Class template basic_fasta

Class template basic_fasta_file

boost::genetics::basic_fasta_file

Synopsis

// In header: <boost/genetics/fasta.hpp>

template<typename ChromosomeType, typename StringType, typename IndexType, 
         bool Writable> 
class basic_fasta_file : public boost::genetics::fasta_file_interface {
public:
  // types
  typedef ChromosomeType chromosome_type;
  typedef IndexType      index_type;     
  typedef StringType     string_type;    

  // construct/copy/destruct
  basic_fasta_file();
  basic_fasta_file(const std::string &);
  basic_fasta_file(mapper &);
  basic_fasta_file & operator=(basic_fasta_file &&);
  ~basic_fasta_file();

  // public member functions
  virtual void append(const std::string &);
  void append(const char *, const char *);
  virtual const chromosome & find_chromosome(size_t) const;
  virtual void 
  find_inexact(std::vector< fasta_result > &, const std::string &, size_t, 
               size_t, size_t, bool);
  virtual const chromosome & get_chromosome(size_t) const;
  virtual size_t get_num_chromosomes() const;
  virtual void make_index(size_t);
  size_t size() const;
  void swap(basic_fasta_file &);
  virtual void write_ascii(std::ostream &) const;
  virtual void write_binary(writer &) const;
};

Description

`basic_fasta_file` public construct/copy/destruct

```
basic_fasta_file();
```
Create an empty FASTA reference file. Use append() to add files.

basic_fasta_file(const std::string & filename);

Create a FASTA reference from a single text file.

```
basic_fasta_file(mapper & map);
```
Use a mapper to instantly load from a mapped file.

basic_fasta_file & operator=(basic_fasta_file && rhs);

Move from another reference of the same type.

```
~basic_fasta_file();
```

`basic_fasta_file` public member functions

virtual void append(const std::string & filename);

Append a single FASTA file to this file.

void append(const char * p, const char * end);

Append the image of a FASTA file to this file.

virtual const chromosome & find_chromosome(size_t location) const;

Find a chomosome for a location.

virtual void 
find_inexact(std::vector< fasta_result > & result, const std::string & dstr, 
             size_t max_distance, size_t max_results, size_t max_gap, 
             bool is_brute_force);

Search the FASTA file for strings with some allowable errors.

virtual const chromosome & get_chromosome(size_t index) const;

Get the chromosomes in this file.

virtual size_t get_num_chromosomes() const;

virtual void make_index(size_t num_indexed_chars);

Must be called after appending FASTA data.

```
size_t size() const;
```
Number of base pairs in this file.
```
void swap(basic_fasta_file & rhs);
```
Swap FASTA files.

virtual void write_ascii(std::ostream & os) const;

copy the bytes in this file to an image.

virtual void write_binary(writer & wr) const;