AP_sequence Class Reference

#include <AP_sequence.hxx>

Inheritance diagram for AP_sequence:

Collaboration diagram for AP_sequence:

Public Member Functions
	AP_sequence (const AliView *aliview)
virtual	~AP_sequence ()
virtual AP_sequence *	dup () const =0
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

Protected Member Functions
void	mark_sequence_set (bool is_set)
virtual void	set (const char *sequence)=0
virtual void	unset ()=0
void	do_lazy_load () const

Protected Attributes
AP_FLOAT	cached_wbc

Detailed Description

Definition at line 33 of file AP_sequence.hxx.

Constructor & Destructor Documentation

AP_sequence::AP_sequence

(

const AliView *

aliview

)

Definition at line 16 of file AP_sequence.cxx.

virtual AP_sequence::~AP_sequence ( )

inlinevirtual

Definition at line 58 of file AP_sequence.hxx.

Member Function Documentation

void AP_sequence::mark_sequence_set ( bool  is_set )

inlineprotected

Definition at line 43 of file AP_sequence.hxx.

References AP_timer().

virtual void AP_sequence::set ( const char *  sequence )

protectedpure virtual

Referenced by do_lazy_load().

virtual void AP_sequence::unset ( )

protectedpure virtual

Referenced by bind_to_species(), forget_sequence(), and unbind_from_species().

void AP_sequence::do_lazy_load ( ) const

protected

Definition at line 46 of file AP_sequence.cxx.

References ap_assert, error(), GB_await_error(), GB_get_grandfather(), GB_read_char_pntr(), GB_warningf(), GBT_get_name_or_description(), seq, set(), and ta.

Referenced by lazy_load_sequence().

virtual AP_sequence* AP_sequence::dup ( ) const

pure virtual

Implemented in AP_combinableSeq, FINAL_TYPE< SEQTYPE >, MostLikelySeq, FINAL_TYPE< SEQTYPE >, and AP_sequence_simple_protein.

GB_ERROR AP_sequence::bind_to_species

(

GBDATA *

gb_species

)

Definition at line 24 of file AP_sequence.cxx.

References ap_assert, error(), GBS_global_string(), GBT_find_sequence(), GBT_get_name_or_description(), AliView::get_aliname(), AliView::get_gb_main(), NULp, ta, and unset().

Referenced by MostLikelySeq::bind_to_species(), and DI_ENTRY::DI_ENTRY().

void AP_sequence::unbind_from_species

(

)

Definition at line 40 of file AP_sequence.cxx.

References ap_assert, NULp, and unset().

Referenced by MostLikelySeq::unbind_from_species(), and MostLikelySeq::~MostLikelySeq().

bool AP_sequence::is_bound_to_species ( ) const

inline

Definition at line 64 of file AP_sequence.hxx.

Referenced by lazy_load_sequence().

GBDATA* AP_sequence::get_bound_species_data ( ) const

inline

Definition at line 65 of file AP_sequence.hxx.

Referenced by MostLikelySeq::get_bound_species_data().

void AP_sequence::lazy_load_sequence ( ) const

inline

Definition at line 67 of file AP_sequence.hxx.

References do_lazy_load(), and is_bound_to_species().

Referenced by DI_ENTRY::DI_ENTRY(), ensure_sequence_loaded(), and FINAL_TYPE< SEQTYPE >::get_sequence().

void AP_sequence::ensure_sequence_loaded ( ) const

inline

Definition at line 70 of file AP_sequence.hxx.

References ap_assert, and lazy_load_sequence().

bool AP_sequence::hasSequence ( ) const

inline

Definition at line 75 of file AP_sequence.hxx.

Referenced by ARB_seqtree::hasSequence().

void AP_sequence::forget_sequence ( )

inline

Definition at line 76 of file AP_sequence.hxx.

References unset().

size_t AP_sequence::get_sequence_length ( ) const

inline

Definition at line 78 of file AP_sequence.hxx.

References AliView::get_length().

const AP_filter* AP_sequence::get_filter ( ) const

inline

Definition at line 79 of file AP_sequence.hxx.

References AliView::get_filter().

const AP_weights* AP_sequence::get_weights ( ) const

inline

Definition at line 80 of file AP_sequence.hxx.

References AliView::get_weights().

const AliView* AP_sequence::get_aliview ( ) const

inline

Definition at line 82 of file AP_sequence.hxx.

Referenced by ARB_seqtree_root::ARB_seqtree_root(), AP_sequence_simple_protein::dup(), and MostLikelySeq::dup().

Member Data Documentation

AP_FLOAT AP_sequence::cached_wbc

mutableprotected

Definition at line 41 of file AP_sequence.hxx.

Referenced by AP_combinableSeq::weighted_base_count().

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

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