IDBoostGraph Class Reference

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	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
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 boost::filtered_graph< Graph, boost::function< bool(edge_t)>, boost::function< bool(vertex_t)> >	FilteredGraph
typedef std::set< IDBoostGraph::vertex_t >	ProteinNodeSet
typedef std::set< IDBoostGraph::vertex_t >	PeptideNodeSet

Public Member Functions
	IDBoostGraph (ProteinIdentification &proteins, std::vector< PeptideIdentification > &idedSpectra)
	Constructors. More...
	IDBoostGraph (ProteinIdentification &proteins, std::vector< PeptideIdentification > &idedSpectra, const ExperimentalDesign &ed)
void	applyFunctorOnCCs (std::function< void(Graph &)> functor)
	Do sth on connected components (your functor object has to inherit from std::function) More...
void	applyFunctorOnCCsST (std::function< void(Graph &)> functor)
void	clusterIndistProteinsAndPeptides ()
void	clusterIndistProteinsAndPeptidesAndExtendGraph ()
	As above but adds charge, replicate and sequence layer of nodes (untested) More...
void	annotateIndistProteins (bool addSingletons=true) const
void	computeConnectedComponents ()
	Splits the initialized graph into connected components and clears it. More...
void	buildGraph (Size use_top_psms)
void	buildGraphWithRunInfo (Size use_top_psms, bool readstore_run_info=true)
Size	getNrConnectedComponents ()

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) const
	internal function to annotate the underlying ID structures based on the given Graph More...
void	printFilteredGraph (std::ostream &out, const FilteredGraph &fg) const
void	printGraph (std::ostream &out, const Graph &fg) const

Private Attributes
Graph	g
	the initial boost Graph More...
Graphs	ccs_
	the Graph split into connected components More...
std::vector< std::pair< Size, double > >	sizes_and_times_ {1}
	sizes and times of last functor execution More...
ProteinIdentification &	proteins_
	underlying protein identification object More...
std::vector< PeptideIdentification > &	idedSpectra_
	underlying peptide identifications More...
const ExperimentalDesign	exp_design_
	underlying experimental design, if not given it will be default constructed More...
std::unordered_map< vertex_t, Size >	pepHitVtx_to_run_
LabelVisitor	lv_
	a visitor that creates labels based on the node type (e.g. for printing) More...

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

FilteredGraph

typedef boost::filtered_graph<Graph, boost::function<bool(edge_t)>, boost::function<bool(vertex_t)> > FilteredGraph

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

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
	)

Constructors.

IDBoostGraph() [2/2]

IDBoostGraph	(	ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	idedSpectra,
		const ExperimentalDesign &	ed
	)

Member Function Documentation

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

)

const

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

annotateIndistProteins_()

void annotateIndistProteins_ ( const Graph &  fg, bool  addSingletons  ) const

private

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

applyFunctorOnCCs()

void applyFunctorOnCCs

(

std::function< void(Graph &)>

functor

)

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

applyFunctorOnCCsST()

void applyFunctorOnCCsST

(

std::function< void(Graph &)>

functor

)

buildGraph()

void buildGraph

(

Size

use_top_psms

)

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_all_psms	If all or just the FIRST psm should be used

buildGraphWithRunInfo()

void buildGraphWithRunInfo	(	Size	use_top_psms,
		bool	readstore_run_info = true
	)

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

(

)

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.

getNrConnectedComponents()

Size getNrConnectedComponents

(

)

printFilteredGraph()

void printFilteredGraph ( std::ostream &  out, const FilteredGraph &  fg  ) const

private

printGraph()

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

private

Member Data Documentation

ccs_

Graphs ccs_

private

the Graph split into connected components

exp_design_

const ExperimentalDesign exp_design_

private

underlying experimental design, if not given it will be default constructed

g

Graph g

private

the initial boost Graph

idedSpectra_

std::vector<PeptideIdentification>& idedSpectra_

private

underlying peptide identifications

lv_

LabelVisitor lv_

private

a visitor that creates labels based on the node type (e.g. for printing)

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.

proteins_

ProteinIdentification& proteins_

private

underlying protein identification object

sizes_and_times_

std::vector<std::pair<Size,double> > sizes_and_times_ {1}

private

sizes and times of last functor execution