System.currentTimeMillis() - buildElapsedTime;%0A%09%09%0A%09%09writer_build.write(Long.toString(buildElapsedTime));%0A%09%09writer_build.close();%0A%09%7D%0A%0A%7D%0A

Test runner added