IDBoostGraph Class Reference

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

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

Collaboration diagram for IDBoostGraph:

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
struct	ProteinGroup
	placeholder for peptides with the same parent proteins or protein groups More...
class	SetPosteriorVisitor

Public Types
typedef boost::variant< ProteinHit *, ProteinGroup, PeptideCluster, Peptide, RunIndex, Charge, PeptideHit * >	IDPointer
	an (currently unmodified) peptide sequence 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, bool best_psms_annotated, 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, bool best_psms_annotated, const boost::optional< const ExperimentalDesign > &ed=boost::optional< const ExperimentalDesign >())
void	applyFunctorOnCCs (const std::function< unsigned long(Graph &, unsigned int)> &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...
void	resolveGraphPeptideCentric (bool removeAssociationsInData=true)
Size	getNrConnectedComponents ()
	Zero means the graph was not split yet. More...
const Graph &	getComponent (Size cc)
	Returns a specific connected component of the graph as a graph itself. More...
const ProteinIdentification &	getProteinIDs ()
	Returns the underlying protein identifications for viewing. More...
void	getUpstreamNodesNonRecursive (std::queue< vertex_t > &q, const Graph &graph, int lvl, bool stop_at_first, std::vector< vertex_t > &result)
	Searches for all upstream nodes from a (set of) start nodes that are lower or equal than a given level. The ordering is the same as in the IDPointer variant typedef. More...
void	getDownstreamNodesNonRecursive (std::queue< vertex_t > &q, const Graph &graph, int lvl, bool stop_at_first, std::vector< vertex_t > &result)
	Searches for all downstream nodes from a (set of) start nodes that are higher or equal than a given level. The ordering is the same as in the IDPointer variant typedef. More...
void	getProteinScores_ (ScoreToTgtDecLabelPairs &scores_and_tgt)
void	getProteinGroupScoresAndTgtFraction (ScoreToTgtDecLabelPairs &scores_and_tgt_fraction)
void	getProteinGroupScoresAndHitchhikingTgtFraction (ScoreToTgtDecLabelPairs &scores_and_tgt_fraction)

Static Public Member Functions
static void	printGraph (std::ostream &out, const Graph &fg)
	Prints a graph (component or if not split, the full graph) in graphviz (i.e. dot) format. More...

Private Member Functions
vertex_t	addVertexWithLookup_ (const 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, bool best_psms_annotated=false)
void	buildGraph_ (ProteinIdentification &proteins, ConsensusMap &cmap, Size use_top_psms, bool use_unassigned_ids, bool best_psms_annotated=false)
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, bool best_psms_annotated)
	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	resolveGraphPeptideCentric_ (Graph &fg, bool removeAssociationsInData)
	see equivalent public method More...
template<class NodeType >
void	getDownstreamNodes (const vertex_t &start, const Graph &graph, std::vector< NodeType > &result)
template<class NodeType >
void	getUpstreamNodes (const vertex_t &start, const 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.

---

Class Documentation

OpenMS::Internal::IDBoostGraph::ProteinGroup

struct OpenMS::Internal::IDBoostGraph::ProteinGroup

placeholder for peptides with the same parent proteins or protein groups

indistinguishable protein groups (size, nr targets, score)

Collaboration diagram for IDBoostGraph::ProteinGroup:

Class Members
double	score
int	size
int	tgts

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

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,
		bool	best_psms_annotated,
		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,
		bool	best_psms_annotated,
		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, bool  best_psms_annotated  )

private

Used during building.

addVertexWithLookup_()

vertex_t addVertexWithLookup_ ( const 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 &, unsigned int)> &

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, bool  best_psms_annotated = false  )

private

buildGraph_() [2/2]

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

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)
best_psms_annotated	Are the PSMs annotated with the "best_per_peptide" meta value. Otherwise all are taken into account.

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

)

Returns a specific connected component of the graph as a graph itself.

Parameters

cc	the index of the component

Returns

the component as graph

getDownstreamNodes()

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

inlineprivate

getDownstreamNodesNonRecursive()

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

Searches for all downstream nodes from a (set of) start nodes that are higher or equal than a given level. The ordering is the same as in the IDPointer variant typedef.

Parameters

q	a queue of start nodes
graph	the graph to look in (q has to be part of it)
lvl	the level to start reporting from
stop_at_first	do you want to stop at the first node >= lvl or also report its upstream "predecessors"
result	vector of reported nodes

getNrConnectedComponents()

Size getNrConnectedComponents

(

)

Zero means the graph was not split yet.

getProteinGroupScoresAndHitchhikingTgtFraction()

void getProteinGroupScoresAndHitchhikingTgtFraction

(

ScoreToTgtDecLabelPairs &

scores_and_tgt_fraction

)

getProteinGroupScoresAndTgtFraction()

void getProteinGroupScoresAndTgtFraction

(

ScoreToTgtDecLabelPairs &

scores_and_tgt_fraction

)

Gets the scores and target decoy fraction from groups and score + binary values for singleton proteins. This function is usually used to create input for FDR calculations

getProteinIDs()

const ProteinIdentification& getProteinIDs

(

)

Returns the underlying protein identifications for viewing.

Returns

const ref to the protein ID run in this graph (can only be one)

getProteinScores_()

void getProteinScores_

(

ScoreToTgtDecLabelPairs &

scores_and_tgt

)

Gets the scores from the proteins included in the graph. The difference to querying the underlying ProteinIdentification structure is that not all proteins might be included in the graph due to using only the best psm per peptide

getUpstreamNodes()

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

inlineprivate

getUpstreamNodesNonRecursive()

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

Searches for all upstream nodes from a (set of) start nodes that are lower or equal than a given level. The ordering is the same as in the IDPointer variant typedef.

Parameters

q	a queue of start nodes
graph	the graph to look in (q has to be part of it)
lvl	the level to start reporting from
stop_at_first	do you want to stop at the first node <= lvl or also report its upstream "predecessors"
result	vector of reported nodes

printGraph()

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

static

Prints a graph (component or if not split, the full graph) in graphviz (i.e. dot) format.

Parameters

out	an ostream to print to
fg	the graph to print

resolveGraphPeptideCentric()

void resolveGraphPeptideCentric

(

bool

removeAssociationsInData = true

)

Todo:

untested Removes all edges from a peptide (and its PSMs) to its parent protein groups (and its proteins) except for the best protein group.

Precondition

Graph must contain PeptideCluster nodes (e.g. with clusterIndistProteinsAndPeptides).

Parameters

removeAssociationsInData

Also removes the corresponding PeptideEvidences in the underlying ID data structure. Only deactivate if you know what you are doing.

resolveGraphPeptideCentric_()

void resolveGraphPeptideCentric_ ( Graph &  fg, bool  removeAssociationsInData  )

private

see equivalent public method

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