| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Friends | List of all members
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

Referenced by UTILProteomicsLFQ::quantifyFraction_().

## ◆ 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)