/*                 CSC 17 Lab 7 Addendum

Hofstra students F. Arman Imal and P. Artyan Imal grew up together and
were raised by the same parents, but they've always felt that they
weren't biological brothers.  "Arman" is rather quiet and introverted
while "Artyan" is outspoken and fun loving.  Each believes that the
other was adopted.  Their father, Dr. Aftan Imal, is a renowned
veterinarian and their mother, Barna N. Imal, is a well known expert
on animal husbandry.  Both are famous Hofstra alumni but they don't
like to discuss this issue with their children. Arman believes that he
is close to his mother.  However, Barna prefers to stay indoors while
Arman loves the open fields.  Artyan shares his father's energy but
Aftan hasn't been pulling his weight lately due to his age.
Determined to find the truth, the Imal brothers managed to obtain DNA
samples from their parents (don't ask how).  Along with samples of
their own DNA, you can help to finally unravel the Imal family's
complicated genetics...

Find dna sequences in the following files:

arman.dna
artyan.dna
mother.dna
father.dna

Your program must be able to distinguish between gaps and "edge gaps".
Use the following scoring scheme to find the maximum alignment
score between these individuals.  Then take the "lab7b quiz" and enter
your numbers.

int score(int i, int k) {
  if ((A.charAt(i)|32) == (B.charAt(k)|32)) return 3; else return -1;
}

int W(boolean edge) {
  if (edge) return 0; else return -2;
}

A parent's DNA should align mostly with the DNA of an offspring
(approximately score 6000, which is close to the maximum alignment
score possible with this scoring scheme).

Conclude based on your analysis whether:

   a. one of the brothers was adopted (determine which one)
   b. they're half brothers (determine same father or same mother)
   c. they don't share a common parent; Aftan is the father of one
      and Barna is the mother of the other.
   d. they're true brothers, with same biological parents
   e. all the Imals are genetically unrelated.

In the following you will find a function that reads a dna string from a
file and returns the string.   Put import java.io.*; at the top of your program
and make sure the files you're reading are in the right directory.
*/
import java.io.*;