libpappsomspp
Library for mass spectrometry
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#include <xtandemspectrumprocess.h>
Private Attributes | |
FilterResampleKeepGreater | m_filter_keep_greater |
FilterGreatestY | m_n_most_intense |
FilterRescaleY | m_filter_rescale |
FilterTandemDeisotope | m_filter_remove_c13 = FilterTandemDeisotope(1.5, 200) |
FilterFloorY | m_filter_floor |
FilterHighPass | m_filter_highpass |
bool | m_isRemoveIsotope = true |
bool | m_isExcludeParent = false |
pappso::pappso_double | m_isExcludeParent_lower_dalton = 2 |
pappso::pappso_double | m_isExcludeParent_upper_dalton = 2 |
bool | m_isExcludeParent_neutral_loss = false |
pappso::pappso_double | m_neutralLossMass = MASSH2O |
pappso::pappso_double | m_neutralLossWindowDalton = 0.5 |
bool | m_isRefineSpectrumModel = true |
bool | _y_ions = true |
bool | _ystar_ions = false |
bool | _b_ions = true |
bool | _bstar_ions = false |
bool | _c_ions = false |
bool | _z_ions = false |
bool | _a_ions = false |
bool | _x_ions = false |
bool | _astar_ions = false |
bool | _ao_ions = false |
bool | _bo_ions = false |
bool | _yo_ions = false |
Definition at line 41 of file xtandemspectrumprocess.h.
pappso::XtandemSpectrumProcess::XtandemSpectrumProcess | ( | ) |
Definition at line 37 of file xtandemspectrumprocess.cpp.
pappso::XtandemSpectrumProcess::XtandemSpectrumProcess | ( | const XtandemSpectrumProcess & | copy | ) |
Definition at line 45 of file xtandemspectrumprocess.cpp.
References _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, m_isExcludeParent, m_isExcludeParent_lower_dalton, m_isExcludeParent_neutral_loss, m_isExcludeParent_upper_dalton, m_isRefineSpectrumModel, m_isRemoveIsotope, m_neutralLossMass, and m_neutralLossWindowDalton.
pappso::XtandemSpectrumProcess::~XtandemSpectrumProcess | ( | ) |
Definition at line 75 of file xtandemspectrumprocess.cpp.
pappso::pappso_double pappso::XtandemSpectrumProcess::getDynamicRange | ( | ) | const |
Definition at line 199 of file xtandemspectrumprocess.cpp.
References pappso::FilterRescaleY::getDynamicRange(), and m_filter_rescale.
bool pappso::XtandemSpectrumProcess::getExcludeParent | ( | ) | const |
Definition at line 209 of file xtandemspectrumprocess.cpp.
References m_isExcludeParent.
bool pappso::XtandemSpectrumProcess::getExcludeParentNeutralLoss | ( | ) | const |
Definition at line 214 of file xtandemspectrumprocess.cpp.
References m_isExcludeParent_neutral_loss.
bool pappso::XtandemSpectrumProcess::getIonScore | ( | PeptideIon | ion_type | ) | const |
Definition at line 237 of file xtandemspectrumprocess.cpp.
References _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, pappso::a, pappso::ao, pappso::astar, pappso::b, pappso::bo, pappso::bstar, pappso::c, pappso::x, pappso::y, pappso::yo, pappso::ystar, and pappso::z.
pappso_double pappso::XtandemSpectrumProcess::getMinimumMz | ( | ) | const |
Definition at line 189 of file xtandemspectrumprocess.cpp.
References pappso::FilterResampleKeepGreater::getThresholdX(), and m_filter_keep_greater.
pappso::pappso_double pappso::XtandemSpectrumProcess::getNeutralLossMass | ( | ) | const |
Definition at line 219 of file xtandemspectrumprocess.cpp.
References m_neutralLossMass.
pappso_double pappso::XtandemSpectrumProcess::getNeutralLossWindowDalton | ( | ) | const |
Definition at line 224 of file xtandemspectrumprocess.cpp.
References m_neutralLossWindowDalton.
unsigned int pappso::XtandemSpectrumProcess::getNmostIntense | ( | ) | const |
Definition at line 194 of file xtandemspectrumprocess.cpp.
References pappso::FilterGreatestY::getNumberOfPoints(), and m_n_most_intense.
bool pappso::XtandemSpectrumProcess::getRefineSpectrumModel | ( | ) | const |
Definition at line 230 of file xtandemspectrumprocess.cpp.
References m_isRefineSpectrumModel.
bool pappso::XtandemSpectrumProcess::getRemoveIsotope | ( | ) | const |
Definition at line 204 of file xtandemspectrumprocess.cpp.
References m_isRemoveIsotope.
MassSpectrum pappso::XtandemSpectrumProcess::process | ( | const MassSpectrum & | spectrum, |
pappso_double | parent_ion_mass, | ||
unsigned int | parent_charge | ||
) | const |
process raw spectrum to prepare hyperscore computation
Definition at line 281 of file xtandemspectrumprocess.cpp.
References pappso::FilterTandemDeisotope::filter(), pappso::MassSpectrumFilterResampleRemoveMzRange::filter(), pappso::FilterHighPass::filter(), pappso::FilterGreatestY::filter(), pappso::FilterRescaleY::filter(), pappso::FilterResampleKeepGreater::filter(), pappso::PrecisionFactory::getDaltonInstance(), m_filter_highpass, m_filter_keep_greater, m_filter_remove_c13, m_filter_rescale, m_isExcludeParent, m_isExcludeParent_lower_dalton, m_isExcludeParent_neutral_loss, m_isExcludeParent_upper_dalton, m_isRemoveIsotope, m_n_most_intense, m_neutralLossMass, m_neutralLossWindowDalton, pappso::MassSpectrum::massSpectrumFilter(), and pappso::MHPLUS().
void pappso::XtandemSpectrumProcess::setDynamicRange | ( | pappso::pappso_double | dynamic_range | ) |
Definition at line 90 of file xtandemspectrumprocess.cpp.
References m_filter_rescale.
void pappso::XtandemSpectrumProcess::setExcludeParent | ( | bool | exclude_parent | ) |
Definition at line 102 of file xtandemspectrumprocess.cpp.
References m_isExcludeParent.
void pappso::XtandemSpectrumProcess::setExcludeParentNeutralLoss | ( | bool | neutral_loss | ) |
Definition at line 107 of file xtandemspectrumprocess.cpp.
References m_isExcludeParent_neutral_loss.
void pappso::XtandemSpectrumProcess::setIonScore | ( | PeptideIon | ion_type, |
bool | compute_score | ||
) |
Definition at line 133 of file xtandemspectrumprocess.cpp.
References _a_ions, _ao_ions, _astar_ions, _b_ions, _bo_ions, _bstar_ions, _c_ions, _x_ions, _y_ions, _yo_ions, _ystar_ions, _z_ions, pappso::a, pappso::ao, pappso::astar, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::c, pappso::x, pappso::y, pappso::yo, pappso::yp, pappso::ystar, and pappso::z.
void pappso::XtandemSpectrumProcess::setMinimumMz | ( | pappso_double | minimum_mz | ) |
Definition at line 80 of file xtandemspectrumprocess.cpp.
References m_filter_keep_greater.
void pappso::XtandemSpectrumProcess::setNeutralLossMass | ( | pappso::pappso_double | neutral_loss_mass | ) |
Definition at line 112 of file xtandemspectrumprocess.cpp.
References m_neutralLossMass.
void pappso::XtandemSpectrumProcess::setNeutralLossWindowDalton | ( | pappso::pappso_double | neutral_loss_precision | ) |
Definition at line 118 of file xtandemspectrumprocess.cpp.
References m_neutralLossWindowDalton.
void pappso::XtandemSpectrumProcess::setNmostIntense | ( | unsigned int | nmost_intense | ) |
Definition at line 85 of file xtandemspectrumprocess.cpp.
References m_n_most_intense.
void pappso::XtandemSpectrumProcess::setRefineSpectrumModel | ( | bool | refine | ) |
Definition at line 126 of file xtandemspectrumprocess.cpp.
References m_isRefineSpectrumModel.
void pappso::XtandemSpectrumProcess::setRemoveIsotope | ( | bool | remove_isotope | ) |
Definition at line 96 of file xtandemspectrumprocess.cpp.
References m_isRemoveIsotope.
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Definition at line 100 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 103 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 102 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 96 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 104 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 97 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 98 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 101 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 94 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 105 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 95 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 99 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getIonScore(), and setIonScore().
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Definition at line 84 of file xtandemspectrumprocess.h.
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Definition at line 85 of file xtandemspectrumprocess.h.
Referenced by process().
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Definition at line 80 of file xtandemspectrumprocess.h.
Referenced by getMinimumMz(), process(), and setMinimumMz().
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Definition at line 83 of file xtandemspectrumprocess.h.
Referenced by process().
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Definition at line 82 of file xtandemspectrumprocess.h.
Referenced by getDynamicRange(), process(), and setDynamicRange().
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Definition at line 87 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getExcludeParent(), process(), and setExcludeParent().
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Definition at line 88 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), and process().
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Definition at line 90 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getExcludeParentNeutralLoss(), process(), and setExcludeParentNeutralLoss().
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Definition at line 89 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), and process().
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Definition at line 93 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getRefineSpectrumModel(), and setRefineSpectrumModel().
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Definition at line 86 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getRemoveIsotope(), process(), and setRemoveIsotope().
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Definition at line 81 of file xtandemspectrumprocess.h.
Referenced by getNmostIntense(), process(), and setNmostIntense().
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Definition at line 91 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getNeutralLossMass(), process(), and setNeutralLossMass().
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Definition at line 92 of file xtandemspectrumprocess.h.
Referenced by XtandemSpectrumProcess(), getNeutralLossWindowDalton(), process(), and setNeutralLossWindowDalton().