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Queue
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‎Queue/Main.java‎

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import java.util.Random;
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public class Main {
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public static void main(String[] args) {
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Random rnd = new Random();
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Queue first_dna = new Queue(1000); // first queue for dna
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Queue comp_dna = new Queue(1000); // second queue for complement dna
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Queue amino = new Queue(1000); // third queue for triple dna code
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Queue aminoAcids_name = new Queue(1000); // fourth queue for the amino acids
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for (int i = 0; i < 21; i++) {
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char symbol; // for the base
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int number = rnd.nextInt(4); // generate base randomly for first dna
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if(number == 0) {
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symbol ='A';
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first_dna.enqueue(symbol);
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}
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else if(number == 1) {
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symbol ='T';
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first_dna.enqueue(symbol);
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}
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else if(number == 2) {
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symbol ='G';
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first_dna.enqueue(symbol);
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}
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else if(number == 3) {
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symbol ='C';
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first_dna.enqueue(symbol);
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}
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}
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Queue saved_dna1 = new Queue(1000);
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System.out.println("-First DNA-"); // print first dna
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for (int i = 0; i <21; i++) {
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System.out.print(first_dna.peek() + " ");
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first_dna.enqueue(first_dna.dequeue());
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}
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System.out.println();
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// construct a new queue which contains the complement of the DNA sequence --- complement dna
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for(int i =0; i < 21; i++) {
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char new_symbol; // complement base
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char symbol; // base
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symbol = (char) first_dna.peek();
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if(symbol == 'A') { // A-T
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new_symbol = 'T';
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comp_dna.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'T') { // T-A
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new_symbol = 'A';
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comp_dna.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'G') { // G-C
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new_symbol = 'C';
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comp_dna.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'C') { // C-G
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new_symbol = 'G';
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comp_dna.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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}
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System.out.println("\n-Complement of first DNA-"); // print the complement dna
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for (int i = 0; i < 21; i++) {
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System.out.print(comp_dna.peek() + " ");
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first_dna.enqueue(comp_dna.dequeue());
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}
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for(int i =0; i<21;i++) { // This is necessary because it will used in crossover part
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saved_dna1.enqueue(first_dna.dequeue());
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}
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Queue saved_dna2 = new Queue(1000); // this is necessary too. It will used in amino acids part
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for(int i =0; i < 21; i++) { // this is the most important part. Without it, amino acids printed wrong. There was a problem in here, when I fix it with adding this code.
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char new_symbol;
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char symbol;
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symbol = (char) first_dna.peek();
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if(symbol == 'A') { // A-T
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new_symbol = 'T';
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saved_dna2.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'T') { // T-A
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new_symbol = 'A';
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saved_dna2.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'G') { // G-C
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new_symbol = 'C';
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saved_dna2.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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else if(symbol == 'C') { // C-G
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new_symbol = 'G';
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saved_dna2.enqueue(new_symbol);
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first_dna.enqueue(first_dna.dequeue());
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}
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}
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System.out.println();
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// for the second part ( amino acids )
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for (int i = 0; i < 7; i++) {
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String amino_acid ="";
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for (int j = 0; j < 3; j++) {
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amino_acid += saved_dna2.dequeue(); // I stored the dna codes 3-3
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}
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amino.enqueue(amino_acid);
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}
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System.out.println("\n**Each 3 letters of DNA code for one amino acid**");
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for (int i = 0; i < 7; i++) {
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System.out.print(amino.peek() + " ");
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amino.enqueue(amino.dequeue());
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}
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System.out.println();
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for (int i = 0; i < 7; i++) { // A DNA sequence codes for a sequence of amino acids that make up a protein. Each 3 letters of DNA code for one amino acid
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String piece = (String) amino.dequeue();
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// starts with A
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if (piece.startsWith("AA")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Lys");
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else aminoAcids_name.enqueue("Asn");
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}
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else if ( piece.startsWith("AC")) aminoAcids_name.enqueue("Thr");
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else if (piece.startsWith("AG")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Arg");
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else aminoAcids_name.enqueue("Ser");
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}
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else if (piece.startsWith("AT")) {
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if (piece.endsWith("G")) aminoAcids_name.enqueue("Stop");
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else aminoAcids_name.enqueue("Ile");
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}
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// starts with C
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else if (piece.startsWith("CA")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Gln");
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else aminoAcids_name.enqueue("His");
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}
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else if ( piece.startsWith("CC")) aminoAcids_name.enqueue("Pro");
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else if ( piece.startsWith("CT")) aminoAcids_name.enqueue("Leu");
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else if ( piece.startsWith("CG")) aminoAcids_name.enqueue("Arg");
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// starts with T
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else if (piece.startsWith("TA")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Stop");
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else aminoAcids_name.enqueue("Tyr");
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}
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else if ( piece.startsWith("TC")) aminoAcids_name.enqueue("Ser");
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else if (piece.startsWith("TT")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Leu");
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else aminoAcids_name.enqueue("Phe");
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}
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else if (piece.startsWith("TG")) {
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if (piece.endsWith("A")) aminoAcids_name.enqueue("Stop");
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else if (piece.endsWith("C") || piece.endsWith("T")) aminoAcids_name.enqueue("Cys");
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else aminoAcids_name.enqueue("Trp");
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}
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// starts with G
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else if (piece.startsWith("GA")) {
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if (piece.endsWith("A") || piece.endsWith("G")) aminoAcids_name.enqueue("Glu");
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else aminoAcids_name.enqueue("Asp");
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}
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else if ( piece.startsWith("GC")) aminoAcids_name.enqueue("Ala");
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else if ( piece.startsWith("GT")) aminoAcids_name.enqueue("Val");
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else if ( piece.startsWith("GG")) aminoAcids_name.enqueue("Gly");
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}
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System.out.println("\n-Amino Acids-"); // printed amino acids
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for (int i = 0; i < 7; i++) {
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System.out.print(aminoAcids_name.peek() + " ");
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aminoAcids_name.enqueue(aminoAcids_name.dequeue());
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}
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System.out.println();
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Queue second_dna = new Queue(1000); // second dna that act in crossover
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for (int i = 0; i < 21; i++) {
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char symbol;
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int number = rnd.nextInt(4); // generate symbols randomly for second dna
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if(number == 0) {
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symbol ='A';
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second_dna.enqueue(symbol);
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}
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else if(number == 1) {
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symbol ='T';
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second_dna.enqueue(symbol);
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}
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else if(number == 2) {
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symbol ='G';
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second_dna.enqueue(symbol);
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}
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else if(number == 3) {
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symbol ='C';
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second_dna.enqueue(symbol);
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}
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}
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System.out.println("\n-Second DNA before crossover-"); // print second dna. It will used for crossover part
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for (int i = 0; i < 21; i++) {
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System.out.print(second_dna.peek() + " ");
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second_dna.enqueue(second_dna.dequeue());
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}
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System.out.println();
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// Crossover part
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int crossover = 1 + rnd.nextInt(20); // random selected crossover point
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System.out.println("\nRandomly generated crossover point:" + crossover);
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for (int i = 0; i < 21; i++) {
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if(i < crossover) {
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saved_dna1.enqueue(saved_dna1.dequeue());
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second_dna.enqueue(second_dna.dequeue());
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}
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else // crossover starting here. it happenes when i>= crossoverpoint
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{
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saved_dna1.enqueue(second_dna.dequeue());
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second_dna.enqueue(saved_dna1.dequeue());
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}
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}
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//print first and second dna after crossover
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System.out.println("\n\t**After Crossover**");
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System.out.println("-First DNA-");
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for (int i = 0; i < 21 ; i++) {
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System.out.print(saved_dna1.peek() + " ");
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saved_dna1.enqueue(saved_dna1.dequeue());
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}
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System.out.println(); // print second one
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System.out.println("-Second DNA-");
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for (int i = 0; i < 21; i++) {
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System.out.print(second_dna.peek() + " ");
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second_dna.enqueue(second_dna.dequeue());
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}
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}
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}

‎Queue/Queue.java‎

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public class Queue {
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private int rear,front;
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private Object[] elements;
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public Queue(int capacity) {
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elements = new Object[capacity];
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rear = -1;
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front = 0;
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}
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public boolean isEmpty() {
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return rear < front; // true döner
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}
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public boolean isFull() {
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return (rear + 1 == elements.length); // trueeeeeeeeeeee
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}
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public void enqueue(Object data) {
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if(isFull()) {
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System.out.println("Queue is full!");
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}
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else {
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rear++;
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elements[rear] = data;
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}
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}
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public Object dequeue() {
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if(isEmpty()) {
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System.out.println("Queue is empty!");
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return null;
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}
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else {
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Object retData = elements[front];
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elements[front] = null;
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front++;
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return retData;
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}
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}
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public Object peek() {
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if(isEmpty()) {
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System.out.println("Queue is empty!");
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return null;
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}
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else {
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Object retData = elements[front];
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return retData;
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}
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}
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public int size() {
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return (rear - front + 1);
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}
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}

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