RNPxlSearch::RNPxlParameterParsing Struct Reference

Public Types
using	NucleotideToFragmentAdductMap = map< char, set< FragmentAdductDefinition_ > >
using	PrecursorsToMS2Adducts = map< String, MS2AdductsOfSinglePrecursorAdduct >

Static Public Member Functions
static vector< ResidueModification >	getModifications (StringList modNames)
	Query ResidueModifications (given as strings) from ModificationsDB. More...
static NucleotideToFragmentAdductMap	getTargetNucleotideToFragmentAdducts (StringList fragment_adducts)
static MS2AdductsOfSinglePrecursorAdduct	getFeasibleFragmentAdducts (const String &exp_pc_adduct, const String &exp_pc_formula, const NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const set< char > &can_xl)
static PrecursorsToMS2Adducts	getAllFeasibleFragmentAdducts (const RNPxlModificationMassesResult &precursor_adducts, const NucleotideToFragmentAdductMap &nucleotide_to_fragment_adducts, const set< char > &can_xl)

Member Typedef Documentation

NucleotideToFragmentAdductMap

using NucleotideToFragmentAdductMap = map<char, set<FragmentAdductDefinition_> >

PrecursorsToMS2Adducts

using PrecursorsToMS2Adducts = map<String, MS2AdductsOfSinglePrecursorAdduct>

Member Function Documentation

getAllFeasibleFragmentAdducts()

RNPxlSearch::RNPxlParameterParsing::PrecursorsToMS2Adducts getAllFeasibleFragmentAdducts ( const RNPxlModificationMassesResult &  precursor_adducts, const NucleotideToFragmentAdductMap &  nucleotide_to_fragment_adducts, const set< char > &  can_xl  )

static

References LOG_DEBUG, RNPxlModificationMassesResult::mod_combinations, and RNPxlModificationMassesResult::mod_masses.

getFeasibleFragmentAdducts()

RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct getFeasibleFragmentAdducts ( const String &  exp_pc_adduct, const String &  exp_pc_formula, const NucleotideToFragmentAdductMap &  nucleotide_to_fragment_adducts, const set< char > &  can_xl  )

static

References RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct::feasible_adducts, RNPxlSearch::FragmentAdductDefinition_::formula, String::hasSubstring(), LOG_DEBUG, RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct::marker_ions, RNPxlSearch::FragmentAdductDefinition_::mass, RNPxlSearch::FragmentAdductDefinition_::name, OpenMS::StringConversions::toString(), and EmpiricalFormula::toString().

getModifications()

vector< ResidueModification > getModifications ( StringList  modNames )

static

Query ResidueModifications (given as strings) from ModificationsDB.

References ResidueModification::C_TERM, ModificationsDB::getInstance(), ModificationsDB::getModification(), and ResidueModification::N_TERM.

getTargetNucleotideToFragmentAdducts()

RNPxlSearch::RNPxlParameterParsing::NucleotideToFragmentAdductMap getTargetNucleotideToFragmentAdducts ( StringList  fragment_adducts )

static

References ModificationsDB::addModification(), ResidueModification::C_TERM, RNPxlSearch::FragmentAdductDefinition_::formula, ModificationsDB::getInstance(), EmpiricalFormula::getMonoWeight(), LOG_WARN, RNPxlSearch::FragmentAdductDefinition_::mass, ResidueModification::N_TERM, RNPxlSearch::FragmentAdductDefinition_::name, ResidueModification::setDiffMonoMass(), ResidueModification::setFullId(), ResidueModification::setId(), ResidueModification::setName(), ResidueModification::setTermSpecificity(), and EmpiricalFormula::toString().