Classes
class	check_imaging_table_column

class	table_populator

Typedefs
typedef std::map< model::metric_base::base_metric::id_t,::uint64_t >	row_offset_map_t

Functions
size_t	count_table_columns (const std::vector< model::table::imaging_column > &columns)

::uint32_t	max_digits ()

size_t	get_column_rounding (const model::table::column_id index)

template<class T , typename R , typename P1 , typename P2 >
R	call_adapter (const T &obj, P2 param1, R(T::*func)(P1) const)

template<class T , typename R , typename P1 >
R	call_adapter (const T &obj, P1, R(T::*func)() const)

template<typename InputIterator , typename OutputIterator >
void	populate_imaging_table_data_by_cycle (InputIterator beg, InputIterator end, const size_t q20_idx, const size_t q30_idx, const constants::tile_naming_method naming_method, const summary::read_cycle_vector_t &cycle_to_read, const std::vector< size_t > &columns, const row_offset_map_t &row_offset, const size_t column_count, OutputIterator data_beg, OutputIterator data_end)

template<class MetricSet , typename OutputIterator >
void	populate_imaging_table_data_by_cycle (const MetricSet &metrics, const size_t q20_idx, const size_t q30_idx, const constants::tile_naming_method naming_method, const summary::read_cycle_vector_t &cycle_to_read, const std::vector< size_t > &columns, const row_offset_map_t &row_offset, const size_t column_count, OutputIterator data_beg, OutputIterator data_end)

template<typename I >
void	zero_first_column (I beg, I end, size_t column_count)

template<typename I >
void	create_imaging_table_data (const model::metrics::run_metrics &metrics, const std::vector< model::table::imaging_column > &columns, const row_offset_map_t &row_offset, I data_beg, I data_end)

template<typename I >
void	populate_imaging_table_data_t (const model::metrics::run_metrics &metrics, const std::vector< model::table::imaging_column > &columns, const row_offset_map_t &row_offset, I data_beg, const size_t n)

void	populate_imaging_table_data (const model::metrics::run_metrics &metrics, const std::vector< model::table::imaging_column > &columns, const row_offset_map_t &row_offset, float *data_beg, const size_t n) INTEROP_THROW_SPEC((model

void	count_table_rows (const model::metrics::run_metrics &metrics, row_offset_map_t &row_offset)

void	create_imaging_table (model::metrics::run_metrics &metrics, model::table::imaging_table &table)

constants::metric_group	to_group (const model::table::column_id type)

void	list_imaging_table_metrics_to_load (std::vector< unsigned char > &valid_to_load)

void	determine_filled_columns (model::metrics::run_metrics &metrics, const model::metrics::run_metrics::tile_metric_map_t &tile_hash, std::vector< bool > &filled)

constants::metric_data	to_data_type (const size_t index)

void	create_imaging_table_columns (const std::vector< std::string > &channels, const std::vector< bool > &filled, std::vector< model::table::imaging_column > &columns) INTEROP_THROW_SPEC((model

void	populate_column_offsets (std::vector< model::table::imaging_column > &columns)

void	create_imaging_table_columns (model::metrics::run_metrics &metrics, std::vector< model::table::imaging_column > &columns) INTEROP_THROW_SPEC((model

Variables
void populate_imaging_table_data(const model::metrics::run_metrics &metrics, const std::vector< model::table::imaging_column > &columns, const row_offset_map_t &row_offset, float *data_beg, const size_t n) INTEROP_THROW_SPEC((model voi	count_table_rows )(const model::metrics::run_metrics &metrics, row_offset_map_t &row_offset)

void create_imaging_table(model::metrics::run_metrics &metrics, model::table::imaging_table &table) INTEROP_THROW_SPEC((model void	list_imaging_table_metrics_to_load (std::vector< unsigned char > &valid_to_load)

Typedef Documentation

typedef std::map<model::metric_base::base_metric::id_t, ::uint64_t> row_offset_map_t

Define a row offset map

Function Documentation

R illumina::interop::logic::table::call_adapter	(	const T &	obj,
		P2	param1,
		R(T::*)(P1) const	func
	)

Function interface for method call with single parameter

Note: This is necessary because you cannot pass anything into an function that expects no arguments, not even void

Parameters

obj	object corresponding to the method
param1	first value to function
func	pointer to member function

Returns: functor wrapper

R illumina::interop::logic::table::call_adapter	(	const T &	obj,
		P1	,
		R(T::*)() const	func
	)

Function interface for method call with single dummy parameter

Note: This is necessary because you cannot pass anything into an function that expects no arguments, not even void

Parameters

obj	object corresponding to the method
func	pointer to member function

Returns: functor wrapper

size_t count_table_columns ( const std::vector< model::table::imaging_column > & columns )

Count the total number of columns for the data table

Parameters

columns vector of table column descriptions

Returns: total number of columns including sub columns

void illumina::interop::logic::table::count_table_rows	(	const model::metrics::run_metrics &	metrics,
		row_offset_map_t &	row_offset
	)

Count the number of rows in the imaging table and setup an ordering

Parameters

metrics	collections of InterOp metric sets
row_offset	ordering for the rows

void illumina::interop::logic::table::create_imaging_table	(	model::metrics::run_metrics &	metrics,
		model::table::imaging_table &	table
	)

Create an imaging table from run metrics

Parameters

metrics	source run metrics
table	destination imaging table

void illumina::interop::logic::table::create_imaging_table_columns	(	const std::vector< std::string > &	channels,
		const std::vector< bool > &	filled,
		std::vector< model::table::imaging_column > &	columns
	)

Create the imaging table columns

Parameters

channels	names of each channel
filled	boolean array indicating whether to include the column
columns	destination column vector

void illumina::interop::logic::table::create_imaging_table_columns	(	model::metrics::run_metrics &	metrics,
		std::vector< model::table::imaging_column > &	columns
	)

Create a vector of column descriptors

Parameters

metrics	source collection of InterOp metrics from the run
columns	destination vector of column descriptors

void illumina::interop::logic::table::create_imaging_table_data	(	const model::metrics::run_metrics &	metrics,
		const std::vector< model::table::imaging_column > &	columns,
		const row_offset_map_t &	row_offset,
		I	data_beg,
		I	data_end
	)

Populate the imaging table with all the metrics in the run

Parameters

metrics	collection of all run metrics
columns	vector of table columns
row_offset	offset for each metric into the sorted table
data_beg	iterator to start of table data
data_end	iterator to end of table data

void illumina::interop::logic::table::determine_filled_columns	(	model::metrics::run_metrics &	metrics,
		const model::metrics::run_metrics::tile_metric_map_t &	tile_hash,
		std::vector< bool > &	filled
	)

Determine whether a column should be filled

Parameters

metrics	run metrics
tile_hash	map between the tile has and base metric
filled	destination array that indicates whether a column should be filled

size_t get_column_rounding ( const model::table::column_id index )

Get the number of digits to round a column

Parameters

index imaging table column id

Returns: number of digits to round a column

void illumina::interop::logic::table::list_imaging_table_metrics_to_load ( std::vector< unsigned char > & valid_to_load )

List the required on demand metrics

Parameters

valid_to_load list of metrics to load on demand

uint32_t max_digits ( )

Get the maximum number of digits to round

Returns: maximum number of rounding digits

void illumina::interop::logic::table::populate_column_offsets ( std::vector< model::table::imaging_column > & columns )

Populate the value offsets from the column headers

Parameters

columns column headers

void illumina::interop::logic::table::populate_imaging_table_data	(	const model::metrics::run_metrics &	metrics,
		const std::vector< model::table::imaging_column > &	columns,
		const row_offset_map_t &	row_offset,
		float *	data_beg,
		const size_t	n
	)

Populate the imaging table with all the metrics in the run

Parameters

metrics	collection of all run metrics
columns	vector of table columns
row_offset	ordering for the rows
data_beg	iterator to start of table data
n	number of cells in the data table

void illumina::interop::logic::table::populate_imaging_table_data_by_cycle	(	InputIterator	beg,
		InputIterator	end,
		const size_t	q20_idx,
		const size_t	q30_idx,
		const constants::tile_naming_method	naming_method,
		const summary::read_cycle_vector_t &	cycle_to_read,
		const std::vector< size_t > &	columns,
		const row_offset_map_t &	row_offset,
		const size_t	column_count,
		OutputIterator	data_beg,
		OutputIterator	data_end
	)

Populate the imaging table with a by cycle InterOp metric set

Parameters

beg	iterator to start of the metric set
end	iterator to end of the metric set
q20_idx	index of the q20 value
q30_idx	index of the q30_idxindex value
naming_method	tile naming method enum
cycle_to_read	map cycle to read/cycle within read
columns	vector of table columns
row_offset	offset for each metric into the sorted table
column_count	number of data columns including sub columns
data_beg	iterator to start of table data
data_end	iterator to end of table data

void illumina::interop::logic::table::populate_imaging_table_data_by_cycle	(	const MetricSet &	metrics,
		const size_t	q20_idx,
		const size_t	q30_idx,
		const constants::tile_naming_method	naming_method,
		const summary::read_cycle_vector_t &	cycle_to_read,
		const std::vector< size_t > &	columns,
		const row_offset_map_t &	row_offset,
		const size_t	column_count,
		OutputIterator	data_beg,
		OutputIterator	data_end
	)

Populate the imaging table with a by cycle InterOp metric set

Parameters

metrics	InterOp metric set
q20_idx	index of the q20 value
q30_idx	index of the q30 value
naming_method	tile naming method enum
cycle_to_read	map cycle to read/cycle within read
columns	vector of table columns
row_offset	offset for each metric into the sorted table
column_count	number of data columns including sub columns
data_beg	iterator to start of table data
data_end	iterator to end of table data

void illumina::interop::logic::table::populate_imaging_table_data_t	(	const model::metrics::run_metrics &	metrics,
		const std::vector< model::table::imaging_column > &	columns,
		const row_offset_map_t &	row_offset,
		I	data_beg,
		const size_t	n
	)

Populate the imaging table with all the metrics in the run

Parameters

metrics	collection of all run metrics
columns	vector of table columns
row_offset	row offset map
data_beg	iterator to start of table data
n	number of cells in the data table

constants::metric_data illumina::interop::logic::table::to_data_type ( const size_t index )

Convert a column type to the data type

Parameters

index imaging table column index

Returns: metric data

constants::metric_group illumina::interop::logic::table::to_group ( const model::table::column_id type )

inline

Convert metric type to metric group

Parameters

type	metric type

Returns: metric group

void illumina::interop::logic::table::zero_first_column	(	I	beg,
		I	end,
		size_t	column_count
	)

Zero out first column of every row

Parameters

beg	iterator to start of colleciton
end	iterator to end of collection
column_count	number of columns

Variable Documentation

void populate_imaging_table_data (const model::metrics::run_metrics& metrics, const std::vector<model::table::imaging_column>& columns, const row_offset_map_t& row_offset, float* data_beg, const size_t n) INTEROP_THROW_SPEC((model voi count_table_rows) (const model::metrics::run_metrics &metrics, row_offset_map_t &row_offset)

Populate the imaging table with all the metrics in the run

Parameters

metrics	collection of all run metrics
columns	vector of table columns
row_offset	ordering for the rows
data_beg	iterator to start of table data
n	number of cells in the data table Count the number of rows in the imaging table and setup an ordering
metrics	collections of InterOp metric sets
row_offset	ordering for the rows

void create_imaging_table (model::metrics::run_metrics& metrics, model::table::imaging_table& table) INTEROP_THROW_SPEC((model void list_imaging_table_metrics_to_load(std::vector< unsigned char > &valid_to_load)

Create an imaging table from run metrics

Parameters

metrics	source run metrics
table	destination imaging table List the required on demand metrics
valid_to_load	list of metrics to load on demand

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation