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#ifndef INPUT_READER_H
#define INPUT_READER_H
#include "configuration.h"
#include <string>
#include <vector>
#include <iostream>
class configuration;
/**
* Base class for input
*
* Use input_reader::build() to construct an instance.
*/
class input_reader
{
public:
enum input_format_t { input_unset, input_fasta };
// Constructor
static input_reader* build(configuration const &);
// Accessors for metadata
std::string const & id(std::size_t i) const
{ return id_[i]; }
std::size_t size(std::size_t i) const
{ return size_[i]; }
std::size_t size() const
{ return size_.size(); }
std::size_t total_size() const
{ return total_size_; }
std::size_t total_seqs() const
{ return total_seqs_; }
virtual ~input_reader()
{ if (fp != &std::cin) delete fp; fp = 0; }
static bool smaller_than_rev_cmpl(std::string const &);
protected:
explicit input_reader(std::string);
std::istream *fp;
std::vector<std::string> id_;
std::vector<std::size_t> size_;
std::size_t total_size_;
unsigned total_seqs_;
private:
input_reader();
// No copy constructor or assignment
input_reader(input_reader const&);
input_reader& operator = (input_reader const&);
};
/**
* Simple FASTA reader
*/
class fasta_input_reader : public input_reader
{
public:
explicit fasta_input_reader(configuration const &);
virtual ~fasta_input_reader()
{ }
private:
fasta_input_reader();
// No copy constructor or assignment
fasta_input_reader(fasta_input_reader const&);
fasta_input_reader& operator = (fasta_input_reader const&);
};
#endif
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