libpappsomspp
Library for mass spectrometry
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#include <msrundatasettree.h>
Public Types | |
using | NodeVector = std::vector< MsRunDataSetTreeNode * > |
using | QualMassSpectraVector = std::vector< QualifiedMassSpectrumCstSPtr > |
using | DoubleNodeVectorMap = std::map< double, NodeVector > |
Public Member Functions | |
MsRunDataSetTree (MsRunIdCstSPtr ms_run_id_csp) | |
virtual | ~MsRunDataSetTree () |
MsRunDataSetTreeNode * | addMassSpectrum (QualifiedMassSpectrumCstSPtr mass_spectrum) |
const std::map< std::size_t, MsRunDataSetTreeNode * > & | getIndexNodeMap () const |
const std::vector< MsRunDataSetTreeNode * > & | getRootNodes () const |
void | accept (MsRunDataSetTreeNodeVisitorInterface &visitor) |
void | accept (MsRunDataSetTreeNodeVisitorInterface &visitor, std::vector< pappso::MsRunDataSetTreeNode * >::const_iterator nodes_begin_iterator, std::vector< pappso::MsRunDataSetTreeNode * >::const_iterator nodes_end_iterator) |
MsRunDataSetTreeNode * | findNode (QualifiedMassSpectrumCstSPtr mass_spectrum_csp) const |
MsRunDataSetTreeNode * | findNode (std::size_t spectrum_index) const |
std::size_t | massSpectrumIndex (const MsRunDataSetTreeNode *node) const |
std::size_t | massSpectrumIndex (QualifiedMassSpectrumCstSPtr qualified_mass_spectrum_csp) const |
std::vector< MsRunDataSetTreeNode * > | flattenedView () |
std::vector< MsRunDataSetTreeNode * > | flattenedViewMsLevel (std::size_t ms_level, bool with_descendants=false) |
MsRunDataSetTreeNode * | precursorNodeByProductSpectrumIndex (std::size_t product_spectrum_index) |
std::vector< MsRunDataSetTreeNode * > | productNodesByPrecursorSpectrumIndex (std::size_t precursor_spectrum_index) |
std::vector< MsRunDataSetTreeNode * > | precursorNodesByPrecursorMz (pappso_double mz, PrecisionPtr precision_ptr) |
std::size_t | depth () const |
std::size_t | size () const |
std::size_t | indexNodeMapSize () const |
std::size_t | getSpectrumCount () const |
std::size_t | addDataSetTreeNodesInsideDtRtRange (double start, double end, NodeVector &nodes, DataKind data_kind) const |
std::size_t | addDataSetTreeNodesInsideDtRtPolygon (const SelectionPolygon &selectionPolygon, NodeVector &nodes, DataKind data_kind) const |
std::size_t | removeDataSetTreeNodesOutsideDtRtRange (double start, double end, NodeVector &nodes, DataKind data_kind) const |
std::size_t | addDataSetQualMassSpectraInsideDtRtRange (double start, double end, QualMassSpectraVector &mass_spectra, DataKind data_kind) const |
std::size_t | removeDataSetQualMassSpectraOutsideDtRtRange (double start, double end, QualMassSpectraVector &mass_spectra, DataKind data_kind) const |
Private Member Functions | |
bool | documentNodeInDtRtMap (double time, MsRunDataSetTreeNode *node_p, DataKind data_kind) |
MsRunDataSetTreeNode * | addMassSpectrum (QualifiedMassSpectrumCstSPtr mass_spectrum, MsRunDataSetTreeNode *parent) |
MsRunDataSetTreeNode * | addMassSpectrum (QualifiedMassSpectrumCstSPtr mass_spectrum, std::size_t precursor_spectrum_index) |
Private Attributes | |
MsRunIdCstSPtr | mcsp_msRunId |
std::size_t | m_spectrumCount = std::numeric_limits<std::size_t>::min() |
std::vector< MsRunDataSetTreeNode * > | m_rootNodes |
std::map< std::size_t, MsRunDataSetTreeNode * > | m_indexNodeMap |
DoubleNodeVectorMap | m_dtDoubleNodeVectorMap |
DoubleNodeVectorMap | m_rtDoubleNodeVectorMap |
Definition at line 28 of file msrundatasettree.h.
using pappso::MsRunDataSetTree::DoubleNodeVectorMap = std::map<double, NodeVector> |
Definition at line 87 of file msrundatasettree.h.
using pappso::MsRunDataSetTree::NodeVector = std::vector<MsRunDataSetTreeNode *> |
Definition at line 84 of file msrundatasettree.h.
using pappso::MsRunDataSetTree::QualMassSpectraVector = std::vector<QualifiedMassSpectrumCstSPtr> |
Definition at line 85 of file msrundatasettree.h.
pappso::MsRunDataSetTree::MsRunDataSetTree | ( | MsRunIdCstSPtr | ms_run_id_csp | ) |
Definition at line 19 of file msrundatasettree.cpp.
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virtual |
Definition at line 25 of file msrundatasettree.cpp.
References m_rootNodes.
void pappso::MsRunDataSetTree::accept | ( | MsRunDataSetTreeNodeVisitorInterface & | visitor | ) |
Definition at line 196 of file msrundatasettree.cpp.
References m_rootNodes, and pappso::MsRunDataSetTreeNodeVisitorInterface::shouldStop().
void pappso::MsRunDataSetTree::accept | ( | MsRunDataSetTreeNodeVisitorInterface & | visitor, |
std::vector< pappso::MsRunDataSetTreeNode * >::const_iterator | nodes_begin_iterator, | ||
std::vector< pappso::MsRunDataSetTreeNode * >::const_iterator | nodes_end_iterator | ||
) |
Definition at line 213 of file msrundatasettree.cpp.
References pappso::MsRunDataSetTreeNodeVisitorInterface::setNodesToProcessCount(), and pappso::MsRunDataSetTreeNodeVisitorInterface::shouldStop().
std::size_t pappso::MsRunDataSetTree::addDataSetQualMassSpectraInsideDtRtRange | ( | double | start, |
double | end, | ||
QualMassSpectraVector & | mass_spectra, | ||
DataKind | data_kind | ||
) | const |
Definition at line 759 of file msrundatasettree.cpp.
References pappso::dt, m_dtDoubleNodeVectorMap, m_rtDoubleNodeVectorMap, and pappso::rt.
std::size_t pappso::MsRunDataSetTree::addDataSetTreeNodesInsideDtRtPolygon | ( | const SelectionPolygon & | selectionPolygon, |
NodeVector & | nodes, | ||
DataKind | data_kind | ||
) | const |
std::size_t pappso::MsRunDataSetTree::addDataSetTreeNodesInsideDtRtRange | ( | double | start, |
double | end, | ||
NodeVector & | nodes, | ||
DataKind | data_kind | ||
) | const |
Definition at line 591 of file msrundatasettree.cpp.
References pappso::dt, m_dtDoubleNodeVectorMap, m_rtDoubleNodeVectorMap, and pappso::rt.
MsRunDataSetTreeNode * pappso::MsRunDataSetTree::addMassSpectrum | ( | QualifiedMassSpectrumCstSPtr | mass_spectrum | ) |
Definition at line 53 of file msrundatasettree.cpp.
References documentNodeInDtRtMap(), pappso::dt, findNode(), pappso::MsRunDataSetTreeNode::m_children, m_indexNodeMap, m_rootNodes, m_spectrumCount, and pappso::rt.
Referenced by addMassSpectrum().
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private |
Definition at line 502 of file msrundatasettree.cpp.
References documentNodeInDtRtMap(), pappso::dt, pappso::MsRunDataSetTreeNode::m_children, m_indexNodeMap, m_rootNodes, m_spectrumCount, and pappso::rt.
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private |
Definition at line 556 of file msrundatasettree.cpp.
References addMassSpectrum(), and findNode().
std::size_t pappso::MsRunDataSetTree::depth | ( | ) | const |
Definition at line 1034 of file msrundatasettree.cpp.
References m_rootNodes.
Referenced by flattenedViewMsLevel().
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private |
Definition at line 444 of file msrundatasettree.cpp.
References pappso::dt, m_dtDoubleNodeVectorMap, m_rtDoubleNodeVectorMap, and pappso::rt.
Referenced by addMassSpectrum().
MsRunDataSetTreeNode * pappso::MsRunDataSetTree::findNode | ( | QualifiedMassSpectrumCstSPtr | mass_spectrum_csp | ) | const |
Definition at line 251 of file msrundatasettree.cpp.
References pappso::MsRunDataSetTreeNode::findNode(), and m_rootNodes.
Referenced by addMassSpectrum(), massSpectrumIndex(), precursorNodeByProductSpectrumIndex(), precursorNodesByPrecursorMz(), and productNodesByPrecursorSpectrumIndex().
MsRunDataSetTreeNode * pappso::MsRunDataSetTree::findNode | ( | std::size_t | spectrum_index | ) | const |
Definition at line 269 of file msrundatasettree.cpp.
References pappso::MsRunDataSetTreeNode::findNode(), and m_rootNodes.
std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTree::flattenedView | ( | ) |
std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTree::flattenedViewMsLevel | ( | std::size_t | ms_level, |
bool | with_descendants = false |
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) |
const std::map< std::size_t, MsRunDataSetTreeNode * > & pappso::MsRunDataSetTree::getIndexNodeMap | ( | ) | const |
Definition at line 149 of file msrundatasettree.cpp.
References m_indexNodeMap.
const std::vector< MsRunDataSetTreeNode * > & pappso::MsRunDataSetTree::getRootNodes | ( | ) | const |
Definition at line 189 of file msrundatasettree.cpp.
References m_rootNodes.
std::size_t pappso::MsRunDataSetTree::getSpectrumCount | ( | ) | const |
Definition at line 1091 of file msrundatasettree.cpp.
References m_spectrumCount.
std::size_t pappso::MsRunDataSetTree::indexNodeMapSize | ( | ) | const |
Definition at line 1084 of file msrundatasettree.cpp.
References m_indexNodeMap.
std::size_t pappso::MsRunDataSetTree::massSpectrumIndex | ( | const MsRunDataSetTreeNode * | node | ) | const |
Definition at line 156 of file msrundatasettree.cpp.
References m_indexNodeMap.
Referenced by massSpectrumIndex().
std::size_t pappso::MsRunDataSetTree::massSpectrumIndex | ( | QualifiedMassSpectrumCstSPtr | qualified_mass_spectrum_csp | ) | const |
Definition at line 179 of file msrundatasettree.cpp.
References findNode(), and massSpectrumIndex().
MsRunDataSetTreeNode * pappso::MsRunDataSetTree::precursorNodeByProductSpectrumIndex | ( | std::size_t | product_spectrum_index | ) |
Definition at line 367 of file msrundatasettree.cpp.
References findNode(), and pappso::MsRunDataSetTreeNode::mcsp_massSpectrum.
std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTree::precursorNodesByPrecursorMz | ( | pappso_double | mz, |
PrecisionPtr | precision_ptr | ||
) |
Definition at line 407 of file msrundatasettree.cpp.
References findNode(), m_rootNodes, and pappso::mz.
std::vector< MsRunDataSetTreeNode * > pappso::MsRunDataSetTree::productNodesByPrecursorSpectrumIndex | ( | std::size_t | precursor_spectrum_index | ) |
Definition at line 387 of file msrundatasettree.cpp.
References findNode(), and pappso::MsRunDataSetTreeNode::m_children.
std::size_t pappso::MsRunDataSetTree::removeDataSetQualMassSpectraOutsideDtRtRange | ( | double | start, |
double | end, | ||
QualMassSpectraVector & | mass_spectra, | ||
DataKind | data_kind | ||
) | const |
Definition at line 897 of file msrundatasettree.cpp.
References pappso::dt, m_dtDoubleNodeVectorMap, m_rtDoubleNodeVectorMap, and pappso::rt.
std::size_t pappso::MsRunDataSetTree::removeDataSetTreeNodesOutsideDtRtRange | ( | double | start, |
double | end, | ||
NodeVector & | nodes, | ||
DataKind | data_kind | ||
) | const |
Definition at line 653 of file msrundatasettree.cpp.
References pappso::dt, m_dtDoubleNodeVectorMap, m_rtDoubleNodeVectorMap, and pappso::rt.
std::size_t pappso::MsRunDataSetTree::size | ( | ) | const |
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private |
Definition at line 126 of file msrundatasettree.h.
Referenced by addDataSetQualMassSpectraInsideDtRtRange(), addDataSetTreeNodesInsideDtRtRange(), documentNodeInDtRtMap(), removeDataSetQualMassSpectraOutsideDtRtRange(), and removeDataSetTreeNodesOutsideDtRtRange().
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Definition at line 121 of file msrundatasettree.h.
Referenced by addMassSpectrum(), getIndexNodeMap(), indexNodeMapSize(), and massSpectrumIndex().
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private |
Definition at line 120 of file msrundatasettree.h.
Referenced by ~MsRunDataSetTree(), accept(), addMassSpectrum(), depth(), findNode(), flattenedView(), flattenedViewMsLevel(), getRootNodes(), precursorNodesByPrecursorMz(), and size().
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private |
Definition at line 127 of file msrundatasettree.h.
Referenced by addDataSetQualMassSpectraInsideDtRtRange(), addDataSetTreeNodesInsideDtRtRange(), documentNodeInDtRtMap(), removeDataSetQualMassSpectraOutsideDtRtRange(), and removeDataSetTreeNodesOutsideDtRtRange().
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private |
Definition at line 118 of file msrundatasettree.h.
Referenced by addMassSpectrum(), and getSpectrumCount().
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private |
Definition at line 116 of file msrundatasettree.h.