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How to print letters(DNA) in a format of (0,10,6)

I am struggling with this code here. I want print out dna in java that shows format of (0, 10, 6) which need to pass a until test
instead of looking like this
ACAAGATGCC ATTGTCCCCC GGCCTCCTGC TGCTGCTGCT CTCCGGGGCC ACGGCCACCG
CTGCCCTGCC CCTGGAGGGT GGCCCCACCG GCCGAGACAG CGAGCATATG CAGGAAGCGG
CAGGAATAAG GAAAAGCAGC CTCCTGACTT TCCTCGCTTG GTGGTTTGAG TGGACCTCCC
AGGCCAGTGC CGGGCCCCTC ATAGGAGAGG AAGCTCGGGA GGTGGCCAGG CGGCAGGAAG
GCGCACCCCC CCAGCAATCC GCGCGCCGGG ACAGAATGCC CTGCAGGAAC TTCTTCTGGA
AGACCTTCTC CTCCTGCAAA TAAAACCTCA CCCATGAATG CTCACGCAAG TTTAATTACA
It looks like this
ATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGG....
here is my code
public String formatInGroups(int index, int basesPerGroup, int groupsPerLine) {
StringBuilder formattedSequence = new StringBuilder();
String sequence = sequences.get(index);
int num = 0;
while(num < sequence.length()) {
for(int i = 0; i < groupsPerLine; i++) {
for( int j = 0; j < basesPerGroup; j++) {
if(num < sequence.length()) {
formattedSequence.append(sequence.charAt(num));
num++;
}
}
}
}
return sequence;
}
}

You should append a white space to the sequence after a dna sequence is appended (at the end of the inner for loop). Also, when a line is full, you should append a new line (\n) character to the sequence(at the end of the outer for loop).
public String formatInGroups(int index, int basesPerGroup, int groupsPerLine) {
StringBuilder formattedSequence = new StringBuilder();
String sequence = sequences.get(index);
int num = 0;
while(num < sequence.length()) {
for(int i = 0; i < groupsPerLine; i++) {
for( int j = 0; j < basesPerGroup; j++) {
if(num < sequence.length()) {
formattedSequence.append(sequence.charAt(num));
formattedSequence.append(" ");
num++;
}
}
formattedSequence.append("\n");
}
}
return formattedSequence.toString();
}

Looking at your code, I think you just missed some little things here and there, add a new line break after a certain character count and a space after some groups, and also you were returning the wrong variable.
Here check this code I edited based on yours, I just added some simple stuff and you got the remaining right.
public String formatInGroups(int index, int basesPerGroup,
int groupsPerLine) {
// I suppose you have a 'sequences' list somewhere
sequences.add(dna());
StringBuilder formattedSequence = new StringBuilder();
String sequence = sequences.get(index);
int num = 0;
while(num < sequence.length()) {
for( int j = 0; j < basesPerGroup; j++) {
if(num < sequence.length()) {
if (num % (basesPerGroup * groupsPerLine) == 0){
formattedSequence.append("\n");
}
formattedSequence.append(sequence.charAt(num));
num++;
}
}
formattedSequence.append(" ");
}
return formattedSequence.toString().trim();
}
Little things to consider on your next problem:
1 - You were returning your original sequence instead of the formattedSequence.toString();
2 - Try to avoid using global variables, you can declare them inside your for loop;
3 - Try using better variable names, instead of num you could name your variable after something that it is doing, like charPositionCounter, it will improve your code readability.

Java stdin not prompting program to run

I am working on a Merge-sort algorithm, and I am currently trying to test if it works.
It should be controlled through stdin with the input format:
array length
element values (separated by " ")
However, when typing in:
3
17 10 3
Nothing happens, and hitting enter, just get me to the next line in the console.
I get no error message (unless I type in wrong input), and so I have a hard time figuring out why the script is not prompted to run with the input given.
(Code is copied below)
package merge;
import java.io.*;
import java.util.*;
public class MergeSort
{
// This method takes two sorted arrays of integers as input parameters
// and it should return one sorted array of integers.
public int[] merge(int[] A1, int[] A2) {
int[] C = new int[A1.length + A2.length];
int i = 0, j = 0, k = 0;
while (i < A1.length && j < A2.length)
C[k++] = A1[i] < A2[j] ? A1[i++] : A2[j++];
while (i < A1.length)
C[k++] = A1[i++];
while (j < A2.length)
C[k++] = A2[j++];
return C;
}
// This method takes an array of integers as input parameter,
// and it should then return the integers sorted
// in ascending order using the MergeSort algorithm.
private int[] sort(int[] numbers) {
//pointers
int i = 0, j = 0, k = 0;
// reference values
int half = numbers.length / 2;
int[] sorted = new int[numbers.length];
if (numbers.length <= 1){
return numbers;
}
//left part of 'numbers'
int[] left = new int[half];
int[] right;
//right part of 'numbers'
if (numbers.length % 2 != 0){
right = new int[half+1];
j = half + 1;
}
else{
right = new int[half];
j = half;
}
//fills out left half of array with values from input array
while (i < half)
left[i] = numbers[i];
i++;
//fills out right half of array with values from input array
while (j < numbers.length)
right[j] = numbers[k];
j++; k++;
left = sort(left);
right = sort(right);
merge(left,right);
return sorted;
}
// ##################################################
// # Stdin part. #
// ##################################################
public static void main(String[] args) throws IOException {
new MergeSort().run();
}
private void run() throws IOException {
BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
int[] numbers = readIntArray(in);
numbers = sort(numbers);
for (int i = 0; i < numbers.length; i++) {
System.out.print(numbers[i] + " ");
}
}
private int[] readIntArray(BufferedReader in) throws IOException {
int length = Integer.parseInt(in.readLine());
int[] array = new int[length];
StringTokenizer st = new StringTokenizer(in.readLine());
for (int i = 0; i < length; i++) {
array[i] = Integer.parseInt(st.nextToken());
}
return array;
}
}

You call readLine() two times, resulting in an attempt to read two lines on the standard input.

Java array reading loop never ends?

Hi I am new to programming and today i was writing a code for one Java array task and in the beginning i tried just to test what i have done and in the first for loop (the array reading ) the program does not stop to read a numbers even i already enter a number (n) for its length. Please help ?
import java.util.Scanner;
public class ReadTwoElementsForArrayAndSum {
public static void main(String[] args) {
// TODO Auto-generated method stub
Scanner in = new Scanner(System.in);
System.out.println("Please enter N element:");
int n = in.nextInt();
System.out.print("Please enter K element, for k < N: ");
int k = in.nextInt();
int[] arrayN = new int[n];
System.out.print("Please enter N numbers for the array: ");
for(int i = 0; i < arrayN.length; i++) {
arrayN[i] = in.nextInt();
}
boolean changed = false;
do {
int temp = 0;
for( int i = 0; i < (arrayN.length-1); i++) {
if(arrayN[i] > arrayN[i+1]){
temp = arrayN[i];
arrayN[i] = arrayN[i+1];
arrayN[i+1] = temp;
changed = true;
}
}
} while (changed);
for(int i = 0; i < arrayN.length; i ++) {
System.out.printf("%d", arrayN[i]);
System.out.print(k);
}
in.close();
}
}

Loop is infinite because once the if condition inside for loop is executed then changed is set to true and its value never changed to false causing infinite loop by do while loop.
Instead you can use Arrays.sort(arrayN) or if you want to use loop only then try below code
int count = 0;
do {
int temp = 0;
count++;
for (int i = 0; i < (arrayN.length - 1); i++) {
if (arrayN[i] > arrayN[i + 1]) {
temp = arrayN[i];
arrayN[i] = arrayN[i + 1];
arrayN[i + 1] = temp;
}
}
} while (count < (arrayN.length));
Demo

in this loop :
do {
int temp = 0;
for( int i = 0; i < (arrayN.length-1); i++) {
if(arrayN[i] > arrayN[i+1]){
temp = arrayN[i];
arrayN[i] = arrayN[i+1];
arrayN[i+1] = temp;
changed = true;
}
}
} while (changed);
you once change the changed to true and never make it false. If you want to end your loop you must some how(it depends on your approach) make changed false so it can end the loop.

what you should be doing in a do-while loop is
boolean flag=true;
do{
(some condition){
flag=false;
}
}while(flag)
this causes correct execution of do-while loop

Given an array with 2 integers that repeat themselves the same no. of times, how do i print the two integers

i'm new to this, Say if you typed 6 6 6 1 4 4 4 in the command line, my code gives the most frequent as only 6 and i need it to print out 6 and 4 and i feel that there should be another loop in my code
public class MostFrequent {
//this method creates an array that calculates the length of an integer typed and returns
//the maximum integer...
public static int freq(final int[] n) {
int maxKey = 0;
//initiates the count to zero
int maxCounts = 0;
//creates the array...
int[] counts = new int[n.length];
for (int i=0; i < n.length; i++) {
for (int j=0; j < n[i].length; j++)
counts[n[i][j]]++;
if (maxCounts < counts[n[i]]) {
maxCounts = counts[n[i]];
maxKey = n[i];
}
}
return maxKey;
}
//method mainly get the argument from the user
public static void main(String[] args) {
int len = args.length;
if (len == 0) {
//System.out.println("Usage: java MostFrequent n1 n2 n3 ...");
return;
}
int[] n = new int[len + 1];
for (int i=0; i<len; i++) {
n[i] = Integer.parseInt(args[i]);
}
System.out.println("Most frequent is "+freq(n));
}
}
Thanks...enter code here

Though this may not be a complete solution, it's a suggestion. If you want to return more than one value, your method should return an array, or better yet, an ArrayList (because you don't know how many frequent numbers there will be). In the method, you can add to the list every number that is the most frequest.
public static ArrayList<Integer> freq(final int[] n) {
ArrayList<Integer> list = new ArrayList<>();
...
if (something)
list.add(thatMostFrequentNumber)
return list;
}

The solutions looks like this:
// To use count sort the length of the array need to be at least as
// large as the maximum number in the list.
int[] counts = new int[MAX_NUM];
for (int i=0; i < n.length; i++)
counts[n[i]]++;
// If your need more than one value return a collection
ArrayList<Integer> mf = new ArrayList<Integer>();
int max = 0;
for (int i = 0; i < MAX_NUM; i++)
if (counts[i] > max)
max = counts[i];
for (int i = 0; i < MAX_NUM; i++)
if (counts[i] == max)
mf.add(i);
return mf;

Well you can just do this easily by using the HashTable class.
Part 1. Figure out the frequency of each number.
You can do this by either a HashTable or just a simple array if your numbers are whole numbrs and have a decent enough upper limit.
Part 2. Find duplicate frequencies.
You can just do a simple for loop to figure out which numbers are repeated more than once and then print them accordingly. This wont necessarily give them to you in order though so you can store the information in the first pass and then print it out accordingly. You can use a HashTable<Integer,ArrayList<Integer> for this. Use the key to store frequency and the ArrayList to store the numbers that fall within that frequency.
You can maintain a "max" here while inserting into our HashTable if you only want to print out only the things with most frequency.

Here is a different way to handle this. First you sort the list, then loop through and keep track of the largest numbers:
class Ideone
{
public static void main (String[] args) throws java.lang.Exception
{
int n[] = { 6, 4, 6, 4, 6, 4, 1 };
List<Integer> maxNums = new ArrayList<Integer>();
int max = Integer.MIN_VALUE;
Integer lastValue = null;
int currentCount = 0;
Arrays.sort(n);
for( int i : n ){
if( lastValue == null || i != lastValue ){
if( currentCount == max ){
maxNums.add(lastValue);
}
else if( currentCount > max ){
maxNums.clear();
maxNums.add(lastValue);
max = currentCount;
}
lastValue = i;
currentCount = 1;
}
else {
currentCount++;
}
System.out.println("i=" + i + ", currentCount=" + currentCount);
}
if( currentCount == max ){
maxNums.add(lastValue);
}
else if( currentCount >= max ){
maxNums.clear();
maxNums.add(lastValue);
}
System.out.println(maxNums);
}
}
You can try it at: http://ideone.com/UbmoZ5

Taking User Input for an Array

A link to the assignment:
http://i.imgur.com/fc86hG9.png
I'm having a bit of trouble discerning how to take a series of numbers and apply them to an array without a loop. Not only that, but I'm having a bit of trouble comparing them. What I have written so far is:
import java.util.Scanner;
public class Lottery {
public static void main(String[] args) {
int userInputs[] = new int[5];
int lotteryNumbers [] = new int[5];
int matchedNumbers =0;
char repeatLottery = '\0';
Scanner in = new Scanner (System.in);
do{
System.out.println("Enter your 5 single-digit lottery numbers.\n (Use the spacebar to separate digits): ");
for(int i = 0; i <5; i++ )
userInputs[i] = in.nextInt();
System.out.println("Your inputs: ");
printArray(userInputs);
System.out.println("\nLottery Numbers: ");
readIn(lotteryNumbers);
for(int i=0; i<5; i++) {
System.out.print(lotteryNumbers[i] + " ");
}
matchedNumbers = compareArr(userInputs, lotteryNumbers);
System.out.println("\n\nYou matched " + matchedNumbers + " numbers");
System.out.println("\nDo you wish to play again?(Enter Y or N): ");
repeatLottery = in.next().charAt(0);
}
while (repeatLottery == 'Y' || repeatLottery == 'y');
}
public static void printArray(int arr[]){
int n = arr.length;
for (int i = 0; i < n; i++) {
System.out.print(arr[i] + " ");
}
}
public static void readIn(int[] List) {
for(int j=0; j<List.length; j++) {
List[j] = (int) (Math.random()*10);
}
}
public static int compareArr (int[] list1, int[] list2) {
int same = 0;
for (int i = 0; i <= list1.length-1; i++) {
for(int j = 0; j <= list2.length-1; j++) {
if (list1[i] == list2[j]) {
same++;
}
}
}
return same;
}
}
As you'll notice, I commented out the input line because I'm not quite sure how to handle it. If I have them in an array, I should be able to compare them fairly easily I think. This is our first assignment handling arrays, and I think it seems a bit in-depth for only having one class-period on it; So, please forgive my ignorance. :P
Edit:
I added a new method at the end to compare the digits, but the problem is it compares them in-general and not from position to position. That seems to be the major issue now.

your question isn't 100% clear but i will try my best.
1- i don't see any problems with reading input from user
int[] userInput = new int[5]; // maybe here you had a mistake
int[] lotterryArray = new int[5]; // and here you were declaring your arrays in a wrong way
Scanner scanner = new Scanner(system.in);
for ( int i = 0 ; i < 5 ; i++)
{
userInput[i] = scanner.nextInt();
} // this will populate your array try to print it to make sure
Edit : important in the link you shared about the assignment the compare need to check the value and location so if there are two 5 one in input one in loterry array they need to be in the same location check the assignment again
// to compare
int result = 0 ; // this will be the number of matched digits
for ( int i = 0 ; i < 5 ; i++)
{
if ( userInput[i] == loterryArray[i] )
result++
}
// in this comparsion if the digits are equale in value and location result will be incremented