cDeNovoGraph Class Reference

The class implementing the de novo graph. More...

#include <cDeNovoGraph.h>

Public Member Functions
	cDeNovoGraph ()
	The constructor.
void	initialize (cMainThread &os, cParameters &parameters)
	Initialize the graph. More...
int	createGraph (bool &terminatecomputation)
	Create the graph. More...
int	removeEdgesFormingPathsNotFinishingInPrecursor (bool &terminatecomputation)
	Remove edges which do not form a path finishing in the precursor. More...
int	removeEdgesFormingPathsNotStartingFromFirstNode (bool &terminatecomputation)
	Remove edges which do not start from system nodes. More...
int	connectEdgesFormingPathsNotFinishingInPrecursor (bool &terminatecomputation)
	Connect edges which do not form a path finishing in the precursor. More...
int	connectEdgesFormingPathsNotStartingFromFirstNode (bool &terminatecomputation)
	Connect edges which do not start from system nodes. More...
int	removePathsWhichCanBeSubstitutedByLongerPath (bool &terminatecomputation)
	Remove paths which can be substituted by longer paths. More...
void	startGraphReader (cCandidateSet &candidates, long long unsigned &count, int scanmode, bool &terminatecomputation)
	Start the graph reader. More...
int	getNumberOfEdges ()
	Get the number of edges. More...
void	printPaths (cMainThread *os, cDeNovoGraphNode &node, vector< string > &path, vector< string > &composition)
	Print all paths in the graph into a stream. More...
string	printGraph ()
	Print the graph to a string. More...
cDeNovoGraphNode &	operator[] (int position)
	Overloaded operator []. More...
void	sortEdgesByPPMError ()
	Sort edges by ppm error.
void	sortEdgesByTargetNodeIntensity ()
	Sort edges by target node intensity.
cBricksDatabase *	getBrickDatabaseWithCombinations ()
	Access to the database of bricks with combinations of bricks. More...

Detailed Description

The class implementing the de novo graph.

Member Function Documentation

connectEdgesFormingPathsNotFinishingInPrecursor()

int cDeNovoGraph::connectEdgesFormingPathsNotFinishingInPrecursor

(

bool &

terminatecomputation

)

Connect edges which do not form a path finishing in the precursor.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

connectEdgesFormingPathsNotStartingFromFirstNode()

int cDeNovoGraph::connectEdgesFormingPathsNotStartingFromFirstNode

(

bool &

terminatecomputation

)

Connect edges which do not start from system nodes.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

createGraph()

int cDeNovoGraph::createGraph

(

bool &

terminatecomputation

)

Create the graph.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

graph[i].ionannotation[parameters->fragmentionsfordenovograph[k]] ||

getBrickDatabaseWithCombinations()

cBricksDatabase * cDeNovoGraph::getBrickDatabaseWithCombinations

(

)

Access to the database of bricks with combinations of bricks.

Return values

cBricksDatabase

pointer to a database of bricks

getNumberOfEdges()

int cDeNovoGraph::getNumberOfEdges

(

)

Get the number of edges.

Return values

int	number of edges

initialize()

void cDeNovoGraph::initialize	(	cMainThread &	os,
		cParameters &	parameters
	)

Initialize the graph.

Parameters

os	reference to the main thread of the application
parameters	reference to program parameters

operator[]()

cDeNovoGraphNode & cDeNovoGraph::operator[]

(

int

position

)

Overloaded operator [].

Parameters

position

position of a node

Return values

cDeNovoGraphNode

reference to a node

printGraph()

string cDeNovoGraph::printGraph

(

)

Print the graph to a string.

Return values

string

the printed graph

printPaths()

void cDeNovoGraph::printPaths	(	cMainThread *	os,
		cDeNovoGraphNode &	node,
		vector< string > &	path,
		vector< string > &	composition
	)

Print all paths in the graph into a stream.

Parameters

os	pointer to the main thread of the application (stream, respectively).
node	reference to a starting node
path	reference to an auxiliary empty vector of strings
composition	reference to an auxiliary empty vector of strings

removeEdgesFormingPathsNotFinishingInPrecursor()

int cDeNovoGraph::removeEdgesFormingPathsNotFinishingInPrecursor

(

bool &

terminatecomputation

)

Remove edges which do not form a path finishing in the precursor.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

removeEdgesFormingPathsNotStartingFromFirstNode()

int cDeNovoGraph::removeEdgesFormingPathsNotStartingFromFirstNode

(

bool &

terminatecomputation

)

Remove edges which do not start from system nodes.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

removePathsWhichCanBeSubstitutedByLongerPath()

int cDeNovoGraph::removePathsWhichCanBeSubstitutedByLongerPath

(

bool &

terminatecomputation

)

Remove paths which can be substituted by longer paths.

Parameters

terminatecomputation

reference to a variable determining that the computation must be stopped

Return values

int	0 = successfully finished, -1 computation terminated

startGraphReader()

void cDeNovoGraph::startGraphReader	(	cCandidateSet &	candidates,
		long long unsigned &	count,
		int	scanmode,
		bool &	terminatecomputation
	)

Start the graph reader.

Parameters

candidates	output set of candidates
count	an output number of peptide sequence candidates
scanmode	0 = get candidates; 1 = calculate the number of peptide sequence candidates
terminatecomputation	reference to a variable determining that the computation must be stopped

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The documentation for this class was generated from the following files:

• core/cDeNovoGraph.h
• core/cDeNovoGraph.cpp