import java.io.File;
import java.io.IOException;
import java.util.Scanner;
import java.util.ArrayList;

/**
* DNA class.
* @author cs416
* @version 1
*/
public class DNA {

    /**
    * Read DNA Profiles from the specified fileName and returns them as
    * an ArrayList.
    * @param fileName The file name containing DNA Profiles
    * @return DNARecord[]
    */
    public static ArrayList<DNARecord> readData(String fileName) throws IOException {
	throw new UnsupportedOperationException("TO BE IMPLEMENTED");
    }

    /**
    * Reads the DNA Sequences from the files and counts the RelationType
    * sequences.
    * @param fileName The file to count sequences from
    * @return Profile
    */
    public static Profile readSequence(String fileName) throws IOException {
	throw new UnsupportedOperationException("TO BE IMPLEMENTED");
    }

    /**
    * Counts the maximum consecutive matches from the match in the given sequence.
    * @param sequence The DNA sequence string to search through
    * @param match The string to match
    * @return int
    */
    public static int countMaximumConsecutiveMatches(String sequence, String match) {
	throw new UnsupportedOperationException("TO BE IMPLEMENTED");
    }

    /**
    * Main function.
    * @param args The command line arguments.
    */
    public static void main(String[] args)  {
        ArrayList<DNARecord> data;

        try {
            data = readData(args[0]);
            Profile profile = readSequence(args[1]);

            for (DNARecord r : data) {
                if (r.getProfile().equals(profile)) {
                    System.out.println("Matched " + r.getName() + ": "
                                       + r.getProfile());
                    return;
                }
            }


            System.out.println("No match for " + profile);

        } catch (IOException e) {
            System.err.println(e);
        }
    }
}