Creating a class with an open file stream - c++

Question

I've created a class which is supposed to read in DNA sequences: It contains an if stream private member:
Interface:
class Sequence_stream {
const char* FileName;
std::ifstream FileStream;
std::string FileFormat;
public:
Sequence_stream(const char* Filename, std::string Format);
NucleotideSequence get();
};
Implementation:
Sequence_stream::Sequence_stream(const char* Filename, std::string Format)
{
FileName = Filename;
FileStream.open(FileName);
FileFormat = Format;
std::cout << "Filestream is open: " << FileStream.is_open() << std::endl;
}
NucleotideSequence Sequence_stream::get()
{
if (FileStream.is_open())
{
char currentchar;
int basepos = 0;
std::string name;
std::vector<Nucleotide> sequence;
currentchar = FileStream.get();
if (currentchar == '>' && false == FileStream.eof()) { // Check that the start of the first line is the fasta head character.
currentchar = FileStream.get(); // Proceed to get the full name of the sequence. Get characters until the newline character.
while(currentchar != '\n' && false == FileStream.eof())
{
if (true == FileStream.eof()) {
std::cout << "The file ends before we have even finished reading in the name. Returning an empty NucleotideSequence" << std::endl;
return NucleotideSequence();
}
name.append(1, currentchar);
currentchar = FileStream.get();
} // done getting names, now let's get the sequence.
currentchar = FileStream.get();
while(currentchar != '>' && false == FileStream.eof())
{
if(currentchar != '\n'){
basepos++;
sequence.push_back(Nucleotide(currentchar, basepos));
}
currentchar = FileStream.get();
}
if(currentchar == '>')
{
FileStream.unget();
}
return NucleotideSequence(name, sequence);
} else {
std::cout << "The first line of the file was not a fasta format description line beginning with '>'. Are you sure the file is of FASTA format?" << std::endl;
return NucleotideSequence();
}
} else {
std::cout << "The filestream is not open..." << std::endl;
return NucleotideSequence();
}
}
However if I test it:
int main()
{
std::cout << "Let's try and read in a sequence!" << std::endl;
std::cout << "First we'll create a stream!" << std::endl;
Sequence_stream MyDNAStream("~/Dropbox/1_20dd5.fasta", "fasta");
std::cout << "Done!" << std::endl;
std::cout << "Now let's try and get a sequence!" << endl;
NucleotideSequence firstsequence = MyDNAStream.get();
return 0;
}
I see that the if stream is not open:
Let's try and read in a sequence!
First we'll create a stream!
Filestream is open: 0
Done!
The filestream is not open...
logout
[Process completed]
Although I thought the constructor function opens the if stream. What do I need to do to correct this so as the object is created and contains an open stream? (I know I'm yet to include a destructor which will close the stream upon destruction of the object).
Thanks,
Ben.

Answer 1

Your example shows that is_open returned false. I think you should check in your constructor that the file is indeed open, and throw if not.
In your case, I suspect this is due to passing "~/Dropbox/1_20dd5.fasta" as an input parameter. Did you test with a full pathname, with no ~? I have no knowledge of a C++ library that handles real path expansion (like python's os.path).