执行基本数量生物学的类的基本用法

Question

我正在写一个程序，执行基本的定量生物学操作。我有两个独立的文件，一个是.h，另一个是.cpp。.h包含带有函数原型的类，.cpp包含函数定义。我觉得我写的代码是正确的，但它不能编译。下面是我的代码：

//.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;
};               

编辑:我已经设法修复了尽可能多的错误。唯一剩下的就是一些编译器错误，希望有人能给我一些提示。错误在底部的注释中

Answer 1

在QubiEngine::QubiEngine(ifstream& dnaFile)中不要这样做

dnaFile("dna.txt");

它已经被初始化了(在main中)，而且它也不是正确的sintax。

在dna2rna中，*it是string，所以在*it == 't'中，您可以尝试将string与char进行比较。它不会工作，但您已经知道如何解决这个问题:在其他地方使用string::iterator，使用它遍历字符串中的所有char，并将char与char进行比较。

在compute_revcom中，您永远不会初始化letter，但可以在switch中使用它，请使用st。您也不能在while中推进string::iterator。您还需要使用't'而不是"t"，一个是char，另一个是字符串。

在nucl_frequency中，再次将a string与char进行比较，使用string::iterator。

在count_CpG中，您忘记了dna的类型，它是一个字符串向量，请使用正确的迭代器类型。此外，*it == CpG将比较两个字符串是否相等，这并不是您想要的。

如果*it是"cgcg“，你希望计数是2，但实际上是0。看看是否可以使用string::iterator完成此任务。

也是

vector<string>& temp = dna;            //A dummy blank vector to store the reverse of the dna vector.

因为那个"&“，它不会像你想的那样，temp将是dna，而不是副本。

可能还有更多。

尽量不要一次写完所有的东西，然后在最后构建。相反，编写一个函数，或函数的一部分，并构建(和测试)。

从一个编译和工作的小程序转移到一个稍微大一点的编译和工作的程序。重复操作，直到完成！

Answer 2

尝试将#include <fstream>添加到您的头文件，似乎您缺少它(对于ifstream)

实际上，尝试将main移动到单独的文件中，比如main.cpp，其中只有#include "jmcready_QubiEngine.h"，没有.cpp