libpappsomspp
Library for mass spectrometry
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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
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.

49 : msp_fragment(sp_fragment), m_ionType(ion_type)
50{
51 m_mass = msp_fragment.get()->getMass();
52 PeptideDirection direction = msp_fragment.get()->getPeptideIonDirection();
53 if(direction != pappso::getPeptideIonDirection(m_ionType))
54 {
55 throw PappsoException(
56 QString("Enums::PeptideIon %1 is not an %2 fragment")
57 .arg(PeptideFragmentIon::getPeptideIonName(m_ionType))
58 .arg(PeptideFragment::getPeptideIonDirectionName(direction)));
59 }
60 m_mass -= MASSH2O;
61 switch(m_ionType)
62 {
63 // -MASSH2O
64 case Enums::PeptideIon::yp:
65 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
66 m_mass -=
67 ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
68 ion_type = Enums::PeptideIon::y;
69 break;
70 case Enums::PeptideIon::bp:
71 m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
72 m_mass -=
73 ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
74 ion_type = Enums::PeptideIon::b;
75 break;
76 default:
77 break;
78 }
79 m_mass += PeptideRawFragmentMasses::getDeltaMass(ion_type);
80}
pappso::PeptideFragmentIon::m_ionType
const Enums::PeptideIon m_ionType
Definition peptidefragmention.h:96
pappso::PeptideFragmentIon::getPeptideIonName
const QString getPeptideIonName() const
Definition peptidefragmention.cpp:138
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:56
pappso::Enums::PeptideIon::y
@ y
Cter amino ions.
Definition types.h:295
pappso::Enums::PeptideIon::b
@ b
Nter acylium ions.
Definition types.h:287
pappso::PeptideDirection
PeptideDirection
Definition peptide.h:46
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(Enums::PeptideIon ion_type)
get the direction of a peptide ion
Definition peptide.cpp:95
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 82 of file peptidefragmention.cpp.

83 : msp_fragment(other.msp_fragment), m_ionType(other.m_ionType)
84{
85 m_mass = other.m_mass;
86}

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

◆ PeptideFragmentIon() [4/4]

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

Definition at line 89 of file peptidefragmention.cpp.

91 : msp_fragment(std::move(toCopy.msp_fragment)),
92 m_ionType(toCopy.m_ionType),
93 m_mass(toCopy.m_mass)
94{
95}

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

◆ ~PeptideFragmentIon()

pappso::PeptideFragmentIon::~PeptideFragmentIon ( )
virtual

Definition at line 97 of file peptidefragmention.cpp.

98{
99}

Member Function Documentation

◆ getCompletePeptideIonName()

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

get a complete ion name string

Parameters
charge

Definition at line 110 of file peptidefragmention.cpp.

111{
112
113 std::size_t size = msp_fragment.get()->size();
114 QString plusstr = "+";
115 plusstr = plusstr.repeated(charge);
116 if(m_ionType == Enums::PeptideIon::yp)
117 {
118 return QString("y%1(-P%2)%3")
119 .arg(size)
120 .arg(m_neutralPhosphoLossNumber)
121 .arg(plusstr);
122 }
123 else if(m_ionType == Enums::PeptideIon::bp)
124 {
125 return QString("b%1(-P%2)%3")
126 .arg(size)
127 .arg(m_neutralPhosphoLossNumber)
128 .arg(plusstr);
129 }
130
131 return QString("%1%2%3")
132 .arg(getPeptideIonName(m_ionType))
133 .arg(size)
134 .arg(plusstr);
135}
pappso::PeptideFragmentIon::size
virtual unsigned int size() const override
Definition peptidefragmention.cpp:557

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 581 of file peptidefragmention.cpp.

582{
583 return m_mass;
584}

References m_mass.

Referenced by PeptideFragmentIon().

◆ getName()

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

Reimplemented from pappso::PeptideInterface.

Definition at line 575 of file peptidefragmention.cpp.

576{
577 return QString("%1-%2").arg(getPeptideIonName(m_ionType)).arg(size());
578}

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 259 of file peptidefragmention.cpp.

260{
261 int number = msp_fragment.get()->getNumberOfAtom(atom);
262 int diff = 0;
263 switch(atom)
264 {
265 case Enums::AtomIsotopeSurvey::C:
266 switch(m_ionType)
267 {
268 case Enums::PeptideIon::y:
269 break;
270 case Enums::PeptideIon::yp:
271 // H 1 O 3 P 1 + H 2 0
272 break;
273 case Enums::PeptideIon::ystar:
274 // m_mass -= MASSNH3;
275 break;
276 case Enums::PeptideIon::yo:
277 // m_mass -= MASSH2O;
278 break;
279 case Enums::PeptideIon::bstar:
280 // m_mass -= MASSH2O;
281 // m_mass -= MASSNH3;
282 break;
283 case Enums::PeptideIon::bo:
284 // m_mass -= MASSH2O;
285 // m_mass -= MASSH2O;
286 break;
287 case Enums::PeptideIon::a:
288 // m_mass -= MASSH2O;
289 // m_mass -= MASSCO;
290 diff = -1;
291 break;
292 case Enums::PeptideIon::c:
293 // m_mass += MASSNH3;
294 break;
295 // SvgIon.moxygen - mN
296 case Enums::PeptideIon::z:
297 // m_mass -= MASSH2O;
298 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
299 break;
300 case Enums::PeptideIon::b:
301 // m_mass -= MASSH2O;
302 break;
303 case Enums::PeptideIon::bp:
304 // H 1 O 3 P 1 + H 2 0
305 break;
306
307 case Enums::PeptideIon::astar:
308 // m_mass -= MASSH2O;
309 // m_mass = - MASSCO - MASSNH3;
310 diff = -1;
311 break;
312 case Enums::PeptideIon::ao:
313 // m_mass -= MASSH2O;
314 // m_mass = - MASSCO - MASSH2O;
315 diff = -1;
316 break;
317 case Enums::PeptideIon::x:
318 // +MASSCO + MASSOXYGEN
319 diff = +1;
320 break;
321 default:
322 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
323 break;
324 }
325 break;
326 case Enums::AtomIsotopeSurvey::H:
327 switch(m_ionType)
328 {
329 case Enums::PeptideIon::y:
330 break;
331 case Enums::PeptideIon::yp:
332 // H 1 O 3 P 1 + H 2 0
333 diff = -3 * m_neutralPhosphoLossNumber;
334 break;
335 case Enums::PeptideIon::ystar:
336 // m_mass -= MASSNH3;
337 diff = -3;
338 break;
339 case Enums::PeptideIon::yo:
340 // m_mass -= MASSH2O;
341 diff = -2;
342 break;
343 case Enums::PeptideIon::bstar:
344 // m_mass -= MASSH2O;
345 // m_mass -= MASSNH3;
346 diff = -5;
347 break;
348 case Enums::PeptideIon::bo:
349 // m_mass -= MASSH2O;
350 // m_mass -= MASSH2O;
351 diff = -4;
352 break;
353 case Enums::PeptideIon::a:
354 // m_mass -= MASSH2O;
355 // m_mass -= MASSCO;
356 diff = -2;
357 break;
358 case Enums::PeptideIon::c:
359 // m_mass += MASSNH3;
360 diff = -3;
361 break;
362 // SvgIon.moxygen - mN
363 case Enums::PeptideIon::z:
364 // m_mass -= MASSH2O;
365 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
366 diff = -3;
367 break;
368 case Enums::PeptideIon::b:
369 // m_mass -= MASSH2O;
370 diff = -2;
371 break;
372 case Enums::PeptideIon::bp:
373 // H 1 O 3 P 1 + H 2 0
374 diff = -3 * m_neutralPhosphoLossNumber;
375 break;
376
377
378 case Enums::PeptideIon::astar:
379 // m_mass -= MASSH2O;
380 // m_mass = - MASSCO - MASSNH3;
381 diff = -5;
382 break;
383 case Enums::PeptideIon::ao:
384 // m_mass -= MASSH2O;
385 // m_mass = - MASSCO - MASSH2O;
386 diff = -4;
387 break;
388 case Enums::PeptideIon::x:
389 // +MASSCO + MASSOXYGEN
390 diff = -2;
391 break;
392 default:
393 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
394 break;
395 }
396 break;
397 case Enums::AtomIsotopeSurvey::N:
398 switch(m_ionType)
399 {
400 case Enums::PeptideIon::y:
401 break;
402 case Enums::PeptideIon::yp:
403 // H 1 O 3 P 1 + H 2 0
404 break;
405
406 case Enums::PeptideIon::ystar:
407 // m_mass -= MASSNH3;
408 diff = -1;
409 break;
410 case Enums::PeptideIon::yo:
411 // m_mass -= MASSH2O;
412 break;
413 case Enums::PeptideIon::bstar:
414 // m_mass -= MASSH2O;
415 // m_mass -= MASSNH3;
416 diff = -1;
417 break;
418 case Enums::PeptideIon::bo:
419 // m_mass -= MASSH2O;
420 // m_mass -= MASSH2O;
421 break;
422 case Enums::PeptideIon::a:
423 // m_mass -= MASSH2O;
424 // m_mass -= MASSCO;
425 break;
426 case Enums::PeptideIon::c:
427 // m_mass += MASSNH3;
428 diff = -1;
429 break;
430 // SvgIon.moxygen - mN
431 case Enums::PeptideIon::z:
432 // m_mass -= MASSH2O;
433 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
434 diff = -1;
435 break;
436 case Enums::PeptideIon::b:
437 // m_mass -= MASSH2O;
438 break;
439 case Enums::PeptideIon::bp:
440 // H 1 O 3 P 1 + H 2 0
441 break;
442
443
444 case Enums::PeptideIon::astar:
445 // m_mass -= MASSH2O;
446 // m_mass = - MASSCO - MASSNH3;
447 diff = -1;
448 break;
449 case Enums::PeptideIon::ao:
450 // m_mass -= MASSH2O;
451 // m_mass = - MASSCO - MASSH2O;
452 break;
453 case Enums::PeptideIon::x:
454 // +MASSCO + MASSOXYGEN
455 break;
456 default:
457 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
458 break;
459 }
460 break;
461 case Enums::AtomIsotopeSurvey::O:
462 switch(m_ionType)
463 {
464 case Enums::PeptideIon::y:
465 break;
466 case Enums::PeptideIon::yp:
467 // H 1 O 3 P 1 + H 2 0
468 diff = -4 * m_neutralPhosphoLossNumber;
469 break;
470
471 case Enums::PeptideIon::ystar:
472 // m_mass -= MASSNH3;
473 break;
474 case Enums::PeptideIon::yo:
475 // m_mass -= MASSH2O;
476 diff = -1;
477 break;
478 case Enums::PeptideIon::bstar:
479 // m_mass -= MASSH2O;
480 // m_mass -= MASSNH3;
481 diff = -1;
482 break;
483 case Enums::PeptideIon::bo:
484 // m_mass -= MASSH2O;
485 // m_mass -= MASSH2O;
486 diff = -2;
487 break;
488 case Enums::PeptideIon::a:
489 // m_mass -= MASSH2O;
490 // m_mass -= MASSCO;
491 diff = -2;
492 break;
493 case Enums::PeptideIon::c:
494 // m_mass += MASSNH3;
495 break;
496 // SvgIon.moxygen - mN
497 case Enums::PeptideIon::z:
498 // m_mass -= MASSH2O;
499 // m_mass += MASSOXYGEN - MASSNITROGEN - MPROTIUM;
500 diff = -2;
501 break;
502 case Enums::PeptideIon::b:
503 // m_mass -= MASSH2O;
504 diff = -1;
505 break;
506 case Enums::PeptideIon::bp:
507 // H 1 O 3 P 1 + H 2 0
508 diff = -4 * m_neutralPhosphoLossNumber;
509 break;
510
511
512 case Enums::PeptideIon::astar:
513 // m_mass -= MASSH2O;
514 // m_mass = - MASSCO - MASSNH3;
515 diff = -2;
516 break;
517 case Enums::PeptideIon::ao:
518 // m_mass -= MASSH2O;
519 // m_mass = - MASSCO - MASSH2O;
520 diff = -3;
521 break;
522 case Enums::PeptideIon::x:
523 // +MASSCO + MASSOXYGEN
524 diff = +1;
525 break;
526 default:
527 throw PappsoException(
528 QObject::tr("Enums::PeptideIon name not implemented"));
529 break;
530 }
531 break;
532 case Enums::AtomIsotopeSurvey::S:
533 break;
534 default:
535 qDebug() << "PeptideFragmentIon::getNumberOfAtom(Enums::AtomIsotopeSurvey "
536 "atom) NOT IMPLEMENTED";
537 }
538 return number + diff;
539}
pappso::Enums::PeptideIon::a
@ a
Nter aldimine ions.
Definition types.h:290
pappso::Enums::PeptideIon::c
@ c
Nter amino ions.
Definition types.h:294
pappso::Enums::PeptideIon::astar
@ astar
Nter aldimine ions + NH3 loss.
Definition types.h:291
pappso::Enums::PeptideIon::ystar
@ ystar
Cter amino ions + NH3 loss.
Definition types.h:296
pappso::Enums::PeptideIon::yo
@ yo
Cter amino ions + H2O loss.
Definition types.h:297
pappso::Enums::PeptideIon::bstar
@ bstar
Nter acylium ions + NH3 loss.
Definition types.h:288
pappso::Enums::PeptideIon::x
@ x
Cter acylium ions.
Definition types.h:300
pappso::Enums::PeptideIon::bo
@ bo
Nter acylium ions + H2O loss.
Definition types.h:289
pappso::Enums::PeptideIon::ao
@ ao
Nter aldimine ions + H2O loss.
Definition types.h:292
pappso::Enums::PeptideIon::z
@ z
Cter carbocations.
Definition types.h:298

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 543 of file peptidefragmention.cpp.

544{
545 int number = msp_fragment.get()->getNumberOfIsotope(isotope);
546 return number;
547}

References msp_fragment.

◆ getNumberOfNeutralPhosphoLoss()

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

Definition at line 597 of file peptidefragmention.cpp.

598{
599 return m_neutralPhosphoLossNumber;
600}

References m_neutralPhosphoLossNumber.

◆ getPeptideFragmentSp()

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

Definition at line 569 of file peptidefragmention.cpp.

570{
571 return msp_fragment;
572}

References msp_fragment.

◆ getPeptideIonColor()

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

Definition at line 204 of file peptidefragmention.cpp.

205{
206 switch(m_ionType)
207 {
208 case Enums::PeptideIon::y:
209 return QColor("red");
210 break;
211 case Enums::PeptideIon::yp:
212 return QColor("red");
213 break;
214 case Enums::PeptideIon::ystar:
215 return QColor("red");
216 break;
217 case Enums::PeptideIon::yo:
218 return QColor("orange");
219 break;
220 case Enums::PeptideIon::x:
221 return QColor("orange");
222 break;
223 case Enums::PeptideIon::bstar:
224 return QColor("blue");
225 break;
226 case Enums::PeptideIon::bo:
227 return QColor("#ff00ff");
228 break;
229 case Enums::PeptideIon::a:
230 return QColor("green");
231 break;
232 case Enums::PeptideIon::astar:
233 return QColor("green");
234 break;
235 case Enums::PeptideIon::ao:
236 return QColor("green");
237 break;
238 case Enums::PeptideIon::c:
239 return QColor("blue");
240 break;
241 // SvgIon.moxygen - mN
242 case Enums::PeptideIon::z:
243 return QColor("red");
244 break;
245 case Enums::PeptideIon::b:
246 return QColor("blue");
247 break;
248 case Enums::PeptideIon::bp:
249 return QColor("blue");
250 break;
251 default:
252 throw PappsoException(QString("Enums::PeptideIon color not implemented %1")
253 .arg(getPeptideIonName(m_ionType)));
254 break;
255 }
256}

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 592 of file peptidefragmention.cpp.

593{
594 return msp_fragment.get()->getPeptideIonDirection();
595}

References msp_fragment.

Referenced by PeptideFragmentIon().

◆ getPeptideIonDirection() [2/2]

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

Definition at line 103 of file peptidefragmention.cpp.

104{
105 return pappso::getPeptideIonDirection(ion_type);
106}

References pappso::getPeptideIonDirection().

◆ getPeptideIonName() [1/2]

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

Definition at line 138 of file peptidefragmention.cpp.

139{
140 if((m_ionType == Enums::PeptideIon::yp) || (m_ionType == Enums::PeptideIon::bp))
141 {
142 return QString("%1(%2)")
143 .arg(getPeptideIonName(m_ionType))
144 .arg(m_neutralPhosphoLossNumber);
145 }
146 return getPeptideIonName(m_ionType);
147}

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 150 of file peptidefragmention.cpp.

151{
152 switch(m_ionType)
153 {
154 case Enums::PeptideIon::y:
155 return "y";
156 break;
157 case Enums::PeptideIon::yp:
158 return "yP";
159 break;
160 case Enums::PeptideIon::ystar:
161 return "y*";
162 break;
163 case Enums::PeptideIon::yo:
164 return "yO";
165 break;
166 case Enums::PeptideIon::bstar:
167 return "b*";
168 break;
169 case Enums::PeptideIon::bo:
170 return "bO";
171 break;
172 case Enums::PeptideIon::a:
173 return "a";
174 break;
175 case Enums::PeptideIon::astar:
176 return "a*";
177 break;
178 case Enums::PeptideIon::ao:
179 return "aO";
180 break;
181 case Enums::PeptideIon::c:
182 return "c";
183 break;
184 // SvgIon.moxygen - mN
185 case Enums::PeptideIon::z:
186 return "z";
187 break;
188 case Enums::PeptideIon::b:
189 return "b";
190 break;
191 case Enums::PeptideIon::bp:
192 return "bP";
193 break;
194 case Enums::PeptideIon::x:
195 return "x";
196 break;
197 default:
198 throw PappsoException(QString("Enums::PeptideIon name not implemented"));
199 break;
200 }
201}

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 587 of file peptidefragmention.cpp.

588{
589 return m_ionType;
590}

References m_ionType.

◆ getSequence()

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

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 563 of file peptidefragmention.cpp.

564{
565 return msp_fragment.get()->getSequence();
566}

References msp_fragment.

◆ isPalindrome()

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

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 603 of file peptidefragmention.cpp.

604{
605 return msp_fragment.get()->isPalindrome();
606}

References msp_fragment.

◆ makePeptideFragmentIonSp()

PeptideFragmentIonSp pappso::PeptideFragmentIon::makePeptideFragmentIonSp ( ) const

Definition at line 550 of file peptidefragmention.cpp.

551{
552 return std::make_shared<PeptideFragmentIon>(*this);
553}

◆ size()

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

Implements pappso::PeptideInterface.

Definition at line 557 of file peptidefragmention.cpp.

558{
559 return msp_fragment.get()->size();
560}

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: