ali_aligner_dellist Struct Reference

#include <ali_aligner.hxx>

Inheritance diagram for ali_aligner_dellist:

Collaboration diagram for ali_aligner_dellist:

Public Member Functions
	ali_aligner_dellist (ALI_PROFILE *p)
	~ali_aligner_dellist ()
void	print ()
void	print_cont (unsigned long position)
unsigned long	length ()
void	make_empty ()
void	insert (unsigned long start, float costs, unsigned char operation)
float	update (unsigned long position)
ALI_TARRAY < ali_pathmap_up_pointer > *	starts (float costs, unsigned long y_offset)
void	optimize (unsigned long position)
Public Member Functions inherited from Noncopyable
	Noncopyable ()

Public Attributes
ALI_PROFILE *	profile
ALI_TLIST < ali_aligner_dellist_elem * >	list_of_dels

Detailed Description

Definition at line 92 of file ali_aligner.hxx.

Constructor & Destructor Documentation

ali_aligner_dellist::ali_aligner_dellist ( ALI_PROFILE *  p )

inline

Definition at line 96 of file ali_aligner.hxx.

ali_aligner_dellist::~ali_aligner_dellist ( )

inline

Definition at line 99 of file ali_aligner.hxx.

References ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), and ALI_TLIST< T >::next().

Member Function Documentation

void ali_aligner_dellist::print ( )

inline

Definition at line 111 of file ali_aligner.hxx.

References ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), ALI_TLIST< T >::next(), and ali_aligner_dellist_elem::print().

void ali_aligner_dellist::print_cont ( unsigned long  position )

inline

Definition at line 122 of file ali_aligner.hxx.

References ALI_TLIST< T >::first(), ALI_PROFILE::gap_percent(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), ALI_TLIST< T >::next(), ali_aligner_dellist_elem::print(), and ali_aligner_dellist_elem::start.

unsigned long ali_aligner_dellist::length ( )

inline

Definition at line 135 of file ali_aligner.hxx.

References ALI_TLIST< T >::cardinality().

void ali_aligner_dellist::make_empty ( )

inline

Definition at line 138 of file ali_aligner.hxx.

References ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), ALI_TLIST< T >::make_empty(), and ALI_TLIST< T >::next().

void ali_aligner_dellist::insert ( unsigned long  start, float  costs, unsigned char  operation  )

inline

Definition at line 150 of file ali_aligner.hxx.

References ALI_TLIST< T >::append_end().

float ali_aligner_dellist::update

(

unsigned long

position

)

Definition at line 16 of file ali_aligner.cxx.

References ali_aligner_dellist_elem::costs, ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), list_of_dels, ALI_TLIST< T >::next(), profile, ali_aligner_dellist_elem::start, and ALI_PROFILE::w_del().

ALI_TARRAY< ali_pathmap_up_pointer > * ali_aligner_dellist::starts	(	float	costs,
		unsigned long	y_offset
	)

Definition at line 37 of file ali_aligner.cxx.

References ali_aligner_dellist_elem::costs, ALI_TLIST< T >::first(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), list_of_dels, ALI_TLIST< T >::next(), NULp, ali_pathmap_up_pointer::operation, ali_aligner_dellist_elem::operation, ALI_TARRAY< T >::set(), ali_pathmap_up_pointer::start, and ali_aligner_dellist_elem::start.

void ali_aligner_dellist::optimize

(

unsigned long

position

)

Definition at line 79 of file ali_aligner.cxx.

References ali_aligner_dellist_elem::costs, ALI_TLIST< T >::current(), ALI_TLIST< T >::delete_element(), ALI_TLIST< T >::first(), ALI_PROFILE::gap_percent(), ALI_TLIST< T >::has_next(), ALI_TLIST< T >::is_empty(), list_of_dels, ALI_TLIST< T >::mark_element(), ALI_TLIST< T >::marked(), ALI_TLIST< T >::next(), NULp, ali_aligner_dellist_elem::operation, profile, and ali_aligner_dellist_elem::start.

Member Data Documentation

ALI_PROFILE* ali_aligner_dellist::profile

Definition at line 93 of file ali_aligner.hxx.

Referenced by optimize(), and update().

ALI_TLIST<ali_aligner_dellist_elem *> ali_aligner_dellist::list_of_dels

Definition at line 94 of file ali_aligner.hxx.

Referenced by optimize(), starts(), and update().

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

• NALIGNER/ali_aligner.hxx
• NALIGNER/ali_aligner.cxx