Basic use of classes to perform basic quantitative biology
<p>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:</p>

<pre><code>//.h file

#ifndef __JMCREADY_QUBIENGINE_H_
#define __JMCREADY_QUBIENGINE_H_
#include &lt;vector&gt;
#include &lt;string&gt;
#include &lt;fstream&gt;
using namespace std;

class QubiEngine{
private:
   vector&lt;string&gt; dna;
public:
   QubiEngine();                    //Default constructor
   QubiEngine(ifstream&amp; 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 &lt;iostream&gt;
  #include &lt;string&gt;
  #include &lt;vector&gt;
  #include &lt;fstream&gt;
  #include &lt;algorithm&gt;
  #include &lt;iterator&gt;
  using namespace std;

  QubiEngine::QubiEngine(ifstream&amp; 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&lt;string&gt;::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 &lt;&lt; *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&lt;string&gt; 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&lt;string&gt;::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 &lt;&lt; "File contains elements that aren't valid, please fix."&lt;&lt; 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&lt;string&gt;::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&lt;string&gt;::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&lt;string&gt;::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 &lt;&lt; "The total number of CG islands is : " &lt;&lt; cpg &lt;&lt; endl;

    if ( qbengine.isPalindromic() )
        cout &lt;&lt; "Palindromic" &lt;&lt; endl;
    else
        cout &lt;&lt; "Not Palindromic" &lt;&lt; endl;
    return 0;
};               
</code></pre>

<p>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</p>
