DNASingleMatcher.java

import java.util.*;
import java.util.regex.*;
import java.text.*;
import java.math.*;
import java.awt.geom.*;

public class DNASingleMatcher
{
	public int longestMatch(String seq1, String seq2)
	{
		int max = 0;
		int n1 = seq1.length(), n2 = seq2.length();
		
		if (n1 > n2)
		{
			String t = seq1;
			seq1 = seq2;
			seq2 = t;
			int n = n1;
			n1 = n2;
			n2 = n;
		}
		for (int s1 = 0; s1 < n1; s1++)
		{
			for (int len = 1; s1+len <= n1; len++)
			{
				for (int s2 = 0; s2+len <= n2; s2++)
				{
					if (seq1.substring(s1, s1+len).equals(seq2.substring(s2, s2+len)))
					{
						if (len > max)
							max = len;
					}
				}
			}
		}
		return max;
	}
	
	public static void main(String[] args)
	{
		long time;
		int answer;
		boolean errors = false;
		int desiredAnswer;
		
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("AAAAAAAAAAAAAAAAAAAAACCCGGGGGGGGGGGGG", "AAAACCCGGGGGGGGGGGGGGGGTTTTTTTTTGGGGGGGGGGGG");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 20;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("CAT", "AT");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 2;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC", "GAGAGGAGAAAGAGAGAGAAGAGAGGAGGAAAGAGAGAGAAAAGAGGGAA");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 0;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC", "GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 48;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("TC", "CATCAT");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 2;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		time = System.currentTimeMillis();
		answer = new DNASingleMatcher().longestMatch("CGCATTAGATTCAGAG", "CGCATGAGTAGATTC");
		System.out.println("Time: " + (System.currentTimeMillis()-time)/1000.0 + " seconds");
		desiredAnswer = 7;
		System.out.println("Your answer:");
		System.out.println("\t" + answer);
		System.out.println("Desired answer:");
		System.out.println("\t" + desiredAnswer);
		if (answer != desiredAnswer)
		{
			errors = true;
			System.out.println("DOESN'T MATCH!!!!");
		}
		else
			System.out.println("Match :-)");
		System.out.println();
		
		if (errors)
			System.out.println("Some of the test cases had errors :-(");
		else
			System.out.println("You're a stud (at least on the test data)! :-D ");
	}
}

//Powered by [KawigiEdit]