Creates and maintains a boost graph based on the OpenMS ID datastructures. More...

#include <OpenMS/ANALYSIS/ID/IDBoostGraph.h>

Classes
class	dfs_ccsplit_visitor
	A boost dfs visitor that copies connected components into a vector of graphs. More...

class	GetPosteriorVisitor

class	LabelVisitor
	Visits nodes in the boost graph (ptrs to an ID Object) and depending on their type creates a label. More...

class	PrintAddressVisitor

class	SetPosteriorVisitor

Public Types
typedef boost::variant< ProteinHit , ProteinGroup, PeptideCluster, Peptide, RunIndex, Charge, PeptideHit >	IDPointer
	placeholder for peptides with the same parent proteins or protein groups More...

typedef boost::variant< const ProteinHit , const ProteinGroup , const PeptideCluster , const Peptide, const RunIndex, const Charge, const PeptideHit >	IDPointerConst

typedef boost::adjacency_list< boost::setS, boost::vecS, boost::undirectedS, IDPointer >	Graph

typedef std::vector< Graph >	Graphs

typedef boost::adjacency_list< boost::setS, boost::vecS, boost::undirectedS, IDPointer >	GraphConst

typedef boost::graph_traits< Graph >::vertex_descriptor	vertex_t

typedef boost::graph_traits< Graph >::edge_descriptor	edge_t

typedef std::set< IDBoostGraph::vertex_t >	ProteinNodeSet

typedef std::set< IDBoostGraph::vertex_t >	PeptideNodeSet

Public Member Functions
	IDBoostGraph (ProteinIdentification &proteins, std::vector< PeptideIdentification > &idedSpectra, Size use_top_psms, bool use_run_info, const boost::optional< const ExperimentalDesign > &ed=boost::optional< const ExperimentalDesign >())
	Constructors. More...

	IDBoostGraph (ProteinIdentification &proteins, ConsensusMap &cmap, Size use_top_psms, bool use_run_info, bool use_unassigned_ids, const boost::optional< const ExperimentalDesign > &ed=boost::optional< const ExperimentalDesign >())

void	applyFunctorOnCCs (const std::function< unsigned long(Graph &)> &functor)
	Do sth on connected components (your functor object has to inherit from std::function or be a lambda) More...

void	applyFunctorOnCCsST (const std::function< void(Graph &)> &functor)
	Do sth on connected components single threaded (your functor object has to inherit from std::function or be a lambda) More...

void	clusterIndistProteinsAndPeptides ()

void	clusterIndistProteinsAndPeptidesAndExtendGraph ()
	(under development) As above but adds charge, replicate and sequence layer of nodes (untested) More...

void	annotateIndistProteins (bool addSingletons=true)

void	calculateAndAnnotateIndistProteins (bool addSingletons=true)

void	computeConnectedComponents ()
	Splits the initialized graph into connected components and clears it. More...

Size	getNrConnectedComponents ()
	Zero means the graph was not split yet. More...

const Graph &	getComponent (Size cc)

ProteinIdentification &	getProteinIDs ()

Static Public Member Functions
static void	printGraph (std::ostream &out, const Graph &fg)

Private Member Functions
vertex_t	addVertexWithLookup_ (IDPointer &ptr, std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &vertex_map)

void	annotateIndistProteins_ (const Graph &fg, bool addSingletons)
	internal function to annotate the underlying ID structures based on the given Graph More...

void	calculateAndAnnotateIndistProteins_ (const Graph &fg, bool addSingletons)

void	buildGraph_ (ProteinIdentification &proteins, std::vector< PeptideIdentification > &idedSpectra, Size use_top_psms)

void	buildGraph_ (ProteinIdentification &proteins, ConsensusMap &cmap, Size use_top_psms, bool use_unassigned_ids)

void	addPeptideIDWithAssociatedProteins_ (PeptideIdentification &spectrum, std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &vertex_map, const std::unordered_map< std::string, ProteinHit * > &accession_map, Size use_top_psms)
	Used during building. More...

void	addPeptideAndAssociatedProteinsWithRunInfo_ (PeptideIdentification &spectrum, std::unordered_map< unsigned, unsigned > &indexToPrefractionationGroup, std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &vertex_map, std::unordered_map< std::string, ProteinHit * > &accession_map, Size use_top_psms)

void	buildGraphWithRunInfo_ (ProteinIdentification &proteins, ConsensusMap &cmap, Size use_top_psms, bool use_unassigned_ids, const ExperimentalDesign &ed)

void	buildGraphWithRunInfo_ (ProteinIdentification &proteins, std::vector< PeptideIdentification > &idedSpectra, Size use_top_psms, const ExperimentalDesign &ed)

void	getUpstreamNodesNonRecursive (std::queue< vertex_t > &q, Graph graph, int lvl, bool stop_at_first, std::vector< vertex_t > &result)

void	resolveGraphPeptideCentric_ (Graph &fg)

template<class NodeType >
void	getDownstreamNodes (vertex_t start, Graph graph, std::vector< NodeType > &result)

template<class NodeType >
void	getUpstreamNodes (vertex_t start, Graph graph, std::vector< NodeType > &result)

Private Attributes
ProteinIdentification &	protIDs_

Graph	g
	the initial boost Graph (will be cleared when split into CCs) More...

Graphs	ccs_
	the Graph split into connected components More...

std::unordered_map< vertex_t, Size >	pepHitVtx_to_run_

Size	nrPrefractionationGroups_ = 0

Detailed Description

Creates and maintains a boost graph based on the OpenMS ID datastructures.

For finding connected components and applying functions to them. Currently assumes that all PeptideIdentifications are from the ProteinID run that is given. Please make sure this is right. VERY IMPORTANT NOTE: If you add Visitors here, make sure they do not touch members of the underlying ID objects that are responsible for the graph structure. E.g. the (protein/peptide)_hits vectors or the lists in ProteinGroups. You can set information like scores or metavalues, though.

Member Typedef Documentation

◆ edge_t

typedef boost::graph_traits<Graph>::edge_descriptor edge_t

◆ Graph

typedef boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS, IDPointer> Graph

◆ GraphConst

typedef boost::adjacency_list<boost::setS, boost::vecS, boost::undirectedS, IDPointer> GraphConst

◆ Graphs

typedef std::vector<Graph> Graphs

◆ IDPointer

typedef boost::variant<ProteinHit*, ProteinGroup, PeptideCluster, Peptide, RunIndex, Charge, PeptideHit*> IDPointer

placeholder for peptides with the same parent proteins or protein groups

indistinguishable protein groups an (currently unmodified) peptide sequence in which run a PSM was observed in which charge state a PSM was observed

◆ IDPointerConst

typedef boost::variant<const ProteinHit*, const ProteinGroup*, const PeptideCluster*, const Peptide, const RunIndex, const Charge, const PeptideHit*> IDPointerConst

◆ PeptideNodeSet

typedef std::set<IDBoostGraph::vertex_t> PeptideNodeSet

◆ ProteinNodeSet

typedef std::set<IDBoostGraph::vertex_t> ProteinNodeSet

◆ vertex_t

typedef boost::graph_traits<Graph>::vertex_descriptor vertex_t

Constructor & Destructor Documentation

◆ IDBoostGraph() [1/2]

IDBoostGraph	(	ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	idedSpectra,
		Size	use_top_psms,
		bool	use_run_info,
		const boost::optional< const ExperimentalDesign > &	ed = `boost::optional< const ExperimentalDesign >()`
	)

Constructors.

◆ IDBoostGraph() [2/2]

IDBoostGraph	(	ProteinIdentification &	proteins,
		ConsensusMap &	cmap,
		Size	use_top_psms,
		bool	use_run_info,
		bool	use_unassigned_ids,
		const boost::optional< const ExperimentalDesign > &	ed = `boost::optional< const ExperimentalDesign >()`
	)

Member Function Documentation

◆ addPeptideAndAssociatedProteinsWithRunInfo_()

void addPeptideAndAssociatedProteinsWithRunInfo_	(	PeptideIdentification &	spectrum,
		std::unordered_map< unsigned, unsigned > &	indexToPrefractionationGroup,
		std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &	vertex_map,
		std::unordered_map< std::string, ProteinHit * > &	accession_map,
		Size	use_top_psms
	)

private

◆ addPeptideIDWithAssociatedProteins_()

void addPeptideIDWithAssociatedProteins_	(	PeptideIdentification &	spectrum,
		std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &	vertex_map,
		const std::unordered_map< std::string, ProteinHit * > &	accession_map,
		Size	use_top_psms
	)

private

Used during building.

◆ addVertexWithLookup_()

vertex_t addVertexWithLookup_	(	IDPointer &	ptr,
		std::unordered_map< IDPointer, vertex_t, boost::hash< IDPointer >> &	vertex_map
	)

private

helper function to add a vertex if it is not present yet, otherwise return the present one needs a temporary filled vertex_map that is modifiable

◆ annotateIndistProteins()

void annotateIndistProteins ( bool addSingletons = true )

Annotate indistinguishable proteins by adding the groups to the underlying ProteinIdentification::ProteinGroups object. This has no effect on the graph itself.

Precondition: Graph must contain ProteinGroup nodes (e.g. with clusterIndistProteinsAndPeptides). Otherwise it does nothing and you should use calculateAndAnnotateIndistProteins instead.

Parameters

addSingletons if you want to annotate groups with just one protein entry

◆ annotateIndistProteins_()

void annotateIndistProteins_	(	const Graph &	fg,
		bool	addSingletons
	)

private

internal function to annotate the underlying ID structures based on the given Graph

◆ applyFunctorOnCCs()

void applyFunctorOnCCs ( const std::function< unsigned long(Graph &)> & functor )

Do sth on connected components (your functor object has to inherit from std::function or be a lambda)

◆ applyFunctorOnCCsST()

void applyFunctorOnCCsST ( const std::function< void(Graph &)> & functor )

Do sth on connected components single threaded (your functor object has to inherit from std::function or be a lambda)

◆ buildGraph_() [1/2]

void buildGraph_	(	ProteinIdentification &	proteins,
		ConsensusMap &	cmap,
		Size	use_top_psms,
		bool	use_unassigned_ids
	)

private

◆ buildGraph_() [2/2]

void buildGraph_	(	ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	idedSpectra,
		Size	use_top_psms
	)

private

Initialize and store the graph IMPORTANT: Once the graph is built, editing members like (protein/peptide)_hits_ will invalidate it!

Parameters

protein	ProteinIdentification object storing IDs and groups
idedSpectra	vector of ProteinIdentifications with links to the proteins and PSMs in its PeptideHits
use_top_psms	Nr of top PSMs used per spectrum (<= 0 means all)

Todo:: we could include building the graph in important "main" functions like inferPosteriors to make the methods safer, but it is also nice to be able to reuse the graph

◆ buildGraphWithRunInfo_() [1/2]

void buildGraphWithRunInfo_	(	ProteinIdentification &	proteins,
		ConsensusMap &	cmap,
		Size	use_top_psms,
		bool	use_unassigned_ids,
		const ExperimentalDesign &	ed
	)

private

Initialize and store the graph. Also stores run information to later group peptides more efficiently. IMPORTANT: Once the graph is built, editing members like (protein/peptide)_hits_ will invalidate it!

Parameters

use_top_psms Nr of top PSMs used per spectrum (<= 0 means all)

Todo:: we could include building the graph in important "main" functions like inferPosteriors to make the methods safer, but it is also nice to be able to reuse the graph

◆ buildGraphWithRunInfo_() [2/2]

void buildGraphWithRunInfo_	(	ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	idedSpectra,
		Size	use_top_psms,
		const ExperimentalDesign &	ed
	)

private

◆ calculateAndAnnotateIndistProteins()

void calculateAndAnnotateIndistProteins ( bool addSingletons = true )

Annotate indistinguishable proteins by adding the groups to the underlying ProteinIdentification::ProteinGroups object. This has no effect on the graph itself.

Parameters

addSingletons if you want to annotate groups with just one protein entry

◆ calculateAndAnnotateIndistProteins_()

void calculateAndAnnotateIndistProteins_	(	const Graph &	fg,
		bool	addSingletons
	)

private

◆ clusterIndistProteinsAndPeptides()

void clusterIndistProteinsAndPeptides ( )

Add intermediate nodes to the graph that represent indist. protein groups and peptides with the same parents this will save computation time and oscillations later on.

◆ clusterIndistProteinsAndPeptidesAndExtendGraph()

void clusterIndistProteinsAndPeptidesAndExtendGraph ( )

(under development) As above but adds charge, replicate and sequence layer of nodes (untested)

◆ computeConnectedComponents()

void computeConnectedComponents ( )

Splits the initialized graph into connected components and clears it.

◆ getComponent()

const Graph& getComponent ( Size cc )

◆ getDownstreamNodes()

void getDownstreamNodes	(	vertex_t	start,
		Graph	graph,
		std::vector< NodeType > &	result
	)

inlineprivate

◆ getNrConnectedComponents()

Size getNrConnectedComponents ( )

Zero means the graph was not split yet.

◆ getProteinIDs()

ProteinIdentification& getProteinIDs ( )

◆ getUpstreamNodes()

void getUpstreamNodes	(	vertex_t	start,
		Graph	graph,
		std::vector< NodeType > &	result
	)

inlineprivate

◆ getUpstreamNodesNonRecursive()

void getUpstreamNodesNonRecursive	(	std::queue< vertex_t > &	q,
		Graph	graph,
		int	lvl,
		bool	stop_at_first,
		std::vector< vertex_t > &	result
	)

private

◆ printGraph()

static void printGraph	(	std::ostream &	out,
		const Graph &	fg
	)

static

◆ resolveGraphPeptideCentric_()

void resolveGraphPeptideCentric_ ( Graph & fg )

private

Member Data Documentation

◆ ccs_

Graphs ccs_

private

the Graph split into connected components

◆ g

Graph g

private

the initial boost Graph (will be cleared when split into CCs)

◆ nrPrefractionationGroups_

Size nrPrefractionationGroups_ = 0

private

this basically stores the number of different values in the pepHitVtx_to_run a Prefractionation group (previously called run) is a unique combination of all non-fractionation related entries in the exp. design i.e. one (sub-)experiment before fractionation

◆ pepHitVtx_to_run_

std::unordered_map<vertex_t, Size> pepHitVtx_to_run_

private

if a graph is built with run information, this will store the run, each peptide hit vertex belongs to. Important for extending the graph.

◆ protIDs_

ProteinIdentification& protIDs_

private

Classes

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ edge_t

◆ Graph

◆ GraphConst

◆ Graphs

◆ IDPointer

◆ IDPointerConst

◆ PeptideNodeSet

◆ ProteinNodeSet

◆ vertex_t

Constructor & Destructor Documentation

◆ IDBoostGraph() [1/2]

◆ IDBoostGraph() [2/2]

Member Function Documentation

◆ addPeptideAndAssociatedProteinsWithRunInfo_()

◆ addPeptideIDWithAssociatedProteins_()

◆ addVertexWithLookup_()

◆ annotateIndistProteins()

◆ annotateIndistProteins_()

◆ applyFunctorOnCCs()

◆ applyFunctorOnCCsST()

◆ buildGraph_() [1/2]

◆ buildGraph_() [2/2]

◆ buildGraphWithRunInfo_() [1/2]

◆ buildGraphWithRunInfo_() [2/2]

◆ calculateAndAnnotateIndistProteins()

◆ calculateAndAnnotateIndistProteins_()

◆ clusterIndistProteinsAndPeptides()

◆ clusterIndistProteinsAndPeptidesAndExtendGraph()

◆ computeConnectedComponents()

◆ getComponent()

◆ getDownstreamNodes()

◆ getNrConnectedComponents()

◆ getProteinIDs()

◆ getUpstreamNodes()

◆ getUpstreamNodesNonRecursive()

◆ printGraph()

◆ resolveGraphPeptideCentric_()

Member Data Documentation

◆ ccs_

◆ g

◆ nrPrefractionationGroups_

◆ pepHitVtx_to_run_

◆ protIDs_