ARB: AP_combinableSeq Class Reference

ARB

#include <AP_sequence.hxx>

Inheritance diagram for AP_combinableSeq:

Inheritance graph

Collaboration diagram for AP_combinableSeq:

Collaboration graph

Public Member Functions
	AP_combinableSeq (const AliView *aliview)

virtual	~AP_combinableSeq ()

virtual AP_combinableSeq *	dup () const =0

virtual int	cmp_combined (const AP_combinableSeq *other) const =0

virtual Mutations	combine_seq (const AP_combinableSeq lefts, const AP_combinableSeq rights, char *mutation_per_site=NULp)=0

virtual Mutations	mutations_if_combined_with (const AP_combinableSeq *other)=0

virtual void	partial_match (const AP_combinableSeq part, long overlap, long *penalty) const =0

virtual uint32_t	checksum () const =0

AP_FLOAT	weighted_base_count () const

Mutations	noncounting_combine_seq (const AP_combinableSeq lefts, const AP_combinableSeq rights)

bool	combinedEquals (const AP_combinableSeq *other) const

Public Member Functions inherited from AP_sequence
	AP_sequence (const AliView *aliview)

virtual	~AP_sequence ()

GB_ERROR	bind_to_species (GBDATA *gb_species)

void	unbind_from_species ()

bool	is_bound_to_species () const

GBDATA *	get_bound_species_data () const

void	lazy_load_sequence () const

void	ensure_sequence_loaded () const

bool	hasSequence () const

void	forget_sequence ()

size_t	get_sequence_length () const

const AP_filter *	get_filter () const

const AP_weights *	get_weights () const

const AliView *	get_aliview () const

Static Public Member Functions
static long	combine_count ()

Protected Member Functions
virtual AP_FLOAT	count_weighted_bases () const =0

Protected Member Functions inherited from AP_sequence
void	mark_sequence_set (bool is_set)

virtual void	set (const char *sequence)=0

virtual void	unset ()=0

void	do_lazy_load () const

Static Protected Member Functions
static void	inc_combine_count ()

Additional Inherited Members
Protected Attributes inherited from AP_sequence
AP_FLOAT	cached_wbc

Detailed Description

Definition at line 102 of file AP_sequence.hxx.

Constructor & Destructor Documentation

AP_combinableSeq::AP_combinableSeq ( const AliView * aliview )

inline

Definition at line 111 of file AP_sequence.hxx.

virtual AP_combinableSeq::~AP_combinableSeq ( )

inlinevirtual

Definition at line 112 of file AP_sequence.hxx.

Member Function Documentation

virtual AP_FLOAT AP_combinableSeq::count_weighted_bases ( ) const

protectedpure virtual

Referenced by weighted_base_count().

static void AP_combinableSeq::inc_combine_count ( )

inlinestaticprotected

Definition at line 108 of file AP_sequence.hxx.

virtual AP_combinableSeq* AP_combinableSeq::dup ( ) const

pure virtual

Implements AP_sequence.

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

virtual int AP_combinableSeq::cmp_combined ( const AP_combinableSeq * other ) const

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

Referenced by combinedEquals().

virtual Mutations AP_combinableSeq::combine_seq	(	const AP_combinableSeq *	lefts,
		const AP_combinableSeq *	rights,
		char *	mutation_per_site = `NULp`
	)

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

Referenced by noncounting_combine_seq().

virtual Mutations AP_combinableSeq::mutations_if_combined_with ( const AP_combinableSeq * other )

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

Referenced by insert_species_into_tree().

virtual void AP_combinableSeq::partial_match	(	const AP_combinableSeq *	part,
		long *	overlap,
		long *	penalty
	)		const

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

virtual uint32_t AP_combinableSeq::checksum ( ) const

pure virtual

Implemented in FINAL_TYPE< SEQTYPE >, and FINAL_TYPE< SEQTYPE >.

static long AP_combinableSeq::combine_count ( )

inlinestatic

Definition at line 123 of file AP_sequence.hxx.

Referenced by PARSIMONY_testenv< SEQTYPE >::combines_performed(), and PARSIMONY_testenv< SEQTYPE >::~PARSIMONY_testenv().

AP_FLOAT AP_combinableSeq::weighted_base_count ( ) const

inline

Definition at line 125 of file AP_sequence.hxx.

References AP_sequence::cached_wbc, and count_weighted_bases().

Referenced by LowDataCheck::count().

Mutations AP_combinableSeq::noncounting_combine_seq	(	const AP_combinableSeq *	lefts,
		const AP_combinableSeq *	rights
	)

inline

Definition at line 130 of file AP_sequence.hxx.

References combine_seq().

bool AP_combinableSeq::combinedEquals ( const AP_combinableSeq * other ) const

inline

Definition at line 136 of file AP_sequence.hxx.

References cmp_combined().

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

SL/SEQUENCE/AP_sequence.hxx
SL/SEQUENCE/AP_sequence.cxx