libpappsomspp
Library for mass spectrometry
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#include <grpexperiment.h>
Public Member Functions | |
GrpProteinSp & | getGrpProteinSp (const QString &acc, const QString &description) |
GrpPeptideSp & | setGrpPeptide (const GrpProteinSp &proteinSp, const QString &sequence, pappso_double mass) |
GrpExperiment (GrpGroupingMonitorInterface *p_monitor) | |
virtual | ~GrpExperiment () |
void | startGrouping () |
std::vector< GrpProteinSpConst > | getGrpProteinSpList () const |
void | setRemoveNonInformativeSubgroups (bool ok) |
void | addPostGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein) |
protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein More... | |
void | addPreGroupingGrpProteinSpRemoval (GrpProteinSp sp_protein) |
protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases More... | |
std::vector< GrpGroupSpConst > | getGrpGroupSpList () const |
Private Member Functions | |
void | addSubGroupSp (GrpMapPeptideToGroup &grp_map_peptide_to_group, GrpSubGroupSp &grpSubGroupSp) const |
void | numbering () |
void | removeNonInformativeSubGroups () |
Private Attributes | |
GrpGroupingMonitorInterface * | mp_monitor = nullptr |
bool | m_isRemoveNonInformativeSubgroups = true |
std::map< QString, GrpProteinSp > | m_mapProteins |
std::map< QString, std::map< unsigned long, GrpPeptideSp > > | m_mapPeptides |
std::list< GrpPeptideSp > | m_grpPeptideList |
std::list< GrpProteinSp > | m_grpProteinList |
bool | m_isGroupingStarted = false |
std::list< GrpProtein * > | m_remainingGrpProteinList |
GrpPeptideSet | m_grpPostGroupingProteinListRemoval |
GrpPeptideSet | m_grpPreGroupingProteinListRemoval |
std::list< GrpGroupSp > | m_grpGroupSpList |
Definition at line 41 of file grpexperiment.h.
GrpExperiment::GrpExperiment | ( | GrpGroupingMonitorInterface * | p_monitor | ) |
Definition at line 37 of file grpexperiment.cpp.
References mp_monitor.
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Definition at line 42 of file grpexperiment.cpp.
void GrpExperiment::addPostGroupingGrpProteinSpRemoval | ( | GrpProteinSp | sp_protein | ) |
protein to remove with its entire group after grouping is completed typically : to use with protein contaminants if you want to ignore any group containing one contaminant protein
Definition at line 52 of file grpexperiment.cpp.
References pappso::GrpPeptideSet::addAll(), and m_grpPostGroupingProteinListRemoval.
void GrpExperiment::addPreGroupingGrpProteinSpRemoval | ( | GrpProteinSp | sp_protein | ) |
protein peptides to remove before grouping typically : remove protein contaminants in special metaproteomics cases
Definition at line 60 of file grpexperiment.cpp.
References pappso::GrpPeptideSet::addAll(), and m_grpPreGroupingProteinListRemoval.
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private |
Definition at line 203 of file grpexperiment.cpp.
References pappso::GrpMapPeptideToGroup::getGroupList(), pappso::GrpGroup::makeGrpGroupSp(), and pappso::GrpMapPeptideToGroup::set().
Referenced by removeNonInformativeSubGroups(), and startGrouping().
std::vector< GrpGroupSpConst > GrpExperiment::getGrpGroupSpList | ( | ) | const |
Definition at line 67 of file grpexperiment.cpp.
References m_grpGroupSpList.
GrpProteinSp & GrpExperiment::getGrpProteinSp | ( | const QString & | acc, |
const QString & | description | ||
) |
Definition at line 78 of file grpexperiment.cpp.
References m_grpProteinList, m_mapProteins, and m_remainingGrpProteinList.
std::vector< GrpProteinSpConst > GrpExperiment::getGrpProteinSpList | ( | ) | const |
Definition at line 281 of file grpexperiment.cpp.
References m_grpProteinList, and m_isGroupingStarted.
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Definition at line 258 of file grpexperiment.cpp.
References m_grpGroupSpList, mp_monitor, and pappso::GrpGroupingMonitorInterface::startNumberingAllGroups().
Referenced by startGrouping().
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Definition at line 300 of file grpexperiment.cpp.
References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), m_grpGroupSpList, mp_monitor, pappso::GrpGroupingMonitorInterface::removingNonInformativeSubGroupsInGroup(), pappso::GrpGroupingMonitorInterface::startRemovingNonInformativeSubGroupsInAllGroups(), and pappso::GrpGroupingMonitorInterface::stopRemovingNonInformativeSubGroupsInAllGroups().
Referenced by startGrouping().
GrpPeptideSp & GrpExperiment::setGrpPeptide | ( | const GrpProteinSp & | proteinSp, |
const QString & | sequence, | ||
pappso_double | mass | ||
) |
Definition at line 93 of file grpexperiment.cpp.
References m_grpPeptideList, and m_mapPeptides.
void GrpExperiment::setRemoveNonInformativeSubgroups | ( | bool | ok | ) |
Definition at line 46 of file grpexperiment.cpp.
References m_isRemoveNonInformativeSubgroups.
void GrpExperiment::startGrouping | ( | ) |
Definition at line 117 of file grpexperiment.cpp.
References addSubGroupSp(), pappso::GrpMapPeptideToGroup::clear(), pappso::GrpGroupingMonitorInterface::groupingProtein(), m_grpGroupSpList, m_grpPeptideList, m_grpPreGroupingProteinListRemoval, m_isGroupingStarted, m_isRemoveNonInformativeSubgroups, m_mapPeptides, m_mapProteins, m_remainingGrpProteinList, pappso::GrpSubGroup::makeGrpSubGroupSp(), mp_monitor, numbering(), removeNonInformativeSubGroups(), pappso::GrpPeptideSet::size(), pappso::GrpGroupingMonitorInterface::startGrouping(), and pappso::GrpGroupingMonitorInterface::stopGrouping().
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Definition at line 58 of file grpexperiment.h.
Referenced by getGrpGroupSpList(), numbering(), removeNonInformativeSubGroups(), and startGrouping().
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Definition at line 49 of file grpexperiment.h.
Referenced by setGrpPeptide(), and startGrouping().
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Definition at line 54 of file grpexperiment.h.
Referenced by addPostGroupingGrpProteinSpRemoval().
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Definition at line 56 of file grpexperiment.h.
Referenced by addPreGroupingGrpProteinSpRemoval(), and startGrouping().
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Definition at line 50 of file grpexperiment.h.
Referenced by getGrpProteinSp(), and getGrpProteinSpList().
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Definition at line 51 of file grpexperiment.h.
Referenced by getGrpProteinSpList(), and startGrouping().
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Definition at line 45 of file grpexperiment.h.
Referenced by setRemoveNonInformativeSubgroups(), and startGrouping().
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Definition at line 47 of file grpexperiment.h.
Referenced by setGrpPeptide(), and startGrouping().
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Definition at line 46 of file grpexperiment.h.
Referenced by getGrpProteinSp(), and startGrouping().
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Definition at line 52 of file grpexperiment.h.
Referenced by getGrpProteinSp(), and startGrouping().
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Definition at line 44 of file grpexperiment.h.
Referenced by GrpExperiment(), numbering(), removeNonInformativeSubGroups(), and startGrouping().