I'm writing a program that performs basic quantitative biology operations. I have two separate files, a .h and .cpp. The .h contains my class with function prototypes and my .cpp contains my function definitions. I feel like I wrote the code correctly but it won't compile. Here is my code:
//.h file
#ifndef __JMCREADY_QUBIENGINE_H_
#define __JMCREADY_QUBIENGINE_H_
#include <vector>
#include <string>
#include <fstream>
using namespace std;
class QubiEngine{
private:
vector<string> dna;
public:
QubiEngine(); //Default constructor
QubiEngine(ifstream& dnaFile); //Reads lines from given input file and pushes every read DNA sequence into the dna vector.
void dna2rna(); //Reads the DNA from the dna vector and computes it's RNA, then stores them in a file rna.txt
void compute_revcom(); //Reads the DNA sequences from the dna vector, computes the reverse, and stores in revcom.txt
void nucl_frequency(); //Counts the total occurances of each nucleotide in the DNA sequence.
int count_CpG(); //Counts the occurance of the string "CG"
bool isPalindromic(); //Checks if the string is palindromic.
};
#endif
//.cpp file
#include "jmcready_QubiEngine.h"
#include <iostream>
#include <string>
#include <vector>
#include <fstream>
#include <algorithm>
#include <iterator>
using namespace std;
QubiEngine::QubiEngine(ifstream& dnaFile){
string neucleotides; //Declares an empty string of nucelotides,
//opens the file to be stored into the vector,
while (getline(dnaFile, neucleotides)){ //and while it is reading the whole line from the
dna.push_back(neucleotides); //dnaFile, it is pushing the nucelotides into the vector.
}
}
void QubiEngine::dna2rna(){
ofstream outfile;
outfile.open("rna.txt"); //Creates a blank text file
const char* foo = "t";
for (vector<string>::iterator it = dna.begin(), endOfString = dna.end(); it != endOfString; it++){
if ( find(dna.begin(), dna.end(), foo) != dna.end() ){ //for loop with a nested if statement to run through each
dna.at(*foo) = "u"; //member of the vector and check if the iterator is equal
outfile << *it; //to "t", if it is, it is changed to "u."
} //Then saves the new iterator value to the outfile.
}
outfile.close(); //Closes the file so no further changes can be made.
}
void QubiEngine::compute_revcom(){
char letter = '\0';
ofstream outfile;
outfile.open ("revcom.txt"); //Another blank text file.
vector<string> temp; //A dummy blank vector to store the reverse of the dna vector.
reverse( dna.begin(), dna.end() ); //Stores the reverse of vector dna to temp vector.
for (vector<string>::iterator it = temp.begin(), endOfString = temp.end(); it != endOfString; it++){
while ( it != dna.end() ){ //For loop with nested while loop to change
switch(letter){ //each element in the temp vector to it's complement element.
case 'a' :
*it = "t";
break;
case 't' :
*it = "a";
break;
case 'c' :
*it = "g";
break;
case 'g' :
*it = "c";
break;
default :
cout << "File contains elements that aren't valid, please fix."<< endl;
break;
}
}
}
outfile.close();
}
void QubiEngine::nucl_frequency(){
int numOfA = 0; //Declares multiple counts and letters
int numOfT = 0; //to keep track of each nucleotide seperately
int numOfC = 0;
int numOfG = 0;
string a = "a";
string t = "t";
string c = "c";
string g = "g";
for (vector<string>::iterator it = dna.begin(), endOfString = dna.end(); it != endOfString; it++){
if (*it == a){ //For loop with multiple nested if statements
numOfA++; //to check each individual element
} //and count it towards the total.
if(*it == t){
numOfT++;
}
if (*it == c){
numOfC++;
}
if (*it == g){
numOfG++;
}
}
}
int QubiEngine::count_CpG(){
int count = 0;
string CpG = "cg";
for (vector<string>::iterator it = dna.begin(), endOfString = dna.end(); it != endOfString; it++){
if (*it == CpG){ //For loop with nested if statement to check
count++; //for the string "cg" and add them to an int
} //counter.
}
return count;
}
bool QubiEngine::isPalindromic(){
for (vector<string>::iterator it = dna.begin(), endOfString = dna.end(); it != endOfString; it++){
if(*it == string(dna.rbegin(), dna.rend())){ //For loop with nested if statement
return true;
} //to check if *it is equal to
else{
return false;
} //the reverse of it's original,
//if it is equal than it is palindromic.
}
}
int main (int args, char* argv[]) { //Main function given in the pdf, calls each
ifstream dnaFile; //public function to check if it works, and how
dnaFile.open("dna.txt");
QubiEngine qbengine(dnaFile); //effectively.
qbengine.dna2rna();
qbengine.compute_revcom();
qbengine.nucl_frequency();
int cpg = qbengine.count_CpG();
cout << "The total number of CG islands is : " << cpg << endl;
if ( qbengine.isPalindromic() )
cout << "Palindromic" << endl;
else
cout << "Not Palindromic" << endl;
return 0;
};
EDIT: I've managed to fix as many mistakes as I can. The only thing left are a few compiler errors, was hoping if someone can give me some tips. The errors are in the comments at the bottom