Transcript Class Reference

Inheritance diagram for Transcript:

Public Member Functions
	Transcript (const Transcript &other)
Transcript &	operator= (const Transcript &other)
virtual Transcript *	clone ()
Transcript *	cloneGeneSequence ()
void	addStatePostProbs (float p)
void	setStatePostProbs (float p)
void	addSampleCount (int k)
void	setSampleCount (int k)
virtual long	geneBegin () const
virtual long	geneEnd () const
virtual bool	isCoding () const
bool	operator< (const Transcript &other) const
bool	operator== (const Transcript &other) const
void	normPostProb (float n)
void	updatePostProb (Transcript *other)
virtual list< State * >	getExInHeads () const
virtual list< State * >	getExInInHeads () const
double	meanStateProb ()
char *	getExonicSequence (AnnoSequence *annoseq=NULL, bool noOffset=false) const
virtual void	shiftCoordinates (long d)
virtual bool	almostIdenticalTo (Transcript *other)
virtual void	printCodingSeq (AnnoSequence *annoseq) const
virtual void	printProteinSeq (AnnoSequence *annoseq) const
virtual void	printBlockSequences (AnnoSequence *annoseq) const
virtual void	printGFF () const
virtual void	printEvidence () const
void	setStateHasScore (bool has)
virtual double	supportingFraction (HintGroup *group)

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

Public Attributes
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	gff3 = false
static bool	print_tss =false
static bool	print_tts =false

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

• include/gene.hh
• src/gene.cc