ARB: probe_struct_global Class Reference

ARB

#include <probe.h>

Collaboration diagram for probe_struct_global:

Collaboration graph

Public Member Functions
void	setup ()

void	cleanup ()

void	enter_stage (Stage stage_)

Stage	get_stage () const

POS_TREE1 *&	TREE_ROOT1 ()

POS_TREE2 *&	TREE_ROOT2 ()

Public Attributes
GB_shell *	gb_shell

GBDATA *	gb_main

char *	alignment_name

GB_HASH *	namehash

int	data_count

struct probe_input_data *	data

char *	ecoli

BI_ecoli_ref *	bi_ecoli

int	max_size

long	char_count

int	reversed

double *	pos_to_weight

MostUsedPos	abs_pos

int	sort_by

char *	main_probe

char *	server_name

aisc_com *	link

T_PT_MAIN	main

Hs_struct *	com_so

probe_statistic_struct	stat

bool	big_db

POS_TREE1 *	p1

POS_TREE2 *	p2

Detailed Description

Definition at line 341 of file probe.h.

Member Function Documentation

void probe_struct_global::setup ( )

Definition at line 70 of file PT_main.cxx.

References alignment_name, char_count, com_so, data, data_count, gb_main, gb_shell, link, main, main_probe, max_size, namehash, NULp, pos_to_weight, reversed, server_name, probe_statistic_struct::setup(), sort_by, and stat.

Referenced by cleanup(), and PT_init_psg().

void probe_struct_global::cleanup ( )

Definition at line 103 of file PT_main.cxx.

References alignment_name, bi_ecoli, com_so, data, ecoli, GB_close(), gb_main, gb_shell, GBS_free_hash(), namehash, NULp, pos_to_weight, pt_assert, and setup().

Referenced by PT_exit_psg().

void probe_struct_global::enter_stage ( Stage stage_ )

Definition at line 141 of file PT_prefixtree.cxx.

References pt_global::init(), Memory::is_clear(), MEM, pt_assert, and PT_GLOBAL.

Referenced by enter_stage_1_build_tree(), and enter_stage_2_load_tree().

Stage probe_struct_global::get_stage ( ) const

inline

Definition at line 387 of file probe.h.

Referenced by PT_dump_POS_TREE_to_file().

POS_TREE1*& probe_struct_global::TREE_ROOT1 ( )

inline

Definition at line 389 of file probe.h.

References pt_assert, and STAGE1.

Referenced by PT_dump_POS_TREE_to_file().

POS_TREE2*& probe_struct_global::TREE_ROOT2 ( )

inline

Definition at line 390 of file probe.h.

References pt_assert, and STAGE2.

Referenced by OutgroupMatcher::calculate_outgroup_matches(), enter_stage_2_load_tree(), find_family(), probe_match(), PT_dump_POS_TREE_to_file(), PT_dump_tree_statistics(), PT_find_exProb(), and remove_tprobes_with_too_many_mishits().

Member Data Documentation

POS_TREE1* probe_struct_global::p1

Definition at line 345 of file probe.h.

POS_TREE2* probe_struct_global::p2

Definition at line 346 of file probe.h.

GB_shell* probe_struct_global::gb_shell

Definition at line 350 of file probe.h.

Referenced by cleanup(), probe_read_data_base(), and setup().

GBDATA* probe_struct_global::gb_main

Definition at line 351 of file probe.h.

Referenced by cleanup(), enter_stage_1_build_tree(), gene_rel_2_abs(), probe_read_data_base(), PT_init_input_data(), pt_init_main_struct(), PT_init_map(), run_command(), and setup().

char* probe_struct_global::alignment_name

Definition at line 352 of file probe.h.

Referenced by cleanup(), PT_init_input_data(), pt_init_main_struct(), and setup().

GB_HASH* probe_struct_global::namehash

Definition at line 353 of file probe.h.

Referenced by cleanup(), PT_build_species_hash(), ptpd_read_names(), and setup().

int probe_struct_global::data_count

Definition at line 355 of file probe.h.

Referenced by enter_stage_1_build_tree(), find_family(), AbsLoc::has_valid_name(), make_PT_family_list(), MP_all_species_string(), MP_count_all_species(), PT_build_species_hash(), PT_init_cache_sizes(), PT_init_input_data(), ptpd_read_names(), and setup().

struct probe_input_data* probe_struct_global::data

char* probe_struct_global::ecoli

Definition at line 358 of file probe.h.

Referenced by cleanup(), detect_format_props(), PT_abs_2_ecoli_rel(), PT_build_species_hash(), and PT_init_input_data().

BI_ecoli_ref* probe_struct_global::bi_ecoli

Definition at line 359 of file probe.h.

Referenced by cleanup(), PT_abs_2_ecoli_rel(), and PT_build_species_hash().

int probe_struct_global::max_size

Definition at line 361 of file probe.h.

Referenced by PT_build_species_hash(), and setup().

long probe_struct_global::char_count

Definition at line 362 of file probe.h.

Referenced by enter_stage_1_build_tree(), PT_build_species_hash(), and setup().

int probe_struct_global::reversed

Definition at line 364 of file probe.h.

Referenced by MatchRequest::add_hit(), probe_match(), and setup().

double* probe_struct_global::pos_to_weight

Definition at line 366 of file probe.h.

Referenced by cleanup(), Mismatches::count_weighted(), pt_build_pos_to_weight(), and setup().

MostUsedPos probe_struct_global::abs_pos

Definition at line 368 of file probe.h.

Referenced by count_mishits_for_all(), ptnd_chain_count_mishits::operator()(), and remove_tprobes_with_too_many_mishits().

int probe_struct_global::sort_by

Definition at line 370 of file probe.h.

Referenced by pt_sort_compare_match(), pt_sort_match_list(), and setup().

char* probe_struct_global::main_probe

Definition at line 372 of file probe.h.

Referenced by MatchRequest::add_hit(), probe_match(), and setup().

char* probe_struct_global::server_name

Definition at line 374 of file probe.h.

Referenced by setup().

aisc_com* probe_struct_global::link

Definition at line 375 of file probe.h.

Referenced by run_command(), and setup().

T_PT_MAIN probe_struct_global::main

Definition at line 376 of file probe.h.

Referenced by run_command(), and setup().

Hs_struct* probe_struct_global::com_so

Definition at line 377 of file probe.h.

Referenced by broadcast(), cleanup(), server_shutdown(), setup(), and start_pt_server().

probe_statistic_struct probe_struct_global::stat

Definition at line 379 of file probe.h.

Referenced by enter_stage_1_build_tree(), PTD_write_node_to_disk(), and setup().

bool probe_struct_global::big_db

Definition at line 381 of file probe.h.

Referenced by PT_statistic::dump(), and PTD_read_leafs_from_disk().

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