基本的な量的生物学操作を実行するプログラムを書いています。.h と .cpp という 2 つの別個のファイルがあります。.h には関数プロトタイプを含むクラスが含まれ、.cpp には関数定義が含まれています。コードを正しく書いたような気がしますが、コンパイルされません。これが私のコードです：
//.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;
};
編集: できる限り多くの間違いを修正することができました。残っているのはいくつかのコンパイルエラーだけです。誰かが私にいくつかのヒントを教えてくれることを望んでいました. エラーは下部のコメントにあります