pappso::Enums Namespace Reference

Enumerations
enum class	TimeUnit { none , s , min , h }
enum class	PrecisionUnit {   none , dalton , ppm , res ,   mz , last }
enum class	AtomIsotopeSurvey : std::int8_t {   C , H , O , N ,   S , P , last }
enum class	Isotope {   C , C13 , H , H2 ,   O , O17 , O18 , N ,   N15 , S , S33 , S34 ,   S36 , P }
enum class	MsDataFormat : std::int8_t {   unknown = 0 , mzML = 1 , mzXML = 2 , MGF = 3 ,   SQLite3 = 4 , xy = 5 , mz5 = 6 , msn = 7 ,   abSciexWiff = 8 , abSciexT2D = 9 , agilentMassHunter = 10 , thermoRaw = 11 ,   watersRaw = 12 , brukerFid = 13 , brukerYep = 14 , brukerBaf = 15 ,   brukerTims = 16 , brukerBafAscii = 17 , mzcbor = 18 , last = 19 }
enum class	FileReaderType {   pwiz , mzcbor , xy , bafascii ,   tims , tims_frames , tims_ms2 , tims_dia }
enum class	AminoAcidChar : char {   alanine = 'A' , cysteine = 'C' , aspartic_acid = 'D' , glutamic_acid = 'E' ,   phenylalanine = 'F' , glycine = 'G' , histidine = 'H' , isoleucine = 'I' ,   lysine = 'K' , leucine = 'L' , methionine = 'M' , asparagine = 'N' ,   proline = 'P' , glutamine = 'Q' , arginine = 'R' , serine = 'S' ,   threonine = 'T' , valine = 'V' , tryptophan = 'W' , tyrosine = 'Y' ,   selenocysteine = 'U' , pyrrolysine = 'O' }
enum class	SortType : std::int8_t { none = 0 , x = 1 , y = 2 }
enum class	SortOrder : std::int8_t { ascending = 0 , descending = 1 }
enum class	DataCompression : std::int8_t { unset = -1 , none = 0 , zlib = 1 }
enum class	DataKind : std::int8_t { unset = -1 , rt = 0 , dt = 1 , mz = 2 }
enum class	Axis : std::int8_t { unset = 0x000 , x = 1 << 0 , y = 1 << 1 , z = 1 << 2 }
enum class	AxisScale : std::int8_t { unset = 0 , orig = 1 , log10 = 2 }
enum class	XicExtractMethod : std::int8_t { sum = 1 , max = 2 }
enum class	PeptideIon : std::int8_t {   b = 0 , bstar = 1 , bo = 2 , a = 3 ,   astar = 4 , ao = 5 , bp = 6 , c = 7 ,   y = 8 , ystar = 9 , yo = 10 , z = 11 ,   yp = 12 , x = 13 }
	Enums::PeptideIon enum defines all types of ions (Nter or Cter). More...

Enumeration Type Documentation

AminoAcidChar

enum class pappso::Enums::AminoAcidChar : char

strong

Enumerator
alanine
cysteine
aspartic_acid
glutamic_acid
phenylalanine
glycine
histidine
isoleucine
lysine
leucine
methionine
asparagine
proline
glutamine
arginine
serine
threonine
valine
tryptophan
tyrosine
selenocysteine
pyrrolysine

Definition at line 195 of file types.h.

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

AtomIsotopeSurvey

enum class pappso::Enums::AtomIsotopeSurvey : std::int8_t

strong

Enumerator
C
H
O
N
S
P
last

Definition at line 109 of file types.h.

{
  C,
  H,
  O,
  N,
  S,
  P,
  last
};

Axis

enum class pappso::Enums::Axis : std::int8_t

strong

Enumerator
unset
x
y
z

Definition at line 257 of file types.h.

{
  unset = 0x000,
  x     = 1 << 0,
  y     = 1 << 1,
  z     = 1 << 2,
};

AxisScale

enum class pappso::Enums::AxisScale : std::int8_t

strong

Enumerator
unset
orig
log10

Definition at line 266 of file types.h.

{
  unset = 0,
  orig  = 1,
  log10 = 2,
};

DataCompression

enum class pappso::Enums::DataCompression : std::int8_t

strong

Enumerator
unset	not net
none	no compression
zlib	zlib compresssion

Definition at line 240 of file types.h.

{
  unset = -1, ///< not net
  none  = 0,  ///< no compression
  zlib  = 1,  ///< zlib compresssion
};

DataKind

enum class pappso::Enums::DataKind : std::int8_t

strong

Enumerator
unset	not set
rt	Retention time.
dt	Drift time.
mz	m/z

Definition at line 248 of file types.h.

{
  unset = -1, ///< not set
  rt    = 0,  ///< Retention time
  dt    = 1,  ///< Drift time
  mz    = 2,  ///< m/z
};

FileReaderType

enum class pappso::Enums::FileReaderType

strong

Enumerator
pwiz	using libpwizlite
mzcbor	using homemade mzcbor parser
xy
bafascii
tims	TimsMsRunReader : each scan is returned as a mass spectrum.
tims_frames	TimsFramesMsRunReader : the whole frame is merged in a single spectrum
tims_ms2	TimsMsRunReaderMs2 : Spectrum are delivered for each precursor (MS1 or MS2)
tims_dia	TimsMsRunReaderDia : Spectrum are delivered for DIA window (slice)

Definition at line 175 of file types.h.

{
  pwiz, ///< using libpwizlite
  mzcbor, ///< using homemade mzcbor parser
  xy,
  bafascii,
  tims,        ///< TimsMsRunReader : each scan is returned as a mass spectrum
  tims_frames, ///< TimsFramesMsRunReader : the whole frame is merged in a
               ///< single spectrum
  tims_ms2,    ///< TimsMsRunReaderMs2 : Spectrum are delivered for each precursor
               ///< (MS1 or MS2)
 
  tims_dia, ///< TimsMsRunReaderDia : Spectrum are delivered for DIA window
            ///< (slice)
};

Isotope

enum class pappso::Enums::Isotope

strong

Enumerator
C
C13
H
H2
O
O17
O18
N
N15
S
S33
S34
S36
P

Definition at line 125 of file types.h.

{
  C,
  C13,
  H,
  H2,
  O,
  O17,
  O18,
  N,
  N15,
  S,
  S33,
  S34,
  S36,
  P
};

MsDataFormat

enum class pappso::Enums::MsDataFormat : std::int8_t

strong

Enumerator
unknown	unknown format
mzML	mzML
mzXML	mzXML
MGF	Mascot format.
SQLite3	SQLite3 format.
xy	(x,y) format
mz5
msn
abSciexWiff
abSciexT2D
agilentMassHunter
thermoRaw
watersRaw
brukerFid
brukerYep
brukerBaf
brukerTims
brukerBafAscii
mzcbor
last

Definition at line 147 of file types.h.

{
  unknown           = 0, ///< unknown format
  mzML              = 1, ///< mzML
  mzXML             = 2, ///< mzXML
  MGF               = 3, ///< Mascot format
  SQLite3           = 4, ///< SQLite3 format
  xy                = 5, ///< (x,y) format
  mz5               = 6, //< MZ5 format
  msn               = 7, //< MS_MS2 format
  abSciexWiff       = 8,
  abSciexT2D        = 9,
  agilentMassHunter = 10,
  thermoRaw         = 11,
  watersRaw         = 12,
  brukerFid         = 13,
  brukerYep         = 14,
  brukerBaf         = 15,
  brukerTims        = 16,
  brukerBafAscii    = 17, // Baf to ascii from Bruker software
  mzcbor            = 18,
  last              = 19
};

PeptideIon

enum class pappso::Enums::PeptideIon : std::int8_t

strong

Enums::PeptideIon enum defines all types of ions (Nter or Cter).

Enumerator
b	Nter acylium ions.
bstar	Nter acylium ions + NH3 loss.
bo	Nter acylium ions + H2O loss.
a	Nter aldimine ions.
astar	Nter aldimine ions + NH3 loss.
ao	Nter aldimine ions + H2O loss.
bp
c	Nter amino ions.
y	Cter amino ions.
ystar	Cter amino ions + NH3 loss.
yo	Cter amino ions + H2O loss.
z	Cter carbocations.
yp
x	Cter acylium ions.

Definition at line 285 of file types.h.

{
  b     = 0, ///< Nter acylium ions
  bstar = 1, ///< Nter acylium ions + NH3 loss
  bo    = 2, ///< Nter acylium ions + H2O loss
  a     = 3, ///< Nter aldimine ions
  astar = 4, ///< Nter aldimine ions + NH3 loss
  ao    = 5, ///< Nter aldimine ions + H2O loss
  bp    = 6,
  c     = 7,  ///< Nter amino ions
  y     = 8,  ///< Cter amino ions
  ystar = 9,  ///< Cter amino ions + NH3 loss
  yo    = 10, ///< Cter amino ions + H2O loss
  z     = 11, ///< Cter carbocations
  yp    = 12,
  x     = 13 ///< Cter acylium ions
};

PrecisionUnit

enum class pappso::Enums::PrecisionUnit

strong

Enumerator
none
dalton
ppm
res
mz
last

Definition at line 95 of file types.h.

{
  none,
  dalton,
  ppm,
  res,
  mz,
  last
};

SortOrder

enum class pappso::Enums::SortOrder : std::int8_t

strong

Enumerator
ascending
descending

Definition at line 230 of file types.h.

{
  ascending  = 0,
  descending = 1,
};

SortType

enum class pappso::Enums::SortType : std::int8_t

strong

Enumerator
none
x
y

Definition at line 222 of file types.h.

{
  none = 0,
  x    = 1,
  y    = 2,
};

TimeUnit

enum class pappso::Enums::TimeUnit

strong

Enumerator
none
s
min
h

Definition at line 84 of file types.h.

                      {
    none,
    s,
    min,
    h,
  };

XicExtractMethod

enum class pappso::Enums::XicExtractMethod : std::int8_t

strong

Enumerator
sum	sum of intensities
max	maximum of intensities

Definition at line 277 of file types.h.

{
  sum = 1, ///< sum of intensities
  max = 2  ///< maximum of intensities
};