libpappsomspp
Library for mass spectrometry
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Enumerations
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 , last = 18
}
 
enum class  FileReaderType {
  pwiz , 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.

196{
197 alanine = 'A',
198 cysteine = 'C',
199 aspartic_acid = 'D',
200 glutamic_acid = 'E',
201 phenylalanine = 'F',
202 glycine = 'G',
203 histidine = 'H',
204 isoleucine = 'I',
205 lysine = 'K',
206 leucine = 'L',
207 methionine = 'M',
208 asparagine = 'N',
209 proline = 'P',
210 glutamine = 'Q',
211 arginine = 'R',
212 serine = 'S',
213 threonine = 'T',
214 valine = 'V',
215 tryptophan = 'W',
216 tyrosine = 'Y',
217 selenocysteine = 'U',
218 pyrrolysine = 'O',
219};

◆ AtomIsotopeSurvey

enum class pappso::Enums::AtomIsotopeSurvey : std::int8_t
strong
Enumerator
C 
H 
O 
N 
S 
P 
last 

Definition at line 111 of file types.h.

112{
113 C,
114 H,
115 O,
116 N,
117 S,
118 P,
119 last
120};

◆ Axis

enum class pappso::Enums::Axis : std::int8_t
strong
Enumerator
unset 
x 
y 
z 

Definition at line 257 of file types.h.

258{
259 unset = 0x000,
260 x = 1 << 0,
261 y = 1 << 1,
262 z = 1 << 2,
263};

◆ AxisScale

enum class pappso::Enums::AxisScale : std::int8_t
strong
Enumerator
unset 
orig 
log10 

Definition at line 266 of file types.h.

267{
268 unset = 0,
269 orig = 1,
270 log10 = 2,
271};

◆ 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.

241{
242 unset = -1, ///< not net
243 none = 0, ///< no compression
244 zlib = 1, ///< zlib compresssion
245};
pappso::Enums::DataCompression::zlib
@ zlib
zlib compresssion
Definition types.h:244

◆ 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.

249{
250 unset = -1, ///< not set
251 rt = 0, ///< Retention time
252 dt = 1, ///< Drift time
253 mz = 2, ///< m/z
254};
pappso::Enums::DataKind::dt
@ dt
Drift time.
Definition types.h:252
pappso::Enums::DataKind::rt
@ rt
Retention time.
Definition types.h:251

◆ FileReaderType

enum class pappso::Enums::FileReaderType
strong
Enumerator
pwiz 

using libpwizlite

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 176 of file types.h.

177{
178 pwiz, ///< using libpwizlite
179 xy,
180 bafascii,
181 tims, ///< TimsMsRunReader : each scan is returned as a mass spectrum
182 tims_frames, ///< TimsFramesMsRunReader : the whole frame is merged in a
183 ///< single spectrum
184 tims_ms2, ///< TimsMsRunReaderMs2 : Spectrum are delivered for each precursor
185 ///< (MS1 or MS2)
186
187 tims_dia, ///< TimsMsRunReaderDia : Spectrum are delivered for DIA window
188 ///< (slice)
189};
pappso::Enums::FileReaderType::pwiz
@ pwiz
using libpwizlite
Definition types.h:178
pappso::Enums::FileReaderType::tims
@ tims
TimsMsRunReader : each scan is returned as a mass spectrum.
Definition types.h:181

◆ 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 127 of file types.h.

128{
129 C,
130 C13,
131 H,
132 H2,
133 O,
134 O17,
135 O18,
136 N,
137 N15,
138 S,
139 S33,
140 S34,
141 S36,
142 P
143};

◆ 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 
last 

Definition at line 149 of file types.h.

150{
151 unknown = 0, ///< unknown format
152 mzML = 1, ///< mzML
153 mzXML = 2, ///< mzXML
154 MGF = 3, ///< Mascot format
155 SQLite3 = 4, ///< SQLite3 format
156 xy = 5, ///< (x,y) format
157 mz5 = 6, //< MZ5 format
158 msn = 7, //< MS_MS2 format
159 abSciexWiff = 8,
160 abSciexT2D = 9,
161 agilentMassHunter = 10,
162 thermoRaw = 11,
163 watersRaw = 12,
164 brukerFid = 13,
165 brukerYep = 14,
166 brukerBaf = 15,
167 brukerTims = 16,
168 brukerBafAscii = 17, // Baf to ascii from Bruker software
169 last = 18
170};
pappso::Enums::MsDataFormat::unknown
@ unknown
unknown format
Definition types.h:151
pappso::Enums::MsDataFormat::SQLite3
@ SQLite3
SQLite3 format.
Definition types.h:155
pappso::Enums::MsDataFormat::MGF
@ MGF
Mascot format.
Definition types.h:154

◆ 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.

286{
287 b = 0, ///< Nter acylium ions
288 bstar = 1, ///< Nter acylium ions + NH3 loss
289 bo = 2, ///< Nter acylium ions + H2O loss
290 a = 3, ///< Nter aldimine ions
291 astar = 4, ///< Nter aldimine ions + NH3 loss
292 ao = 5, ///< Nter aldimine ions + H2O loss
293 bp = 6,
294 c = 7, ///< Nter amino ions
295 y = 8, ///< Cter amino ions
296 ystar = 9, ///< Cter amino ions + NH3 loss
297 yo = 10, ///< Cter amino ions + H2O loss
298 z = 11, ///< Cter carbocations
299 yp = 12,
300 x = 13 ///< Cter acylium ions
301};
pappso::masschroq::PeakQualityCategory::a
@ a
peak detected using a single direct MS2 observation
Definition types.h:46

◆ PrecisionUnit

enum class pappso::Enums::PrecisionUnit
strong
Enumerator
none 
dalton 
ppm 
res 
mz 
last 

Definition at line 97 of file types.h.

98{
99 none,
100 dalton,
101 ppm,
102 res,
103 mz,
104 last
105};

◆ SortOrder

enum class pappso::Enums::SortOrder : std::int8_t
strong
Enumerator
ascending 
descending 

Definition at line 230 of file types.h.

231{
232 ascending = 0,
233 descending = 1,
234};

◆ SortType

enum class pappso::Enums::SortType : std::int8_t
strong
Enumerator
none 
x 
y 

Definition at line 222 of file types.h.

223{
224 none = 0,
225 x = 1,
226 y = 2,
227};

◆ TimeUnit

enum class pappso::Enums::TimeUnit
strong
Enumerator
none 
s 
min 
h 

Definition at line 85 of file types.h.

86{
87 none,
88 s,
89 min,
90 h,
91};

◆ 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.

278{
279 sum = 1, ///< sum of intensities
280 max = 2 ///< maximum of intensities
281};
pappso::Enums::XicExtractMethod::sum
@ sum
sum of intensities
Definition types.h:279
pappso::Enums::XicExtractMethod::max
@ max
maximum of intensities
Definition types.h:280