libpappsomspp
Library for mass spectrometry
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38 : m_filter_keep_greater(150),
39 m_n_most_intense(100),
40 m_filter_rescale(100),
41 m_filter_highpass(0.9)
46 const XtandemSpectrumProcess ©)
47 : m_filter_keep_greater(copy.m_filter_keep_greater),
48 m_n_most_intense(copy.m_n_most_intense),
49 m_filter_rescale(copy.m_filter_rescale),
50 m_filter_highpass(copy.m_filter_highpass)
52 m_isRemoveIsotope = copy.m_isRemoveIsotope;
53 m_isExcludeParent_neutral_loss = copy.m_isExcludeParent_neutral_loss;
54 m_neutralLossMass = copy.m_neutralLossMass;
55 m_neutralLossWindowDalton = copy.m_neutralLossWindowDalton;
57 m_isExcludeParent = copy.m_isExcludeParent;
58 m_isExcludeParent_lower_dalton = copy.m_isExcludeParent_lower_dalton;
59 m_isExcludeParent_upper_dalton = copy.m_isExcludeParent_upper_dalton;
60 m_isRefineSpectrumModel = copy.m_isRefineSpectrumModel;
61 _y_ions = copy._y_ions;
62 _b_ions = copy._b_ions;
63 _ystar_ions = copy._ystar_ions;
64 _bstar_ions = copy._bstar_ions;
65 _c_ions = copy._c_ions;
66 _z_ions = copy._z_ions;
67 _a_ions = copy._a_ions;
68 _x_ions = copy._x_ions;
70 _astar_ions = copy._astar_ions;
71 _ao_ions = copy._ao_ions;
72 _bo_ions = copy._bo_ions;
73 _yo_ions = copy._yo_ions;
283 unsigned int parent_charge)
const
285 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__
286 <<
" parent_charge==" << parent_charge;
289 MassSpectrum spectrum_process(spectrum);
292 spectrum_process.massSpectrumFilter(FilterTandemDeisotope());
294 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"()";
298 spectrum_process.massSpectrumFilter(
299 MassSpectrumFilterResampleRemoveMzRange(
300 MzRange(parent_ion_mz,
306 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"() ";
310 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"()";
312 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"()";
316 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"()";
321 ((parent_ion_mz - (
MHPLUS * parent_charge)) * parent_charge) +
MHPLUS;
327 filter_parent.
filter(spectrum_process);
331 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__
332 <<
" parent_charge==" << parent_charge;
338 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"() "
339 << spectrum_process.size();
340 return spectrum_process;
MassSpectrum & filter(MassSpectrum &spectrum) const override
double pappso_double
A type definition for doubles.
void setMinimumMz(pappso_double minimum_mz)
const pappso_double MHPLUS(1.007276466879)
void setRemoveIsotope(bool remove_isotope)
Trace & filter(Trace &data_points) const override
@ yo
Cter amino ions + H2O loss.
double getThresholdX() const
@ astar
Nter aldimine ions + NH3 loss.
bool getRefineSpectrumModel() const
pappso_double getMinimumMz() const
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
void setExcludeParentNeutralLoss(bool neutral_loss)
bool getIonScore(PeptideIon ion_type) const
@ bstar
Nter acylium ions + NH3 loss.
pappso::pappso_double getNeutralLossMass() const
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
std::size_t getNumberOfPoints() const
Trace & filter(Trace &data_points) const override
MassSpectrum process(const MassSpectrum &spectrum, pappso_double parent_ion_mass, unsigned int parent_charge) const
process raw spectrum to prepare hyperscore computation
void setRefineSpectrumModel(bool refine)
void setNmostIntense(unsigned int nmost_intense)
static PrecisionPtr getDaltonInstance(pappso_double value)
bool getExcludeParentNeutralLoss() const
void setIonScore(PeptideIon ion_type, bool compute_score)
pappso::pappso_double getDynamicRange() const
@ bo
Nter acylium ions + H2O loss.
pappso::pappso_double m_neutralLossMass
void setNeutralLossMass(pappso::pappso_double neutral_loss_mass)
MassSpectrum & filter(MassSpectrum &data_points) const override
Trace & filter(Trace &trace) const override
pappso::pappso_double m_isExcludeParent_lower_dalton
void setNeutralLossWindowDalton(pappso::pappso_double neutral_loss_precision)
@ ao
Nter aldimine ions + H2O loss.
unsigned int getNmostIntense() const
bool getRemoveIsotope() const
FilterRescaleY m_filter_rescale
bool getExcludeParent() const
FilterTandemDeisotope m_filter_remove_c13
pappso::pappso_double m_neutralLossWindowDalton
bool m_isExcludeParent_neutral_loss
pappso::pappso_double m_isExcludeParent_upper_dalton
FilterHighPass m_filter_highpass
FilterResampleKeepGreater m_filter_keep_greater
~XtandemSpectrumProcess()
bool m_isRefineSpectrumModel
void setExcludeParent(bool exclude_parent)
double getDynamicRange() const
@ ystar
Cter amino ions + NH3 loss.
FilterGreatestY m_n_most_intense
Trace & filter(Trace &data_points) const override
void setDynamicRange(pappso::pappso_double dynamic_range)
pappso::pappso_double getNeutralLossWindowDalton() const