DNA Analysis

//
//  a5q1.cpp
//  DNA Analysis
//
//  Created by Hayden Lueck on 2014-11-17.
//  Copyright (c) 2014 Hayden Lueck. All rights reserved.
//
// dna.txt: http://pastebin.com/jshtBzX5

#include <iostream>
#include <string>
#include <fstream>

void SetGene(char[]); //sets genes from input file
void PrintGene(char[]); //prints out a gene (used for testing, unused in program)
bool SameGene(char[], char[], int); //checks if 2 genes are the same
std::string SickleType(char[], char[]); //checks whether person is normal, anemic, or a carrier
std::string AreTheyRelated(char[], char[], char[], char[], int); //first 2 for first person's genes,
                                                     //second 2 for second person's genes, int for size
std::ifstream inFile; //declare for input
std::ofstream outFile; //declare for output

const int GENE_SIZE = 444; //constant integer for size of genes

int main() {
    /***** bind input and output files *****/
    inFile.open("dna.txt");
    outFile.open("DNAanalysis.txt");

    /****** check files exist ******/
    if(!inFile){
        std::cout << "Cannot find input file dna.txt Exiting..." << std::endl;
        return 1;
    }
    if(!outFile){
        std::cout << "Cannot find output file DNAanalysis.txt Exiting..." << std::endl;
        return 2;
    }

    /***** declare gene arrays *****/
    char gene1A[GENE_SIZE];
    char gene2A[GENE_SIZE];
    char gene1B[GENE_SIZE];
    char gene2B[GENE_SIZE];
    char gene1C[GENE_SIZE];
    char gene2C[GENE_SIZE];
    char gene1D[GENE_SIZE];
    char gene2D[GENE_SIZE];

    /***** set genes *****/
    SetGene(gene1A);
    SetGene(gene2A);
    SetGene(gene1B);
    SetGene(gene2B);
    SetGene(gene1C);
    SetGene(gene2C);
    SetGene(gene1D);
    SetGene(gene2D);

    /***** check if genes are normal/sickle ******/
    outFile << "Person A is " << SickleType(gene1A, gene2A) << std::endl;
    outFile << "Person B is " << SickleType(gene1B, gene2B) << std::endl;
    outFile << "Person C is " << SickleType(gene1C, gene2C) << std::endl;
    outFile << "Person D is " << SickleType(gene1D, gene2D) << std::endl;

    outFile << std::endl;

    /***** related people *****/
    outFile << "Person A " << AreTheyRelated(gene1A, gene2A, gene1B, gene2B, GENE_SIZE)
              << "person B" << std::endl;
    outFile << "Person A " << AreTheyRelated(gene1A, gene2A, gene1C, gene2C, GENE_SIZE)
              << "person C" << std::endl;
    outFile << "Person A " << AreTheyRelated(gene1A, gene2A, gene1D, gene2D, GENE_SIZE)
              << "person D" << std::endl;
    outFile << "Person B " << AreTheyRelated(gene1B, gene2B, gene1C, gene2C, GENE_SIZE)
              << "person C" << std::endl;
    outFile << "Person B " << AreTheyRelated(gene1B, gene2B, gene1D, gene2D, GENE_SIZE)
              << "person D" << std::endl;
    outFile << "Person C " << AreTheyRelated(gene1C, gene2C, gene1D, gene2D, GENE_SIZE)
              << "person D" << std::endl;

    /***** close input/output files *****/
    inFile.close();
    outFile.close();

    return 0;
}

void PrintGene(char gene[])
{
    for(int i = 0; i < GENE_SIZE; i++) //go through 444 times
    {
        outFile << gene[i]; //print out each letter in the gene
    }
    outFile << std::endl;
}

void SetGene(char gene[])
{
    for (int i = 0; i < GENE_SIZE; i++) //go through 444 times
    {
        inFile.get(gene[i]); //get the next character in the file, set it to the char in the array
    }
}

bool SameGene(char gene1[], char gene2[], int size)
{
    bool sameGene = false; //prime sameGene
    for(int i = 0; i < size; i++) //go through 444 times
    {
        if(gene1[i] == gene2[i]) //if current letter in gene1 is same as gene2
            sameGene = true; //set to true, go through again with next letter to make sure it's still true
        else //if one letter is off
        {
            sameGene = false; //set to false
            break; //break out of loop
        }
    }
    return sameGene; //return true/false value of sameGene
}

std::string SickleType(char gene1[], char gene2[])
{
    bool geneOneSickle = false, geneTwoSickle = false; //set gene1 and gene2 to not sickle

    if(gene1[19] == 'T') //if 20th char is T
        geneOneSickle = true; //gene is sickle
    if(gene2[19] == 'T') //if 20th char is T
        geneTwoSickle = true; //gene is sickle

    if(geneOneSickle || geneTwoSickle) //if either is sickle
    {
        if(geneTwoSickle && geneTwoSickle) //check if both are sickle, if they are...
            return "a carrier"; //they're a carrier
        else //only one is sickle
            return "anemic"; //they're anemic
    }
    else //neither genes are sickle
        return "normal"; //the person is normal
}

std::string AreTheyRelated(char person1Gene1[], char person1Gene2[], char person2Gene1[], char person2Gene2[], int size)
{
    if(SameGene(person1Gene1, person2Gene1, size) ||
       SameGene(person1Gene1, person2Gene2, size) ||
       SameGene(person1Gene2, person2Gene1, size) ||
       SameGene(person1Gene2, person2Gene2, size)) //compare all genes, check if any are the same
    {
        return " is related to "; //if true, they're related
    }
    else //if false...
        return " is not related to "; //they're not related
}