libpappsomspp
Library for mass spectrometry
pappso::PeptideVariableModificationBuilder Class Reference

Modify a peptide shared pointer with a variable modification on one AA. More...

#include <peptidevariablemodificationbuilder.h>

Inheritance diagram for pappso::PeptideVariableModificationBuilder:
pappso::PeptideModificatorBase pappso::PeptideModificatorInterface pappso::PeptideSpSinkInterface pappso::PeptideVariableModificationReplacement

Public Member Functions

 PeptideVariableModificationBuilder (AaModificationP mod)
 
virtual ~PeptideVariableModificationBuilder ()
 
void setPeptideSp (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
 function to give the products of modifications for a digested peptide More...
 
void addAa (char aa)
 
void setMaxNumberMod (unsigned int max_num)
 
void setMinNumberMod (unsigned int min_num)
 
void setModificationCounter (unsigned int counter)
 
void setSink (PeptideModificatorInterface *sink) override
 
void setProtNter (bool arg1)
 this modification concerns the Nter peptide More...
 
void setProtCter (bool arg1)
 this modification concerns the Cter peptide More...
 
void setProtElse (bool arg1)
 this modification concerns all peptides between Nter and Cter More...
 
- Public Member Functions inherited from pappso::PeptideModificatorBase
 PeptideModificatorBase ()
 
virtual ~PeptideModificatorBase ()
 
virtual void setModificationPattern (QString &pattern) final
 set the pattern on which the modification will be applied (usually the list of concerned AA) More...
 
- Public Member Functions inherited from pappso::PeptideModificatorInterface
virtual ~PeptideModificatorInterface ()
 

Static Protected Member Functions

static bool next_combination (const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last)
 

Protected Attributes

PeptideModificatorInterfacem_sink = nullptr
 
AaModificationP mp_mod
 
unsigned int m_minNumberMod = 0
 
unsigned int m_maxNumberMod = 30000
 
unsigned int m_modificationCount = 0
 
bool m_isProtNterMod = true
 
bool m_isProtCterMod = true
 
bool m_isProtElseMod = true
 
- Protected Attributes inherited from pappso::PeptideModificatorBase
QRegularExpression m_pattern
 

Private Attributes

QString m_aaModificationList
 

Additional Inherited Members

- Protected Member Functions inherited from pappso::PeptideModificatorBase
virtual void getModificationPositionList (std::vector< unsigned int > &position_list, const QString &peptide_str) final
 
virtual void getModificationPositionList (std::vector< unsigned int > &position_list, const Peptide *p_peptide, AaModificationP mod, unsigned int modification_counter)
 

Detailed Description

Modify a peptide shared pointer with a variable modification on one AA.

Definition at line 36 of file peptidevariablemodificationbuilder.h.

Constructor & Destructor Documentation

◆ PeptideVariableModificationBuilder()

pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder ( AaModificationP  mod)

Definition at line 72 of file peptidevariablemodificationbuilder.cpp.

◆ ~PeptideVariableModificationBuilder()

pappso::PeptideVariableModificationBuilder::~PeptideVariableModificationBuilder ( )
virtual

Definition at line 78 of file peptidevariablemodificationbuilder.cpp.

79 {
80 }

Member Function Documentation

◆ addAa()

void pappso::PeptideVariableModificationBuilder::addAa ( char  aa)

◆ next_combination()

bool pappso::PeptideVariableModificationBuilder::next_combination ( const std::vector< unsigned int >::iterator  first,
std::vector< unsigned int >::iterator  k,
const std::vector< unsigned int >::iterator  last 
)
staticprotected

Definition at line 30 of file peptidevariablemodificationbuilder.cpp.

34 {
35  /* Credits: Mark Nelson http://marknelson.us */
36  if((first == last) || (first == k) || (last == k))
37  return false;
38  std::vector<unsigned int>::iterator i1 = first;
39  std::vector<unsigned int>::iterator i2 = last;
40  ++i1;
41  if(last == i1)
42  return false;
43  i1 = last;
44  --i1;
45  i1 = k;
46  --i2;
47  while(first != i1)
48  {
49  if(*--i1 < *i2)
50  {
51  std::vector<unsigned int>::iterator j = k;
52  while(!(*i1 < *j))
53  ++j;
54  std::iter_swap(i1, j);
55  ++i1;
56  ++j;
57  i2 = k;
58  std::rotate(i1, j, last);
59  while(last != j)
60  {
61  ++j;
62  ++i2;
63  }
64  std::rotate(k, i2, last);
65  return true;
66  }
67  }
68  std::rotate(first, k, last);
69  return false;
70 }

References pappso::last.

Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().

◆ setMaxNumberMod()

void pappso::PeptideVariableModificationBuilder::setMaxNumberMod ( unsigned int  max_num)
inline

◆ setMinNumberMod()

void pappso::PeptideVariableModificationBuilder::setMinNumberMod ( unsigned int  min_num)
inline

◆ setModificationCounter()

void pappso::PeptideVariableModificationBuilder::setModificationCounter ( unsigned int  counter)
inline

◆ setPeptideSp()

void pappso::PeptideVariableModificationBuilder::setPeptideSp ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const PeptideSp peptide_sp,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
overridevirtual

function to give the products of modifications for a digested peptide

Parameters
sequence_database_idinteger that references the sequence fatabase (file, stream, url...)
protein_spshared pointer on the protein that was initialy digested
is_decoytell if the current protein is a decoy (true) or normal (false) protein
peptidePeptide object containing sequence and possible modifications
startthe position of the first amino acid of the peptide in the original protein sequence. the first amino acid of the protein is at position 1.
is_nterboolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal)
missed_cleavage_numbernumber of missed cleavage sites (that the enzyme has not cut) fot the product
semi_enzymeboolean that tells if this peptide is the produce of a semi enzymatic lysis

Implements pappso::PeptideModificatorInterface.

Reimplemented in pappso::PeptideVariableModificationReplacement.

Definition at line 92 of file peptidevariablemodificationbuilder.cpp.

101 {
102  // QString s = "Banana";
103  // s.replace(QRegExp("a[mn]"), "ox");
104 
105 
106  bool modify_this_peptide = true;
108  {
109  modify_this_peptide = false;
110  if((m_isProtNterMod) && (is_nter))
111  {
112  // this an Nter peptide
113  modify_this_peptide = true;
114  }
115  else if((m_isProtCterMod) &&
116  (protein_sp.get()->size() ==
117  (start + peptide_sp_original.get()->size())))
118  {
119  // this is a Cter peptide
120  modify_this_peptide = true;
121  }
122  else if(m_isProtElseMod)
123  {
124  modify_this_peptide = true;
125  }
126  }
127 
128  if(modify_this_peptide)
129  {
130 
131  std::vector<unsigned int> position_list;
133  position_list, peptide_sp_original.get(), mp_mod, m_modificationCount);
134 
135 
136  // std::vector< unsigned int > position_list =
137  // peptide_sp_original.get()->getAaPositionList(m_aaModificationList);
138  // std::string s = "12345";
139  // no AA modification :
140  if(m_minNumberMod == 0)
141  {
142  m_sink->setPeptideSp(sequence_database_id,
143  protein_sp,
144  is_decoy,
145  peptide_sp_original,
146  start,
147  is_nter,
148  missed_cleavage_number,
149  semi_enzyme);
150  }
151 
152  unsigned int nb_pos = position_list.size();
153  if(nb_pos > 0)
154  {
155  // loop to find 1 to n-1 AA modification combinations
156  unsigned int comb_size = 1;
157  while((comb_size < nb_pos) && (comb_size <= m_maxNumberMod))
158  {
159  do
160  {
161  // std::cout << std::string(being,begin + comb_size) <<
162  // std::endl;
163  Peptide new_peptide(*(peptide_sp_original.get()));
164  for(unsigned int i = 0; i < comb_size; i++)
165  {
166  new_peptide.addAaModification(mp_mod, position_list[i]);
167  }
168  PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
169  m_sink->setPeptideSp(sequence_database_id,
170  protein_sp,
171  is_decoy,
172  new_peptide_sp,
173  start,
174  is_nter,
175  missed_cleavage_number,
176  semi_enzyme);
177  }
178  while(next_combination(position_list.begin(),
179  position_list.begin() + comb_size,
180  position_list.end()));
181  comb_size++;
182  }
183 
184  if(nb_pos <= m_maxNumberMod)
185  {
186  // the last combination : all aa are modified :
187  Peptide new_peptide(*(peptide_sp_original.get()));
188  for(unsigned int i = 0; i < nb_pos; i++)
189  {
190  new_peptide.addAaModification(mp_mod, position_list[i]);
191  }
192  PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
193  m_sink->setPeptideSp(sequence_database_id,
194  protein_sp,
195  is_decoy,
196  new_peptide_sp,
197  start,
198  is_nter,
199  missed_cleavage_number,
200  semi_enzyme);
201  }
202  }
203  }
204  else
205  {
206  // no modification
207  m_sink->setPeptideSp(sequence_database_id,
208  protein_sp,
209  is_decoy,
210  peptide_sp_original,
211  start,
212  is_nter,
213  missed_cleavage_number,
214  semi_enzyme);
215  }
216 }
virtual void getModificationPositionList(std::vector< unsigned int > &position_list, const QString &peptide_str) final
virtual void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of modifications for a digested peptide
static bool next_combination(const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last)
std::shared_ptr< const Peptide > PeptideSp

References pappso::Peptide::addAaModification(), pappso::PeptideModificatorBase::getModificationPositionList(), m_isProtCterMod, m_isProtElseMod, m_isProtNterMod, m_maxNumberMod, m_minNumberMod, m_modificationCount, m_sink, pappso::Peptide::makePeptideSp(), mp_mod, next_combination(), and pappso::PeptideModificatorInterface::setPeptideSp().

◆ setProtCter()

void pappso::PeptideVariableModificationBuilder::setProtCter ( bool  arg1)
inline

this modification concerns the Cter peptide

Definition at line 86 of file peptidevariablemodificationbuilder.h.

87  {
88  m_isProtCterMod = arg1;
89  };

Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().

◆ setProtElse()

void pappso::PeptideVariableModificationBuilder::setProtElse ( bool  arg1)
inline

this modification concerns all peptides between Nter and Cter

Definition at line 93 of file peptidevariablemodificationbuilder.h.

94  {
95  m_isProtElseMod = arg1;
96  };

Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().

◆ setProtNter()

void pappso::PeptideVariableModificationBuilder::setProtNter ( bool  arg1)
inline

this modification concerns the Nter peptide

Definition at line 79 of file peptidevariablemodificationbuilder.h.

80  {
81  m_isProtNterMod = arg1;
82  };

Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().

◆ setSink()

void pappso::PeptideVariableModificationBuilder::setSink ( PeptideModificatorInterface sink)
inlineoverridevirtual

Member Data Documentation

◆ m_aaModificationList

QString pappso::PeptideVariableModificationBuilder::m_aaModificationList
private

Definition at line 121 of file peptidevariablemodificationbuilder.h.

Referenced by addAa().

◆ m_isProtCterMod

bool pappso::PeptideVariableModificationBuilder::m_isProtCterMod = true
protected

◆ m_isProtElseMod

bool pappso::PeptideVariableModificationBuilder::m_isProtElseMod = true
protected

◆ m_isProtNterMod

bool pappso::PeptideVariableModificationBuilder::m_isProtNterMod = true
protected

◆ m_maxNumberMod

unsigned int pappso::PeptideVariableModificationBuilder::m_maxNumberMod = 30000
protected

◆ m_minNumberMod

unsigned int pappso::PeptideVariableModificationBuilder::m_minNumberMod = 0
protected

◆ m_modificationCount

◆ m_sink

PeptideModificatorInterface* pappso::PeptideVariableModificationBuilder::m_sink = nullptr
protected

◆ mp_mod


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