libpappsomspp
Library for mass spectrometry
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pappso::PeptideVariableModificationReplacement Class Reference

#include <peptidevariablemodificationreplacement.h>

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

Public Member Functions

 PeptideVariableModificationReplacement (AaModificationP mod_before, AaModificationP mod_after)
 
virtual ~PeptideVariableModificationReplacement ()
 
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
 
- Public Member Functions inherited from pappso::PeptideVariableModificationBuilder
 PeptideVariableModificationBuilder (AaModificationP mod)
 
virtual ~PeptideVariableModificationBuilder ()
 
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
 
void setProtCter (bool arg1)
 this modification concerns the Cter peptide
 
void setProtElse (bool arg1)
 this modification concerns all peptides between Nter and Cter
 
- 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)
 
- Public Member Functions inherited from pappso::PeptideModificatorInterface
virtual ~PeptideModificatorInterface ()
 

Private Member Functions

void replaceModificationsAtPosition (Peptide &new_peptide, unsigned int position)
 

Private Attributes

AaModificationP mp_modAfter
 

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)
 
- Static Protected Member Functions inherited from pappso::PeptideVariableModificationBuilder
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 inherited from pappso::PeptideVariableModificationBuilder
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
 

Detailed Description

Definition at line 39 of file peptidevariablemodificationreplacement.h.

Constructor & Destructor Documentation

◆ PeptideVariableModificationReplacement()

pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement ( AaModificationP  mod_before,
AaModificationP  mod_after 
)

this forces to check that the targetted modified sites really has the mod_before

Definition at line 35 of file peptidevariablemodificationreplacement.cpp.

38{
39 mp_modAfter = mod_after;
40 /** this forces to check that the targetted modified sites really has the
41 * mod_before */
43}

References pappso::PeptideVariableModificationBuilder::m_modificationCount, and mp_modAfter.

◆ ~PeptideVariableModificationReplacement()

pappso::PeptideVariableModificationReplacement::~PeptideVariableModificationReplacement ( )
virtual

Definition at line 45 of file peptidevariablemodificationreplacement.cpp.

47{
48}

Member Function Documentation

◆ replaceModificationsAtPosition()

void pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition ( Peptide new_peptide,
unsigned int  position 
)
private

Definition at line 52 of file peptidevariablemodificationreplacement.cpp.

54{
55 // replace all mod_before by mod_after :
56 Aa &aa = new_peptide.getAa(position);
57 aa.removeAaModification(mp_mod);
58 unsigned int i = 0;
59 while(i < m_modificationCount)
60 {
61 aa.addAaModification(mp_modAfter);
62 i++;
63 }
64}

References pappso::Aa::addAaModification(), pappso::Peptide::getAa(), pappso::PeptideVariableModificationBuilder::m_modificationCount, pappso::PeptideVariableModificationBuilder::mp_mod, mp_modAfter, and pappso::Aa::removeAaModification().

Referenced by setPeptideSp().

◆ setPeptideSp()

void pappso::PeptideVariableModificationReplacement::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

Reimplemented from pappso::PeptideVariableModificationBuilder.

Definition at line 68 of file peptidevariablemodificationreplacement.cpp.

77{
78 // QString s = "Banana";
79 // s.replace(QRegExp("a[mn]"), "ox");
80
81
82 bool modify_this_peptide = true;
84 {
85 modify_this_peptide = false;
86 if((m_isProtNterMod) && (is_nter))
87 {
88 // this an Nter peptide
89 modify_this_peptide = true;
90 }
91 else if((m_isProtCterMod) &&
92 (protein_sp.get()->size() ==
93 (start + peptide_sp_original.get()->size())))
94 {
95 // this is a Cter peptide
96 modify_this_peptide = true;
97 }
98 else if(m_isProtElseMod)
99 {
100 modify_this_peptide = true;
101 }
102 }
103
104 if(modify_this_peptide)
105 {
106 std::vector<unsigned int> position_list;
108 position_list, peptide_sp_original.get(), mp_mod, m_modificationCount);
109
110 // std::vector< unsigned int > position_list =
111 // peptide_sp_original.get()->getAaPositionList(_aamp_modification_list);
112 // std::string s = "12345";
113 // no AA modification :
114 if(m_minNumberMod == 0)
115 {
116 m_sink->setPeptideSp(sequence_database_id,
117 protein_sp,
118 is_decoy,
119 peptide_sp_original,
120 start,
121 is_nter,
122 missed_cleavage_number,
123 semi_enzyme);
124 }
125
126 unsigned int nb_pos = position_list.size();
127 if(nb_pos > 0)
128 {
129 // loop to find 1 to n-1 AA modification combinations
130 unsigned int comb_size = 1;
131 while((comb_size < nb_pos) && (comb_size <= m_maxNumberMod))
132 {
133 do
134 {
135 // std::cout << std::string(being,begin + comb_size) <<
136 // std::endl;
137 Peptide new_peptide(*(peptide_sp_original.get()));
138 for(unsigned int i = 0; i < comb_size; i++)
139 {
140 // new_peptide.addAaModification(mp_mod,position_list[i]);
141 this->replaceModificationsAtPosition(new_peptide,
142 position_list[i]);
143 }
144 PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
145 m_sink->setPeptideSp(sequence_database_id,
146 protein_sp,
147 is_decoy,
148 new_peptide_sp,
149 start,
150 is_nter,
151 missed_cleavage_number,
152 semi_enzyme);
153 }
154 while(next_combination(position_list.begin(),
155 position_list.begin() + comb_size,
156 position_list.end()));
157 comb_size++;
158 }
159
160 if(nb_pos <= m_maxNumberMod)
161 {
162 // the last combination : all aa are modified :
163 Peptide new_peptide(*(peptide_sp_original.get()));
164 for(unsigned int i = 0; i < nb_pos; i++)
165 {
166 // new_peptide.addAaModification(mp_mod,position_list[i]);
167
168 this->replaceModificationsAtPosition(new_peptide,
169 position_list[i]);
170 }
171 PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
172 m_sink->setPeptideSp(sequence_database_id,
173 protein_sp,
174 is_decoy,
175 new_peptide_sp,
176 start,
177 is_nter,
178 missed_cleavage_number,
179 semi_enzyme);
180 }
181 }
182 }
183 else
184 {
185 // no modification
186 m_sink->setPeptideSp(sequence_database_id,
187 protein_sp,
188 is_decoy,
189 peptide_sp_original,
190 start,
191 is_nter,
192 missed_cleavage_number,
193 semi_enzyme);
194 }
195}
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)
void replaceModificationsAtPosition(Peptide &new_peptide, unsigned int position)
std::shared_ptr< const Peptide > PeptideSp

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

Member Data Documentation

◆ mp_modAfter

AaModificationP pappso::PeptideVariableModificationReplacement::mp_modAfter
private

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