ConsensusMapNormalizerAlgorithmMedian Class Reference

Algorithms of ConsensusMapNormalizer. More...

#include <OpenMS/ANALYSIS/MAPMATCHING/ConsensusMapNormalizerAlgorithmMedian.h>

Public Types
enum	NormalizationMethod { NM_SCALE , NM_SHIFT }
	The NormalizationMethod enum Whether to scale to same median using division/multiplication or shift using subtraction/addition. More...

Public Member Functions
	ConsensusMapNormalizerAlgorithmMedian ()
	default constructor is not implemented -> private
virtual	~ConsensusMapNormalizerAlgorithmMedian ()
	destructor is not implemented -> private

Static Public Member Functions
static void	normalizeMaps (ConsensusMap &map, NormalizationMethod method, const std::string &acc_filter, const std::string &desc_filter)
	normalizes the maps of the consensusMap
static Size	computeMedians (const ConsensusMap &map, std::vector< double > &medians, const std::string &acc_filter, const std::string &desc_filter)
	computes medians of all maps and returns index of map with most features
static bool	passesFilters_ (ConsensusMap::ConstIterator cf_it, const ConsensusMap &map, const std::string &acc_filter, const std::string &desc_filter)
	returns whether consensus feature passes filters returns whether consensus feature cf_it in map passes accession regexp acc_filter and description regexp desc_filter
static std::map< UInt64, Size >	mapPositions_ (const ConsensusMap &map)
	Position of every map index among the column headers of map (in map index order)
static Size	mapPosition_ (const std::map< UInt64, Size > &positions, UInt64 map_index)
	Position of map_index in positions (from mapPositions_())

Private Member Functions
	ConsensusMapNormalizerAlgorithmMedian (const ConsensusMapNormalizerAlgorithmMedian &copyin)
	copy constructor is not implemented -> private
ConsensusMapNormalizerAlgorithmMedian &	operator= (const ConsensusMapNormalizerAlgorithmMedian &rhs)
	assignment operator is not implemented -> private

Friends
class	ConsensusMapNormalizerAlgorithmThreshold
	our friend can use our passesWhitelist_() method in order to avoid code duplication (without overdesigning this)

Detailed Description

Algorithms of ConsensusMapNormalizer.

Member Enumeration Documentation

NormalizationMethod

enum NormalizationMethod

The NormalizationMethod enum Whether to scale to same median using division/multiplication or shift using subtraction/addition.

Enumerator
NM_SCALE
NM_SHIFT

Constructor & Destructor Documentation

ConsensusMapNormalizerAlgorithmMedian() [1/2]

ConsensusMapNormalizerAlgorithmMedian ( const ConsensusMapNormalizerAlgorithmMedian &  copyin )

private

copy constructor is not implemented -> private

ConsensusMapNormalizerAlgorithmMedian() [2/2]

ConsensusMapNormalizerAlgorithmMedian

(

)

default constructor is not implemented -> private

~ConsensusMapNormalizerAlgorithmMedian()

virtual ~ConsensusMapNormalizerAlgorithmMedian ( )

virtual

destructor is not implemented -> private

Member Function Documentation

computeMedians()

static Size computeMedians ( const ConsensusMap &  map, std::vector< double > &  medians, const std::string &  acc_filter, const std::string &  desc_filter  )

static

computes medians of all maps and returns index of map with most features

The maps are numbered by their position among the column headers (see mapPositions_()); for maps numbered 0 ... N-1 this is the map index.

Parameters

[in]	map	ConsensusMap
[out]	medians	vector of medians to be filled, one per map (by position)
[in]	acc_filter	string describing the regular expression for filtering accessions
[in]	desc_filter	string describing the regular expression for filtering descriptions

Returns

position of the map with the largest number of features (ColumnHeader::size)

Exceptions

Exception::ElementNotFound

if a feature handle's map index has no column header

mapPosition_()

static Size mapPosition_ ( const std::map< UInt64, Size > &  positions, UInt64  map_index  )

static

Position of map_index in positions (from mapPositions_())

Exceptions

Exception::ElementNotFound

if map_index has no column header

mapPositions_()

static std::map< UInt64, Size > mapPositions_ ( const ConsensusMap &  map )

static

Position of every map index among the column headers of map (in map index order)

Map indices need not be consecutive: FileFilter keeps them when it extracts maps (-consensus:map). The per-map vectors of the normalization algorithms are therefore indexed by these positions. For maps numbered 0 ... N-1 the position is the map index.

Parameters

[in]

map

consensus map

Returns

map index -> position

normalizeMaps()

static void normalizeMaps ( ConsensusMap &  map, NormalizationMethod  method, const std::string &  acc_filter, const std::string &  desc_filter  )

static

normalizes the maps of the consensusMap

Parameters

[in]	map	ConsensusMap
[in]	method	whether to use scaling or shifting to same median
[in]	acc_filter	string describing the regular expression for filtering accessions
[in]	desc_filter	string describing the regular expression for filtering descriptions

operator=()

ConsensusMapNormalizerAlgorithmMedian & operator= ( const ConsensusMapNormalizerAlgorithmMedian &  rhs )

private

assignment operator is not implemented -> private

passesFilters_()

static bool passesFilters_ ( ConsensusMap::ConstIterator  cf_it, const ConsensusMap &  map, const std::string &  acc_filter, const std::string &  desc_filter  )

static

returns whether consensus feature passes filters returns whether consensus feature cf_it in map passes accession regexp acc_filter and description regexp desc_filter

Parameters

[in]	cf_it	consensus feature
[in]	map	consensus map
[in]	acc_filter	string describing the regular expression for filtering accessions
[in]	desc_filter	string describing the regular expression for filtering descriptions

Friends And Related Symbol Documentation

ConsensusMapNormalizerAlgorithmThreshold

friend class ConsensusMapNormalizerAlgorithmThreshold

friend

our friend can use our passesWhitelist_() method in order to avoid code duplication (without overdesigning this)