#include <metric_set.h>

Inheritance diagram for metric_set< T >:

Public Types
enum	{ TYPE =metric_attributes<T>::TYPE, LATEST_VERSION =metric_attributes<T>::LATEST_VERSION }

typedef std::vector< T >	metric_array_t

typedef T::header_type	header_type

typedef T::base_t	base_t

typedef T	metric_type

typedef metric_set< T >	metric_set_type

typedef T::id_t	id_t

typedef T::uint_t	uint_t

typedef std::vector< uint_t >	id_vector

typedef std::vector< id_t >	key_vector

typedef metric_array_t::size_type	size_type

typedef std::set< uint_t >	id_set_t

typedef std::map< id_t, size_t >	offset_map_t

typedef metric_comparison< T >	metric_comparison_t

typedef metric_array_t::const_iterator	const_iterator

typedef metric_array_t::iterator	iterator

Public Member Functions
	metric_set (const ::int16_t version)

	metric_set (const header_type &header=header_type::default_header(), const ::int16_t version=0)

	metric_set (const metric_array_t &vec, const ::int16_t version, const header_type &header)

void	copy_by_tile (const metric_set< T > &origin, const base_metric &tile_id)

void	append_tiles (const metric_set< T > &origin, const base_metric &tile_id)

bool	data_source_exists () const

void	data_source_exists (const bool exists)

const_iterator	begin () const

const_iterator	end () const

iterator	begin ()

iterator	end ()

void	sort ()

void	rebuild_index (const bool update_ids=false)

void	resize (const size_t n)

void	reserve (const size_t n)

void	trim (const size_t n)

void	insert (const metric_type &metric)

void	insert (const id_t id, const metric_type &metric)

void	remove (iterator &it)

metric_type &	operator[] (const size_t n) INTEROP_THROW_SPEC((model

const metric_type &	operator[] (const size_t n) const INTEROP_THROW_SPEC((model

metric_type &	at (const size_t n) INTEROP_THROW_SPEC((model

const metric_type &	at (const size_t n) const INTEROP_THROW_SPEC((model

void	set_version (const ::int16_t version)

key_vector	keys () const

id_vector	lanes () const

size_t	lane_count () const

size_t	max_lane () const

id_vector	tile_numbers_for_lane (const uint_t lane) const

void	populate_tile_numbers_for_lane (id_set_t &tile_number_set, const uint_t lane) const

void	populate_tile_numbers_for_lane_surface (id_set_t &tile_number_set, const uint_t lane, const uint_t surface, const constants::tile_naming_method naming_convention) const

id_vector	tile_numbers () const

metric_array_t	metrics_for_lane (const uint_t lane) const

void	metrics_for_lane (metric_array_t &lane_metrics, const uint_t lane) const

id_vector	cycles () const

metric_array_t	metrics_for_cycle (const uint_t cycle) const

size_t	size () const

bool	empty () const

::int16_t	version () const

void	clear ()

const metric_array_t &	metrics () const

offset_map_t &	offset_map ()

metric_type &	get_metric_ref (uint_t lane, uint_t tile, uint_t cycle=0) INTEROP_THROW_SPEC((model

metric_type &	get_metric_ref (id_t key) INTEROP_THROW_SPEC((model

size_t	find (const uint_t lane, const uint_t tile, const uint_t cycle=0) const

size_t	find (const id_t id) const

const metric_type &	get_metric (const uint_t lane, const uint_t tile, const uint_t cycle=0) const INTEROP_THROW_SPEC((model

bool	has_metric (const uint_t lane, const uint_t tile, const uint_t cycle=0) const

const metric_type &	get_metric (const id_t key) const INTEROP_THROW_SPEC((model

bool	has_metric (const id_t id) const

void	clear_lookup ()

Static Public Member Functions
static const char *	prefix ()

static const char *	suffix ()

Protected Attributes
metric_array_t	m_data

::int16_t	m_version

bool	m_data_source_exists

offset_map_t	m_id_map

Detailed Description

template<typename T>
class illumina::interop::model::metric_base::metric_set< T >

Metric set holds a collection metrics

This class holds a map that maps a unique id to the metric.

Member Typedef Documentation

typedef T::base_t base_t

Define the base type for the metric

typedef metric_array_t::const_iterator const_iterator

Const metric iterator

typedef T::header_type header_type

Define a write header

typedef std::set<uint_t> id_set_t

Define a set of ids

typedef T::id_t id_t

Define a ID type

typedef std::vector<uint_t> id_vector

Define an id vector

typedef metric_array_t::iterator iterator

Metric iterator

typedef std::vector<id_t> key_vector

Define an key vector

typedef std::vector<T> metric_array_t

Define a collection of metrics

typedef metric_comparison<T> metric_comparison_t

Define a safe comparison for ids

typedef metric_set<T> metric_set_type

Define a metric set type

typedef T metric_type

Define a metric type

typedef std::map<id_t, size_t> offset_map_t

Define offset map

typedef metric_array_t::size_type size_type

Define the size type

typedef T::uint_t uint_t

Define a lane/tile/cycle id type

Member Enumeration Documentation

anonymous enum

Enumerator
TYPE	Group type enum
LATEST_VERSION	Latest version of the format

Constructor & Destructor Documentation

metric_set ( const ::int16_t version )

inline

Constructor

Parameters

version version of the file format

metric_set	(	const header_type &	header = `header_type::default_header()`,
		const ::int16_t	version = `0`
	)

inline

Constructor

Parameters

header	header information for the metric set
version	version of the file format

metric_set	(	const metric_array_t &	vec,
		const ::int16_t	version,
		const header_type &	header
	)

inline

Constructor

Parameters

vec	array of metrics
version	of the metric format
header	header information for the metric set

Member Function Documentation

void append_tiles	(	const metric_set< T > &	origin,
		const base_metric &	tile_id
	)

inline

Adds records only for a specific tile

Parameters

origin	full metric set
tile_id	selected tile

metric_type& at ( const size_t n )

inline

Get a metric at the given index

Deprecated:

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: metric

const metric_type& at ( const size_t n ) const

inline

Get a metric at the given index

Deprecated:

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: metric

const_iterator begin ( ) const

inline

Get start of metric collection

Returns: iterator to start of metric collection

iterator begin ( )

inline

Get start of metric collection

Returns: iterator to start of metric collection

void clear ( )

inline

Clear the metrics in the metric set

void clear_lookup ( )

inline

Clear the lookup table.

void copy_by_tile	(	const metric_set< T > &	origin,
		const base_metric &	tile_id
	)

inline

Copy records only for a specific tile

Parameters

origin	full metric set
tile_id	selected tile

id_vector cycles ( ) const

inline

Get a list of all cycles listed in the metric set

Note: Returns empty array for metrics that do not have a cycle identifier

Returns: vector of cycle numbers

bool data_source_exists ( ) const

inline

Flag that indicates whether the data source exists

Returns: true if the data source, e.g. file, exists

void data_source_exists ( const bool exists )

inline

Set flag that indicates whether the data source exists

Parameters

exists true if the data source, e.g. file, exists

bool empty ( ) const

inline

Test if metric set is empty

Returns: true if metric set is empty

const_iterator end ( ) const

inline

Get end of metric collection

Returns: iterator to end of metric collection

iterator end ( )

inline

Get end of metric collection

Returns: iterator to end of metric collection

size_t find	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle = `0`
	)		const

inline

Find index of metric given the id. If not found, return number of metrics

Parameters

lane	lane
tile	tile
cycle	cycle

Returns: index of metric or number of metrics

size_t find ( const id_t id ) const

inline

Find index of metric given the id. If not found, return number of metrics

Parameters

id id

Returns: index of metric or number of metrics

const metric_type& get_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle = `0`
	)		const

inline

Get metric for lane, tile and cycle

Parameters

lane	lane
tile	tile
cycle	cycle

Returns: metric

const metric_type& get_metric ( const id_t key ) const

inline

Get metric for a unique identifier

Parameters

key	unique id built from lane, tile and cycle (if available)

Returns: metric

metric_type& get_metric_ref	(	uint_t	lane,
		uint_t	tile,
		uint_t	cycle = `0`
	)

inline

Get metric for lane, tile and cycle

Parameters

lane	lane
tile	tile
cycle	cycle

Returns: metric

metric_type& get_metric_ref ( id_t key )

inline

Get metric for a unique identifier

Parameters

key	unique id built from lane, tile and cycle (if available)

Returns: metric

bool has_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle = `0`
	)		const

inline

Test if set has metric

Parameters

lane	lane
tile	tile
cycle	cycle

bool has_metric ( const id_t id ) const

inline

Test if set has metric

Parameters

id id

void insert ( const metric_type & metric )

inline

Add a metric to the metric set

Parameters

metric metric to add to set

void insert	(	const id_t	id,
		const metric_type &	metric
	)

inline

Add a metric to the metric set

Parameters

id	unique id for metric
metric	metric to add to set

key_vector keys ( ) const

inline

Get a list of all available lane numbers

Returns: vector of lane numbers

size_t lane_count ( ) const

inline

Get the number of lanes in the data

Returns: number of lanes

id_vector lanes ( ) const

inline

Get a list of all available lane numbers

Returns: vector of lane numbers

size_t max_lane ( ) const

inline

Get maximum lane number

Returns: maximum lane number

const metric_array_t& metrics ( ) const

inline

Get the metrics in a vector

Returns: vector of metrics

metric_array_t metrics_for_cycle ( const uint_t cycle ) const

inline

Get a list of all available metrics for the specified cycle

Note: Returns empty array for Tile Metrics, which does not contain a cycle identifier

Parameters

cycle cycle number

Returns: vector of metrics that map to the given cycle

metric_array_t metrics_for_lane ( const uint_t lane ) const

inline

Get a list of all available metrics for the specified lane

Parameters

lane	lane number

Returns: vector of tile numbers

void metrics_for_lane	(	metric_array_t &	lane_metrics,
		const uint_t	lane
	)		const

inline

Get a list of all available metrics for the specified lane

Parameters

lane_metrics	destination metric array
lane	lane number

offset_map_t& offset_map ( )

inline

Get the current id offset map

Returns: id offset map

metric_type& operator[] ( const size_t n )

inline

Get a metric at the given index

Parameters

n index

Returns: metric

const metric_type& operator[] ( const size_t n ) const

inline

Get a metric at the given index

Parameters

n index

Returns: metric

void populate_tile_numbers_for_lane	(	id_set_t &	tile_number_set,
		const uint_t	lane
	)		const

inline

Get a list of all available tile numbers for the specified lane

Note: this does not clear the set!

Parameters

tile_number_set	destination set to ensure unique tile numbers
lane	lane number

void populate_tile_numbers_for_lane_surface	(	id_set_t &	tile_number_set,
		const uint_t	lane,
		const uint_t	surface,
		const constants::tile_naming_method	naming_convention
	)		const

inline

Get a list of all available tile numbers for the specified lane

Note: this does not clear the set!

Parameters

tile_number_set	destination set to ensure unique tile numbers
lane	lane number
surface	surface number
naming_convention	tile naming convetion enum

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: prefix

void rebuild_index ( const bool update_ids = false )

inline

Rebuild the index map and update the cycle state

Note: This function clears the lookup table for most metrics if update_ids is false (exceptions are Tile and DynamicPhasing

Parameters

update_ids rebuild the lookup table with new ids

void remove ( iterator & it )

inline

Remove a metric from the metric set

Parameters

it	iterator to metric to remove

void reserve ( const size_t n )

inline

Reserve the number of places in the metric vector

Parameters

n	maximum number of elements

void resize ( const size_t n )

inline

Resize the number of places in the metric vector

Parameters

n	expected number of elements

void set_version ( const ::int16_t version )

inline

Set the version of the InterOp file

The InterOp file version determines which metric fields are populated. Each metric lists which version is supported.

Parameters

version version number

size_t size ( ) const

inline

Number of metrics in the metric set

Returns: number of metrics

void sort ( )

inline

Sort the metric collection

static const char* suffix ( )

inlinestatic

Get the suffix of the InterOp filename

Returns: suffix

id_vector tile_numbers ( ) const

inline

Get a list of all available tile numbers

Returns: vector of tile numbers

id_vector tile_numbers_for_lane ( const uint_t lane ) const

inline

Get a list of all available tile numbers for the specified lane

Parameters

lane	lane number

Returns: vector of tile numbers

void trim ( const size_t n )

inline

Trim the set to the proper number of metrics

Parameters

n	actual size of the metric set

::int16_t version ( ) const

inline

Version of the InterOp file parsed

The InterOp file version determines which metric fields are populated. Each metric lists which version is supported.

Returns: interop file version

Member Data Documentation

metric_array_t m_data

protected

Array of metric data

bool m_data_source_exists

protected

Does the file or other source exist

offset_map_t m_id_map

protected

Map unique identifiers to the index of the metric

::int16_t m_version

protected

Version of the metric read

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

/io/interop/model/metric_base/metric_set.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

template<typename T> class illumina::interop::model::metric_base::metric_set< T >

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename T>
class illumina::interop::model::metric_base::metric_set< T >