import java.io.BufferedReader;
import java.io.FileReader;

/**
 * COMP 322 S13
 *
 * This file is a template for your UsefulParScoring implementation. You may add
 * anything to it that you like, but please do not modify the main() function as
 * declared, though you may add your own code below the existing template.
 */
public class UsefulParScoring
{

    public static String initString (String fname) throws java.io.IOException {
        BufferedReader r = new BufferedReader(new FileReader(fname));
        StringBuilder text = new StringBuilder();
        String line;
        while( (line = r.readLine()) != null){
            text.append(line);
        }
        return text.toString();
    }

    /**
     *  This program takes as input two sequences, passed as the only two
     *  command line arguments, seq1 and seq2
     */
    public static void main(String[] args) throws java.io.IOException {
        if(args.length != 2) {
            System.out.println("usage: java UsefulParScoring file1 file2");
            return;
        }
        String filename1 = args[0];
        String filename2 = args[1];
        String seq1 = initString(filename1);
        String seq2 = initString(filename2);
        System.out.println("Processing sequences \""+
                seq1.substring(0, seq1.length() < 5 ? seq1.length() : 5)+
                (seq1.length() > 5 ? "..." : "")+
                "\" and \""+
                seq2.substring(0, seq2.length() < 5 ? seq2.length() : 5)+
                (seq2.length() > 5 ? "...\"" : "\""));
        // ...
    }

}