11 #include "../pappsoexception.h"
12 #include "../exception/exceptionnotpossible.h"
20 : mcsp_msRunId(ms_run_id_csp)
58 if(mass_spectrum_csp ==
nullptr)
59 qFatal(
"Cannot be nullptr");
61 if(mass_spectrum_csp.get() ==
nullptr)
62 qFatal(
"Cannot be nullptr");
69 std::size_t precursor_spectrum_index =
70 mass_spectrum_csp->getPrecursorSpectrumIndex();
74 if(precursor_spectrum_index == std::numeric_limits<std::size_t>::max())
95 if(mass_spectrum_csp->getMsLevel() <= 1)
98 "msrundatasettree.cpp -- ERROR the MS level needs to be > 1 in a "
99 "fragmentation spectrum.");
105 if(parent_node_p ==
nullptr)
108 "msrundatasettree.cpp -- ERROR could not find "
109 "a tree node matching the index.");
120 parent_node_p->
m_children.push_back(new_node_p);
124 m_indexNodeMap.insert(std::pair<std::size_t, MsRunDataSetTreeNode *>(
125 mass_spectrum_csp->getMassSpectrumId().getSpectrumIndex(), new_node_p));
131 mass_spectrum_csp->getRtInMinutes(), new_node_p,
DataKind::rt);
136 mass_spectrum_csp->getDtInMilliSeconds(), new_node_p,
DataKind::dt);
148 const std::map<std::size_t, MsRunDataSetTreeNode *> &
161 throw(
"Cannot be that the node pointer is nullptr");
163 std::map<std::size_t, MsRunDataSetTreeNode *>::const_iterator iterator =
167 [node](
const std::pair<std::size_t, MsRunDataSetTreeNode *> pair) {
168 return pair.second == node;
172 return iterator->first;
174 return std::numeric_limits<std::size_t>::max();
188 const std::vector<MsRunDataSetTreeNode *> &
207 node->accept(visitor);
215 std::vector<MsRunDataSetTreeNode *>::const_iterator nodes_begin_iterator,
216 std::vector<MsRunDataSetTreeNode *>::const_iterator nodes_end_iterator)
222 using Iterator = std::vector<MsRunDataSetTreeNode *>::const_iterator;
224 Iterator iter = nodes_begin_iterator;
228 std::size_t node_count =
229 std::distance(nodes_begin_iterator, nodes_end_iterator);
233 while(iter != nodes_end_iterator)
244 (*iter)->accept(visitor);
260 if(iterNode !=
nullptr)
278 if(iterNode !=
nullptr)
286 std::vector<MsRunDataSetTreeNode *>
291 std::vector<MsRunDataSetTreeNode *> nodes;
296 node->flattenedView(nodes,
true );
303 std::vector<MsRunDataSetTreeNode *>
305 bool with_descendants)
307 std::vector<MsRunDataSetTreeNode *> nodes;
314 "msrundatasettree.cpp -- ERROR the MS level cannot be 0.");
322 std::size_t
depth = 0;
339 node->flattenedView(nodes, with_descendants);
359 node->flattenedViewMsLevelNodes(ms_level,
depth, nodes, with_descendants);
368 std::size_t product_spectrum_index)
378 node =
findNode(product_spectrum_index);
386 std::vector<MsRunDataSetTreeNode *>
388 std::size_t precursor_spectrum_index)
390 std::vector<MsRunDataSetTreeNode *> nodes;
396 if(precursor_node ==
nullptr)
399 nodes.assign(precursor_node->
m_children.begin(),
406 std::vector<MsRunDataSetTreeNode *>
414 if(precision_ptr ==
nullptr)
416 "msrundatasettree.cpp -- ERROR precision_ptr cannot be nullptr.");
418 std::vector<MsRunDataSetTreeNode *> product_nodes;
426 node->productNodesByPrecursorMz(
mz, precision_ptr, product_nodes);
431 std::vector<MsRunDataSetTreeNode *> precursor_nodes;
433 for(
auto &&node : product_nodes)
435 precursor_nodes.push_back(
436 findNode(node->mcsp_massSpectrum->getPrecursorSpectrumIndex()));
439 return precursor_nodes;
450 using NodeVector = std::vector<MsRunDataSetTreeNode *>;
452 using MapPair = std::pair<double, NodeVector>;
453 using MapIterator = DoubleNodeVectorMap::iterator;
466 qFatal(
"Programming error.");
476 MapIterator found_iterator = map_p->find(time);
478 if(found_iterator != map_p->end())
482 found_iterator->second.push_back(node_p);
492 map_p->insert(MapPair(time, node_vector));
516 if(parent_p ==
nullptr)
533 m_indexNodeMap.insert(std::pair<std::size_t, MsRunDataSetTreeNode *>(
534 mass_spectrum_csp->getMassSpectrumId().getSpectrumIndex(), new_node_p));
540 mass_spectrum_csp->getRtInMinutes(), new_node_p,
DataKind::rt);
545 mass_spectrum_csp->getDtInMilliSeconds(), new_node_p,
DataKind::dt);
558 std::size_t precursor_spectrum_index)
576 if(mass_spec_data_node_p ==
nullptr)
579 "msrundatasettree.cpp -- ERROR could not find a a "
580 "tree node matching the index.");
596 using NodeVector = std::vector<MsRunDataSetTreeNode *>;
598 using MapIterator = DoubleNodeVectorMap::const_iterator;
611 qFatal(
"Programming error.");
613 std::size_t added_nodes = 0;
618 MapIterator start_iterator = map_p->lower_bound(start);
620 if(start_iterator == map_p->end())
625 MapIterator end_iterator = map_p->upper_bound(end);
630 for(MapIterator iterator = start_iterator; iterator != end_iterator;
640 for(
auto &&node_p : node_vector)
642 nodes.push_back(node_p);
656 using NodeVector = std::vector<MsRunDataSetTreeNode *>;
657 using NodeVectorIterator = NodeVector::iterator;
660 using MapIterator = DoubleNodeVectorMap::const_iterator;
673 qFatal(
"Programming error.");
675 std::size_t removed_vector_items = 0;
684 MapIterator first_end_iterator = (*map_p).upper_bound(start);
689 for(MapIterator iterator = map_p->begin(); iterator != first_end_iterator;
701 for(
auto &&node_p : node_vector)
703 NodeVectorIterator iterator =
704 std::find(nodes.begin(), nodes.end(), node_p);
706 if(iterator != nodes.end())
710 nodes.erase(iterator);
712 ++removed_vector_items;
724 MapIterator second_first_iterator = map_p->upper_bound(end);
725 if(second_first_iterator != map_p->begin())
726 --second_first_iterator;
728 for(MapIterator iterator = second_first_iterator; iterator != map_p->end();
738 for(
auto &&node_p : node_vector)
740 NodeVectorIterator iterator =
741 std::find(nodes.begin(), nodes.end(), node_p);
743 if(iterator != nodes.end())
747 nodes.erase(iterator);
749 ++removed_vector_items;
754 return removed_vector_items;
768 qDebug() <<
"Special case, start and end are equal:" << start;
776 using MapIterator = DoubleNodeVectorMap::const_iterator;
797 qFatal(
"Programming error.");
802 std::size_t added_mass_spectra = 0;
807 MapIterator start_iterator = map_p->lower_bound(start);
809 if(start_iterator == map_p->end())
811 qDebug() <<
"The start iterator is end()!";
823 MapIterator end_iterator = map_p->upper_bound(end);
826 if(!std::distance(start_iterator, end_iterator))
828 qDebug() <<
"No range of mass spectra could be selected.";
832 if(end_iterator == map_p->end())
853 for(MapIterator iterator = start_iterator; iterator != end_iterator;
863 for(
auto &&node_p : node_vector)
866 node_p->getQualifiedMassSpectrum();
871 if(qualified_mass_spectrum_csp ==
nullptr ||
872 qualified_mass_spectrum_csp.get() ==
nullptr)
875 "The QualifiedMassSpectrumCstSPtr cannot be nullptr.");
884 mass_spectra.push_back(qualified_mass_spectrum_csp);
886 ++added_mass_spectra;
892 return added_mass_spectra;
903 using QualMassSpectraVectorIterator = QualMassSpectraVector::iterator;
906 using MapIterator = DoubleNodeVectorMap::const_iterator;
927 qFatal(
"Programming error.");
929 std::size_t removed_vector_items = 0;
941 MapIterator first_end_iterator = (*map_p).lower_bound(start);
954 for(MapIterator iterator = map_p->begin(); iterator != first_end_iterator;
966 for(
auto &&node_p : node_vector)
968 QualMassSpectraVectorIterator iterator =
969 std::find(mass_spectra.begin(),
971 node_p->getQualifiedMassSpectrum());
973 if(iterator != mass_spectra.end())
977 mass_spectra.erase(iterator);
979 ++removed_vector_items;
992 MapIterator second_first_iterator = map_p->upper_bound(end);
1001 for(MapIterator iterator = second_first_iterator; iterator != map_p->end();
1011 for(
auto &&node_p : node_vector)
1013 QualMassSpectraVectorIterator iterator =
1014 std::find(mass_spectra.begin(),
1016 node_p->getQualifiedMassSpectrum());
1018 if(iterator != mass_spectra.end())
1022 mass_spectra.erase(iterator);
1024 ++removed_vector_items;
1029 return removed_vector_items;
1048 std::size_t
depth = 1;
1049 std::size_t tmp_depth = 0;
1050 std::size_t greatest_depth = 0;
1054 tmp_depth = node->depth(
depth);
1058 if(tmp_depth > greatest_depth)
1059 greatest_depth = tmp_depth;
1062 return greatest_depth;
1070 std::size_t cumulative_node_count = 0;
1074 node->size(cumulative_node_count);
1079 return cumulative_node_count;
virtual bool shouldStop() const =0
virtual void setNodesToProcessCount(std::size_t)=0
QualifiedMassSpectrumCstSPtr mcsp_massSpectrum
MsRunDataSetTreeNode * findNode(std::size_t spectrum_index)
std::vector< MsRunDataSetTreeNode * > m_children
MsRunDataSetTreeNode * findNode(QualifiedMassSpectrumCstSPtr mass_spectrum_csp) const
const std::vector< MsRunDataSetTreeNode * > & getRootNodes() const
std::vector< QualifiedMassSpectrumCstSPtr > QualMassSpectraVector
std::vector< MsRunDataSetTreeNode * > flattenedViewMsLevel(std::size_t ms_level, bool with_descendants=false)
std::size_t indexNodeMapSize() const
void accept(MsRunDataSetTreeNodeVisitorInterface &visitor)
virtual ~MsRunDataSetTree()
MsRunDataSetTree(MsRunIdCstSPtr ms_run_id_csp)
bool documentNodeInDtRtMap(double time, MsRunDataSetTreeNode *node_p, DataKind data_kind)
std::vector< MsRunDataSetTreeNode * > flattenedView()
std::size_t getSpectrumCount() const
std::map< std::size_t, MsRunDataSetTreeNode * > m_indexNodeMap
std::vector< MsRunDataSetTreeNode * > m_rootNodes
std::size_t addDataSetTreeNodesInsideDtRtRange(double start, double end, NodeVector &nodes, DataKind data_kind) const
std::map< double, NodeVector > DoubleNodeVectorMap
std::size_t removeDataSetTreeNodesOutsideDtRtRange(double start, double end, NodeVector &nodes, DataKind data_kind) const
std::vector< MsRunDataSetTreeNode * > precursorNodesByPrecursorMz(pappso_double mz, PrecisionPtr precision_ptr)
std::vector< MsRunDataSetTreeNode * > NodeVector
std::size_t addDataSetQualMassSpectraInsideDtRtRange(double start, double end, QualMassSpectraVector &mass_spectra, DataKind data_kind) const
std::size_t depth() const
MsRunDataSetTreeNode * precursorNodeByProductSpectrumIndex(std::size_t product_spectrum_index)
const std::map< std::size_t, MsRunDataSetTreeNode * > & getIndexNodeMap() const
MsRunDataSetTreeNode * addMassSpectrum(QualifiedMassSpectrumCstSPtr mass_spectrum)
std::size_t removeDataSetQualMassSpectraOutsideDtRtRange(double start, double end, QualMassSpectraVector &mass_spectra, DataKind data_kind) const
std::size_t massSpectrumIndex(const MsRunDataSetTreeNode *node) const
DoubleNodeVectorMap m_rtDoubleNodeVectorMap
std::vector< MsRunDataSetTreeNode * > productNodesByPrecursorSpectrumIndex(std::size_t precursor_spectrum_index)
std::size_t m_spectrumCount
DoubleNodeVectorMap m_dtDoubleNodeVectorMap
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
double pappso_double
A type definition for doubles.
std::shared_ptr< const QualifiedMassSpectrum > QualifiedMassSpectrumCstSPtr