gistfile1.java

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package skuska.zapocet;

/**
 * 
 * @author Mišel
 */
public class SkuskaZapocet {

	/**
	 * @param args
	 *            the command line arguments
	 */
	static String genom = "agaactttagagag";
	public static Integer globalCounter = 0;

	public static void main(String[] args) {

		
		sortAndPrintCodons(statistics(genom),globalCounter);

	}

	public static int findCodon(String codon, String[][] codonArray) {
		int found = -1;
		for (int i = 0; i < codonArray.length; i++) {
			if (codonArray[i][0] == null) {
				break;
			}
			if (codonArray[i][0].isEmpty()) {
				break;
			}
			if (codonArray[i][0].equals(codon)) {
				found = i;
				break;
			}
		}
		return found;
	}

	public static void sortAndPrintCodons(String[][] codons, int globalCounter) {
		int shortestStringIndex;

		for (int j = 0; j < globalCounter - 1; j++) {
			shortestStringIndex = j;

			for (int i = j + 1; i < globalCounter; i++) {
				if (codons[i][0].trim().compareTo(codons[shortestStringIndex][0].trim()) < 0) {
					shortestStringIndex = i;
				}
			}
			if (shortestStringIndex != j) {
				String temp = codons[j][0];
				codons[j][0] = codons[shortestStringIndex][0];
				codons[shortestStringIndex][0] = temp;
			}
		}
		System.out.println("Codons\t" + "Occurrence");
		for (int i = 0; i < globalCounter; i++) {
			if (codons[i][0] == null) {
				break;
			}
			if (codons[i][0].isEmpty()) {
				break;
			}
			System.out.println(codons[i][0] + "\t" + String.valueOf(codons[i][1]));
		}
	}

	public static String[][] statistics(String genom) {

		String[][] codons = new String[genom.length()][2];

		for (int i = 0; i < genom.length() - 2; i++) {
			String codon = genom.substring(i, i + 3);
			int indexOfCodon = findCodon(codon, codons);
			if (indexOfCodon != -1) {
				Integer count = Integer.valueOf(codons[indexOfCodon][1]);
				count++;
				codons[indexOfCodon][1] = String.valueOf(count);
			} else {
				codons[globalCounter][1] = String.valueOf(1);
				codons[globalCounter][0] = codon;
				globalCounter++;
			}
		}
		return codons;
	}
}