OpenMS  2.8.0
Public Member Functions | Private Member Functions | Private Attributes | List of all members
Tagger Class Reference

Calculate sequence tags from m/z values. More...

#include <OpenMS/CHEMISTRY/Tagger.h>

Collaboration diagram for Tagger:
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Public Member Functions

 Tagger (size_t min_tag_length, double ppm, size_t max_tag_length=65535, size_t min_charge=1, size_t max_charge=1, const StringList &fixed_mods=StringList(), const StringList &var_mods=StringList())
 Constructor for Tagger. More...
 
void getTag (const std::vector< double > &mzs, std::vector< std::string > &tags) const
 Generate tags from mass vector mzs. More...
 
void getTag (const MSSpectrum &spec, std::vector< std::string > &tags) const
 Generate tags from an MSSpectrum. More...
 
void setMaxCharge (size_t max_charge)
 Change the maximal charge considered by the tagger. More...
 

Private Member Functions

char getAAByMass_ (double m) const
 get a residue one letter code by matching the mass m to the map of residues mass2aa_, returns ' ' if there is no match More...
 
void getTag_ (std::string &tag, const std::vector< double > &mzs, const size_t i, std::vector< std::string > &tags, const size_t charge) const
 start searching for tags starting from peak i of the mz vector mzs More...
 

Private Attributes

double min_gap_
 will be set to smallest residue mass in ResidueDB More...
 
double max_gap_
 will be set to highest residue mass in ResidueDB More...
 
double ppm_
 tolerance More...
 
size_t min_tag_length_
 minimum tag length More...
 
size_t max_tag_length_
 maximum tag length More...
 
size_t min_charge_
 minimal fragment charge More...
 
size_t max_charge_
 maximal fragment charge More...
 
std::map< double, char > mass2aa_
 mapping of residue masses to their one letter codes More...
 

Detailed Description

Calculate sequence tags from m/z values.

Current restrictions and potential extensions:

Constructor & Destructor Documentation

◆ Tagger()

Tagger ( size_t  min_tag_length,
double  ppm,
size_t  max_tag_length = 65535,
size_t  min_charge = 1,
size_t  max_charge = 1,
const StringList fixed_mods = StringList(),
const StringList var_mods = StringList() 
)

Constructor for Tagger.

The parameter max_charge_ should be >= min_charge_. Also max_tag_length should be >= min_tag_length.

Parameters
min_tag_lengththe minimal sequence tag length.
ppmthe tolerance for matching residue masses to peak delta masses.
max_tag_lengththe maximal sequence tag length.
min_chargeminimal fragment charge considered for each sequence tag.
max_chargemaximal fragment charge considered for each sequence tag.
fixed_modsa list of modification names. The modified residues replace the unmodified versions.
var_modsa list of modification names. The modified residues are added as additional entries to the list of residues.

Member Function Documentation

◆ getAAByMass_()

char getAAByMass_ ( double  m) const
private

get a residue one letter code by matching the mass m to the map of residues mass2aa_, returns ' ' if there is no match

◆ getTag() [1/2]

void getTag ( const MSSpectrum spec,
std::vector< std::string > &  tags 
) const

Generate tags from an MSSpectrum.

The parameter tags is filled with one string per sequence tag. It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor.

Parameters
speca centroided fragment spectrum.
tagsthe vector of tags, that is filled with this function.

◆ getTag() [2/2]

void getTag ( const std::vector< double > &  mzs,
std::vector< std::string > &  tags 
) const

Generate tags from mass vector mzs.

The parameter tags is filled with one string per sequence tag. It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor.

Parameters
mzsa vector of mz values, containing the mz values from a centroided fragment spectrum.
tagsthe vector of tags, that is filled with this function.

◆ getTag_()

void getTag_ ( std::string &  tag,
const std::vector< double > &  mzs,
const size_t  i,
std::vector< std::string > &  tags,
const size_t  charge 
) const
private

start searching for tags starting from peak i of the mz vector mzs

◆ setMaxCharge()

void setMaxCharge ( size_t  max_charge)

Change the maximal charge considered by the tagger.

Allows to change the maximal considered charge e.g. based on a spectra precursor charge without calling the constructor multiple times.

Parameters
max_chargethe new maximal charge.

Member Data Documentation

◆ mass2aa_

std::map<double, char> mass2aa_
private

mapping of residue masses to their one letter codes

◆ max_charge_

size_t max_charge_
private

maximal fragment charge

◆ max_gap_

double max_gap_
private

will be set to highest residue mass in ResidueDB

◆ max_tag_length_

size_t max_tag_length_
private

maximum tag length

◆ min_charge_

size_t min_charge_
private

minimal fragment charge

◆ min_gap_

double min_gap_
private

will be set to smallest residue mass in ResidueDB

◆ min_tag_length_

size_t min_tag_length_
private

minimum tag length

◆ ppm_

double ppm_
private

tolerance