libpappsomspp
Library for mass spectrometry
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#include <peptidenaturalisotopelist.h>
Public Types | |
typedef std::list< PeptideNaturalIsotopeSp >::const_iterator | const_iterator |
Public Member Functions | |
PeptideNaturalIsotopeList (const PeptideInterfaceSp &peptide, pappso_double minimum_ratio_to_compute=0.001) | |
compute the list of possible isotopes for a peptide More... | |
PeptideNaturalIsotopeList (const PeptideNaturalIsotopeList &other) | |
~PeptideNaturalIsotopeList () | |
PeptideNaturalIsotopeListSp | makePeptideNaturalIsotopeListSp () const |
const_iterator | begin () const |
const_iterator | end () const |
const std::map< unsigned int, pappso_double > | getIntensityRatioPerIsotopeNumber () const |
std::vector< PeptideNaturalIsotopeSp > | getByIsotopeNumber (unsigned int isotopeLevel, unsigned int charge) const |
std::vector< PeptideNaturalIsotopeAverageSp > | getByIntensityRatio (unsigned int charge, PrecisionPtr precision, pappso_double minimum_isotope_pattern_ratio) const |
get the list of natural isotopes representing at least a minimum ratio of the whole isotope pattern More... | |
unsigned int | size () const |
const PeptideInterfaceSp & | getPeptideInterfaceSp () const |
Private Attributes | |
const PeptideInterfaceSp | msp_peptide |
std::list< PeptideNaturalIsotopeSp > | msp_peptide_natural_isotope_list |
Definition at line 48 of file peptidenaturalisotopelist.h.
typedef std::list<PeptideNaturalIsotopeSp>::const_iterator pappso::PeptideNaturalIsotopeList::const_iterator |
Definition at line 67 of file peptidenaturalisotopelist.h.
pappso::PeptideNaturalIsotopeList::PeptideNaturalIsotopeList | ( | const PeptideInterfaceSp & | peptide, |
pappso_double | minimum_ratio_to_compute = 0.001 |
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) |
compute the list of possible isotopes for a peptide
peptide | the peptide |
minimu_ratio_to_compute | the limit under which we stop to compute because the ratio is too thin and not informative (default is 0.001). This limit is the same for each atom to survey : CHNOS |
Definition at line 38 of file peptidenaturalisotopelist.cpp.
References pappso::C, pappso::C13, pappso::H, pappso::H2, msp_peptide, msp_peptide_natural_isotope_list, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.
pappso::PeptideNaturalIsotopeList::PeptideNaturalIsotopeList | ( | const PeptideNaturalIsotopeList & | other | ) |
Definition at line 281 of file peptidenaturalisotopelist.cpp.
pappso::PeptideNaturalIsotopeList::~PeptideNaturalIsotopeList | ( | ) |
Definition at line 288 of file peptidenaturalisotopelist.cpp.
PeptideNaturalIsotopeList::const_iterator pappso::PeptideNaturalIsotopeList::begin | ( | ) | const |
Definition at line 513 of file peptidenaturalisotopelist.cpp.
References msp_peptide_natural_isotope_list.
PeptideNaturalIsotopeList::const_iterator pappso::PeptideNaturalIsotopeList::end | ( | ) | const |
Definition at line 519 of file peptidenaturalisotopelist.cpp.
References msp_peptide_natural_isotope_list.
std::vector< PeptideNaturalIsotopeAverageSp > pappso::PeptideNaturalIsotopeList::getByIntensityRatio | ( | unsigned int | charge, |
PrecisionPtr | precision, | ||
pappso_double | minimumIntensityRatio | ||
) | const |
get the list of natural isotopes representing at least a minimum ratio of the whole isotope pattern
charge | gives the number of H+, important to take into account for isotope ratio |
precision | the mass accuracy to take into acount each isotope (C13 != H2) |
minimum_isotope_pattern_ratio | the minimum ratio of the isotope pattern to represent |
/brief get a sorted (by expected intensity) vector of natural isotope average
Definition at line 425 of file peptidenaturalisotopelist.cpp.
References pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), getIntensityRatioPerIsotopeNumber(), pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), and pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp().
std::vector< PeptideNaturalIsotopeSp > pappso::PeptideNaturalIsotopeList::getByIsotopeNumber | ( | unsigned int | isotope_number, |
unsigned int | charge | ||
) | const |
/brief get a sorted (by expected intensity) vector of isotopes of the same level
Definition at line 323 of file peptidenaturalisotopelist.cpp.
References msp_peptide_natural_isotope_list.
Referenced by pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage().
const std::map< unsigned int, pappso_double > pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber | ( | ) | const |
Definition at line 293 of file peptidenaturalisotopelist.cpp.
References msp_peptide_natural_isotope_list.
Referenced by pappso::MassSpectrumWidget::computeIsotopeMassList(), and getByIntensityRatio().
const PeptideInterfaceSp & pappso::PeptideNaturalIsotopeList::getPeptideInterfaceSp | ( | ) | const |
Definition at line 531 of file peptidenaturalisotopelist.cpp.
References msp_peptide.
PeptideNaturalIsotopeListSp pappso::PeptideNaturalIsotopeList::makePeptideNaturalIsotopeListSp | ( | ) | const |
Definition at line 276 of file peptidenaturalisotopelist.cpp.
unsigned int pappso::PeptideNaturalIsotopeList::size | ( | ) | const |
Definition at line 525 of file peptidenaturalisotopelist.cpp.
References msp_peptide_natural_isotope_list.
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private |
Definition at line 51 of file peptidenaturalisotopelist.h.
Referenced by PeptideNaturalIsotopeList(), and getPeptideInterfaceSp().
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private |
Definition at line 52 of file peptidenaturalisotopelist.h.
Referenced by PeptideNaturalIsotopeList(), begin(), end(), getByIsotopeNumber(), getIntensityRatioPerIsotopeNumber(), and size().