ali_main.cxx File Reference

#include "ali_global.hxx"

Include dependency graph for ali_main.cxx:

Go to the source code of this file.

Macros
#define	HELIX_PAIRS   "helix_pairs"
#define	HELIX_LINE   "helix_line"
#define	ALI_CONSENSUS   "ALI_CON"
#define	ALI_ERROR   "ALI_ERR"
#define	ALI_INTERVALS   "ALI_INT"

Functions
void	message (char *errortext)
static void	print_man ()
void	ali_fatal_error (const char *message, const char *func)
void	ali_error (const char *message, const char *func)
static int	get_species (char *species_string, unsigned int species_number, char *buffer)
static int	check_base_invariance (char *seq1, char *seq2)
static int	convert_for_back_write (char *seq_new, char *seq_orig)
int	ARB_main (int argc, char *argv[])

Variables
static ALI_GLOBAL	aligs
static const char *	ali_version
static const char *	ali_man_line []

Macro Definition Documentation

#define HELIX_PAIRS   "helix_pairs"

Definition at line 14 of file ali_main.cxx.

#define HELIX_LINE   "helix_line"

Definition at line 15 of file ali_main.cxx.

#define ALI_CONSENSUS   "ALI_CON"

Definition at line 16 of file ali_main.cxx.

#define ALI_ERROR   "ALI_ERR"

Definition at line 17 of file ali_main.cxx.

#define ALI_INTERVALS   "ALI_INT"

Definition at line 18 of file ali_main.cxx.

Function Documentation

void message

(

char *

errortext

)

Referenced by alignToNextRelative(), aw_insert_message_in_tmp_message_delayed(), EDB_root_bact::fill_species(), LineAttachedMessage::Message(), ArbProbeCollection::openXML(), setCfgError(), and startup_gui().

static void print_man ( )

static

Definition at line 76 of file ali_main.cxx.

Referenced by ARB_main().

void ali_fatal_error	(	const char *	message,
		const char *	func
	)

Definition at line 85 of file ali_main.cxx.

Referenced by ali_number_to_base(), ali_out_of_memory_if(), ALI_PT::ALI_PT(), ALI_TARRAY< ali_pathmap_up_pointer >::ALI_TARRAY(), ARB_main(), ALI_PROFILE::base_weight(), ALI_SEQUENCE::check(), convert_for_back_write(), ali_prealigner_mask::delete_expensive(), ALI_PT::find_family(), ALI_PATHMAP::get(), ALI_TARRAY< ali_pathmap_up_pointer >::get(), ALI_TSTACK< T >::get(), ALI_PATHMAP::get_value(), ali_prealigner_mask::insert(), ALI_MAP::is_inserted(), ALI_MAP::is_undefined(), ALI_SUB_SOLUTION::make_one_map(), ALI_TLIST< ali_pt_member * >::marked(), ALI_TSTACK< T >::pop(), ALI_MAP::position(), ALI_TSTACK< T >::push(), ALI_PATHMAP::set(), ALI_TARRAY< ali_pathmap_up_pointer >::set(), ALI_MAP::set(), ALI_TSTACK< T >::top(), ALI_MAP::undefine(), and ALI_MAP::unundefine().

void ali_error	(	const char *	message,
		const char *	func
	)

Definition at line 90 of file ali_main.cxx.

Referenced by ALI_PROFILE::ALI_PROFILE(), ARB_main(), convert_for_back_write(), ALI_PT::find_family(), and ALI_GLOBAL::init().

static int get_species ( char *  species_string, unsigned int  species_number, char *  buffer  )

static

Definition at line 97 of file ali_main.cxx.

Referenced by ARB_main().

static int check_base_invariance ( char *  seq1, char *  seq2  )

static

Definition at line 120 of file ali_main.cxx.

References ali_is_base().

Referenced by ARB_main().

static int convert_for_back_write ( char *  seq_new, char *  seq_orig  )

static

Definition at line 143 of file ali_main.cxx.

References ali_error(), ali_fatal_error(), ali_is_dot(), and ali_is_gap().

Referenced by ARB_main().

int ARB_main	(	int	argc,
		char *	argv[]
	)

Definition at line 217 of file ali_main.cxx.

References ali_error(), ali_fatal_error(), ali_message(), ali_warning(), ALI_PREALIGNER::approximation(), ALI_GLOBAL::arbdb, ALI_ARBDB::begin_transaction(), ALI_PROFILE::borders_sequence(), ALI_TLIST< T >::cardinality(), ALI_PROFILE::cheapest_sequence(), check_base_invariance(), ALI_ARBDB::commit_transaction(), convert_for_back_write(), ALI_TLIST< T >::first(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), get_species(), ALI_GLOBAL::init(), ali_prealigner_approx_element::ins_marker, ALI_TLIST< T >::is_empty(), ALI_PROFILE::length(), ali_prealigner_approx_element::map, ALI_GLOBAL::mark_species_flag, ALI_GLOBAL::preali_context, ALI_SUB_SOLUTION::print(), print_man(), ALI_GLOBAL::prof_context, ALI_ARBDB::put_SAI(), ALI_ARBDB::put_sequence_string(), ALI_MAP::sequence(), ALI_PROFILE::sequence(), ALI_PREALIGNER::sequence(), ALI_PROFILE::sequence_length(), ALI_PREALIGNER::sequence_without_inserts(), ALI_PREALIGNER::solution(), ALI_GLOBAL::species_name, and ALI_SEQUENCE::string().

Variable Documentation

ALI_GLOBAL aligs

static

Definition at line 20 of file ali_main.cxx.

const char* ali_version

static

Initial value:

=
    "\nALIGNER   V2.0  (Boris Reichel 5/95)\n"

Definition at line 26 of file ali_main.cxx.

const char* ali_man_line[]

static

Definition at line 29 of file ali_main.cxx.