I've got a function that should read from file line by line, the reading stops when a line does not begin with '>' or ' '. It should store the lines in vector and return it.
This is code:
#include
#include
#include
#include
#include
#include
using namespace std;
string getseq(char * db_file) // gets sequences from file
{
string seqdb;
vector seqs;
ifstream ifs(db_file);
string line;
//vector seqs[size/3];
while(ifs.good())
{
getline(ifs, seqdb);
if (seqdb[0] != '>' & seqdb[0]!=' ')
{
seqs.push_back(seqdb);
}
}
ifs.close();
//return seqs;
//return seqs;
}
int main(int argc, char * argv[1])
{
cout << "Sequences: \n" << getseq(argv[1]) << endl;
return 0;
}
Compiler (g++) returns:
fasta_parser.cpp: In function ‘std::string getseq(char*)’:
fasta_parser.cpp:32: error: conversion from ‘std::vector, std::allocator >, std::allocator, std::allocator > > >’ to non-scalar type ‘std::string’ requested`
Anyone has any idea?
Edit:
As Skurmendel ask, I am adding whole code because of memory security violation after
executing compiled code:
#include
#include
#include
#include
#include
#include
using namespace std;
vector getseq(char * db_file) // pobiera sekwencje z pliku
{
string seqdb;
vector seqs;
ifstream ifs(db_file);
string line;
//vector seqs[size/3];
while(ifs.good())
{
getline(ifs, seqdb);
if (seqdb[0] != '>' & seqdb[0]!=' ')
{
seqs.push_back(seqdb);
}
}
ifs.close();
return seqs;
}
int main(int argc, char * argv[1])
{
vector seqs; // Holds our strings.
getseq(argv[1]); // We don't return anything.
// This is just a matter of taste, we create an alias for the vector iterator type.
typedef vector::iterator string_iter;
// Print prelude.
cout << "Sekwencje: \n";
// Loop till we hit the end of the vector.
for (string_iter i = seqs.begin(); i != seqs.end(); i++)
{
cout << *i << " "; // Do processing, add endlines, commas here etc.
}
cout << endl;
}
Answer
If I understood you, your getseq() should return a vector of strings. Therefore you should change
string getseq(char * db_file)
to
vector getseq(char * db_file)
And if you want to print it on main() you should do it in a loop.
int main() {
vector str_vec = getseq(argv[1]);
for(vector::iterator it = str_vec.begin(); it != str_vec.end(); it++) {
cout << *it << endl;
}
}
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