ALI_NORM_SEQUENCE Class Reference

#include <ali_sequence.hxx>

Inheritance diagram for ALI_NORM_SEQUENCE:

Collaboration diagram for ALI_NORM_SEQUENCE:

Public Member Functions
	ALI_NORM_SEQUENCE (char *name, char *str)
	ALI_NORM_SEQUENCE (ALI_SEQUENCE *sequence)
	~ALI_NORM_SEQUENCE ()
unsigned char *	sequence ()
unsigned char	base (unsigned long position)
char *	string ()
char *	name ()
unsigned long	length ()
int	is_begin (unsigned long pos)

Detailed Description

Definition at line 62 of file ali_sequence.hxx.

Constructor & Destructor Documentation

ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE	(	char *	name,
		char *	str
	)

Definition at line 51 of file ali_sequence.cxx.

References ali_base_to_number(), ali_is_base(), ali_is_dot(), ali_out_of_memory_if(), ARB_strdup(), CALLOC(), and s.

ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE

(

ALI_SEQUENCE *

sequence

)

Definition at line 86 of file ali_sequence.cxx.

References ali_is_base(), ali_is_dot(), ali_out_of_memory_if(), ARB_strdup(), CALLOC(), ALI_SEQUENCE::length(), ALI_SEQUENCE::name(), s, and ALI_SEQUENCE::sequence().

ALI_NORM_SEQUENCE::~ALI_NORM_SEQUENCE ( )

inline

Definition at line 70 of file ali_sequence.hxx.

Member Function Documentation

unsigned char* ALI_NORM_SEQUENCE::sequence ( )

inline

Definition at line 78 of file ali_sequence.hxx.

unsigned char ALI_NORM_SEQUENCE::base ( unsigned long  position )

inline

Definition at line 81 of file ali_sequence.hxx.

Referenced by ALI_MAP::sequence(), ALI_MAP::sequence_without_inserts(), and ALI_PROFILE::w_sub().

char * ALI_NORM_SEQUENCE::string

(

)

Definition at line 122 of file ali_sequence.cxx.

References ali_out_of_memory_if(), ali_sequence_to_string(), and CALLOC().

char* ALI_NORM_SEQUENCE::name ( )

inline

Definition at line 85 of file ali_sequence.hxx.

Referenced by ALI_MAP::sequence(), and ALI_MAP::sequence_without_inserts().

unsigned long ALI_NORM_SEQUENCE::length ( )

inline

Definition at line 88 of file ali_sequence.hxx.

Referenced by ALI_PROFILE::sequence_length().

int ALI_NORM_SEQUENCE::is_begin ( unsigned long  pos )

inline

Definition at line 91 of file ali_sequence.hxx.

Referenced by ALI_PROFILE::is_internal_last(), ALI_MAP::sequence(), and ALI_MAP::sequence_without_inserts().

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

• NALIGNER/ali_sequence.hxx
• NALIGNER/ali_sequence.cxx