Modify a peptide shared pointer with a variable modification on one AA.
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#include <peptidevariablemodificationbuilder.h>
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static bool | next_combination (const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last) |
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Modify a peptide shared pointer with a variable modification on one AA.
Definition at line 57 of file peptidevariablemodificationbuilder.h.
◆ PeptideVariableModificationBuilder()
pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder |
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AaModificationP |
mod | ) |
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◆ ~PeptideVariableModificationBuilder()
pappso::PeptideVariableModificationBuilder::~PeptideVariableModificationBuilder |
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◆ addAa()
void pappso::PeptideVariableModificationBuilder::addAa |
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char |
aa | ) |
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◆ next_combination()
bool pappso::PeptideVariableModificationBuilder::next_combination |
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const std::vector< unsigned int >::iterator |
first, |
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std::vector< unsigned int >::iterator |
k, |
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const std::vector< unsigned int >::iterator |
last |
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staticprotected |
◆ setMaxNumberMod()
void pappso::PeptideVariableModificationBuilder::setMaxNumberMod |
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unsigned int |
max_num | ) |
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inline |
◆ setMinNumberMod()
void pappso::PeptideVariableModificationBuilder::setMinNumberMod |
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unsigned int |
min_num | ) |
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inline |
◆ setModificationCounter()
void pappso::PeptideVariableModificationBuilder::setModificationCounter |
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unsigned int |
counter | ) |
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inline |
◆ setPeptideSp()
void pappso::PeptideVariableModificationBuilder::setPeptideSp |
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std::int8_t |
sequence_database_id, |
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const ProteinSp & |
protein_sp, |
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bool |
is_decoy, |
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const PeptideSp & |
peptide_sp, |
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unsigned int |
start, |
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bool |
is_nter, |
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unsigned int |
missed_cleavage_number, |
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bool |
semi_enzyme |
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overridevirtual |
function to give the products of modifications for a digested peptide
- Parameters
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sequence_database_id | integer that references the sequence fatabase (file, stream, url...) |
protein_sp | shared pointer on the protein that was initialy digested |
is_decoy | tell if the current protein is a decoy (true) or normal (false) protein |
peptide | Peptide object containing sequence and possible modifications |
start | the 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_nter | boolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal) |
missed_cleavage_number | number of missed cleavage sites (that the enzyme has not cut) fot the product |
semi_enzyme | boolean that tells if this peptide is the produce of a semi enzymatic lysis |
Implements pappso::PeptideModificatorInterface.
Reimplemented in pappso::PeptideVariableModificationReplacement.
Definition at line 113 of file peptidevariablemodificationbuilder.cpp.
120 modify_this_peptide =
true;
124 modify_this_peptide =
true;
128 if(modify_this_peptide)
131 std::vector<unsigned int> position_list;
148 missed_cleavage_number,
152 unsigned int nb_pos = position_list.size();
156 unsigned int comb_size = 1;
163 Peptide new_peptide(*(peptide_sp_original.get()));
164 for(
unsigned int i = 0; i < comb_size; i++)
166 new_peptide.addAaModification(
mp_mod, position_list[i]);
168 PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
175 missed_cleavage_number,
179 position_list.begin() + comb_size,
180 position_list.end()));
187 Peptide new_peptide(*(peptide_sp_original.get()));
188 for(
unsigned int i = 0; i < nb_pos; i++)
190 new_peptide.addAaModification(
mp_mod, position_list[i]);
192 PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
199 missed_cleavage_number,
213 missed_cleavage_number,
◆ setProtCter()
void pappso::PeptideVariableModificationBuilder::setProtCter |
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bool |
arg1 | ) |
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◆ setProtElse()
void pappso::PeptideVariableModificationBuilder::setProtElse |
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bool |
arg1 | ) |
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◆ setProtNter()
void pappso::PeptideVariableModificationBuilder::setProtNter |
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bool |
arg1 | ) |
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inline |
◆ setSink()
◆ m_aaModificationList
QString pappso::PeptideVariableModificationBuilder::m_aaModificationList |
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private |
◆ m_isProtCterMod
bool pappso::PeptideVariableModificationBuilder::m_isProtCterMod = true |
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◆ m_isProtElseMod
bool pappso::PeptideVariableModificationBuilder::m_isProtElseMod = true |
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◆ m_isProtNterMod
bool pappso::PeptideVariableModificationBuilder::m_isProtNterMod = true |
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◆ m_maxNumberMod
unsigned int pappso::PeptideVariableModificationBuilder::m_maxNumberMod = 30000 |
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◆ m_minNumberMod
unsigned int pappso::PeptideVariableModificationBuilder::m_minNumberMod = 0 |
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◆ m_modificationCount
unsigned int pappso::PeptideVariableModificationBuilder::m_modificationCount = 0 |
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◆ m_sink
◆ mp_mod
The documentation for this class was generated from the following files: