libpappsomspp
Library for mass spectrometry
types.h File Reference

This header contains all the type re-definitions and all the global variables definitions used in the PAPPSOms++ library. More...

#include <QString>

Go to the source code of this file.

Namespaces

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

Macros

#define PEPTIDE_ION_TYPE_COUNT   14
 only usefull for inernal usefull DO not change this value : it is used to define static array size More...
 

Typedefs

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

Enumerations

enum  pappso::PrecisionUnit {
  pappso::PrecisionUnit::none, pappso::PrecisionUnit::dalton, pappso::PrecisionUnit::ppm, pappso::PrecisionUnit::res,
  pappso::PrecisionUnit::mz, pappso::PrecisionUnit::last
}
 
enum  pappso::AtomIsotopeSurvey : std::int8_t {
  pappso::AtomIsotopeSurvey::C, pappso::AtomIsotopeSurvey::H, pappso::AtomIsotopeSurvey::O, pappso::AtomIsotopeSurvey::N,
  pappso::AtomIsotopeSurvey::S, pappso::AtomIsotopeSurvey::last
}
 
enum  pappso::Isotope {
  pappso::Isotope::C13, pappso::Isotope::H2, pappso::Isotope::O17, pappso::Isotope::O18,
  pappso::Isotope::N15, pappso::Isotope::S33, pappso::Isotope::S34, pappso::Isotope::S36
}
 
enum  pappso::MzFormat : std::int8_t {
  pappso::MzFormat::unknown = 0, pappso::MzFormat::mzML = 1, pappso::MzFormat::mzXML = 2, pappso::MzFormat::MGF = 3,
  pappso::MzFormat::SQLite3 = 4, pappso::MzFormat::xy = 5, pappso::MzFormat::mz5 = 6, pappso::MzFormat::msn = 7,
  pappso::MzFormat::abSciexWiff = 8, pappso::MzFormat::abSciexT2D = 9, pappso::MzFormat::agilentMassHunter = 10, pappso::MzFormat::thermoRaw = 11,
  pappso::MzFormat::watersRaw = 12, pappso::MzFormat::brukerFid = 13, pappso::MzFormat::brukerYep = 14, pappso::MzFormat::brukerBaf = 15,
  pappso::MzFormat::brukerTims = 16, pappso::MzFormat::last = 17
}
 
enum  pappso::AminoAcidChar : char {
  pappso::AminoAcidChar::alanine = 'A', pappso::AminoAcidChar::cysteine = 'C', pappso::AminoAcidChar::aspartic_acid = 'D', pappso::AminoAcidChar::glutamic_acid = 'E',
  pappso::AminoAcidChar::phenylalanine = 'F', pappso::AminoAcidChar::glycine = 'G', pappso::AminoAcidChar::histidine = 'H', pappso::AminoAcidChar::isoleucine = 'I',
  pappso::AminoAcidChar::lysine = 'K', pappso::AminoAcidChar::leucine = 'L', pappso::AminoAcidChar::methionine = 'M', pappso::AminoAcidChar::asparagine = 'N',
  pappso::AminoAcidChar::proline = 'P', pappso::AminoAcidChar::glutamine = 'Q', pappso::AminoAcidChar::arginine = 'R', pappso::AminoAcidChar::serine = 'S',
  pappso::AminoAcidChar::threonine = 'T', pappso::AminoAcidChar::valine = 'V', pappso::AminoAcidChar::tryptophan = 'W', pappso::AminoAcidChar::tyrosine = 'Y',
  pappso::AminoAcidChar::selenocysteine = 'U', pappso::AminoAcidChar::pyrrolysine = 'O'
}
 
enum  pappso::DataCompression : std::int8_t { pappso::DataCompression::unset = -1, pappso::DataCompression::none = 0, pappso::DataCompression::zlib = 1 }
 
enum  pappso::DataKind : std::int8_t { pappso::DataKind::unset = -1, pappso::DataKind::rt = 0, pappso::DataKind::dt = 1, pappso::DataKind::mz = 2 }
 
enum  pappso::Axis : std::int8_t { pappso::Axis::unset = 0, pappso::Axis::x = 1, pappso::Axis::y = 2, pappso::Axis::z = 3 }
 
enum  pappso::AxisScale : std::int8_t { pappso::AxisScale::unset = 0, pappso::AxisScale::orig = 1, pappso::AxisScale::log10 = 2 }
 
enum  pappso::XicExtractMethod : std::int8_t { pappso::XicExtractMethod::sum = 1, pappso::XicExtractMethod::max = 2 }
 
enum  pappso::PeptideIon : std::int8_t {
  pappso::PeptideIon::b = 0, pappso::PeptideIon::bstar = 1, pappso::PeptideIon::bo = 2, pappso::PeptideIon::a = 3,
  pappso::PeptideIon::astar = 4, pappso::PeptideIon::ao = 5, pappso::PeptideIon::bp = 6, pappso::PeptideIon::c = 7,
  pappso::PeptideIon::y = 8, pappso::PeptideIon::ystar = 9, pappso::PeptideIon::yo = 10, pappso::PeptideIon::z = 11,
  pappso::PeptideIon::yp = 12, pappso::PeptideIon::x = 13
}
 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 (31.97207100)
 
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 (32.97145876 - MASSSULFUR)
 
const pappso_double pappso::DIFFS32S34 (33.96786690 - MASSSULFUR)
 
const pappso_double pappso::DIFFS32S36 (35.96708076 - 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 (0.00015574)
 
const pappso_double pappso::ABUNDANCEN15 (0.003663)
 
const pappso_double pappso::ABUNDANCEO17 (0.000372)
 
const pappso_double pappso::ABUNDANCEO18 (0.0020004)
 
const pappso_double pappso::ABUNDANCEC13 (0.011078)
 
const pappso_double pappso::ABUNDANCEC12 (0.988922)
 
const pappso_double pappso::ABUNDANCES33 (0.00750)
 
const pappso_double pappso::ABUNDANCES34 (0.04215)
 
const pappso_double pappso::ABUNDANCES36 (0.00020)
 

Detailed Description

This header contains all the type re-definitions and all the global variables definitions used in the PAPPSOms++ library.

Date
4/3/2015
Author
Olivier Langella

Definition in file types.h.

Macro Definition Documentation

◆ PEPTIDE_ION_TYPE_COUNT

#define PEPTIDE_ION_TYPE_COUNT   14

only usefull for inernal usefull DO not change this value : it is used to define static array size

Definition at line 371 of file types.h.