libpappsomspp
Library for mass spectrometry
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#include <peptidemodificatorbase.h>
Public Member Functions | |
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... | |
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virtual | ~PeptideModificatorInterface () |
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 More... | |
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virtual void | setSink (PeptideModificatorInterface *sink)=0 |
Protected Member Functions | |
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) |
Protected Attributes | |
QRegularExpression | m_pattern |
Definition at line 40 of file peptidemodificatorbase.h.
pappso::PeptideModificatorBase::PeptideModificatorBase | ( | ) |
Definition at line 35 of file peptidemodificatorbase.cpp.
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virtual |
Definition at line 39 of file peptidemodificatorbase.cpp.
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protectedvirtual |
Definition at line 86 of file peptidemodificatorbase.cpp.
References pappso::Peptide::getConstAa(), pappso::Aa::getNumberOfModification(), pappso::Peptide::getSequence(), and m_pattern.
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finalprotectedvirtual |
Definition at line 50 of file peptidemodificatorbase.cpp.
References m_pattern.
Referenced by pappso::PeptideFixedModificationBuilder::setPeptideSp(), pappso::PeptideVariableModificationBuilder::setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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finalvirtual |
set the pattern on which the modification will be applied (usually the list of concerned AA)
the pattern is a standard regular expression : it describes the target site to modify. This standard regular expression is used to make a replacement of all motifs describes by an underscore ("_") The underscore is taken as a landmark to apply the modification.
pattern | the regular expression pattern ( [YST] to replace Y, S and T with _ and modify it ). The pattern can also contain the / separator to eventually specify the replacement motif. This can be used to described very complex modification patterns |
Definition at line 44 of file peptidemodificatorbase.cpp.
References m_pattern.
Referenced by pappso::PeptideModificatorPipeline::parseFixedModification(), pappso::PeptideModificatorPipeline::parseLabeledModification(), and pappso::PeptideModificatorPipeline::parsePotentialModification().
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protected |
Definition at line 66 of file peptidemodificatorbase.h.
Referenced by pappso::PeptideFixedModificationBuilder::addAa(), pappso::PeptideVariableModificationBuilder::addAa(), getModificationPositionList(), and setModificationPattern().