libpappsomspp
Library for mass spectrometry
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, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
 
 PeptideFragmentIon (const PeptideFragmentSp &sp_fragment, 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 More...
 
virtual const PeptideFragmentSp & getPeptideFragmentSp () const
 
virtual int getNumberOfAtom (AtomIsotopeSurvey atom) const override
 get the number of atom C, O, N, H in the molecule More...
 
virtual int getNumberOfIsotope (Isotope isotope) const override
 get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...
 
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 More...
 
PeptideIon getPeptideIonType () const
 
PeptideDirection getPeptideIonDirection () const
 
unsigned int getNumberOfNeutralPhosphoLoss () const
 
virtual bool isPalindrome () const override
 tells if the peptide sequence is a palindrome More...
 
- Public Member Functions inherited from pappso::PeptideInterface
virtual const QString getSequenceLi () const
 amino acid sequence without modification where L are replaced by I More...
 
virtual const QString getFormula (unsigned int charge) const final
 
virtual bool matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
 
- Public Member Functions inherited from pappso::Ion
 Ion ()
 
 ~Ion ()
 
virtual pappso_double getMz (unsigned int charge) const final
 

Static Public Member Functions

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

Private Attributes

const PeptideFragmentSp msp_fragment
 
const 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,
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("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 PeptideIon::yp:
65  m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
66  m_mass -=
67  ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
68  ion_type = PeptideIon::y;
69  break;
70  case PeptideIon::bp:
71  m_neutralPhosphoLossNumber = number_of_neutral_phospho_loss;
72  m_mass -=
73  ((MASSH2O + MASSPHOSPHORYLATEDR) * m_neutralPhosphoLossNumber);
74  ion_type = PeptideIon::b;
75  break;
76  default:
77  break;
78  }
79  m_mass += PeptideRawFragmentMasses::getDeltaMass(ion_type);
80 }
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:98
pappso::PeptideRawFragmentMasses::getDeltaMass
static pappso_double getDeltaMass(PeptideIon ion_type)
Definition: peptiderawfragmentmasses.cpp:56
pappso::PeptideIon::y
@ y
Cter amino ions.
pappso::PeptideIon::b
@ b
Nter acylium ions.
pappso::PeptideDirection
PeptideDirection
Definition: peptide.h:46
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
Definition: peptide.cpp:54
pappso::MASSH2O
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
pappso::MASSPHOSPHORYLATEDR
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)

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

◆ PeptideFragmentIon() [2/4]

pappso::PeptideFragmentIon::PeptideFragmentIon ( const PeptideFragmentSp &  sp_fragment,
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, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
Definition: peptidefragmention.cpp:45

◆ 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 m_mass.

◆ 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 }

◆ ~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 == 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 == 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::bp, getPeptideIonName(), m_ionType, m_neutralPhosphoLossNumber, msp_fragment, size(), and pappso::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.

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

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

◆ getNumberOfIsotope()

int pappso::PeptideFragmentIon::getNumberOfIsotope ( 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 ( PeptideIon  ion_type)
static

Definition at line 204 of file peptidefragmention.cpp.

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

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

◆ getPeptideIonDirection() [2/2]

PeptideDirection pappso::PeptideFragmentIon::getPeptideIonDirection ( 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 == PeptideIon::yp) || (m_ionType == 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::bp, m_ionType, m_neutralPhosphoLossNumber, and pappso::yp.

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

◆ getPeptideIonName() [2/2]

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

Definition at line 150 of file peptidefragmention.cpp.

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

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

◆ getPeptideIonType()

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 getCompletePeptideIonName(), and getName().

Member Data Documentation

◆ m_ionType

const PeptideIon pappso::PeptideFragmentIon::m_ionType
private

Definition at line 96 of file peptidefragmention.h.

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

◆ m_mass

pappso_double pappso::PeptideFragmentIon::m_mass = 0
private

Definition at line 98 of file peptidefragmention.h.

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

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