#include <OpenMS/KERNEL/StandardTypes.h>
#include "NuXLReport.h"
#include <OpenMS/MATH/MathFunctions.h>
#include <boost/range/adaptor/reversed.hpp>
#include <OpenMS/ANALYSIS/ID/IDBoostGraph.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>

Classes
struct	AALevelLocalization

struct	AALevelLocalization::LocalizedXL

struct	RegionLevelLocalization

struct	RegionLevelLocalization::UnlocalizedXL

struct	ProteinReport

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Typedefs
using	ProteinsReport = map< std::string, ProteinReport >

Functions
ProteinsReport	getProteinReportEntries (const PeptideIdentificationList &peps, const map< std::string, ProteinHit * > &acc2protein_targets, const std::map< string, set< string > > &peptide2proteins)

set< string >	printXLSiteDetails (TextFile &tsv_file, const std::string &accession, size_t position, const AALevelLocalization &aa_loc, map< string, vector< RegionLevelLocalization::UnlocalizedXL > > &peptides2unlocalizedXL, std::map< std::string, std::set< std::string > > &peptide2proteins, map< string, map< string, set< pair< size_t, size_t > > > > &peptides2proteins2regions, map< string, set< string > > &protein2proteins)

void	printXLRegionDetails (TextFile &tsv_file, const std::string &accession, const RegionLevelLocalization &region_loc, const set< string > &remaining_peptides, std::map< std::string, std::set< std::string > > &peptide2proteins, map< string, map< string, set< pair< size_t, size_t > > > > &peptides2proteins2regions, map< string, set< string > > &protein2proteins)

Variables
std::unordered_map< std::string, double >	peptide_seq2XLFDR

Class Documentation

◆ OpenMS::AALevelLocalization

struct OpenMS::AALevelLocalization

Class Members
string	AA
map< string, vector< LocalizedXL > >	peptide2XL

◆ OpenMS::AALevelLocalization::LocalizedXL

struct OpenMS::AALevelLocalization::LocalizedXL

Class Members
string	adduct
int	charge = 0
string	NT

◆ OpenMS::RegionLevelLocalization

struct OpenMS::RegionLevelLocalization

Class Members
map< string, vector< UnlocalizedXL > >	peptide2unlocalizedXL

◆ OpenMS::RegionLevelLocalization::UnlocalizedXL

struct OpenMS::RegionLevelLocalization::UnlocalizedXL

Class Members
string	adduct
int	charge = 0

◆ OpenMS::ProteinReport

struct OpenMS::ProteinReport

Class Members
map< size_t, AALevelLocalization >	aa_level_localization
size_t	CSMs_of_shared_peptides = 0
size_t	CSMs_of_unique_peptides = 0
map< pair< size_t, size_t >, RegionLevelLocalization >	region_level_localization
string	sequence

Classes

Namespaces

Typedefs