gistfile1.java

import java.util.Arrays;

public class tupples {

	public static void main(String args[]) {

		String gen = "agcaaagagagactgtttagtccacataaagcgtcgttggacgcaaattacgc" + "ggggggtgcaaacgaacgagaggaggtttgagatagctgtatattc";

		String[][] tuples = new String[gen.length()][2];
		int globalCounter = 0;

		for (int i = 0; i < gen.length() - 2; i++) { // loop through the whole string

			String tuple = gen.substring(i, i + 3);

			int tupleIndex = findTuple(tuple, tuples); // tupleIndex will be -1 if not found, and real value if found

			if (tupleIndex != -1) { // if tuple WAS found, then increase counter on that index

				Integer myCount = Integer.valueOf(tuples[tupleIndex][1]);
				myCount++;
				tuples[tupleIndex][1] = String.valueOf(myCount);
			}

			else { // if it wasn't found

				tuples[globalCounter][1] = String.valueOf(1); // mark 1 as its first occurence of the tuple
				tuples[globalCounter][0] = tuple; // add the tuple
				globalCounter++; // move tuple conuter by one
			}
		}

		// Keeps track of the smallest string's index
		int shortestStringIndex;

		// /I reduced the upper bound from Array.length to (Array.length - 1)
		for (int j = 0; j < globalCounter - 1; j++) {
			shortestStringIndex = j;

			for (int i = j + 1; i < globalCounter; i++) {
				// We keep track of the index to the smallest string
				if (tuples[i][0].trim().compareTo(tuples[shortestStringIndex][0].trim()) < 0) {
					shortestStringIndex = i;
				}
			}
			// We only swap with the smallest string
			if (shortestStringIndex != j) {
				String temp = tuples[j][0];
				tuples[j][0] = tuples[shortestStringIndex][0];
				tuples[shortestStringIndex][0] = temp;
			}
		}

		for (int i = 0; i < globalCounter; i++) {
			if (tuples[i][0] == null)
				break;
			if (tuples[i][0].isEmpty())
				break;

			System.out.println("tuple:" + tuples[i][0] + ",counts:" + String.valueOf(tuples[i][1]));
		}

	}

	private static int findTuple(String tuple, String[][] tuppleArray) {

		int found = -1;

		for (int i = 0; i < tuppleArray.length; i++) {

			if (tuppleArray[i][0] == null)
				break;
			if (tuppleArray[i][0].isEmpty())
				break;

			if (tuppleArray[i][0].equals(tuple)) {

				found = i;
				break;
			}
		}
		return found;
	}

}