jade::basic_ped_reader< TValue > Class Template Reference

A template for a class that reads PED data. More...

#include <jade.ped_reader.hpp>

Collaboration diagram for jade::basic_ped_reader< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...

Public Member Functions
	basic_ped_reader (std::istream &in)
	Initializes a new instance of the class. More...
std::string	str () const
void	write (std::ostream &out) const
	Writes the PED data to the specified output stream. More...
void	write (char const *const path)
	Writes the PED data to the specified output file. More...
void	write (const std::string &path)
	Writes the PED data to the specified output file. More...

Detailed Description

template<typename TValue>
class jade::basic_ped_reader< TValue >

A template for a class that reads PED data.

Definition at line 18 of file jade.ped_reader.hpp.

Member Typedef Documentation

value_type

template<typename TValue >

typedef TValue jade::basic_ped_reader< TValue >::value_type

The value type.

Definition at line 22 of file jade.ped_reader.hpp.

Constructor & Destructor Documentation

basic_ped_reader()

template<typename TValue >

jade::basic_ped_reader< TValue >::basic_ped_reader ( std::istream &  in )

inlineexplicit

Initializes a new instance of the class.

Parameters

in	The input stream.

Definition at line 27 of file jade.ped_reader.hpp.

            : _buf  ()
            , _rows (0)
            , _cols (0)
        {
            size_t line = 1;
            size_t col  = 0;
            for (;;)
            {
                const auto ch = in.get();
 
                if (ch < 0)
                {
                    if (col > 0)
                        throw error("unexpected end of data");
                    break;
                }
 
                if (ch == '\n')
                {
                    if (col > 0)
                        throw error() << "premature end of line " << line;
                    line++;
                    continue;
                }
 
                if (ch != '\t')
                    continue;
 
                if (++col < 6)
                    continue;
 
                col = 1;
                for (;;)
                {
                    const auto ch1 = _read(in, line);
 
                    _require(in, line, ' ');
 
                    const auto ch2 = _read(in, line);
 
                    const auto symbol =
                        ch1 == '0' || ch2 == '0' ? '3' :
                        ch1 != ch2 ? '1' :
                        ch1 == '2' ? '0' :
                        '2';
 
                    _buf.push_back(symbol);
 
                    if (in.peek() < 0 || in.peek() == '\n')
                        break;
 
                    _require(in, line, '\t');
 
                    if (_rows > 0 && col == _cols)
                        throw error()
                            << "expected " << _cols << " pairs but encountered "
                            << "at least " << col + 1 << " on line " << line;
 
                    col++;
                }
 
                if (_rows == 0)
                    _cols = col;
 
                else if (col != _cols)
                    throw error()
                        << "expected " << _cols << " genotype pairs but "
                        << "encountered " << col << " on line " << line;
 
                col = 0;
                _rows++;
            }
 
            if (_cols == 0)
                _rows = 0;
        }

Member Function Documentation

str()

template<typename TValue >

std::string jade::basic_ped_reader< TValue >::str ( ) const

inline

Returns

A string representation of this instance.

Definition at line 109 of file jade.ped_reader.hpp.

        {
            std::ostringstream out;
            write(out);
            return out.str();
        }

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write() [1/3]

template<typename TValue >

void jade::basic_ped_reader< TValue >::write ( char const *const  path )

inline

Writes the PED data to the specified output file.

Parameters

path	The output path.

Definition at line 136 of file jade.ped_reader.hpp.

        {
            assert(path != nullptr);
            std::ofstream out (path);
            if (!out.good())
                throw error() << "error opening '" << path << "' for writing";
            write(out);
        }

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write() [2/3]

template<typename TValue >

void jade::basic_ped_reader< TValue >::write ( const std::string &  path )

inline

Writes the PED data to the specified output file.

Parameters

path	The output path.

Definition at line 149 of file jade.ped_reader.hpp.

        {
            write(path.c_str());
        }

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write() [3/3]

template<typename TValue >

void jade::basic_ped_reader< TValue >::write ( std::ostream &  out ) const

inline

Writes the PED data to the specified output stream.

Parameters

out	The output stream.

Definition at line 119 of file jade.ped_reader.hpp.

        {
            out << _rows << ' ' << _cols << std::endl;
 
            if (_cols == 0)
                return;
 
            size_t i = 0;
            for (const auto ch : _buf)
                out << ch << (++i % _cols == 0 ? '\n' : ' ');
        }

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The documentation for this class was generated from the following file:

• jade.ped_reader.hpp