For the countBase method I need to check if the base passed, in this case 'A' matches the letter in all the positions in the arrays...that way the other methods will output correctly. And then return a filled array with the totals. I only need help starting out the countBase method, everything else is finished..
Thanks! And I know it's wrong, I just don't know how to start it.. :S

Java Code:
import java.io.*;
import java.util.*;

public class Lab6
{

	public static void main(String[] args) throws FileNotFoundException
	{
		Scanner inFile = new Scanner(new File("seq.txt"));   //text data file with DNA bases
		
		char base = 'A';		  //base passed to countBase method
		int size = 8;             //size of the arrays
		char[] array1 = new char[size];   //first array with 8 indexes
		char[] array2 = new char[size];   //second array with 8 indexes
		char[] array3 = new char[size];   //third array with 8 indexes
		char[] array4 = new char[size];   //fourth array with 8 indexes
		
		int i = 0;
		while(inFile.hasNext())
		{	
			array1[i] = inFile.next().charAt(0);
			array2[i] = inFile.next().charAt(0);
			array3[i] = inFile.next().charAt(0);
			array4[i] = inFile.next().charAt(0);
			i++;
		}
	
		System.out.println(array1);
		System.out.println(array2);
		System.out.println(array3);
		System.out.println(array4);
		
		int[] result = countBase(array1, array2, array3, array4, base);
		int mostIndex = findMost(result);
		double average = computeAvg(result);
		
		System.out.println(result);
		System.out.println("The largest value in the counter array is " + result[mostIndex]);
		System.out.println("The average for the counter array is " + average);

	}
public static int[] countBase(char[] one, char[] two, char[] three, char[] four, char letter)   //count number of times a base appears
  	{
		int counter = 0;
		int index = 0;
		if(one[index] == letter)
		{
			counter++;
		}
	
		int[] base = new int[counter];
  		return base;
  	}
public static int findMost(int[] counter)    //find index position of largest element
	{
		int largeIndex = 0;

		for(int i = 0; i < counter.length; i++)
		{
			if(counter[i] > counter[largeIndex])
			{
				largeIndex = i;
			}
		}
			return largeIndex;
	}
	public static double computeAvg(int[] counter)    //compute average
	{
		int sum = 0;

		for(int i = 0; i < counter.length; i++)
		{
			sum = sum + counter[i];
		}
		double avg = (double)(sum) / counter.length;
		return avg;
	}
}