#include <filter_options.h>

Public Types
enum	UseAll { ALL_IDS = 0, ALL_CHANNELS = -1, ALL_BASES = -1 }

typedef constants::dna_bases	dna_base_t

typedef ::int16_t	channel_t

typedef model::metric_base::base_metric::uint_t	id_t

Public Member Functions
	filter_options (const constants::tile_naming_method naming_method, const id_t lane=ALL_IDS, const channel_t channel=ALL_CHANNELS, const dna_base_t base=static_cast< dna_base_t >(ALL_BASES), const id_t surface=ALL_IDS, const id_t read=ALL_IDS, const id_t cycle=ALL_IDS, const id_t tile_number=ALL_IDS, const id_t swath=ALL_IDS, const id_t section=ALL_IDS, const size_t subsample=0)

void	reset ()

void	validate (const constants::metric_type type, const run::info &run_info, const bool check_ignored=false) const INTEROP_THROW_SPEC((model

template<class Metric >
bool	valid_tile (const Metric &metric) const

template<class Metric >
bool	valid_tile_cycle (const Metric &metric) const

template<class Metric >
bool	valid_read (const Metric &metric) const

bool	all_channels (const constants::metric_type type) const

bool	all_channels () const

bool	all_bases (const constants::metric_type type) const

bool	all_bases () const

bool	all_reads () const

bool	all_cycles () const

bool	all_lanes () const

bool	all_tile_numbers () const

bool	all_swaths () const

bool	all_sections () const

bool	is_specific_read (const constants::metric_type type) const

bool	is_specific_read () const

bool	is_specific_surface () const

bool	valid_lane (const id_t lane) const

bool	valid_surface (const id_t surface) const

bool	valid_read (const id_t read) const

bool	valid_cycle (const id_t cycle) const

bool	valid_tile_number (const id_t tile_number) const

bool	valid_swath (const id_t swath) const

bool	valid_section (const id_t section) const

bool	valid_channel (const channel_t channel) const

bool	valid_base (const dna_base_t base) const

void	subsample (const size_t count)

void	tile_naming_method (const constants::tile_naming_method naming_method)

void	channel (const channel_t channel)

void	dna_base (const dna_base_t base)

void	read (const id_t r)

void	cycle (const id_t c)

void	surface (const id_t s)

void	swath (const id_t s)

void	section (const id_t s)

void	tile_number (const id_t s)

void	lane (const id_t l)

id_t	lane () const

channel_t	channel () const

dna_base_t	dna_base () const

id_t	read () const

id_t	cycle () const

id_t	surface () const

std::string	cycle_description () const

std::string	lane_description () const

std::string	channel_description (const std::vector< std::string > &channels) const

std::string	base_description () const

std::string	surface_description () const

std::string	read_description () const

constants::tile_naming_method	naming_method () const

util::chain_range_iterator	option_iterator (const model::run::info &info, const constants::metric_type metric_type, const constants::plot_types plot_type, const bool keep_state=false)

bool	supports_section (const constants::plot_types, const model::run::info &info) const

bool	supports_swath (const constants::plot_types) const

bool	supports_tile (const constants::plot_types) const

bool	supports_all_lanes (const constants::plot_types plot_type) const

bool	supports_lane (const constants::plot_types plot_type) const

bool	supports_all_bases (const constants::plot_types plot_type) const

bool	supports_base (const constants::metric_type metric_type) const

bool	supports_all_channels (const constants::plot_types plot_type) const

bool	supports_channel (const constants::metric_type metric_type) const

bool	supports_all_cycles (const constants::plot_types plot_type) const

bool	supports_cycle (const constants::metric_type metric_type, const constants::plot_types plot_type) const

bool	supports_all_reads (const constants::plot_types plot_type) const

bool	supports_read (const constants::metric_type metric_type, const constants::plot_types plot_type) const

bool	supports_surface (const constants::metric_type metric_type, const model::run::info &info) const

size_t	subsample () const

Friends
std::ostream &	operator<< (std::ostream &out, const filter_options &options)

Detailed Description

Options to filter metrics

Member Typedef Documentation

typedef ::int16_t channel_t

Channel type - Range: 0-N - All: -1

typedef constants::dna_bases dna_base_t

DNA base enumerated type - Range: A,C,G,T - All: NC

typedef model::metric_base::base_metric::uint_t id_t

ID type - Range: 1-N - All: 0

Member Enumeration Documentation

enum UseAll

Sentinels for use all of a specific type

Enumerator
ALL_IDS	All sentinel for id types
ALL_CHANNELS	All sentinel for channel types
ALL_BASES	All sentinel for base types

Constructor & Destructor Documentation

filter_options	(	const constants::tile_naming_method	naming_method,
		const id_t	lane = `ALL_IDS`,
		const channel_t	channel = `ALL_CHANNELS`,
		const dna_base_t	base = `static_cast<dna_base_t>(ALL_BASES)`,
		const id_t	surface = `ALL_IDS`,
		const id_t	read = `ALL_IDS`,
		const id_t	cycle = `ALL_IDS`,
		const id_t	tile_number = `ALL_IDS`,
		const id_t	swath = `ALL_IDS`,
		const id_t	section = `ALL_IDS`,
		const size_t	subsample = `0`
	)

inline

Constructor

Parameters

naming_method	tile naming method
lane	lane number
channel	channel number (order based on RunInfo.xml)
base	enumerate type
surface	surface number
read	read number
cycle	cycle number
tile_number	tile number
swath	swath number
section	section number
subsample	amount to subsample points

Member Function Documentation

bool all_bases ( const constants::metric_type type ) const

inline

Test if all bases were requested

Parameters

type	metric type

Returns: true if metric type supports bases and all bases requested

bool all_bases ( ) const

inline

Test if all bases were requested

Returns: true if all bases requested

bool all_channels ( const constants::metric_type type ) const

inline

Test if all channels were requested

Parameters

type	metric type

Returns: true if metric supports channels and all channels requested

bool all_channels ( ) const

inline

Test if all channels were requested

Returns: true if metric supports channels and all channels requested

bool all_cycles ( ) const

inline

Test if all cycles were requested

Returns: true if all cycles were requested

bool all_lanes ( ) const

inline

Test if all lanes were requested

Returns: true if all lanes were requested

bool all_reads ( ) const

inline

Test if all reads were requested

Returns: true if all reads were requested

bool all_sections ( ) const

inline

Test if all sections were requested

Returns: true if all sections were requested

bool all_swaths ( ) const

inline

Test if all swaths were requested

Returns: true if all swaths were requested

bool all_tile_numbers ( ) const

inline

Test if all tile numbers were requested

Returns: true if all tile numbers were requested

std::string base_description ( ) const

inline

Get a description of the base filter options

Returns: description

channel_t channel ( ) const

inline

Get channel to display

Returns: channel

std::string channel_description ( const std::vector< std::string > & channels ) const

inline

Get a description of the channel filter options

Returns: description

id_t cycle ( ) const

inline

Get cycle to display

Returns: cycle

std::string cycle_description ( ) const

inline

Get a description for the cycle filter option

Returns: description for the cycle filter option

dna_base_t dna_base ( ) const

inline

Get base to display

Returns: base

bool is_specific_read ( const constants::metric_type type ) const

inline

Test if metric is read metric and specific read is chosen

Parameters

type	metric type

Returns: true if metric type supports reads and a specific read is requested

bool is_specific_read ( ) const

inline

Test if specific read is chosen

Returns: true if a specific read is requested

bool is_specific_surface ( ) const

inline

Test if specific surface is chosen

Returns: true if a specific surface is requested

id_t lane ( ) const

inline

Get the lane to display

Returns: lane

std::string lane_description ( ) const

inline

Get a description of the lane filter options

Returns: description

constants::tile_naming_method naming_method ( ) const

inline

Get the tile naming convention

Returns: tile naming convention

util::chain_range_iterator option_iterator	(	const model::run::info &	info,
		const constants::metric_type	metric_type,
		const constants::plot_types	plot_type,
		const bool	keep_state = `false`
	)

inline

Create an iterator that updates the current object

flowcell - does not support lanes

Parameters

info	run info
metric_type	metric type
plot_type	type of the plot
keep_state	keep the current state of the options

Returns: iterator

id_t read ( ) const

inline

Get read to display

Returns: read

std::string read_description ( ) const

inline

Get a description of the read filter options

Returns: description

void reset ( )

inline

Reset all options to default values (except naming_method)

size_t subsample ( ) const

inline

Number of points to subsample

Returns: maximum number of points

bool supports_all_bases ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by all bases

Parameters

plot_type plot type

Returns: true if plot supports filtering by base

bool supports_all_channels ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by all channels

Parameters

plot_type plot type

Returns: true if plot supports filtering all channels

bool supports_all_cycles ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by all cycles

Parameters

plot_type plot type

Returns: true if plot supports filtering by all cycles

bool supports_all_lanes ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by all lanes

Parameters

plot_type type of plot

Returns: true if metric supports filtering by all lanes

bool supports_all_reads ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by all reads

Parameters

plot_type plot type

Returns: true if plot supports filtering by all reads

bool supports_base ( const constants::metric_type metric_type ) const

inline

Test if metric supports filtering by base

Parameters

metric_type metric type

Returns: true if metric supports filtering by base

bool supports_channel ( const constants::metric_type metric_type ) const

inline

Test if metric supports filtering by channel

Parameters

metric_type metric type

Returns: true if metric supports filtering by channel

bool supports_cycle	(	const constants::metric_type	metric_type,
		const constants::plot_types	plot_type
	)		const

inline

Test if metric and plot combination supports filtering by cycle

Parameters

metric_type	metric type
plot_type	plot type

Returns: true if metric supports filtering by cycle

bool supports_lane ( const constants::plot_types plot_type ) const

inline

Test if plot supports filtering by lane

Parameters

plot_type type of plot

Returns: true if metric supports filtering by lane

bool supports_read	(	const constants::metric_type	metric_type,
		const constants::plot_types	plot_type
	)		const

inline

Test if metric and plot combination supports filtering by read

Parameters

metric_type	metric type
plot_type	type of plot

Returns: true if metric supports filtering by read

bool supports_section	(	const constants::plot_types	,
		const model::run::info &	info
	)		const

inline

Test if the combination of the plot and run info support filtering by section

param plot_type type of plot

Parameters

info run info

Returns: true if metric supports filtering by swath

bool supports_surface	(	const constants::metric_type	metric_type,
		const model::run::info &	info
	)		const

inline

Test if metric and run info combination supports filtering by surface

Parameters

metric_type	metric type
info	run info

Returns: true if metric supports filtering by surface

bool supports_swath ( const constants::plot_types ) const

inline

Test if plot supports filtering by swath

param plot_type type of plot

Returns: true if metric supports filtering by swath

bool supports_tile ( const constants::plot_types ) const

inline

Test if plot supports filtering by tile

param plot_type type of plot

Returns: true if metric supports filtering by tile

id_t surface ( ) const

inline

Get surface to display

Returns: cycle

std::string surface_description ( ) const

inline

Get a description of the surface filter options

Returns: description

bool valid_base ( const dna_base_t base ) const

inline

Test if the base if valid

Returns: true if base should not be filtered

bool valid_channel ( const channel_t channel ) const

inline

Test if the channel if valid

Returns: true if channel should not be filtered

bool valid_cycle ( const id_t cycle ) const

inline

Test if the cycle if valid

Returns: true if cycle should not be filtered

bool valid_lane ( const id_t lane ) const

inline

Test if the lane if valid

Returns: true if lane should not be filtered

bool valid_read ( const Metric & metric ) const

inline

Test if metric is a valid read

Parameters

metric any metric type

Returns: true if the tile should not be filtered

bool valid_read ( const id_t read ) const

inline

Test if the read if valid

Returns: true if read should not be filtered

bool valid_section ( const id_t section ) const

inline

Test if the section if valid

Returns: true if section should not be filtered

bool valid_surface ( const id_t surface ) const

inline

Test if the surface if valid

Returns: true if surface should not be filtered

bool valid_swath ( const id_t swath ) const

inline

Test if the swath if valid

Returns: true if swath should not be filtered

bool valid_tile ( const Metric & metric ) const

inline

Test if metric is a valid tile

Parameters

metric any metric type

Returns: true if the tile should not be filtered

bool valid_tile_cycle ( const Metric & metric ) const

inline

Test if metric is a valid tile

Parameters

metric any metric type

Returns: true if the tile should not be filtered

bool valid_tile_number ( const id_t tile_number ) const

inline

Test if the tile number if valid

Returns: true if tile number should not be filtered

void validate	(	const constants::metric_type	type,
		const run::info &	run_info,
		const bool	check_ignored = `false`
	)		const

inline

Test if the filter options are valid, if not throw an exception

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const filter_options &	options
	)

friend

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

/io/interop/model/plot/filter_options.h

Public Types

Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation