Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
AP_sequence Class Referenceabstract

#include <AP_sequence.hxx>

Inheritance diagram for AP_sequence:
Inheritance graph
Collaboration diagram for AP_sequence:
Collaboration graph

Public Member Functions

 AP_sequence (const AliView *aliview)
virtual ~AP_sequence ()
virtual AP_sequencedup () const =0
GB_ERROR bind_to_species (GBDATA *gb_species)
void unbind_from_species ()
bool is_bound_to_species () const
GBDATAget_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_filterget_filter () const
const AP_weightsget_weights () const
const AliViewget_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 ( )

Definition at line 58 of file AP_sequence.hxx.

Member Function Documentation

void AP_sequence::mark_sequence_set ( bool  is_set)

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
void AP_sequence::do_lazy_load ( ) const
virtual AP_sequence* AP_sequence::dup ( ) const
pure virtual
GB_ERROR AP_sequence::bind_to_species ( GBDATA gb_species)
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

Definition at line 64 of file AP_sequence.hxx.

Referenced by lazy_load_sequence().

GBDATA* AP_sequence::get_bound_species_data ( ) const

Definition at line 65 of file AP_sequence.hxx.

Referenced by MostLikelySeq::get_bound_species_data().

void AP_sequence::lazy_load_sequence ( ) const
void AP_sequence::ensure_sequence_loaded ( ) const

Definition at line 70 of file AP_sequence.hxx.

References ap_assert, and lazy_load_sequence().

bool AP_sequence::hasSequence ( ) const

Definition at line 75 of file AP_sequence.hxx.

Referenced by ARB_seqtree::hasSequence().

void AP_sequence::forget_sequence ( )

Definition at line 76 of file AP_sequence.hxx.

References unset().

size_t AP_sequence::get_sequence_length ( ) const

Definition at line 78 of file AP_sequence.hxx.

References AliView::get_length().

const AP_filter* AP_sequence::get_filter ( ) const

Definition at line 79 of file AP_sequence.hxx.

References AliView::get_filter().

const AP_weights* AP_sequence::get_weights ( ) const

Definition at line 80 of file AP_sequence.hxx.

References AliView::get_weights().

const AliView* AP_sequence::get_aliview ( ) const

Member Data Documentation

AP_FLOAT AP_sequence::cached_wbc

Definition at line 41 of file AP_sequence.hxx.

Referenced by AP_combinableSeq::weighted_base_count().

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