Try this code.

char[] firstArray = {'a', 'b', 'c'};
char[] secondArray = {'a', 'b', 'c'};

if (firstArray.length != secondArray.length) {
    System.out.println("False.they are not equal");
} else {
    boolean isEqual = true;
    for (int i = 0; i < firstArray.length; i++) {
        if (firstArray[i] != secondArray[i]) {
            System.out.println("False.they are not equal");
            isEqual = false;
            break;
        }
    }
    if (isEqual)
        System.out.println("true.they are equal");
}

From what I see you just try to see if they are equal, if this is true, just go with something like this:

boolean areEqual = Arrays.equals(arr1, arr2);

This is the standard way of doing it.

Please note that the arrays must be also sorted to be considered equal, from the JavaDoc:

Two arrays are considered equal if both arrays contain the same number of elements, and all corresponding pairs of elements in the two arrays are equal. In other words, two arrays are equal if they contain the same elements in the same order.

Sorry for missing that.

Here is how you will compare your two double arrays for equality:

public static boolean compArray (double[] a, double[] b, int n) {
    //if the arrays dont have the same length, then they are not equals
    if (a.length != b.length) {
        return false;
    }

    for (int i = 0; i < a.length; i++) {
            //if one element at array a is different than the other at array b, 
            //at the same index, then the arrays are not equals
            if (a[i] != b[i]) {
                return false;
            }
        }
    }
    
    //otherwise, the two arrays are equals
    return true;
}

I'm not 100% clear on how your algorithm is supposed to work, but it seems you may want to replace the line

pozita[i] = j;

with

pozita[i] = kodimi[j];

Right now, you are only writing the matching index to pozita, not a replacement character.

If my assumption is correct, you would also change

int[] pozita;

to

char[] pozita;

and initialize it to an array of length input.Length.