#include <base_metric.h>

Inheritance diagram for base_metric:

Public Types
enum	{ LANE_BIT_COUNT = 6, TILE_BIT_COUNT = 26, CYCLE_BIT_COUNT = 16, READ_BIT_COUNT = 16, RESERVED_BIT_COUNT = 16, READ_BIT_SHIFT = RESERVED_BIT_COUNT, CYCLE_BIT_SHIFT = RESERVED_BIT_COUNT, TILE_BIT_SHIFT = CYCLE_BIT_SHIFT+CYCLE_BIT_COUNT, LANE_BIT_SHIFT = TILE_BIT_SHIFT+TILE_BIT_COUNT }

typedef ::uint64_t	ulong_t

typedef ulong_t	id_t

typedef ::uint16_t	ushort_t

typedef ::uint32_t	uint_t

typedef base_metric_header	header_type

typedef ::uint8_t	lane_t

typedef ::uint32_t	tile_t

typedef constants::base_tile_t	base_t

Public Types inherited from empty_metric
typedef ::uint32_t	id_t

typedef ::uint32_t	uint_t

typedef constants::base_run_t	base_t

Public Member Functions
	base_metric (const uint_t lane=0, const uint_t tile=0)

void	set_base (const uint_t lane, const uint_t tile)

template<class BaseMetric >
void	set_base (const BaseMetric &base)

id_t	id () const

id_t	tile_hash () const

uint_t	lane () const

uint_t	tile () const

uint_t	number (const illumina::interop::constants::tile_naming_method) const

uint_t	section (const illumina::interop::constants::tile_naming_method method) const

uint_t	surface (const illumina::interop::constants::tile_naming_method method) const

uint_t	swath (const illumina::interop::constants::tile_naming_method method) const

uint_t	phyiscalLocationIndex (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationColumn (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationRow (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

size_t	physical_location_index (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_column (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_row (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

bool	operator< (const base_metric &metric2) const

Public Member Functions inherited from empty_metric
template<class BaseMetric >
void	set_base (const BaseMetric &)

void	set_base (const uint_t, const uint_t)

bool	operator< (const empty_metric &) const

Static Public Member Functions
static id_t	create_id (const id_t lane, const id_t tile, const id_t=0)

static id_t	lane_from_id (const id_t id)

static id_t	tile_hash_from_id (const id_t id)

static id_t	tile_from_id (const id_t id)

static const char *	suffix ()

Static Public Member Functions inherited from empty_metric
static const char *	suffix ()

static id_t	create_id (const id_t, const id_t, const id_t=0)

Detailed Description

Base class for InterOp classes that contain tile specific metrics

These classes define both a lane and tile identifier.

Member Typedef Documentation

typedef constants::base_tile_t base_t

Define the base type

typedef base_metric_header header_type

Base metric header that adds no functionality

typedef ulong_t id_t

Defines the type of a unique identifier

typedef ::uint8_t lane_t

Define lane type

typedef ::uint32_t tile_t

Define tile type

typedef ::uint32_t uint_t

Unsigned int

typedef ::uint64_t ulong_t

Unsigned long

typedef ::uint16_t ushort_t

Unsigned int16_t

Member Enumeration Documentation

anonymous enum

Enumerator
LANE_BIT_COUNT
TILE_BIT_COUNT
CYCLE_BIT_COUNT
READ_BIT_COUNT
RESERVED_BIT_COUNT
READ_BIT_SHIFT
CYCLE_BIT_SHIFT
TILE_BIT_SHIFT
LANE_BIT_SHIFT

Constructor & Destructor Documentation

base_metric	(	const uint_t	lane = `0`,
		const uint_t	tile = `0`
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number

Member Function Documentation

static id_t create_id	(	const id_t	lane,
		const id_t	tile,
		const id_t	= `0`
	)

inlinestatic

Unique id created from both the lane and tile

Parameters

lane	lane number
tile	tile number

Returns: unique id

id_t id ( ) const

inline

Unique id created from both the lane and tile

Returns: unique identifier

uint_t lane ( ) const

inline

Lane number

Returns: lane number

static id_t lane_from_id ( const id_t id )

inlinestatic

Get the lane from the unique lane/tile id

Parameters

id	unique lane/tile id

Returns: lane number

uint_t number ( const illumina::interop::constants::tile_naming_method ) const

inline

Tile number

Calculates the number of the tile from the tile id.

Returns: number of the tile.

bool operator< ( const base_metric & metric2 ) const

inline

Comparison operator used to sort the entries in order of their IDs

Parameters

metric2 metric to compare with the current object

Returns: true if this object's ID is less than metric2's ID

uint_t phyiscalLocationColumn	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	swath_count,
		const bool	all_surfaces
	)		const

inline

Column of the physical location of tile within the flowcell

Deprecated:

Will be removed in 1.1.x (use phyiscal_location_column instead)

Parameters

method	the tile naming method
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: column of the physical location within the flowcell

uint_t phyiscalLocationIndex	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	section_per_lane,
		const uint_t	tile_count,
		const uint_t	swath_count,
		const bool	all_surfaces
	)		const

inline

Index of the physical location of tile within the flowcell

Deprecated:

Will be removed in 1.1.x (use physical_location_index instead)

Parameters

method	the tile naming method
section_per_lane	number of sections per lane
tile_count	number of tiles
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: index of the physical location within the flowcell

uint_t phyiscalLocationRow	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	section_per_lane,
		const uint_t	tile_count
	)		const

inline

Row of the physical location of tile within the flowcell

Deprecated:

Will be removed in 1.1.x (use phyiscal_location_row instead)

Parameters

method	the tile naming method
section_per_lane	number of sections per lane (number of cameras that cover the lane)
tile_count	number of tiles

Returns: row of the physical location within the flowcell

uint_t physical_location_column	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	swath_count,
		const bool	all_surfaces
	)		const

inline

Column of the physical location of tile within the flowcell

Parameters

method	the tile naming method
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: column of the physical location within the flowcell

size_t physical_location_index	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	section_per_lane,
		const uint_t	tile_count,
		const uint_t	swath_count,
		const bool	all_surfaces
	)		const

inline

Index of the physical location of tile within the flowcell

Parameters

method	the tile naming method
section_per_lane	number of sections per lane (number of cameras that cover the lane)
tile_count	number of tiles
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: index of the physical location within the flowcell

uint_t physical_location_row	(	const illumina::interop::constants::tile_naming_method	method,
		const uint_t	section_per_lane,
		const uint_t	tile_count
	)		const

inline

Row of the physical location of tile within the flowcell

Parameters

method	the tile naming method
section_per_lane	number of sections per lane
tile_count	number of tiles

Returns: row of the physical location within the flowcell

uint_t section ( const illumina::interop::constants::tile_naming_method method ) const

inline

Section number

Calculates the section of the tile from the tile id.

Returns: section of the tile.

void set_base	(	const uint_t	lane,
		const uint_t	tile
	)

inline

Set id

Parameters

lane	lane number
tile	tile number

void set_base ( const BaseMetric & base )

inline

Set the base metric identifiers

Parameters

base	layout base

static const char* suffix ( )

inlinestatic

Get the metric name suffix

Returns: empty string

uint_t surface ( const illumina::interop::constants::tile_naming_method method ) const

inline

Surface number

Calculates the surface of the tile from the tile id.

Returns: surface of the tile.

uint_t swath ( const illumina::interop::constants::tile_naming_method method ) const

inline

Swath number

Calculates the surface of the tile from the tile id.

Returns: surface of the tile.

uint_t tile ( ) const

inline

Tile id

The tile id can have either a 4-digit format or a 5-digit format.

4-digit: 1234 -> surface (1) swath (2) tile_number (34)

5-digit: 12345 -> surface (1) swath (2) section(3) tile_number (45)

Returns: tile number

static id_t tile_from_id ( const id_t id )

inlinestatic

Get the tile hash from the unique lane/tile/cycle id

Parameters

id	unique lane/tile/cycle id

Returns: tile hash number

id_t tile_hash ( ) const

inline

Unique id created from both the lane and tile

Returns: unique identifier

static id_t tile_hash_from_id ( const id_t id )

inlinestatic

Get the tile hash from the unique lane/tile/cycle id

Parameters

id	unique lane/tile/cycle id

Returns: tile hash number

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

/io/interop/model/metric_base/base_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation