ali_prealigner_mask Struct Reference

#include <ali_prealigner.hxx>

Collaboration diagram for ali_prealigner_mask:

Public Member Functions
	ali_prealigner_mask ()
void	insert (ALI_MAP *in_map, float costs)
void	delete_expensive (ALI_PREALIGNER_CONTEXT *context, ALI_PROFILE *profile)
void	clear ()

Public Attributes
ALI_MAP *	map
float	cost_of_binding
unsigned long	calls
unsigned long	joins
unsigned long	last_new
unsigned long	last_joins

Detailed Description

Definition at line 67 of file ali_prealigner.hxx.

Constructor & Destructor Documentation

ali_prealigner_mask::ali_prealigner_mask ( )

inline

Definition at line 73 of file ali_prealigner.hxx.

References NULp.

Member Function Documentation

void ali_prealigner_mask::insert	(	ALI_MAP *	in_map,
		float	costs
	)

Definition at line 14 of file ali_prealigner.cxx.

References ali_fatal_error(), calls, cost_of_binding, ALI_MAP::first_base(), ALI_MAP::first_reference_base(), ALI_MAP::is_undefined(), joins, ALI_MAP::last_base(), last_joins, last_new, ALI_MAP::last_reference_base(), map, ALI_MAP::position(), and ALI_MAP::undefine().

void ali_prealigner_mask::delete_expensive	(	ALI_PREALIGNER_CONTEXT *	context,
		ALI_PROFILE *	profile
	)

Definition at line 52 of file ali_prealigner.cxx.

References ali_fatal_error(), ALI_GAP_CODE, calls, ALI_PROFILE::complement_position(), ALI_PREALIGNER_CONTEXT::error_count, ALI_MAP::first_base(), ALI_MAP::first_reference_base(), ALI_PREALIGNER_CONTEXT::interval_border, ALI_PREALIGNER_CONTEXT::interval_center, ALI_MAP::inverse_without_inserts(), ALI_PROFILE::is_in_helix(), ALI_MAP::is_inserted(), ALI_MAP::is_undefined(), joins, ALI_MAP::last_base(), last_joins, last_new, long, map, ALI_PREALIGNER_CONTEXT::max_cost_of_helix, ALI_PREALIGNER_CONTEXT::max_cost_of_sub_percent, ALI_MAP::position(), ALI_PROFILE::sequence(), ALI_MAP::undefine(), ALI_PROFILE::w_bind(), ALI_PROFILE::w_sub(), and ALI_PROFILE::w_sub_maximum().

Referenced by ALI_PREALIGNER::ALI_PREALIGNER().

void ali_prealigner_mask::clear ( )

inline

Definition at line 81 of file ali_prealigner.hxx.

References map.

Member Data Documentation

ALI_MAP* ali_prealigner_mask::map

Definition at line 68 of file ali_prealigner.hxx.

Referenced by ALI_PREALIGNER::ALI_PREALIGNER(), clear(), delete_expensive(), insert(), ALI_PREALIGNER::sequence(), and ALI_PREALIGNER::sequence_without_inserts().

float ali_prealigner_mask::cost_of_binding

Definition at line 69 of file ali_prealigner.hxx.

Referenced by insert().

unsigned long ali_prealigner_mask::calls

Definition at line 71 of file ali_prealigner.hxx.

Referenced by delete_expensive(), and insert().

unsigned long ali_prealigner_mask::joins

Definition at line 71 of file ali_prealigner.hxx.

Referenced by delete_expensive(), and insert().

unsigned long ali_prealigner_mask::last_new

Definition at line 71 of file ali_prealigner.hxx.

Referenced by delete_expensive(), and insert().

unsigned long ali_prealigner_mask::last_joins

Definition at line 71 of file ali_prealigner.hxx.

Referenced by delete_expensive(), and insert().

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

• NALIGNER/ali_prealigner.hxx
• NALIGNER/ali_prealigner.cxx