ALI_ARBDB Class Reference

#include <ali_arbdb.hxx>

Inheritance diagram for ALI_ARBDB:

Collaboration diagram for ALI_ARBDB:

Public Member Functions
	ALI_ARBDB ()
	~ALI_ARBDB ()
int	open (char *name, char *use_alignment=NULp)
void	close ()
void	begin_transaction ()
void	commit_transaction ()
char *	get_sequence_string (char *name, int and_mark=0)
ALI_SEQUENCE *	get_sequence (char *name, int and_mark=0)
char *	get_SAI (char *name)
int	put_sequence_string (char *name, char *sequence)
int	put_sequence (char *name, ALI_SEQUENCE *sequence)
int	put_SAI (const char *name, char *sequence)

Public Attributes
GBDATA *	gb_main

Detailed Description

Definition at line 19 of file ali_arbdb.hxx.

Constructor & Destructor Documentation

ALI_ARBDB::ALI_ARBDB ( )

inline

Definition at line 26 of file ali_arbdb.hxx.

References NULp.

ALI_ARBDB::~ALI_ARBDB

(

)

Definition at line 19 of file ali_arbdb.cxx.

References GB_close(), and gb_main.

Member Function Documentation

int ALI_ARBDB::open	(	char *	name,
		char *	use_alignment = NULp
	)

Definition at line 24 of file ali_arbdb.cxx.

References ARB_strdup(), GB_begin_transaction(), GB_commit_transaction(), gb_main, GB_open(), GB_print_error(), and GBT_get_default_alignment().

Referenced by ALI_GLOBAL::init().

void ALI_ARBDB::close

(

)

Definition at line 48 of file ali_arbdb.cxx.

References GB_close(), and gb_main.

void ALI_ARBDB::begin_transaction ( )

inline

Definition at line 35 of file ali_arbdb.hxx.

References GB_begin_transaction().

Referenced by ARB_main().

void ALI_ARBDB::commit_transaction ( )

inline

Definition at line 38 of file ali_arbdb.hxx.

References GB_commit_transaction().

Referenced by ARB_main().

char * ALI_ARBDB::get_sequence_string	(	char *	name,
		int	and_mark = 0
	)

Definition at line 53 of file ali_arbdb.cxx.

References GB_brother(), GB_entry(), GB_find_string(), GB_get_father(), GB_IGNORE_CASE, gb_main, GB_read_string(), gb_species_data, GB_write_flag(), GBT_get_species_data(), NULp, and SEARCH_GRANDCHILD.

Referenced by ARB_main().

ALI_SEQUENCE * ALI_ARBDB::get_sequence	(	char *	name,
		int	and_mark = 0
	)

Definition at line 74 of file ali_arbdb.cxx.

References GB_brother(), GB_entry(), GB_find_string(), GB_get_father(), GB_IGNORE_CASE, gb_main, GB_read_string(), gb_species_data, GB_write_flag(), GBT_get_species_data(), NULp, and SEARCH_GRANDCHILD.

Referenced by ARB_main().

char * ALI_ARBDB::get_SAI

(

char *

name

)

Definition at line 101 of file ali_arbdb.cxx.

References GB_brother(), GB_entry(), GB_find_string(), GB_IGNORE_CASE, gb_main, GB_read_string(), GBT_get_SAI_data(), NULp, and SEARCH_GRANDCHILD.

int ALI_ARBDB::put_sequence_string	(	char *	name,
		char *	sequence
	)

Definition at line 119 of file ali_arbdb.cxx.

References GB_brother(), GB_find_string(), GB_IGNORE_CASE, gb_main, GB_search(), gb_species_data, GB_STRING, GB_write_string(), GBT_get_species_data(), and SEARCH_GRANDCHILD.

Referenced by ARB_main().

int ALI_ARBDB::put_sequence	(	char *	name,
		ALI_SEQUENCE *	sequence
	)

Definition at line 136 of file ali_arbdb.cxx.

References GB_brother(), GB_find_string(), GB_IGNORE_CASE, gb_main, GB_search(), gb_species_data, GB_STRING, GB_write_string(), GBT_get_species_data(), SEARCH_GRANDCHILD, and ALI_SEQUENCE::string().

int ALI_ARBDB::put_SAI	(	const char *	name,
		char *	sequence
	)

Definition at line 155 of file ali_arbdb.cxx.

References gb_main, GB_STRING, GB_write_string(), GBT_add_data(), and GBT_find_or_create_SAI().

Referenced by ARB_main().

Member Data Documentation

GBDATA* ALI_ARBDB::gb_main

Definition at line 24 of file ali_arbdb.hxx.

Referenced by close(), get_SAI(), get_sequence(), get_sequence_string(), ALI_GLOBAL::init(), open(), put_SAI(), put_sequence(), put_sequence_string(), and ~ALI_ARBDB().

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

• NALIGNER/ali_arbdb.hxx
• NALIGNER/ali_arbdb.cxx