NuXLParameterParsing Struct Reference

#include <OpenNuXL/include/NuXLParameterParsing.h>

Public Types
using	NucleotideToFragmentAdductMap = std::map< char, std::set< NuXLFragmentAdductDefinition > >
using	PrecursorsToMS2Adducts = std::map< std::string, MS2AdductsOfSinglePrecursorAdduct >

Static Public Member Functions
static std::vector< ResidueModification >	getModifications (StringList modNames)
	Query ResidueModifications (given as strings) from ModificationsDB.
static NucleotideToFragmentAdductMap	getTargetNucleotideToFragmentAdducts (StringList fragment_adducts)
static MS2AdductsOfSinglePrecursorAdduct	getFeasibleFragmentAdducts (const std::string &exp_pc_adduct, const std::string &exp_pc_formula, const NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const std::set< char > &can_xl, const bool always_add_default_marker_ions, const bool default_marker_ions_RNA)
static std::vector< NuXLFragmentAdductDefinition >	getMarkerIonsMassSet (const PrecursorsToMS2Adducts &pc2adducts)
static PrecursorsToMS2Adducts	getAllFeasibleFragmentAdducts (const NuXLModificationMassesResult &precursor_adducts, const NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const std::set< char > &can_xl, const bool always_add_default_marker_ions, const bool default_marker_ions_RNA)

Member Typedef Documentation

NucleotideToFragmentAdductMap

using NucleotideToFragmentAdductMap = std::map<char, std::set<NuXLFragmentAdductDefinition> >

PrecursorsToMS2Adducts

using PrecursorsToMS2Adducts = std::map<std::string, MS2AdductsOfSinglePrecursorAdduct>

Member Function Documentation

getAllFeasibleFragmentAdducts()

NuXLParameterParsing::PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts ( const NuXLModificationMassesResult &  precursor_adducts, const NucleotideToFragmentAdductMap &  nucleotide_to_fragment_adducts, const std::set< char > &  can_xl, const bool  always_add_default_marker_ions, const bool  default_marker_ions_RNA  )

static

References NuXLModificationMassesResult::formula2mass, NuXLParameterParsing::getFeasibleFragmentAdducts(), NuXLModificationMassesResult::mod_combinations, and OPENMS_LOG_DEBUG.

getFeasibleFragmentAdducts()

MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts ( const std::string &  exp_pc_adduct, const std::string &  exp_pc_formula, const NucleotideToFragmentAdductMap &  nucleotide_to_fragment_adducts, const std::set< char > &  can_xl, const bool  always_add_default_marker_ions, const bool  default_marker_ions_RNA  )

static

References MS2AdductsOfSinglePrecursorAdduct::feasible_adducts, NuXLFragmentAdductDefinition::formula, OpenMS::StringUtils::hasSubstring(), MS2AdductsOfSinglePrecursorAdduct::marker_ions, NuXLFragmentAdductDefinition::mass, NuXLFragmentAdductDefinition::name, OPENMS_LOG_DEBUG, OPENMS_LOG_WARN, OpenMS::StringUtils::toStr(), and EmpiricalFormula::toString().

Referenced by NuXLParameterParsing::getAllFeasibleFragmentAdducts().

getMarkerIonsMassSet()

std::vector< NuXLFragmentAdductDefinition > getMarkerIonsMassSet ( const PrecursorsToMS2Adducts &  pc2adducts )

static

References NuXLFragmentAdductDefinition::mass, and NuXLFragmentAdductDefinition::name.

getModifications()

vector< ResidueModification > getModifications ( StringList  modNames )

static

Query ResidueModifications (given as strings) from ModificationsDB.

References ResidueModification::C_TERM, ModificationsDB::getInstance(), ModificationsDB::getModification(), OpenMS::StringUtils::hasSubstring(), ResidueModification::N_TERM, and OpenMS::StringUtils::substitute().

getTargetNucleotideToFragmentAdducts()

NuXLParameterParsing::NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts ( StringList  fragment_adducts )

static

References ModificationsDB::addModification(), ResidueModification::C_TERM, ResidueModification::DEFINED, NuXLFragmentAdductDefinition::formula, ModificationsDB::getInstance(), EmpiricalFormula::getMonoWeight(), NuXLFragmentAdductDefinition::mass, ResidueModification::N_TERM, NuXLFragmentAdductDefinition::name, OPENMS_LOG_WARN, OpenMS::StringUtils::removeWhitespaces(), ResidueModification::setId(), OpenMS::StringUtils::split(), OpenMS::StringUtils::substr(), EmpiricalFormula::toString(), and ResidueModification::toString().