libpappsomspp
Library for mass spectrometry
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types.h
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1/**
2 * \file pappsomspp/types.h
3 * \date 4/3/2015
4 * \author Olivier Langella
5 * \brief This header contains all the type re-definitions and all
6 * the global variables definitions used in the PAPPSOms++ library.
7 */
8
9/*******************************************************************************
10 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
11 *
12 * This file is part of the PAPPSOms++ library.
13 *
14 * PAPPSOms++ is free software: you can redistribute it and/or modify
15 * it under the terms of the GNU General Public License as published by
16 * the Free Software Foundation, either version 3 of the License, or
17 * (at your option) any later version.
18 *
19 * PAPPSOms++ is distributed in the hope that it will be useful,
20 * but WITHOUT ANY WARRANTY; without even the implied warranty of
21 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 * GNU General Public License for more details.
23 *
24 * You should have received a copy of the GNU General Public License
25 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26 *
27 * Contributors:
28 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
29 *implementation
30 ******************************************************************************/
31
32#pragma once
33
34#include <QString>
35#include <cstdint>
36
37namespace pappso
38{
39
40/************ Typedefs **************************************************/
41
42/** \var typedef QString PeptideStr
43 \brief A type definition for PeptideStr
44 */
45typedef QString PeptideStr;
46
47/** \var typedef double pappso_double
48 \brief A type definition for doubles
49 */
50typedef double pappso_double;
51
52/** \var typedef float mcq_float
53 \brief A type definition for floats
54 */
55typedef float pappso_float;
56
57typedef unsigned int uint;
58
59/*********** enumerations *********************************/
60
61/** \def TimeUnit (s, min, h)
62 */
63enum class TimeUnit
64{
65 none,
66 s,
67 min,
68 h,
69};
70
71
72/** \def PrecisionUnit ppm or dalton
73 *
74 */
75enum class PrecisionUnit
76{
77 none,
78 dalton,
79 ppm,
80 res,
81 mz,
82 last
83};
84
85/** \def AtomIsotopeSurvey list of atoms on which isotopes may occurs
86 *
87 */
88enum class AtomIsotopeSurvey : std::int8_t
89{
90 C,
91 H,
92 O,
93 N,
94 S,
95 last
96};
97
98
99/** \def Isotope list of isotopes taken into account for peptide abundance
100 * calculation
101 *
102 */
103enum class Isotope
104{
105 C13,
106 H2,
107 O17,
108 O18,
109 N15,
110 S33,
111 S34,
112 S36
113};
114
115
116/** \def MzFormat mz data file format types
117 *
118 */
119enum class MsDataFormat : std::int8_t
120{
121 unknown = 0, ///< unknown format
122 mzML = 1, ///< mzML
123 mzXML = 2, ///< mzXML
124 MGF = 3, ///< Mascot format
125 SQLite3 = 4, ///< SQLite3 format
126 xy = 5, ///< (x,y) format
127 mz5 = 6, //< MZ5 format
128 msn = 7, //< MS_MS2 format
129 abSciexWiff = 8,
130 abSciexT2D = 9,
132 thermoRaw = 11,
133 watersRaw = 12,
134 brukerFid = 13,
135 brukerYep = 14,
136 brukerBaf = 15,
137 brukerTims = 16,
138 brukerBafAscii = 17, // Baf to ascii from Bruker software
139 last = 18
140};
141
142
143/** \def FileReaderType mass data file reader types
144 *
145 */
147{
148 pwiz,
149 xy,
150 bafascii,
151 tims,
153 tims_ms2,
154};
155
156
157/** \def AminoAcidChar Amino-acid full name and code correspondence
158 *
159 */
160enum class AminoAcidChar : char
161{
162 alanine = 'A',
163 cysteine = 'C',
164 aspartic_acid = 'D',
165 glutamic_acid = 'E',
166 phenylalanine = 'F',
167 glycine = 'G',
168 histidine = 'H',
169 isoleucine = 'I',
170 lysine = 'K',
171 leucine = 'L',
172 methionine = 'M',
173 asparagine = 'N',
174 proline = 'P',
175 glutamine = 'Q',
176 arginine = 'R',
177 serine = 'S',
178 threonine = 'T',
179 valine = 'V',
180 tryptophan = 'W',
181 tyrosine = 'Y',
182 selenocysteine = 'U',
183 pyrrolysine = 'O',
184};
185
186
187enum class SortType : std::int8_t
188{
189 no_sort = 0,
190 x = 1,
191 y = 2,
192};
193
194
195enum class SortOrder : std::int8_t
196{
197 ascending = 0,
198 descending = 1,
199};
200
201/** \def Data compression types
202 *
203 */
204enum class DataCompression : std::int8_t
205{
206 unset = -1, ///< not net
207 none = 0, ///< no compression
208 zlib = 1, ///< zlib compresssion
209};
210
211
212enum class DataKind : std::int8_t
213{
214 unset = -1, ///< not set
215 rt = 0, ///< Retention time
216 dt = 1, ///< Drift time
217 mz = 2, ///< m/z
218};
219
220
221enum class Axis : std::int8_t
222{
223 unset = 0x000,
224 x = 1 << 0,
225 y = 1 << 1,
226 z = 1 << 2,
227};
228
229
230enum class AxisScale : std::int8_t
231{
232 unset = 0,
233 orig = 1,
234 log10 = 2,
235};
236
237
238/** \def XixExtactMethod method to extract Xic
239 *
240 */
241enum class XicExtractMethod : std::int8_t
242{
243 sum = 1, ///< sum of intensities
244 max = 2 ///< maximum of intensities
245};
246
247
248/*********** Global variables definitions*********************************/
249
250/** \def MHPLUS 1.007276466879
251 \brief The (monoisotopic) mass of the H+ ion
252 https://en.wikipedia.org/wiki/Proton (One Proton alone)
253 1.007276466879
254 */
255const pappso_double MHPLUS(1.007276466879);
256const pappso_double MPROTON(1.007276466879);
257
258/** \def MPROTIUM 1.00782503207
259 \brief The (monoisotopic) mass of the H atom
260 https://en.wikipedia.org/wiki/Isotopes_of_hydrogen (One proton + One electron)
261 1.00782503207
262
263 Note that as of 20191028, that same page says: 1.007825032241
264 */
265const pappso_double MPROTIUM(1.007825032241);
266
267
268/** \def ONEMILLION 1000000
269 \brief One million integer, why not.
270 */
272
273
274/** @file
275 * https://forgemia.inra.fr/pappso/massxpert/-/blob/be60e53480f68d36afa95c809cffd68d4fb46c79/data/polChemDefs/protein-1-letter-libisospec-atomic-data/protein-1-letter-libisospec-atomic-data.xml
276 * abundance of sulfur extracted from 'massXpert' polymer definitions
277 */
278// <name>Sulfur</name>
279// <symbol>S</symbol>
280// <isotope>
281// <mass>31.9720711741</mass>
282// <abund>94.985001199904004920426814351230859756469726562500000000000000</abund>
283// </isotope>
284// <isotope>
285// <mass>32.9714589101</mass>
286// <abund>0.751939844812414937003097747947322204709053039550781250000000</abund>
287// </isotope>
288// <isotope>
289// <mass>33.9678670300</mass>
290// <abund>4.252059835213182203972337447339668869972229003906250000000000</abund>
291// </isotope>
292// <isotope>
293// <mass>35.9670812000</mass>
294// <abund>0.010999120070394368536836893213148869108408689498901367187500</abund>
295// </isotope>
296
297
298const pappso_double MASSOXYGEN(15.99491461956);
301const pappso_double MASSNITROGEN(14.0030740048);
304const pappso_double MASSPHOSPHORUS(30.973761998);
305const pappso_double MASSSULFUR(31.9720711741);
306
307// id: MOD:00696 name: phosphorylated residue H 1 O 3 P 1
310
311// Selenium : warning lot of isotopes
312const pappso_double MASSSELENIUM(79.916520); // 79.916520 //78.971
313
314// CHNOS
315
316/** \def DIFFC12C13 1.0033548378
317 \brief The (monoisotopic) mass difference between C12 (12u) and C13 stable
318 isotope of carbon
319 */
320const pappso_double DIFFC12C13(1.0033548378);
321
322/** \def DIFFS32S33 0.99938776
323 \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S33
324 (32.97145876u) stable isotope of sulfur
325 https://en.wikipedia.org/wiki/Isotopes_of_sulfur
326 */
327const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR);
328
329/** \def DIFFS32S34 1.9957959
330 \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S34
331 (33.96786690u) stable isotope of sulfur
332 */
333const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR);
334
335/** \def DIFFS32S36 3.99500976
336 \brief The (monoisotopic) mass difference between S32 (31.97207100u) and S36
337 (35.96708076u) stable isotope of sulfur
338 */
339const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR);
340
341
342/** \def DIFFH1H2
343 \brief The (monoisotopic) mass difference between H1 and H2 stable isotope of
344 hydrogen
345 */
346const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM);
347
348/** \def DIFFO16O18
349 \brief The (monoisotopic) mass difference between O16 and O18 stable isotope of
350 oxygen
351 */
353
354/** \def DIFFO16O17
355 \brief The (monoisotopic) mass difference between O16 and O17 stable isotope of
356 oxygen
357 */
359
360/** \def DIFFN14N15
361 \brief The (monoisotopic) mass difference between N14 and N15 stable isotope of
362 nitrogen
363 */
364const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN);
365
366
367// http://education.expasy.org/student_projects/isotopident/htdocs/motza.html
368/** \def ABUNDANCEH2 0.0156%
369 \brief H2 isotope abundance
370 */
371const pappso_double
372 ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250);
373
374/** \def ABUNDANCEN15 0.00364
375 \brief N15 isotope abundance
376 */
378 0.00364198543205827118818262988497735932469367980957031250000000);
379
380/** \def ABUNDANCEO17
381 \brief O17 isotope abundance
382 */
384 0.00038099847600609595965615028489992255344986915588378906250000);
385
386/** \def ABUNDANCEO18 0.2%
387 \brief O18 isotope abundance
388 */
390 0.00205139179443282221315669744399201590567827224731445312500000);
391
392/** \def ABUNDANCEC13 1.109%
393 \brief C13 isotope abundance
394 */
396 0.01078805814953308406245469086570665240287780761718750000000000);
397
398/** \def ABUNDANCEC12 98.89%
399 \brief C12 abundance
400 */
402 0.98921194185046687152862432412803173065185546875000000000000000);
403
404
405/** \def ABUNDANCES33 0.00750
406 \brief S33 abundance
407 */
409 0.00751939844812414937003097747947322204709053039550781250000000);
410
411/** \def ABUNDANCES34 0.0429
412 \brief S34 abundance
413 */
415 0.04252059835213182203972337447339668869972229003906250000000000);
416
417/** \def ABUNDANCES36 0.00020
418 \brief S36 abundance
419 */
421 0.00010999120070394368536836893213148869108408689498901367187500);
422
423
424/** \brief PeptideIon enum defines all types of ions (Nter or Cter)
425 */
426enum class PeptideIon : std::int8_t
427{
428 b = 0, ///< Nter acylium ions
429 bstar = 1, ///< Nter acylium ions + NH3 loss
430 bo = 2, ///< Nter acylium ions + H2O loss
431 a = 3, ///< Nter aldimine ions
432 astar = 4, ///< Nter aldimine ions + NH3 loss
433 ao = 5, ///< Nter aldimine ions + H2O loss
434 bp = 6,
435 c = 7, ///< Nter amino ions
436 y = 8, ///< Cter amino ions
437 ystar = 9, ///< Cter amino ions + NH3 loss
438 yo = 10, ///< Cter amino ions + H2O loss
439 z = 11, ///< Cter carbocations
440 yp = 12,
441 x = 13 ///< Cter acylium ions
442};
443
444/** \brief only useful for internal use
445 * DO not change this value : it is used to define static array size
446 */
447#define PEPTIDE_ION_TYPE_COUNT 14
448} // namespace pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
const pappso_double MPROTON(1.007276466879)
const pappso_double ABUNDANCEC12(0.98921194185046687152862432412803173065185546875000000000000000)
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:427
AminoAcidChar
Definition types.h:161
MsDataFormat
Definition types.h:120
@ xy
(x,y) format
@ unknown
unknown format
@ SQLite3
SQLite3 format.
@ MGF
Mascot format.
const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR)
PrecisionUnit
Definition types.h:76
const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR)
const pappso_double DIFFO16O17(16.99913150 - MASSOXYGEN)
const pappso_double MASSCARBON(12)
const pappso_double MASSPHOSPHORUS(30.973761998)
const pappso_double MASSSULFUR(31.9720711741)
const pappso_double ABUNDANCES36(0.00010999120070394368536836893213148869108408689498901367187500)
QString PeptideStr
A type definition for PeptideStr.
Definition types.h:45
DataCompression
Definition types.h:205
@ zlib
zlib compresssion
const pappso_double MASSCO(MASSCARBON+MASSOXYGEN)
const pappso_double ONEMILLION(1000000)
const pappso_double ABUNDANCEN15(0.00364198543205827118818262988497735932469367980957031250000000)
const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR)
const pappso_double MASSSELENIUM(79.916520)
const pappso_double MHPLUS(1.007276466879)
AtomIsotopeSurvey
Definition types.h:89
double pappso_double
A type definition for doubles.
Definition types.h:50
Isotope
Definition types.h:104
AxisScale
Definition types.h:231
SortType
Definition types.h:188
const pappso_double ABUNDANCEC13(0.01078805814953308406245469086570665240287780761718750000000000)
const pappso_double MPROTIUM(1.007825032241)
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
const pappso_double ABUNDANCEO17(0.00038099847600609595965615028489992255344986915588378906250000)
const pappso_double ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250)
DataKind
Definition types.h:213
@ dt
Drift time.
@ rt
Retention time.
const pappso_double MASSNH3((MPROTIUM *3)+MASSNITROGEN)
unsigned int uint
Definition types.h:57
const pappso_double ABUNDANCES34(0.04252059835213182203972337447339668869972229003906250000000000)
const pappso_double MASSNITROGEN(14.0030740048)
const pappso_double MASSOXYGEN(15.99491461956)
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
FileReaderType
Definition types.h:147
const pappso_double ABUNDANCEO18(0.00205139179443282221315669744399201590567827224731445312500000)
const pappso_double DIFFO16O18(17.9991610 - MASSOXYGEN)
const pappso_double ABUNDANCES33(0.00751939844812414937003097747947322204709053039550781250000000)
const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN)
TimeUnit
Definition types.h:64
XicExtractMethod
Definition types.h:242
@ sum
sum of intensities
@ max
maximum of intensities
const pappso_double DIFFC12C13(1.0033548378)
float pappso_float
Definition types.h:55
SortOrder
Definition types.h:196
const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM)