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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>`
`#include <cstdint>`

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

## 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::TimeUnit { pappso::none , pappso::s , pappso::min , pappso::h }
enum class | pappso::PrecisionUnit { pappso::none , pappso::dalton , pappso::ppm , pappso::res , pappso::mz , pappso::last }
enum class | pappso::AtomIsotopeSurvey : std::int8_t { pappso::C , pappso::H , pappso::O , pappso::N , pappso::S , pappso::last }
enum class | pappso::Isotope { pappso::C13 , pappso::H2 , pappso::O17 , pappso::O18 , pappso::N15 , pappso::S33 , pappso::S34 , pappso::S36 }

enum class

pappso::MsDataFormat : std::int8_t {
pappso::unknown = 0 , pappso::mzML = 1 , pappso::mzXML = 2 , pappso::MGF = 3 ,
pappso::SQLite3 = 4 , pappso::xy = 5 , pappso::mz5 = 6 , pappso::msn = 7 ,
pappso::abSciexWiff = 8 , pappso::abSciexT2D = 9 , pappso::agilentMassHunter = 10 , pappso::thermoRaw = 11 ,
pappso::watersRaw = 12 , pappso::brukerFid = 13 , pappso::brukerYep = 14 , pappso::brukerBaf = 15 ,
pappso::brukerTims = 16 , pappso::brukerBafAscii = 17 , pappso::last = 18
}

enum class | pappso::FileReaderType { pappso::pwiz , pappso::xy , pappso::bafascii , pappso::tims , pappso::tims_frames , pappso::tims_ms2 , pappso::tims_dia }

enum class

pappso::AminoAcidChar : char {
pappso::alanine = 'A' , pappso::cysteine = 'C' , pappso::aspartic_acid = 'D' , pappso::glutamic_acid = 'E' ,
pappso::phenylalanine = 'F' , pappso::glycine = 'G' , pappso::histidine = 'H' , pappso::isoleucine = 'I' ,
pappso::lysine = 'K' , pappso::leucine = 'L' , pappso::methionine = 'M' , pappso::asparagine = 'N' ,
pappso::proline = 'P' , pappso::glutamine = 'Q' , pappso::arginine = 'R' , pappso::serine = 'S' ,
pappso::threonine = 'T' , pappso::valine = 'V' , pappso::tryptophan = 'W' , pappso::tyrosine = 'Y' ,
pappso::selenocysteine = 'U' , pappso::pyrrolysine = 'O'
}

enum class | pappso::SortType : std::int8_t { pappso::no_sort = 0 , pappso::x = 1 , pappso::y = 2 }
enum class | pappso::SortOrder : std::int8_t { pappso::ascending = 0 , pappso::descending = 1 }
enum class | pappso::DataCompression : std::int8_t { pappso::unset = -1 , pappso::none = 0 , pappso::zlib = 1 }
enum class | pappso::DataKind : std::int8_t { pappso::unset = -1 , pappso::rt = 0 , pappso::dt = 1 , pappso::mz = 2 }
enum class | pappso::Axis : std::int8_t { pappso::unset = 0x000 , pappso::x = 1 << 0 , pappso::y = 1 << 1 , pappso::z = 1 << 2 }
enum class | pappso::AxisScale : std::int8_t { pappso::unset = 0 , pappso::orig = 1 , pappso::log10 = 2 }
enum class | pappso::XicExtractMethod : std::int8_t { pappso::sum = 1 , pappso::max = 2 }
enum class | pappso::PeptideIon : std::int8_t { pappso::b = 0 , pappso::bstar = 1 , pappso::bo = 2 , pappso::a = 3 , pappso::astar = 4 , pappso::ao = 5 , pappso::bp = 6 , pappso::c = 7 , pappso::y = 8 , pappso::ystar = 9 , pappso::yo = 10 , pappso::z = 11 , pappso::yp = 12 , pappso::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 (31.9720711741)
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

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

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 452 of file types.h.