libpappsomspp
Library for mass spectrometry
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#include <posttreatment.h>
Public Member Functions | |
PostTreatment (pappso::PrecisionPtr precision, const PeptideModel &peptide_model) | |
virtual | ~PostTreatment () |
const PeptideModel & | getBetterPeptideModel () const |
const PeptideModel & | getOriginalPeptideModel () const |
bool | findReplaceMutations () |
Private Member Functions | |
void | findBetterPeptideModel () |
whole processus to find a better peptide model | |
void | tryBetterPositionOffsets () |
try to move offset (mass difference) | |
void | tryToRemoveOffsets () |
try to remove offset (mass difference) | |
void | tryToCumulateOffSets () |
try to assign residual mass delta to non aligned elements | |
Private Attributes | |
PeptideModel | m_originalPeptideModel |
PeptideModel | m_betterPeptideModel |
pappso::PrecisionPtr | m_precision |
Definition at line 52 of file posttreatment.h.
pappso::specglob::PostTreatment::PostTreatment | ( | pappso::PrecisionPtr | precision, |
const PeptideModel & | peptide_model ) |
Default constructor
Definition at line 45 of file posttreatment.cpp.
References findBetterPeptideModel(), m_originalPeptideModel, m_precision, and pappso::specglob::PeptideModel::matchExperimentalPeaks().
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whole processus to find a better peptide model
assign residual mass to Cter remove complementary mass delta eliminate negative offsets (perhaps neutral loss) check negative offsets for amino acid mass sums to remove try better positions for mass delta
Definition at line 66 of file posttreatment.cpp.
References pappso::specglob::PeptideModel::assignResidualMass2Cter(), pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::eliminateComplementaryDelta(), pappso::specglob::PeptideModel::eliminateNegativeOffset(), pappso::specglob::PeptideModel::getCountSharedPeaks(), pappso::specglob::PeptideModel::getMassDelta(), pappso::PrecisionBase::getNominal(), m_betterPeptideModel, m_originalPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), pappso::specglob::PeptideModel::removeBracketsForAlignedAA(), pappso::specglob::PeptideModel::toString(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().
Referenced by PostTreatment().
bool pappso::specglob::PostTreatment::findReplaceMutations | ( | ) |
Definition at line 307 of file posttreatment.cpp.
References pappso::alanine, pappso::arginine, pappso::asparagine, pappso::aspartic_acid, pappso::cysteine, pappso::AaModification::getInstance(), pappso::glutamic_acid, pappso::glutamine, pappso::glycine, pappso::histidine, pappso::isoleucine, pappso::leucine, pappso::lysine, m_betterPeptideModel, m_precision, pappso::methionine, pappso::phenylalanine, pappso::proline, pappso::serine, pappso::threonine, pappso::tryptophan, pappso::tyrosine, and pappso::valine.
const PeptideModel & pappso::specglob::PostTreatment::getBetterPeptideModel | ( | ) | const |
Definition at line 60 of file posttreatment.cpp.
References m_betterPeptideModel.
const PeptideModel & pappso::specglob::PostTreatment::getOriginalPeptideModel | ( | ) | const |
Definition at line 301 of file posttreatment.cpp.
References m_originalPeptideModel.
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try to move offset (mass difference)
for each mass difference position, try to move to other position if the amino acid is not aligned, count matched peaks and compare to the previous solution. Keep only the better position
Definition at line 147 of file posttreatment.cpp.
References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), and pappso::specglob::PeptideModel::toString().
Referenced by findBetterPeptideModel().
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try to assign residual mass delta to non aligned elements
This method is run only if there is not-aligned offSets. It may be explained by an inadequate alignment at the start because we give some advance to non-tryptic peptides. But, at the end of the alignment, we can consider it was not the best choice Trying to improve this alignment by adding not-aligned offSet with another one
Definition at line 260 of file posttreatment.cpp.
References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), pappso::specglob::PeptideModel::getMassDelta(), m_betterPeptideModel, m_precision, and pappso::specglob::PeptideModel::matchExperimentalPeaks().
Referenced by findBetterPeptideModel().
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try to remove offset (mass difference)
for each mass difference position, count matched peaks and compare to the previous solution. Removes mass difference if it does not degrade the number of matched peaks
Definition at line 217 of file posttreatment.cpp.
References pappso::specglob::PeptideModel::copyDeep(), pappso::specglob::PeptideModel::getCountSharedPeaks(), m_betterPeptideModel, m_precision, pappso::specglob::PeptideModel::matchExperimentalPeaks(), and pappso::specglob::PeptideModel::toString().
Referenced by findBetterPeptideModel().
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Definition at line 113 of file posttreatment.h.
Referenced by findBetterPeptideModel(), findReplaceMutations(), getBetterPeptideModel(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().
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Definition at line 112 of file posttreatment.h.
Referenced by PostTreatment(), findBetterPeptideModel(), and getOriginalPeptideModel().
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Definition at line 114 of file posttreatment.h.
Referenced by PostTreatment(), findBetterPeptideModel(), findReplaceMutations(), tryBetterPositionOffsets(), tryToCumulateOffSets(), and tryToRemoveOffsets().