Represents a simple set of unique genes. More...

#include <genome.h>

Inheritance diagram for Sleipnir::CGenes:

Public Member Functions
	CGenes (CGenome &Genome)
	Construct a new gene set containing genomes drawn from the given underlying genome.
bool	Open (std::istream &istm, bool fCreate=true)
	Construct a new gene set by loading genes from the given text stream, one per line.
bool	Open (const std::vector< std::string > &vecstrGenes, bool fCreate=true)
	Construct a new gene set containing the given gene IDs.
bool	OpenWeighted (std::istream &istm, bool fCreate=true)
	Construct a new weighted gene set by loading genes from the given text stream, one per line.
void	Filter (const CGenes &GenesExclude)
	Remove the given genes from the gene set.
size_t	CountAnnotations (const IOntology pOntology, size_t iTerm, bool fRecursive=true, const CGenes pBackground=NULL) const
	Return the number of genes in the set annotated at or, optionally, below the given ontology term.
std::vector< std::string >	GetGeneNames () const
	Return the primary identifiers of all genes in the set.
bool	Open (const char *szFile, bool fCreate=true)
	Construct a new gene set by loading genes from the given text file, one per line.
bool	OpenWeighted (const char *szFile, bool fCreate=true)
	Construct a new weighted gene set by loading genes from the given text stream, one per line.
size_t	GetGenes () const
	Return the number of genes in the set.
bool	IsGene (const std::string &strGene) const
	Return true if the given name is a primary identifier of a gene in the set.
bool	IsWeighted () const
	Determine whether genes are weighted.
CGenome &	GetGenome () const
	Return the gene set's underlying genome.
const CGene &	GetGene (size_t iGene) const
	Return the gene at the requested index.
const float	GetGeneWeight (size_t iGene) const
	Return weight of the gene at the requested index.
size_t	GetGene (const std::string &strGene) const
	Return the index of the gene with the given primary identifier, or -1 if none exists.
bool	AddGene (const std::string &strGene)
	Adds a new gene with the given ID to the gene set.
Static Public Member Functions
static bool	Open (const char szFile, CGenome &Genome, std::vector< std::string > &vecstrNames, std::vector< CGenes > &vecpGenes)
	Simultaneously construct multiple new gene sets loaded from the given file, one per line, with tab-delimited genes.

Detailed Description

Represents a simple set of unique genes.

Remarks:: Genes are represented by index only and not explicitly checked for uniqueness, so most of the naming issues of CGenome are avoided. Gene comparisons generally assume a constant gene pool drawn from the base CGenome and are thus performed by pointer comparisons for efficiency; in other words, don't expect two different CGene objects with the same primary ID to behave correctly.

Definition at line 373 of file genome.h.

Constructor & Destructor Documentation

Sleipnir::CGenes::CGenes ( CGenome & Genome )

Construct a new gene set containing genomes drawn from the given underlying genome.

Parameters:

Genome Genome containing all genes which might become members of this gene set.

Definition at line 548 of file genome.cpp.

Referenced by Open().

Member Function Documentation

bool Sleipnir::CGenes::AddGene ( const std::string & strGene ) [inline]

Adds a new gene with the given ID to the gene set.

Parameters:

strGene Gene ID to be added.

Returns:: True if gene was added, false if it was already included.

See also:: Open | GetGene

Definition at line 565 of file genome.h.

References Sleipnir::CGenome::AddGene(), and GetGene().

size_t Sleipnir::CGenes::CountAnnotations	(	const IOntology *	pOntology,
		size_t	iTerm,
		bool	fRecursive = `true`,
		const CGenes *	pBackground = `NULL`
	)		const

Return the number of genes in the set annotated at or, optionally, below the given ontology term.

Parameters:

pOntology	Ontology in which annotations are counted.
iTerm	Ontology term at or below which annotations are counted.
fRecursive	If true, count annotations at or below the given term; otherwise, count only direct annotations to the term.
pBackground	If non-null, count only annotations for genes also contained in the given background set.

Returns:: Number of genes in the gene set annotated at or below the given ontology term.

See also:: IOntology::IsAnnotated

Definition at line 711 of file genome.cpp.

References Sleipnir::IOntology::IsAnnotated(), and IsGene().

void Sleipnir::CGenes::Filter ( const CGenes & GenesExclude )

Remove the given genes from the gene set.

Parameters:

GenesExclude Genes to be removed from the current gene set.

Remarks:: Comparisons are performed using pointers to CGene objects, so both gene sets should use the same underlying CGenome for proper behavior.

Definition at line 769 of file genome.cpp.

References GetGene(), and GetGenes().

const CGene& Sleipnir::CGenes::GetGene ( size_t iGene ) const [inline]

Return the gene at the requested index.

Parameters:

iGene Gene index to retrieve.

Returns:: Gene at the requested index.

Remarks:: For efficiency, no bounds checking is performed. The given index must be smaller than GetGenes.

Definition at line 512 of file genome.h.

Referenced by AddGene(), Sleipnir::CPCL::Distance(), Filter(), Sleipnir::CDat::FilterGenes(), Sleipnir::CDat::Open(), and Sleipnir::CDatasetCompact::Open().

size_t Sleipnir::CGenes::GetGene ( const std::string & strGene ) const [inline]

Return the index of the gene with the given primary identifier, or -1 if none exists.

Parameters:

strGene Primary gene identifier for which the set is searched.

Returns:: Index of the gene with the given primary identifier; -1 if none exists.

See also:: IsGene

Definition at line 546 of file genome.h.

vector< string > Sleipnir::CGenes::GetGeneNames ( ) const

Return the primary identifiers of all genes in the set.

Returns:: Vector of primary identifiers of all genes in the set.

Definition at line 789 of file genome.cpp.

Referenced by Sleipnir::CPCL::Distance().

size_t Sleipnir::CGenes::GetGenes ( ) const [inline]

Return the number of genes in the set.

Returns:: Number of genes in the set.

Definition at line 457 of file genome.h.

Referenced by Sleipnir::CPCL::Distance(), Filter(), Sleipnir::CDat::FilterGenes(), Sleipnir::CDataFilter::IsExample(), Sleipnir::CSVM::Learn(), Sleipnir::CDat::Open(), and Sleipnir::CDatasetCompact::Open().

const float Sleipnir::CGenes::GetGeneWeight ( size_t iGene ) const [inline]

Return weight of the gene at the requested index.

Parameters:

iGene Gene index to retrieve.

Returns:: Gene weight at the requested index. NULL if gene requested doesn't exist.

Remarks:: For efficiency, no bounds checking is performed. The given index must be smaller than GetGenes.

Definition at line 529 of file genome.h.

CGenome& Sleipnir::CGenes::GetGenome ( ) const [inline]

Return the gene set's underlying genome.

Returns:: Gene set's underlying genome.

Definition at line 495 of file genome.h.

Referenced by Sleipnir::CSVM::Learn().

bool Sleipnir::CGenes::IsGene ( const std::string & strGene ) const [inline]

Return true if the given name is a primary identifier of a gene in the set.

Parameters:

strGene Primary gene identifier for which the set is searched.

Returns:: True if the set contains a gene with the given primary identifier.

See also:: GetGene

Definition at line 474 of file genome.h.

Referenced by Sleipnir::CDataFilter::Attach(), CountAnnotations(), Sleipnir::CDat::Open(), and Sleipnir::CDatasetCompact::Open().

bool Sleipnir::CGenes::IsWeighted ( ) const [inline]

Determine whether genes are weighted.

Returns:: Value at the requested location, or NaN if it does not exist or has been filtered.

Definition at line 485 of file genome.h.

bool Sleipnir::CGenes::Open	(	const char *	szFile,
		CGenome &	Genome,
		std::vector< std::string > &	vecstrNames,
		std::vector< CGenes * > &	vecpGenes
	)		`[static]`

Simultaneously construct multiple new gene sets loaded from the given file, one per line, with tab-delimited genes.

Parameters:

szFile	File from which gene sets are loaded.
Genome	Genome containing all genes which might become members of these gene sets.
vecstrNames	Human-readable identifiers for the loaded gene sets.
vecpGenes	Vector to which loaded gene sets are appended.

Returns:: True on success, false otherwise.

Opens multiple gene sets from the given tab-delimited text file. Each line should contain a single tab-delimited gene set, and the first token on each line should be a human-readable identifier for that line's gene set.

See also:: Open

Definition at line 507 of file genome.cpp.

References CGenes(), and Sleipnir::CMeta::Tokenize().

Referenced by Sleipnir::CPCL::Distance(), Sleipnir::CDat::FilterGenes(), Sleipnir::CDatasetCompact::FilterGenes(), and Open().

bool Sleipnir::CGenes::Open	(	std::istream &	istm,
		bool	fCreate = `true`
	)

Construct a new gene set by loading genes from the given text stream, one per line.

Parameters:

istm	Stream containing gene IDs to load, one per line.
fCreate	If true, add unknown genes to the underlying genome; otherwise, unknown gene IDs are ignored.

Returns:: True if gene set was constructed successfully.

Loads a text file of the form:

 GENE1
 GENE2
 GENE3

containing one primary gene identifier per line. If these gene identifiers are found in the gene set's underlying genome, CGene objects are loaded from there. Otherwise, if fCreate is true, new genes are created from the loaded IDs. If fCreate is false, unrecognized genes are skipped with a warning.

See also:: CGenome::AddGene

Definition at line 578 of file genome.cpp.

References Sleipnir::CGenome::AddGene(), Sleipnir::CGenome::FindGene(), Sleipnir::CGenome::GetGene(), and Sleipnir::CGene::GetName().

bool Sleipnir::CGenes::Open	(	const std::vector< std::string > &	vecstrGenes,
		bool	fCreate = `true`
	)

Construct a new gene set containing the given gene IDs.

Parameters:

vecstrGenes	Primary identifiers of genes in the new gene set.
fCreate	If true, add unknown genes to the underlying genome; otherwise, unknown gene IDs are ignored.

Returns:: True if gene set was constructed successfully.

If the given gene identifiers are found in the gene set's underlying genome, CGene objects are loaded from there. Otherwise, if fCreate is true, new genes are created from the loaded IDs. If fCreate is false, unrecognized genes are skipped with a warning.

See also:: CGenome::AddGene

Definition at line 742 of file genome.cpp.

References Sleipnir::CGenome::AddGene(), Sleipnir::CGenome::FindGene(), and Sleipnir::CGenome::GetGene().

bool Sleipnir::CGenes::Open	(	const char *	szFile,
		bool	fCreate = `true`
	)		`[inline]`

Construct a new gene set by loading genes from the given text file, one per line.

Parameters:

szFile	File containing gene IDs to load, one per line.
fCreate	If true, add unknown genes to the underlying genome; otherwise, unknown gene IDs are ignored.

Returns:: True if gene set was constructed successfully.

Loads a text file of the form:

 GENE1
 GENE2
 GENE3

containing one primary gene identifier per line. If these gene identifiers are found in the gene set's underlying genome, CGene objects are loaded from there. Otherwise, if fCreate is true, new genes are created from the loaded IDs. If fCreate is false, unrecognized genes are skipped with a warning.

See also:: CGenome::AddGene

Definition at line 414 of file genome.h.

References Open().

bool Sleipnir::CGenes::OpenWeighted	(	std::istream &	istm,
		bool	fCreate = `true`
	)

Construct a new weighted gene set by loading genes from the given text stream, one per line.

Parameters:

istm	Stream containing gene IDs and corresponding weights to load, one per line.
fCreate	If true, add unknown genes to the underlying genome; otherwise, unknown gene IDs are ignored.

Returns:: True if gene set was constructed successfully.

Loads a text file of the form:

 GENE1 WEIGHT1
 GENE2 WEIGHT2
 GENE3 WEIGHT3

containing one primary gene identifier per line. If these gene identifiers are found in the gene set's underlying genome, CGene objects are loaded from there. Otherwise, if fCreate is true, new genes are created from the loaded IDs. If fCreate is false, unrecognized genes are skipped with a warning.

See also:: CGenome::AddGene

Definition at line 639 of file genome.cpp.

References Sleipnir::CGenome::AddGene(), Sleipnir::CGenome::FindGene(), Sleipnir::CGenome::GetGene(), Sleipnir::CGene::GetName(), and Sleipnir::CMeta::Tokenize().

Referenced by OpenWeighted().

bool Sleipnir::CGenes::OpenWeighted	(	const char *	szFile,
		bool	fCreate = `true`
	)		`[inline]`

Construct a new weighted gene set by loading genes from the given text stream, one per line.

Parameters:

istm	Stream containing gene IDs and corresponding weights to load, one per line.
fCreate	If true, add unknown genes to the underlying genome; otherwise, unknown gene IDs are ignored.

Returns:: True if gene set was constructed successfully.

Loads a text file of the form:

 GENE1 WEIGHT1
 GENE2 WEIGHT2
 GENE3 WEIGHT3

containing one primary gene identifier per line. If these gene identifiers are found in the gene set's underlying genome, CGene objects are loaded from there. Otherwise, if fCreate is true, new genes are created from the loaded IDs. If fCreate is false, unrecognized genes are skipped with a warning.

See also:: CGenome::AddGene

Definition at line 445 of file genome.h.

References OpenWeighted().

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

src/genome.h
src/genome.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation