#include <mutable_path_metadata.hpp>

Inheritance diagram for handlegraph::MutablePathMetadata:

Public Member Functions
virtual	~MutablePathMetadata ()=default

virtual path_handle_t	create_path (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange, bool is_circular=false)

Public Member Functions inherited from handlegraph::PathMetadata
virtual	~PathMetadata ()=default

virtual PathSense	get_sense (const path_handle_t &handle) const
	What is the given path meant to be representing? More...

virtual std::string	get_sample_name (const path_handle_t &handle) const

virtual std::string	get_locus_name (const path_handle_t &handle) const

virtual size_t	get_haplotype (const path_handle_t &handle) const

virtual size_t	get_phase_block (const path_handle_t &handle) const

virtual subrange_t	get_subrange (const path_handle_t &handle) const

template<typename Iteratee >
bool	for_each_path_of_sense (const PathSense &sense, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_of_sample (const std::string &sample, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > senses, const std::unordered_set< std::string > samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_step_of_sense (const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const

Protected Member Functions
virtual path_handle_t	create_path_handle (const std::string &name, bool is_circular=false)=0

Protected Member Functions inherited from handlegraph::PathMetadata
virtual bool	for_each_path_matching_impl (const std::unordered_set< PathSense > senses, const std::unordered_set< std::string > samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) const

virtual bool	for_each_step_of_sense_impl (const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const

virtual std::string	get_path_name (const path_handle_t &path_handle) const =0
	Look up the name of a path from a handle to it. More...

virtual path_handle_t	get_path_handle_of_step (const step_handle_t &step_handle) const =0
	Returns a handle to the path that an step is on. More...

virtual bool	for_each_path_handle_impl (const std::function< bool(const path_handle_t &)> &iteratee) const =0

virtual bool	for_each_step_on_handle_impl (const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0

Additional Inherited Members
Static Public Member Functions inherited from handlegraph::PathMetadata
static PathSense	parse_sense (const std::string &path_name)

static std::string	parse_sample_name (const std::string &path_name)

static std::string	parse_locus_name (const std::string &path_name)

static size_t	parse_haplotype (const std::string &path_name)

static size_t	parse_phase_block (const std::string &path_name)

static subrange_t	parse_subrange (const std::string &path_name)

static void	parse_path_name (const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange)
	Decompose a formatted path name into metadata. More...

static std::string	create_path_name (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange)

Static Public Attributes inherited from handlegraph::PathMetadata
static const std::string	NO_SAMPLE_NAME = ""

static const std::string	NO_LOCUS_NAME = ""

static const size_t	NO_HAPLOTYPE = std::numeric_limits<size_t>::max()

static const size_t	NO_PHASE_BLOCK = std::numeric_limits<size_t>::max()

static const subrange_t	NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION}

static const offset_t	NO_END_POSITION = std::numeric_limits<offset_t>::max()

Detailed Description

This is the interface for mutable embedded path and haplotype thread metadata (see PathMetadata).

Comes with a default implementation of this interface, based on a name-based create_path_handle() and special path name formatting.

Constructor & Destructor Documentation

◆ ~MutablePathMetadata()

virtual handlegraph::MutablePathMetadata::~MutablePathMetadata ( )

virtualdefault

Member Function Documentation

◆ create_path()

path_handle_t handlegraph::MutablePathMetadata::create_path	(	const PathSense &	sense,
		const std::string &	sample,
		const std::string &	locus,
		const size_t &	haplotype,
		const size_t &	phase_block,
		const subrange_t &	subrange,
		bool	is_circular = `false`
	)

virtual

Add a path with the given metadata. Any item can be the corresponding unset sentinel (PathMetadata::NO_LOCUS_NAME, PathMetadata::NO_PHASE_BLOCK, etc.).

Implementations may refuse to store paths-or-threads of certain senses when relevant fields are unset.

Handles to other paths must remain valid.

◆ create_path_handle()

virtual path_handle_t handlegraph::MutablePathMetadata::create_path_handle	(	const std::string &	name,
		bool	is_circular = `false`
	)

protectedpure virtual

Create a path with the given name. The caller must ensure that no path with the given name exists already, or the behavior is undefined. Returns a handle to the created empty path. Handles to other paths must remain valid.

Implemented in handlegraph::MutablePathHandleGraph.

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

deps/libhandlegraph/src/include/handlegraph/mutable_path_metadata.hpp
deps/libhandlegraph/src/mutable_path_metadata.cpp

Public Member Functions