Gene Class Reference

Inheritance diagram for Gene:

Public Member Functions
	Gene (const Gene &other)
virtual Gene *	clone ()
list< State * >	getExInHeads () const
list< State * >	getExInInHeads () const
bool	hasInFrameStop (AnnoSequence *annoseq) const
int	numExons () const
State *	lastExon () const
bool	identicalCDS (Gene *other)
virtual bool	almostIdenticalTo (Gene *other)
void	shiftCoordinates (long d)
long	geneBegin () const
long	geneEnd () const
virtual bool	isCoding () const
void	addUTR (State *mrnaRanges, bool complete_l=true, bool complete_r=true)
void	compileExtrinsicEvidence (list< HintGroup > *groupList)
double	supportingFraction (HintGroup *group)
void	addSupportedStates (HintGroup *group)
double	getPercentSupported () const
long	getCDSCoord (long loc, bool comp) const
bool	completeCDS () const
void	print ()
void	printGFF () const
void	printCodingSeq (AnnoSequence *annoseq) const
void	printProteinSeq (AnnoSequence *annoseq) const
void	printBlockSequences (AnnoSequence *annoseq) const
virtual void	printEvidence () const
void	truncateMaskedUTR (AnnoSequence *annoseq)
virtual bool	almostIdenticalTo (Transcript *other)
Public Member Functions inherited from Transcript
	Transcript (const Transcript &other)
Transcript &	operator= (const Transcript &other)
Transcript *	cloneGeneSequence ()
void	addStatePostProbs (float p)
void	setStatePostProbs (float p)
void	addSampleCount (int k)
void	setSampleCount (int k)
bool	operator< (const Transcript &other) const
bool	operator== (const Transcript &other) const
void	normPostProb (float n)
void	updatePostProb (Transcript *other)
double	meanStateProb ()
char *	getExonicSequence (AnnoSequence *annoseq=NULL, bool noOffset=false) const
void	setStateHasScore (bool has)

Static Public Member Functions
static void	init ()
Static Public Member Functions inherited from Transcript
static void	destroyGeneSequence (Transcript *head)
static Transcript *	getGenesOnStrand (Transcript *genes, Strand strand)
static void	filterTranscriptsByMaxTracks (list< Transcript * > &gl, int maxTracks)

Public Attributes
State *	utr5exons
	members for UnTranslated Region
State *	utr3exons
State *	utr5introns
State *	utr3introns
long	codingstart
long	codingend
bool	complete5utr
bool	complete3utr
int	length
	The length of the span of the coding part (with introns)
int	clength
	The coding length of the gene.
int	frame
	The reading frame position of the first base (usually 0)
BaseCount	bc
int	weight
Evidence *	supportingEvidence
Evidence *	incompatibleEvidence
Evidence *	CDSexonEvidence
Evidence *	CDSintronEvidence
Evidence *	UTR5stateEvidence
Evidence *	UTR3stateEvidence
list< PP::Match >	proteinMatches
Public Attributes inherited from Transcript
State *	exons
State *	introns
long	transstart
long	transend
Transcript *	next
string	id
string	seqname
string	source
Strand	strand
Boolean	complete
string	geneid
float	apostprob
bool	hasProbs
bool	throwaway
bool	viterbi

Static Public Attributes
static bool	print_start =false
	output options
static bool	print_stop =false
static bool	print_introns =false
static bool	print_cds =true
static bool	print_exonnames =false
static bool	stopCodonExcludedFromCDS =false
static bool	print_utr =false
static bool	print_blocks = false
Static Public Attributes inherited from Transcript
static bool	gff3 = false
static bool	print_tss =false
static bool	print_tts =false

Member Function Documentation

almostIdenticalTo()

bool Transcript::almostIdenticalTo ( Transcript * other )

virtual

Reimplemented from Transcript.

clone()

virtual Gene * Gene::clone ( )

inlinevirtual

Reimplemented from Transcript.

geneBegin()

long Gene::geneBegin ( ) const

inlinevirtual

Reimplemented from Transcript.

geneEnd()

long Gene::geneEnd ( ) const

inlinevirtual

Reimplemented from Transcript.

getExInHeads()

list< State * > Gene::getExInHeads ( ) const

inlinevirtual

Reimplemented from Transcript.

getExInInHeads()

list< State * > Gene::getExInInHeads ( ) const

inlinevirtual

Reimplemented from Transcript.

isCoding()

virtual bool Gene::isCoding ( ) const

inlinevirtual

Reimplemented from Transcript.

printBlockSequences()

void Gene::printBlockSequences ( AnnoSequence * annoseq ) const

virtual

Reimplemented from Transcript.

printCodingSeq()

void Gene::printCodingSeq ( AnnoSequence * annoseq ) const

virtual

Reimplemented from Transcript.

printEvidence()

void Gene::printEvidence ( ) const

virtual

Reimplemented from Transcript.

printGFF()

void Gene::printGFF ( ) const

virtual

Reimplemented from Transcript.

printProteinSeq()

void Gene::printProteinSeq ( AnnoSequence * annoseq ) const

virtual

Reimplemented from Transcript.

shiftCoordinates()

void Gene::shiftCoordinates ( long d )

virtual

Reimplemented from Transcript.

supportingFraction()

double Gene::supportingFraction ( HintGroup * group )

virtual

Reimplemented from Transcript.

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

• include/gene.hh
• src/gene.cc