38 : m_filter_keep_greater(150),
39 m_n_most_intense(100),
40 m_filter_rescale(100),
41 m_filter_highpass(0.9)
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)
283 unsigned int parent_charge)
const
285 qDebug() << __FILE__ <<
" " << __FUNCTION__ <<
" " << __LINE__
286 <<
" parent_charge==" << parent_charge;
294 qDebug() << __FILE__ <<
"@" << __LINE__ << __FUNCTION__ <<
"()";
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;
keep N datapoints form the greatest intensities to the lowest
Trace & filter(Trace &data_points) const override
std::size_t getNumberOfPoints() const
Trace & filter(Trace &data_points) const override
double getThresholdX() const
Trace & filter(Trace &trace) const override
rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
Trace & filter(Trace &data_points) const override
double getDynamicRange() const
Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based m...
MassSpectrum & filter(MassSpectrum &data_points) const override
MassSpectrum & filter(MassSpectrum &spectrum) const override
Class to represent a mass spectrum.
virtual MassSpectrum & massSpectrumFilter(const MassSpectrumFilterInterface &filter) final
apply a filter on this MassSpectrum
static PrecisionPtr getDaltonInstance(pappso_double value)
get a Dalton precision pointer
pappso::pappso_double m_isExcludeParent_upper_dalton
void setRemoveIsotope(bool remove_isotope)
bool getRemoveIsotope() const
bool m_isRefineSpectrumModel
void setRefineSpectrumModel(bool refine)
pappso::pappso_double getDynamicRange() const
FilterResampleKeepGreater m_filter_keep_greater
void setIonScore(PeptideIon ion_type, bool compute_score)
bool getRefineSpectrumModel() const
~XtandemSpectrumProcess()
bool getExcludeParentNeutralLoss() const
pappso::pappso_double getNeutralLossMass() const
unsigned int getNmostIntense() const
pappso::pappso_double m_isExcludeParent_lower_dalton
void setExcludeParentNeutralLoss(bool neutral_loss)
FilterRescaleY m_filter_rescale
void setNeutralLossMass(pappso::pappso_double neutral_loss_mass)
bool getIonScore(PeptideIon ion_type) const
FilterGreatestY m_n_most_intense
pappso_double getMinimumMz() const
pappso::pappso_double m_neutralLossMass
FilterTandemDeisotope m_filter_remove_c13
void setMinimumMz(pappso_double minimum_mz)
void setNeutralLossWindowDalton(pappso::pappso_double neutral_loss_precision)
pappso::pappso_double getNeutralLossWindowDalton() const
void setDynamicRange(pappso::pappso_double dynamic_range)
pappso::pappso_double m_neutralLossWindowDalton
bool getExcludeParent() const
MassSpectrum process(const MassSpectrum &spectrum, pappso_double parent_ion_mass, unsigned int parent_charge) const
process raw spectrum to prepare hyperscore computation
FilterHighPass m_filter_highpass
void setExcludeParent(bool exclude_parent)
void setNmostIntense(unsigned int nmost_intense)
bool m_isExcludeParent_neutral_loss
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
@ astar
Nter aldimine ions + NH3 loss.
@ ystar
Cter amino ions + NH3 loss.
@ yo
Cter amino ions + H2O loss.
@ bstar
Nter acylium ions + NH3 loss.
@ bo
Nter acylium ions + H2O loss.
@ ao
Nter aldimine ions + H2O loss.
const pappso_double MHPLUS(1.007276466879)
double pappso_double
A type definition for doubles.