ARB: ALI_MAP Class Reference

ARB

#include <ali_solution.hxx>

Inheritance diagram for ALI_MAP:

Inheritance graph

Collaboration diagram for ALI_MAP:

Collaboration graph

Public Member Functions
	ALI_MAP (unsigned long first_seq_base, unsigned long last_seq_base, unsigned long first_ref_base, unsigned long last_ref_base)

	ALI_MAP (ALI_MAP *map)

	~ALI_MAP ()

unsigned long	first_base ()

unsigned long	last_base ()

unsigned long	first_reference_base ()

unsigned long	last_reference_base ()

void	set (unsigned long base, unsigned long pos, int insert=-1)

long	position (unsigned long base)

unsigned long	insertations ()

int	is_inserted (unsigned long base)

void	undefine (unsigned long base)

void	unundefine (unsigned long base)

int	is_undefined (unsigned long base)

int	have_undefined ()

int	is_konsistent ()

int	is_equal (ALI_MAP *map)

ALI_SEQUENCE *	sequence (ALI_NORM_SEQUENCE *ref_seq)

ALI_SEQUENCE *	sequence_without_inserts (ALI_NORM_SEQUENCE *ref_seq)

ALI_MAP *	inverse_without_inserts ()

char *	insert_marker ()

void	print ()

Detailed Description

Definition at line 18 of file ali_solution.hxx.

Constructor & Destructor Documentation

ALI_MAP::ALI_MAP	(	unsigned long	first_seq_base,
		unsigned long	last_seq_base,
		unsigned long	first_ref_base,
		unsigned long	last_ref_base
	)

Definition at line 17 of file ali_solution.cxx.

References ali_out_of_memory_if(), and CALLOC().

Referenced by inverse_without_inserts().

ALI_MAP::ALI_MAP ( ALI_MAP * map )

Definition at line 38 of file ali_solution.cxx.

References ali_out_of_memory_if(), and CALLOC().

ALI_MAP::~ALI_MAP ( )

inline

Definition at line 29 of file ali_solution.hxx.

Member Function Documentation

unsigned long ALI_MAP::first_base ( )

inline

Definition at line 37 of file ali_solution.hxx.

Referenced by ali_prealigner_mask::delete_expensive(), ALI_SUB_SOLUTION::free_area(), ali_prealigner_mask::insert(), ALI_SUB_SOLUTION::insert(), ALI_SUB_SOLUTION::is_konsistent(), ALI_SUB_SOLUTION::make_one_map(), ALI_SUB_SOLUTION::number_of_free_areas(), and ALI_SUB_SOLUTION::print().

unsigned long ALI_MAP::last_base ( )

inline

Definition at line 40 of file ali_solution.hxx.

Referenced by ali_prealigner_mask::delete_expensive(), ALI_SUB_SOLUTION::free_area(), ali_prealigner_mask::insert(), ALI_SUB_SOLUTION::insert(), ALI_SUB_SOLUTION::is_konsistent(), ALI_SUB_SOLUTION::make_one_map(), ALI_SUB_SOLUTION::number_of_free_areas(), and ALI_SUB_SOLUTION::print().

unsigned long ALI_MAP::first_reference_base ( )

inline

Definition at line 43 of file ali_solution.hxx.

Referenced by ali_prealigner_mask::delete_expensive(), ALI_SUB_SOLUTION::free_area(), ali_prealigner_mask::insert(), ALI_SUB_SOLUTION::insert(), ALI_SUB_SOLUTION::is_konsistent(), ALI_SUB_SOLUTION::make_one_map(), ALI_SUB_SOLUTION::number_of_free_areas(), and ALI_SUB_SOLUTION::print().

unsigned long ALI_MAP::last_reference_base ( )

inline

Definition at line 46 of file ali_solution.hxx.

Referenced by ALI_SUB_SOLUTION::free_area(), ali_prealigner_mask::insert(), ALI_SUB_SOLUTION::insert(), ALI_SUB_SOLUTION::is_konsistent(), ALI_SUB_SOLUTION::make_one_map(), and ALI_SUB_SOLUTION::print().

void ALI_MAP::set	(	unsigned long	base,
		unsigned long	pos,
		int	insert = `-1`
	)

inline

Definition at line 50 of file ali_solution.hxx.

References ali_fatal_error().

Referenced by inverse_without_inserts(), and ALI_SUB_SOLUTION::make_one_map().

long ALI_MAP::position ( unsigned long base )

inline

Definition at line 80 of file ali_solution.hxx.

References ali_fatal_error().

Referenced by ali_prealigner_mask::delete_expensive(), ali_prealigner_mask::insert(), and ALI_SUB_SOLUTION::make_one_map().

unsigned long ALI_MAP::insertations ( )

inline

Definition at line 85 of file ali_solution.hxx.

int ALI_MAP::is_inserted ( unsigned long base )

inline

Definition at line 88 of file ali_solution.hxx.

References ali_fatal_error().

Referenced by ali_prealigner_mask::delete_expensive(), and ALI_SUB_SOLUTION::make_one_map().

void ALI_MAP::undefine ( unsigned long base )

inline

Definition at line 98 of file ali_solution.hxx.

References ali_fatal_error().

Referenced by ali_prealigner_mask::delete_expensive(), and ali_prealigner_mask::insert().

void ALI_MAP::unundefine ( unsigned long base )

inline

Definition at line 105 of file ali_solution.hxx.

References ali_fatal_error().

int ALI_MAP::is_undefined ( unsigned long base )

inline

Definition at line 112 of file ali_solution.hxx.

References ali_fatal_error().

Referenced by ali_prealigner_mask::delete_expensive(), have_undefined(), ali_prealigner_mask::insert(), ALI_SUB_SOLUTION::make_one_map(), and print().

int ALI_MAP::have_undefined ( )

inline

Definition at line 122 of file ali_solution.hxx.

References is_undefined().

int ALI_MAP::is_konsistent ( )

Definition at line 61 of file ali_solution.cxx.

int ALI_MAP::is_equal ( ALI_MAP * map )

inline

Definition at line 131 of file ali_solution.hxx.

ALI_SEQUENCE * ALI_MAP::sequence ( ALI_NORM_SEQUENCE * ref_seq )

Definition at line 71 of file ali_solution.cxx.

References ALI_DOT_CODE, ALI_GAP_CODE, ali_out_of_memory_if(), ALI_NORM_SEQUENCE::base(), CALLOC(), ALI_NORM_SEQUENCE::is_begin(), long, ALI_NORM_SEQUENCE::name(), and seq.

Referenced by ARB_main(), and ALI_PREALIGNER::sequence().

ALI_SEQUENCE * ALI_MAP::sequence_without_inserts ( ALI_NORM_SEQUENCE * ref_seq )

Definition at line 120 of file ali_solution.cxx.

References ALI_DOT_CODE, ALI_GAP_CODE, ali_out_of_memory_if(), ALI_NORM_SEQUENCE::base(), CALLOC(), ALI_NORM_SEQUENCE::is_begin(), long, ALI_NORM_SEQUENCE::name(), and seq.

Referenced by ALI_PREALIGNER::sequence_without_inserts().

ALI_MAP * ALI_MAP::inverse_without_inserts ( )

Definition at line 162 of file ali_solution.cxx.

References ALI_MAP(), and set().

Referenced by ali_prealigner_mask::delete_expensive().

char * ALI_MAP::insert_marker ( )

Definition at line 180 of file ali_solution.cxx.

References CALLOC(), long, and seq.

void ALI_MAP::print ( )

inline

Definition at line 150 of file ali_solution.hxx.

References is_undefined().

Referenced by ali_prealigner_approx_element::print().

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

NALIGNER/ali_solution.hxx
NALIGNER/ali_solution.cxx