libpappsomspp
Library for mass spectrometry
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Namespaces | Macros | Typedefs | Enumerations | Functions
types.h File Reference
#include <cstdint>
#include <map>
#include <QString>
#include <QtQml>
#include "pappsomspp/export-import-config.h"
#include "pappsomspp/config.h"

Go to the source code of this file.

Namespaces

namespace  pappso
 tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
 
namespace  pappso::Enums
 

Macros

#define PEPTIDE_ION_TYPE_COUNT   14
 only useful for internal use DO not change this value : it is used to define static array size
 

Typedefs

typedef QString pappso::PeptideStr
 A type definition for PeptideStr.
 
typedef double pappso::pappso_double
 A type definition for doubles.
 
typedef float pappso::pappso_float
 
typedef unsigned int pappso::uint
 

Enumerations

enum class  pappso::Enums::TimeUnit { pappso::Enums::none , pappso::Enums::s , pappso::Enums::min , pappso::Enums::h }
 
enum class  pappso::Enums::PrecisionUnit {
  pappso::Enums::none , pappso::Enums::dalton , pappso::Enums::ppm , pappso::Enums::res ,
  pappso::Enums::mz , pappso::Enums::last
}
 
enum class  pappso::Enums::AtomIsotopeSurvey : std::int8_t {
  pappso::Enums::C , pappso::Enums::H , pappso::Enums::O , pappso::Enums::N ,
  pappso::Enums::S , pappso::Enums::P , pappso::Enums::last
}
 
enum class  pappso::Enums::Isotope {
  pappso::Enums::C , pappso::Enums::C13 , pappso::Enums::H , pappso::Enums::H2 ,
  pappso::Enums::O , pappso::Enums::O17 , pappso::Enums::O18 , pappso::Enums::N ,
  pappso::Enums::N15 , pappso::Enums::S , pappso::Enums::S33 , pappso::Enums::S34 ,
  pappso::Enums::S36 , pappso::Enums::P
}
 
enum class  pappso::Enums::MsDataFormat : std::int8_t {
  pappso::Enums::unknown = 0 , pappso::Enums::mzML = 1 , pappso::Enums::mzXML = 2 , pappso::Enums::MGF = 3 ,
  pappso::Enums::SQLite3 = 4 , pappso::Enums::xy = 5 , pappso::Enums::mz5 = 6 , pappso::Enums::msn = 7 ,
  pappso::Enums::abSciexWiff = 8 , pappso::Enums::abSciexT2D = 9 , pappso::Enums::agilentMassHunter = 10 , pappso::Enums::thermoRaw = 11 ,
  pappso::Enums::watersRaw = 12 , pappso::Enums::brukerFid = 13 , pappso::Enums::brukerYep = 14 , pappso::Enums::brukerBaf = 15 ,
  pappso::Enums::brukerTims = 16 , pappso::Enums::brukerBafAscii = 17 , pappso::Enums::last = 18
}
 
enum class  pappso::Enums::FileReaderType {
  pappso::Enums::pwiz , pappso::Enums::xy , pappso::Enums::bafascii , pappso::Enums::tims ,
  pappso::Enums::tims_frames , pappso::Enums::tims_ms2 , pappso::Enums::tims_dia
}
 
enum class  pappso::Enums::AminoAcidChar : char {
  pappso::Enums::alanine = 'A' , pappso::Enums::cysteine = 'C' , pappso::Enums::aspartic_acid = 'D' , pappso::Enums::glutamic_acid = 'E' ,
  pappso::Enums::phenylalanine = 'F' , pappso::Enums::glycine = 'G' , pappso::Enums::histidine = 'H' , pappso::Enums::isoleucine = 'I' ,
  pappso::Enums::lysine = 'K' , pappso::Enums::leucine = 'L' , pappso::Enums::methionine = 'M' , pappso::Enums::asparagine = 'N' ,
  pappso::Enums::proline = 'P' , pappso::Enums::glutamine = 'Q' , pappso::Enums::arginine = 'R' , pappso::Enums::serine = 'S' ,
  pappso::Enums::threonine = 'T' , pappso::Enums::valine = 'V' , pappso::Enums::tryptophan = 'W' , pappso::Enums::tyrosine = 'Y' ,
  pappso::Enums::selenocysteine = 'U' , pappso::Enums::pyrrolysine = 'O'
}
 
enum class  pappso::Enums::SortType : std::int8_t { pappso::Enums::none = 0 , pappso::Enums::x = 1 , pappso::Enums::y = 2 }
 
enum class  pappso::Enums::SortOrder : std::int8_t { pappso::Enums::ascending = 0 , pappso::Enums::descending = 1 }
 
enum class  pappso::Enums::DataCompression : std::int8_t { pappso::Enums::unset = -1 , pappso::Enums::none = 0 , pappso::Enums::zlib = 1 }
 
enum class  pappso::Enums::DataKind : std::int8_t { pappso::Enums::unset = -1 , pappso::Enums::rt = 0 , pappso::Enums::dt = 1 , pappso::Enums::mz = 2 }
 
enum class  pappso::Enums::Axis : std::int8_t { pappso::Enums::unset = 0x000 , pappso::Enums::x = 1 << 0 , pappso::Enums::y = 1 << 1 , pappso::Enums::z = 1 << 2 }
 
enum class  pappso::Enums::AxisScale : std::int8_t { pappso::Enums::unset = 0 , pappso::Enums::orig = 1 , pappso::Enums::log10 = 2 }
 
enum class  pappso::Enums::XicExtractMethod : std::int8_t { pappso::Enums::sum = 1 , pappso::Enums::max = 2 }
 
enum class  pappso::Enums::PeptideIon : std::int8_t {
  pappso::Enums::b = 0 , pappso::Enums::bstar = 1 , pappso::Enums::bo = 2 , pappso::Enums::a = 3 ,
  pappso::Enums::astar = 4 , pappso::Enums::ao = 5 , pappso::Enums::bp = 6 , pappso::Enums::c = 7 ,
  pappso::Enums::y = 8 , pappso::Enums::ystar = 9 , pappso::Enums::yo = 10 , pappso::Enums::z = 11 ,
  pappso::Enums::yp = 12 , pappso::Enums::x = 13
}
 Enums::PeptideIon enum defines all types of ions (Nter or Cter) More...
 

Functions

const pappso_double pappso::MHPLUS (1.007276466879)
 
const pappso_double pappso::MPROTON (1.007276466879)
 
const pappso_double pappso::MPROTIUM (1.007825032241)
 
const pappso_double pappso::ONEMILLION (1000000)
 
const pappso_double pappso::MASSOXYGEN (15.99491461956)
 
const pappso_double pappso::MASSCARBON (12)
 
const pappso_double pappso::MASSH2O ((MPROTIUM *2)+MASSOXYGEN)
 
const pappso_double pappso::MASSNITROGEN (14.0030740048)
 
const pappso_double pappso::MASSNH3 ((MPROTIUM *3)+MASSNITROGEN)
 
const pappso_double pappso::MASSCO (MASSCARBON+MASSOXYGEN)
 
const pappso_double pappso::MASSPHOSPHORUS (30.973761998)
 
const pappso_double pappso::MASSSULFUR (31.9720711741)
 
const pappso_double pappso::MASSPHOSPHORYLATEDR (MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
 
const pappso_double pappso::MASSSELENIUM (79.916520)
 
const pappso_double pappso::DIFFC12C13 (1.0033548378)
 
const pappso_double pappso::DIFFS32S33 (32.9714589101 - MASSSULFUR)
 
const pappso_double pappso::DIFFS32S34 (33.9678670300 - MASSSULFUR)
 
const pappso_double pappso::DIFFS32S36 (35.9670812000 - MASSSULFUR)
 
const pappso_double pappso::DIFFH1H2 (2.0141017778 - MPROTIUM)
 
const pappso_double pappso::DIFFO16O18 (17.9991610 - MASSOXYGEN)
 
const pappso_double pappso::DIFFO16O17 (16.99913150 - MASSOXYGEN)
 
const pappso_double pappso::DIFFN14N15 (15.0001088982 - MASSNITROGEN)
 
const pappso_double pappso::ABUNDANCEH2 (0.00011570983569203332000374651045149221317842602729797363281250)
 
const pappso_double pappso::ABUNDANCEN15 (0.00364198543205827118818262988497735932469367980957031250000000)
 
const pappso_double pappso::ABUNDANCEO17 (0.00038099847600609595965615028489992255344986915588378906250000)
 
const pappso_double pappso::ABUNDANCEO18 (0.00205139179443282221315669744399201590567827224731445312500000)
 
const pappso_double pappso::ABUNDANCEC13 (0.01078805814953308406245469086570665240287780761718750000000000)
 
const pappso_double pappso::ABUNDANCEC12 (0.98921194185046687152862432412803173065185546875000000000000000)
 
const pappso_double pappso::ABUNDANCES33 (0.00751939844812414937003097747947322204709053039550781250000000)
 
const pappso_double pappso::ABUNDANCES34 (0.04252059835213182203972337447339668869972229003906250000000000)
 
const pappso_double pappso::ABUNDANCES36 (0.00010999120070394368536836893213148869108408689498901367187500)
 

Detailed Description

https://forgemia.inra.fr/pappso/massxpert/-/blob/be60e53480f68d36afa95c809cffd68d4fb46c79/data/polChemDefs/protein-1-letter-libisospec-atomic-data/protein-1-letter-libisospec-atomic-data.xml abundance of sulfur extracted from 'massXpert' polymer definitions

Definition in file types.h.

Macro Definition Documentation

◆ PEPTIDE_ION_TYPE_COUNT

#define PEPTIDE_ION_TYPE_COUNT   14

only useful for internal use DO not change this value : it is used to define static array size

Definition at line 478 of file types.h.

Referenced by pappso::XtandemHyperscoreBis::reset().