When i runt he code and try to get the size of the 2 files something goes wrong with the msgIn file. I'm using the same method for both files and the bookIn will work but msgIn just returns 0 as if it never ran.

this is the method that gets the size of the file

int getSize (istream& file)
{
	int num = 0;
	char c =file.get();
	while (file)
	{
		++num;
		c = file.get();
	}
	return num;
}

This code runs the method to get the size

int bookSize = 0;
		int msgSize = 0;
		//msgSize = getSize(msgIn);
		//msgIn.clear();
		//msgIn.seekg(0, ios::beg);
		bookSize = getSize(bookIn);
		bookIn.clear();
		bookIn.seekg(0, ios::beg);
		cout << "\nthe size of the book is: " << bookSize << endl;
		cout << "\nthe size of the msg is: " << msgSize << endl;
#define _CRT_RAND_S
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <cstdlib>
#include <cmath>
using namespace std;

int getSize (istream& file)
{
	int num = 0;
	char c =file.get();
	while (file)
	{
		++num;
		c = file.get();
	}
	return num;
}

int random(int low, int high)
{
	unsigned num;
	rand_s(&num);
	double normalized = static_cast<double>(num) / UINT_MAX;
	return static_cast<int>(normalized * (high - low +1)) + low;
}

int main(int argc, char *argv[])
{
	if (argc != 4)
	{
		cout << "Usage: encode.exe bookFile.txt msgFile.txt outFile.txt" << endl;
	}
	else
	{
		ifstream bookIn(argv[1]);
		ifstream msgIn(argv[2]);
		ofstream out(argv[3]);
		vector<char> msgVector;
		while (msgIn)
		{
			msgVector.push_back(msgIn.get());
		}
		cout << "contents of vector: " << endl;
		for(int i=0; i < msgVector.size(); ++i) cout << msgVector[i];

		//count number of chars in the book file and set the char size
		int bookSize = 0;
		int msgSize = 0;
		//msgSize = getSize(msgIn);
		//msgIn.clear();
		//msgIn.seekg(0, ios::beg);
		bookSize = getSize(bookIn);
		bookIn.clear();
		bookIn.seekg(0, ios::beg);
		cout << "\nthe size of the book is: " << bookSize << endl;
		cout << "\nthe size of the msg is: " << msgSize << endl;
		int startingPoint = 0;
		char c = bookIn.get();

		for (int i=0; i < msgSize; ++i)
		{
			//select a random number from the generator
			startingPoint = random(0,bookSize);

			//go to that number in the book
			for (int ii=0; ii < startingPoint; ++ii)
			{
				c = bookIn.get();
			}
			cout << "\nRandom number is: " << startingPoint << endl;
			cout << "\nmsgVector is: " << msgVector[0] << endl;
			cout << "\nc is: " << c << endl;
	
			//find the next char that is = to the char of the msg
			for(int ii=startingPoint; ii < bookSize; ++ii)
			{
				c = bookIn.get();
				if (msgVector[0] == c)
				{
					//print number of char in bookFile to outFile, print a space before next char.
					out << ii << " ";
					break;
				}
			}//end for
		}//end for

	}//end stream

	cin.ignore();

	return 0;
}//end main

Line 42: while (msgIn)
You're at the end of the file when you call your size function.
So it returns immediately.

Make sure the file location pointer is reset back to the start of the file, and the eof() state has been cleared.

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