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 More...
virtual	~ConsensusMapNormalizerAlgorithmMedian ()
	destructor is not implemented -> private More...

Static Public Member Functions
static void	normalizeMaps (ConsensusMap &map, NormalizationMethod method, const String &acc_filter, const String &desc_filter)
	normalizes the maps of the consensusMap More...
static Size	computeMedians (const ConsensusMap &map, std::vector< double > &medians, const String &acc_filter, const String &desc_filter)
	computes medians of all maps and returns index of map with most features More...
static bool	passesFilters_ (ConsensusMap::ConstIterator cf_it, const ConsensusMap &map, const String &acc_filter, const 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 More...

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

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

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 String &  acc_filter, const String &  desc_filter  )

static

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

Parameters

map	ConsensusMap
medians	vector of medians to be filled
acc_filter	string describing the regular expression for filtering accessions
desc_filter	string describing the regular expression for filtering descriptions

Returns

index of map with largest number of features

normalizeMaps()

static void normalizeMaps ( ConsensusMap &  map, NormalizationMethod  method, const String &  acc_filter, const String &  desc_filter  )

static

normalizes the maps of the consensusMap

Parameters

map	ConsensusMap
method	whether to use scaling or shifting to same median
acc_filter	string describing the regular expression for filtering accessions
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 String &  acc_filter, const 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

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

Friends And Related Function Documentation

ConsensusMapNormalizerAlgorithmThreshold

friend class ConsensusMapNormalizerAlgorithmThreshold

friend

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