libpappsomspp
Library for mass spectrometry
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pappso::PeptideFragmentIon Class Reference

#include <peptidefragmention.h>

Inheritance diagram for pappso::PeptideFragmentIon:
pappso::PeptideInterface pappso::Ion pappso::AtomNumberInterface

Public Member Functions

 PeptideFragmentIon (const PeptideFragmentSp &sp_fragment, Enums::PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
 PeptideFragmentIon (const PeptideFragmentSp &sp_fragment, Enums::PeptideIon ion_type)
 PeptideFragmentIon (const PeptideFragmentIon &other)
 PeptideFragmentIon (PeptideFragmentIon &&toCopy)
virtual ~PeptideFragmentIon ()
PeptideFragmentIonSp makePeptideFragmentIonSp () const
virtual unsigned int size () const override
virtual const QString getSequence () const override
 amino acid sequence without modification
virtual const PeptideFragmentSp & getPeptideFragmentSp () const
virtual int getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const override
 get the number of atom C, O, N, H in the molecule
virtual int getNumberOfIsotope (Enums::Isotope isotope) const override
 get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
virtual const QString getName () const override
pappso_double getMass () const override
const QString getPeptideIonName () const
const QString getCompletePeptideIonName (unsigned int charge) const
 get a complete ion name string
Enums::PeptideIon getPeptideIonType () const
PeptideDirection getPeptideIonDirection () const
unsigned int getNumberOfNeutralPhosphoLoss () const
virtual bool isPalindrome () const override
 tells if the peptide sequence is a palindrome
Public Member Functions inherited from pappso::PeptideInterface
virtual const QString getSequenceLi () const
 amino acid sequence without modification where L are replaced by I
virtual const ChemicalFormula getChemicalFormulaCharge (unsigned int charge) const
virtual const QString getFormula (unsigned int charge) const final
virtual bool matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
 tells if the peptide m/z matches a given experimental mass
Public Member Functions inherited from pappso::Ion
 Ion ()
 ~Ion ()
virtual pappso_double getMz (unsigned int charge) const final
Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula getChemicalFormula () const

Static Public Member Functions

static PeptideDirection getPeptideIonDirection (Enums::PeptideIon ion_type)
static const QString getPeptideIonName (Enums::PeptideIon ion_type)
static const QColor getPeptideIonColor (Enums::PeptideIon ion_type)

Private Attributes

const PeptideFragmentSp msp_fragment
const Enums::PeptideIon m_ionType
pappso_double m_mass = 0
unsigned int m_neutralPhosphoLossNumber = 0

Detailed Description

Definition at line 49 of file peptidefragmention.h.

Constructor & Destructor Documentation

◆ PeptideFragmentIon() [1/4]

pappso::PeptideFragmentIon::PeptideFragmentIon ( const PeptideFragmentSp & sp_fragment,
Enums::PeptideIon ion_type,
unsigned int number_of_neutral_phospho_loss )

Definition at line 45 of file peptidefragmention.cpp.

48 : msp_fragment(sp_fragment), m_ionType(ion_type)
49{
50 m_mass = msp_fragment.get()->getMass();
51 PeptideDirection direction = msp_fragment.get()->getPeptideIonDirection();
52 if(direction != pappso::getPeptideIonDirection(m_ionType))
53 {
54 throw PappsoException(QString("Enums::PeptideIon %1 is not an %2 fragment")
55 .arg(PeptideFragmentIon::getPeptideIonName(m_ionType))
56 .arg(PeptideFragment::getPeptideIonDirectionName(direction)));
57 }
58 m_mass -= MASSH2O;
59 switch(m_ionType)
60 {
61 // -MASSH2O
62 case Enums::PeptideIon::yp:
63 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
64 m_mass -= ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
65 ion_type = Enums::PeptideIon::y;
66 break;
67 case Enums::PeptideIon::bp:
68 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
69 m_mass -= ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
70 ion_type = Enums::PeptideIon::b;
71 break;
72 default:
73 break;
74 }
75 m_mass += PeptideRawFragmentMasses::getDeltaMass(ion_type);
76}
pappso::PeptideFragmentIon::m_ionType
const Enums::PeptideIon m_ionType
Definition peptidefragmention.h:96
pappso::PeptideFragmentIon::getPeptideIonName
const QString getPeptideIonName() const
Definition peptidefragmention.cpp:122
pappso::PeptideFragmentIon::msp_fragment
const PeptideFragmentSp msp_fragment
Definition peptidefragmention.h:95
pappso::PeptideFragment::getPeptideIonDirectionName
static const QString getPeptideIonDirectionName(PeptideDirection direction)
Definition peptidefragment.cpp:103
pappso::PeptideRawFragmentMasses::getDeltaMass
static pappso_double getDeltaMass(Enums::PeptideIon ion_type)
Definition peptiderawfragmentmasses.cpp:55
pappso::Enums::PeptideIon::y
@ y
Cter amino ions.
Definition types.h:281
pappso::Enums::PeptideIon::b
@ b
Nter acylium ions.
Definition types.h:273
pappso::PeptideDirection
PeptideDirection
Definition peptide.h:47
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(Enums::PeptideIon ion_type)
get the direction of a peptide ion
Definition peptide.cpp:97
pappso::MASSH2O
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
pappso::MASSPHOSPHORYLATEDR
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)

References pappso::Enums::b, pappso::Enums::bp, pappso::PeptideRawFragmentMasses::getDeltaMass(), getMass(), pappso::getPeptideIonDirection(), getPeptideIonDirection(), pappso::PeptideFragment::getPeptideIonDirectionName(), getPeptideIonName(), m_ionType, m_mass, m_neutralPhosphoLossNumber, pappso::MASSH2O(), pappso::MASSPHOSPHORYLATEDR(), msp_fragment, pappso::Enums::y, and pappso::Enums::yp.

Referenced by PeptideFragmentIon(), PeptideFragmentIon(), and PeptideFragmentIon().

◆ PeptideFragmentIon() [2/4]

pappso::PeptideFragmentIon::PeptideFragmentIon ( const PeptideFragmentSp & sp_fragment,
Enums::PeptideIon ion_type )

Definition at line 39 of file peptidefragmention.cpp.

41 : PeptideFragmentIon(sp_fragment, ion_type, 0)
42{
43}
pappso::PeptideFragmentIon::PeptideFragmentIon
PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, Enums::PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
Definition peptidefragmention.cpp:45

References PeptideFragmentIon().

◆ PeptideFragmentIon() [3/4]

pappso::PeptideFragmentIon::PeptideFragmentIon ( const PeptideFragmentIon & other)

Definition at line 78 of file peptidefragmention.cpp.

79 : msp_fragment(other.msp_fragment), m_ionType(other.m_ionType)
80{
81 m_mass = other.m_mass;
82}

References PeptideFragmentIon(), m_ionType, m_mass, and msp_fragment.

◆ PeptideFragmentIon() [4/4]

pappso::PeptideFragmentIon::PeptideFragmentIon ( PeptideFragmentIon && toCopy)

Definition at line 85 of file peptidefragmention.cpp.

86 : msp_fragment(std::move(toCopy.msp_fragment)), m_ionType(toCopy.m_ionType), m_mass(toCopy.m_mass)
87{
88}

References PeptideFragmentIon(), m_ionType, m_mass, and msp_fragment.

◆ ~PeptideFragmentIon()

pappso::PeptideFragmentIon::~PeptideFragmentIon ( )
virtual

Definition at line 90 of file peptidefragmention.cpp.

91{
92}

Member Function Documentation

◆ getCompletePeptideIonName()

const QString pappso::PeptideFragmentIon::getCompletePeptideIonName ( unsigned int charge) const

get a complete ion name string

Parameters
charge

Definition at line 103 of file peptidefragmention.cpp.

104{
105
106 std::size_t size = msp_fragment.get()->size();
107 QString plusstr = "+";
108 plusstr = plusstr.repeated(charge);
109 if(m_ionType == Enums::PeptideIon::yp)
110 {
111 return QString("y%1(-P%2)%3").arg(size).arg(m_neutralPhosphoLossNumber).arg(plusstr);
112 }
113 else if(m_ionType == Enums::PeptideIon::bp)
114 {
115 return QString("b%1(-P%2)%3").arg(size).arg(m_neutralPhosphoLossNumber).arg(plusstr);
116 }
117
118 return QString("%1%2%3").arg(getPeptideIonName(m_ionType)).arg(size).arg(plusstr);
119}
pappso::PeptideFragmentIon::size
virtual unsigned int size() const override
Definition peptidefragmention.cpp:538

References pappso::Enums::bp, getPeptideIonName(), m_ionType, m_neutralPhosphoLossNumber, msp_fragment, size(), and pappso::Enums::yp.

◆ getMass()

pappso_double pappso::PeptideFragmentIon::getMass ( ) const
overridevirtual

Implements pappso::Ion.

Definition at line 562 of file peptidefragmention.cpp.

563{
564 return m_mass;
565}

References m_mass.

Referenced by PeptideFragmentIon().

◆ getName()

const QString pappso::PeptideFragmentIon::getName ( ) const
overridevirtual

Reimplemented from pappso::PeptideInterface.

Definition at line 556 of file peptidefragmention.cpp.

557{
558 return QString("%1-%2").arg(getPeptideIonName(m_ionType)).arg(size());
559}

References getPeptideIonName(), m_ionType, and size().

◆ getNumberOfAtom()

int pappso::PeptideFragmentIon::getNumberOfAtom ( Enums::AtomIsotopeSurvey atom) const
overridevirtual

get the number of atom C, O, N, H in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 241 of file peptidefragmention.cpp.

242{
243 int number = msp_fragment.get()->getNumberOfAtom(atom);
244 int diff = 0;
245 switch(atom)
246 {
247 case Enums::AtomIsotopeSurvey::C:
248 switch(m_ionType)
249 {
250 case Enums::PeptideIon::y:
251 break;
252 case Enums::PeptideIon::yp:
253 // H 1 O 3 P 1 + H 2 0
254 break;
255 case Enums::PeptideIon::ystar:
256 // m_mass -= MASSNH3;
257 break;
258 case Enums::PeptideIon::yo:
259 // m_mass -= MASSH2O;
260 break;
261 case Enums::PeptideIon::bstar:
262 // m_mass -= MASSH2O;
263 // m_mass -= MASSNH3;
264 break;
265 case Enums::PeptideIon::bo:
266 // m_mass -= MASSH2O;
267 // m_mass -= MASSH2O;
268 break;
269 case Enums::PeptideIon::a:
270 // m_mass -= MASSH2O;
271 // m_mass -= MASSCO;
272 diff = -1;
273 break;
274 case Enums::PeptideIon::c:
275 // m_mass += MASSNH3;
276 break;
277 // SvgIon.moxygen - mN
278 case Enums::PeptideIon::z:
279 // m_mass -= MASSH2O;
280 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
281 break;
282 case Enums::PeptideIon::b:
283 // m_mass -= MASSH2O;
284 break;
285 case Enums::PeptideIon::bp:
286 // H 1 O 3 P 1 + H 2 0
287 break;
288
289 case Enums::PeptideIon::astar:
290 // m_mass -= MASSH2O;
291 // m_mass = - MASSCO - MASSNH3;
292 diff = -1;
293 break;
294 case Enums::PeptideIon::ao:
295 // m_mass -= MASSH2O;
296 // m_mass = - MASSCO - MASSH2O;
297 diff = -1;
298 break;
299 case Enums::PeptideIon::x:
300 // +MASSCO + MASSOXYGEN
301 diff = +1;
302 break;
303 default:
304 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
305 break;
306 }
307 break;
308 case Enums::AtomIsotopeSurvey::H:
309 switch(m_ionType)
310 {
311 case Enums::PeptideIon::y:
312 break;
313 case Enums::PeptideIon::yp:
314 // H 1 O 3 P 1 + H 2 0
315 diff = -3 * m_neutralPhosphoLossNumber;
316 break;
317 case Enums::PeptideIon::ystar:
318 // m_mass -= MASSNH3;
319 diff = -3;
320 break;
321 case Enums::PeptideIon::yo:
322 // m_mass -= MASSH2O;
323 diff = -2;
324 break;
325 case Enums::PeptideIon::bstar:
326 // m_mass -= MASSH2O;
327 // m_mass -= MASSNH3;
328 diff = -5;
329 break;
330 case Enums::PeptideIon::bo:
331 // m_mass -= MASSH2O;
332 // m_mass -= MASSH2O;
333 diff = -4;
334 break;
335 case Enums::PeptideIon::a:
336 // m_mass -= MASSH2O;
337 // m_mass -= MASSCO;
338 diff = -2;
339 break;
340 case Enums::PeptideIon::c:
341 // m_mass += MASSNH3;
342 diff = -3;
343 break;
344 // SvgIon.moxygen - mN
345 case Enums::PeptideIon::z:
346 // m_mass -= MASSH2O;
347 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
348 diff = -3;
349 break;
350 case Enums::PeptideIon::b:
351 // m_mass -= MASSH2O;
352 diff = -2;
353 break;
354 case Enums::PeptideIon::bp:
355 // H 1 O 3 P 1 + H 2 0
356 diff = -3 * m_neutralPhosphoLossNumber;
357 break;
358
359
360 case Enums::PeptideIon::astar:
361 // m_mass -= MASSH2O;
362 // m_mass = - MASSCO - MASSNH3;
363 diff = -5;
364 break;
365 case Enums::PeptideIon::ao:
366 // m_mass -= MASSH2O;
367 // m_mass = - MASSCO - MASSH2O;
368 diff = -4;
369 break;
370 case Enums::PeptideIon::x:
371 // +MASSCO + MASSOXYGEN
372 diff = -2;
373 break;
374 default:
375 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
376 break;
377 }
378 break;
379 case Enums::AtomIsotopeSurvey::N:
380 switch(m_ionType)
381 {
382 case Enums::PeptideIon::y:
383 break;
384 case Enums::PeptideIon::yp:
385 // H 1 O 3 P 1 + H 2 0
386 break;
387
388 case Enums::PeptideIon::ystar:
389 // m_mass -= MASSNH3;
390 diff = -1;
391 break;
392 case Enums::PeptideIon::yo:
393 // m_mass -= MASSH2O;
394 break;
395 case Enums::PeptideIon::bstar:
396 // m_mass -= MASSH2O;
397 // m_mass -= MASSNH3;
398 diff = -1;
399 break;
400 case Enums::PeptideIon::bo:
401 // m_mass -= MASSH2O;
402 // m_mass -= MASSH2O;
403 break;
404 case Enums::PeptideIon::a:
405 // m_mass -= MASSH2O;
406 // m_mass -= MASSCO;
407 break;
408 case Enums::PeptideIon::c:
409 // m_mass += MASSNH3;
410 diff = -1;
411 break;
412 // SvgIon.moxygen - mN
413 case Enums::PeptideIon::z:
414 // m_mass -= MASSH2O;
415 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
416 diff = -1;
417 break;
418 case Enums::PeptideIon::b:
419 // m_mass -= MASSH2O;
420 break;
421 case Enums::PeptideIon::bp:
422 // H 1 O 3 P 1 + H 2 0
423 break;
424
425
426 case Enums::PeptideIon::astar:
427 // m_mass -= MASSH2O;
428 // m_mass = - MASSCO - MASSNH3;
429 diff = -1;
430 break;
431 case Enums::PeptideIon::ao:
432 // m_mass -= MASSH2O;
433 // m_mass = - MASSCO - MASSH2O;
434 break;
435 case Enums::PeptideIon::x:
436 // +MASSCO + MASSOXYGEN
437 break;
438 default:
439 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
440 break;
441 }
442 break;
443 case Enums::AtomIsotopeSurvey::O:
444 switch(m_ionType)
445 {
446 case Enums::PeptideIon::y:
447 break;
448 case Enums::PeptideIon::yp:
449 // H 1 O 3 P 1 + H 2 0
450 diff = -4 * m_neutralPhosphoLossNumber;
451 break;
452
453 case Enums::PeptideIon::ystar:
454 // m_mass -= MASSNH3;
455 break;
456 case Enums::PeptideIon::yo:
457 // m_mass -= MASSH2O;
458 diff = -1;
459 break;
460 case Enums::PeptideIon::bstar:
461 // m_mass -= MASSH2O;
462 // m_mass -= MASSNH3;
463 diff = -1;
464 break;
465 case Enums::PeptideIon::bo:
466 // m_mass -= MASSH2O;
467 // m_mass -= MASSH2O;
468 diff = -2;
469 break;
470 case Enums::PeptideIon::a:
471 // m_mass -= MASSH2O;
472 // m_mass -= MASSCO;
473 diff = -2;
474 break;
475 case Enums::PeptideIon::c:
476 // m_mass += MASSNH3;
477 break;
478 // SvgIon.moxygen - mN
479 case Enums::PeptideIon::z:
480 // m_mass -= MASSH2O;
481 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
482 diff = -2;
483 break;
484 case Enums::PeptideIon::b:
485 // m_mass -= MASSH2O;
486 diff = -1;
487 break;
488 case Enums::PeptideIon::bp:
489 // H 1 O 3 P 1 + H 2 0
490 diff = -4 * m_neutralPhosphoLossNumber;
491 break;
492
493
494 case Enums::PeptideIon::astar:
495 // m_mass -= MASSH2O;
496 // m_mass = - MASSCO - MASSNH3;
497 diff = -2;
498 break;
499 case Enums::PeptideIon::ao:
500 // m_mass -= MASSH2O;
501 // m_mass = - MASSCO - MASSH2O;
502 diff = -3;
503 break;
504 case Enums::PeptideIon::x:
505 // +MASSCO + MASSOXYGEN
506 diff = +1;
507 break;
508 default:
509 throw PappsoException(QObject::tr("Enums::PeptideIon name not implemented"));
510 break;
511 }
512 break;
513 case Enums::AtomIsotopeSurvey::S:
514 break;
515 default:
516 qDebug() << "PeptideFragmentIon::getNumberOfAtom(Enums::AtomIsotopeSurvey "
517 "atom) NOT IMPLEMENTED";
518 }
519 return number + diff;
520}
pappso::Enums::PeptideIon::a
@ a
Nter aldimine ions.
Definition types.h:276
pappso::Enums::PeptideIon::c
@ c
Nter amino ions.
Definition types.h:280
pappso::Enums::PeptideIon::astar
@ astar
Nter aldimine ions + NH3 loss.
Definition types.h:277
pappso::Enums::PeptideIon::ystar
@ ystar
Cter amino ions + NH3 loss.
Definition types.h:282
pappso::Enums::PeptideIon::yo
@ yo
Cter amino ions + H2O loss.
Definition types.h:283
pappso::Enums::PeptideIon::bstar
@ bstar
Nter acylium ions + NH3 loss.
Definition types.h:274
pappso::Enums::PeptideIon::x
@ x
Cter acylium ions.
Definition types.h:286
pappso::Enums::PeptideIon::bo
@ bo
Nter acylium ions + H2O loss.
Definition types.h:275
pappso::Enums::PeptideIon::ao
@ ao
Nter aldimine ions + H2O loss.
Definition types.h:278
pappso::Enums::PeptideIon::z
@ z
Cter carbocations.
Definition types.h:284

References pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::C, pappso::Enums::c, pappso::Enums::H, m_ionType, m_neutralPhosphoLossNumber, msp_fragment, pappso::Enums::N, pappso::Enums::O, pappso::Enums::S, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

◆ getNumberOfIsotope()

int pappso::PeptideFragmentIon::getNumberOfIsotope ( Enums::Isotope isotope) const
overridevirtual

get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 524 of file peptidefragmention.cpp.

525{
526 int number = msp_fragment.get()->getNumberOfIsotope(isotope);
527 return number;
528}

References msp_fragment.

◆ getNumberOfNeutralPhosphoLoss()

unsigned int pappso::PeptideFragmentIon::getNumberOfNeutralPhosphoLoss ( ) const

Definition at line 578 of file peptidefragmention.cpp.

579{
580 return m_neutralPhosphoLossNumber;
581}

References m_neutralPhosphoLossNumber.

◆ getPeptideFragmentSp()

const PeptideFragmentSp & pappso::PeptideFragmentIon::getPeptideFragmentSp ( ) const
virtual

Definition at line 550 of file peptidefragmention.cpp.

551{
552 return msp_fragment;
553}

References msp_fragment.

◆ getPeptideIonColor()

const QColor pappso::PeptideFragmentIon::getPeptideIonColor ( Enums::PeptideIon ion_type)
static

Definition at line 186 of file peptidefragmention.cpp.

187{
188 switch(m_ionType)
189 {
190 case Enums::PeptideIon::y:
191 return QColor("red");
192 break;
193 case Enums::PeptideIon::yp:
194 return QColor("red");
195 break;
196 case Enums::PeptideIon::ystar:
197 return QColor("red");
198 break;
199 case Enums::PeptideIon::yo:
200 return QColor("orange");
201 break;
202 case Enums::PeptideIon::x:
203 return QColor("orange");
204 break;
205 case Enums::PeptideIon::bstar:
206 return QColor("blue");
207 break;
208 case Enums::PeptideIon::bo:
209 return QColor("#ff00ff");
210 break;
211 case Enums::PeptideIon::a:
212 return QColor("green");
213 break;
214 case Enums::PeptideIon::astar:
215 return QColor("green");
216 break;
217 case Enums::PeptideIon::ao:
218 return QColor("green");
219 break;
220 case Enums::PeptideIon::c:
221 return QColor("blue");
222 break;
223 // SvgIon.moxygen - mN
224 case Enums::PeptideIon::z:
225 return QColor("red");
226 break;
227 case Enums::PeptideIon::b:
228 return QColor("blue");
229 break;
230 case Enums::PeptideIon::bp:
231 return QColor("blue");
232 break;
233 default:
234 throw PappsoException(
235 QString("Enums::PeptideIon color not implemented %1").arg(getPeptideIonName(m_ionType)));
236 break;
237 }
238}

References pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::c, getPeptideIonName(), m_ionType, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

Referenced by pappso::QCPSpectrum::QCPSpectrum(), and pappso::MassSpectrumWidget::plot().

◆ getPeptideIonDirection() [1/2]

PeptideDirection pappso::PeptideFragmentIon::getPeptideIonDirection ( ) const

Definition at line 573 of file peptidefragmention.cpp.

574{
575 return msp_fragment.get()->getPeptideIonDirection();
576}

References msp_fragment.

Referenced by PeptideFragmentIon().

◆ getPeptideIonDirection() [2/2]

PeptideDirection pappso::PeptideFragmentIon::getPeptideIonDirection ( Enums::PeptideIon ion_type)
static

Definition at line 96 of file peptidefragmention.cpp.

97{
98 return pappso::getPeptideIonDirection(ion_type);
99}

References pappso::getPeptideIonDirection().

◆ getPeptideIonName() [1/2]

const QString pappso::PeptideFragmentIon::getPeptideIonName ( ) const

Definition at line 122 of file peptidefragmention.cpp.

123{
124 if((m_ionType == Enums::PeptideIon::yp) || (m_ionType == Enums::PeptideIon::bp))
125 {
126 return QString("%1(%2)").arg(getPeptideIonName(m_ionType)).arg(m_neutralPhosphoLossNumber);
127 }
128 return getPeptideIonName(m_ionType);
129}

References pappso::Enums::bp, getPeptideIonName(), m_ionType, m_neutralPhosphoLossNumber, and pappso::Enums::yp.

Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getName(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), getPeptideIonColor(), and getPeptideIonName().

◆ getPeptideIonName() [2/2]

const QString pappso::PeptideFragmentIon::getPeptideIonName ( Enums::PeptideIon ion_type)
static

Definition at line 132 of file peptidefragmention.cpp.

133{
134 switch(m_ionType)
135 {
136 case Enums::PeptideIon::y:
137 return "y";
138 break;
139 case Enums::PeptideIon::yp:
140 return "yP";
141 break;
142 case Enums::PeptideIon::ystar:
143 return "y*";
144 break;
145 case Enums::PeptideIon::yo:
146 return "yO";
147 break;
148 case Enums::PeptideIon::bstar:
149 return "b*";
150 break;
151 case Enums::PeptideIon::bo:
152 return "bO";
153 break;
154 case Enums::PeptideIon::a:
155 return "a";
156 break;
157 case Enums::PeptideIon::astar:
158 return "a*";
159 break;
160 case Enums::PeptideIon::ao:
161 return "aO";
162 break;
163 case Enums::PeptideIon::c:
164 return "c";
165 break;
166 // SvgIon.moxygen - mN
167 case Enums::PeptideIon::z:
168 return "z";
169 break;
170 case Enums::PeptideIon::b:
171 return "b";
172 break;
173 case Enums::PeptideIon::bp:
174 return "bP";
175 break;
176 case Enums::PeptideIon::x:
177 return "x";
178 break;
179 default:
180 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
181 break;
182 }
183}

References pappso::Enums::a, pappso::Enums::ao, pappso::Enums::astar, pappso::Enums::b, pappso::Enums::bo, pappso::Enums::bp, pappso::Enums::bstar, pappso::Enums::c, m_ionType, pappso::Enums::x, pappso::Enums::y, pappso::Enums::yo, pappso::Enums::yp, pappso::Enums::ystar, and pappso::Enums::z.

◆ getPeptideIonType()

Enums::PeptideIon pappso::PeptideFragmentIon::getPeptideIonType ( ) const

Definition at line 568 of file peptidefragmention.cpp.

569{
570 return m_ionType;
571}

References m_ionType.

◆ getSequence()

const QString pappso::PeptideFragmentIon::getSequence ( ) const
overridevirtual

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 544 of file peptidefragmention.cpp.

545{
546 return msp_fragment.get()->getSequence();
547}

References msp_fragment.

◆ isPalindrome()

bool pappso::PeptideFragmentIon::isPalindrome ( ) const
overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 584 of file peptidefragmention.cpp.

585{
586 return msp_fragment.get()->isPalindrome();
587}

References msp_fragment.

◆ makePeptideFragmentIonSp()

PeptideFragmentIonSp pappso::PeptideFragmentIon::makePeptideFragmentIonSp ( ) const

Definition at line 531 of file peptidefragmention.cpp.

532{
533 return std::make_shared<PeptideFragmentIon>(*this);
534}

◆ size()

unsigned int pappso::PeptideFragmentIon::size ( ) const
overridevirtual

Implements pappso::PeptideInterface.

Definition at line 538 of file peptidefragmention.cpp.

539{
540 return msp_fragment.get()->size();
541}

References msp_fragment.

Referenced by pappso::findComplementIonType(), getCompletePeptideIonName(), and getName().

Member Data Documentation

◆ m_ionType

const Enums::PeptideIon pappso::PeptideFragmentIon::m_ionType
private

Definition at line 96 of file peptidefragmention.h.

Referenced by PeptideFragmentIon(), PeptideFragmentIon(), PeptideFragmentIon(), getCompletePeptideIonName(), getName(), getNumberOfAtom(), getPeptideIonColor(), getPeptideIonName(), getPeptideIonName(), and getPeptideIonType().

◆ m_mass

pappso_double pappso::PeptideFragmentIon::m_mass = 0
private

Definition at line 98 of file peptidefragmention.h.

Referenced by PeptideFragmentIon(), PeptideFragmentIon(), PeptideFragmentIon(), and getMass().

◆ m_neutralPhosphoLossNumber

unsigned int pappso::PeptideFragmentIon::m_neutralPhosphoLossNumber = 0
private

Definition at line 102 of file peptidefragmention.h.

Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getNumberOfAtom(), getNumberOfNeutralPhosphoLoss(), and getPeptideIonName().

◆ msp_fragment

const PeptideFragmentSp pappso::PeptideFragmentIon::msp_fragment
private

Definition at line 95 of file peptidefragmention.h.

Referenced by PeptideFragmentIon(), PeptideFragmentIon(), PeptideFragmentIon(), getCompletePeptideIonName(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideFragmentSp(), getPeptideIonDirection(), getSequence(), isPalindrome(), and size().

The documentation for this class was generated from the following files: