#include <ali_global.hxx>
Public Member Functions | |
| void | init (int *argc, const char *argv[]) |
Public Attributes | |
| const char * | prog_name |
| char * | species_name |
| char * | default_file |
| char * | db_server |
| char * | pt_server |
| ALI_ARBDB | arbdb |
| ALI_PT * | pt |
| int | mark_species_flag |
| float | cost_low |
| float | cost_middle |
| float | cost_high |
| ALI_PT_CONTEXT | pt_context |
| ALI_PROFILE_CONTEXT | prof_context |
| ALI_PREALIGNER_CONTEXT | preali_context |
Detailed Description
Definition at line 18 of file ali_global.hxx.
Member Function Documentation
Definition at line 62 of file ali_global.cxx.
References ali_error(), ali_message(), ali_warning(), ARB_strdup(), arb_trace_argv(), ALI_PROFILE_CONTEXT::arbdb, arbdb, ALI_PROFILE_CONTEXT::binding_matrix, cost_high, COST_HIGH_DEFAULT, cost_low, COST_LOW_DEFAULT, cost_middle, COST_MIDDLE_DEFAULT, arb_params::db_server, db_server, default_binding_matrix, arb_params::default_file, default_file, default_substitute_matrix, ALI_PREALIGNER_CONTEXT::error_count, ERROR_COUNT_DEFAULT, ALI_PROFILE_CONTEXT::exclusive_flag, EXCLUSIVE_FLAG_DEFAULT, ALI_PT_CONTEXT::ext_list_max, EXT_LIST_MAX_DEFAULT, ALI_PROFILE_CONTEXT::ext_max_weight, EXT_MAX_WEIGHT_DEFAULT, ALI_PT_CONTEXT::fam_list_max, FAM_LIST_MAX_DEFAULT, ALI_PROFILE_CONTEXT::find_family_mode, FIND_FAMILY_MODE_DEFAULT, ALI_ARBDB::gb_main, ALI_PT_CONTEXT::gb_main, ALI_PROFILE_CONTEXT::insert_factor, INSERT_FACTOR_DEFAULT, ALI_PREALIGNER_CONTEXT::interval_border, INTERVAL_BORDER_DEFAULT, ALI_PREALIGNER_CONTEXT::interval_center, INTERVAL_CENTER_DEFAULT, MARK_EXTENSION_FLAG_DEFAULT, ALI_PROFILE_CONTEXT::mark_family_extension_flag, ALI_PROFILE_CONTEXT::mark_family_flag, MARK_FAMILY_FLAG_DEFAULT, mark_species_flag, ALI_PT_CONTEXT::matches_min, MATCHES_MIN_DEFAULT, MAX_COST_OF_HELIX, ALI_PREALIGNER_CONTEXT::max_cost_of_helix, ALI_PREALIGNER_CONTEXT::max_cost_of_sub_percent, MAX_COST_OF_SUB_PERCENT_DEFAULT, ALI_PROFILE_CONTEXT::max_family_size, MAX_FAMILY_SIZE_DEFAULT, ALI_PREALIGNER_CONTEXT::max_number_of_maps, ALI_PREALIGNER_CONTEXT::max_number_of_maps_aligner, MAX_NUMBER_OF_MAPS_ALIGNER_DEFAULT, MAX_NUMBER_OF_MAPS_DEFAULT, ALI_PROFILE_CONTEXT::min_family_size, MIN_FAMILY_SIZE_DEFAULT, ALI_PROFILE_CONTEXT::min_weight, MIN_WEIGHT_DEFAULT, ALI_PROFILE_CONTEXT::multi_gap_factor, MULTI_GAP_FACTOR_DEFAULT, ALI_PROFILE_CONTEXT::multi_insert_factor, MULTI_INSERT_FACTOR_DEFAULT, ALI_ARBDB::open(), ALI_PT_CONTEXT::percent_min, PERCENT_MIN_DEFAULT, preali_context, prof_context, prog_name, ALI_PROFILE_CONTEXT::pt, pt, pt_context, arb_params::pt_server, ALI_PT_CONTEXT::servername, arb_params::species_name, species_name, ALI_PROFILE_CONTEXT::substitute_matrix, ALI_PT_CONTEXT::use_specified_family, and USE_SPECIFIED_FAMILY_DEFAULT.
Referenced by ARB_main().
Member Data Documentation
| const char* ALI_GLOBAL::prog_name |
Definition at line 23 of file ali_global.hxx.
Referenced by init().
| char* ALI_GLOBAL::species_name |
Definition at line 24 of file ali_global.hxx.
Referenced by ARB_main(), and init().
| char* ALI_GLOBAL::default_file |
Definition at line 25 of file ali_global.hxx.
Referenced by init().
| char* ALI_GLOBAL::db_server |
Definition at line 26 of file ali_global.hxx.
Referenced by init().
| char* ALI_GLOBAL::pt_server |
Definition at line 27 of file ali_global.hxx.
| ALI_ARBDB ALI_GLOBAL::arbdb |
Definition at line 30 of file ali_global.hxx.
Referenced by ARB_main(), and init().
| ALI_PT* ALI_GLOBAL::pt |
Definition at line 31 of file ali_global.hxx.
Referenced by init().
| int ALI_GLOBAL::mark_species_flag |
Definition at line 34 of file ali_global.hxx.
Referenced by ARB_main(), and init().
| float ALI_GLOBAL::cost_low |
Definition at line 37 of file ali_global.hxx.
Referenced by init().
| float ALI_GLOBAL::cost_middle |
Definition at line 38 of file ali_global.hxx.
Referenced by init().
| float ALI_GLOBAL::cost_high |
Definition at line 39 of file ali_global.hxx.
Referenced by init().
| ALI_PT_CONTEXT ALI_GLOBAL::pt_context |
Definition at line 42 of file ali_global.hxx.
Referenced by init().
| ALI_PROFILE_CONTEXT ALI_GLOBAL::prof_context |
Definition at line 43 of file ali_global.hxx.
Referenced by ARB_main(), and init().
| ALI_PREALIGNER_CONTEXT ALI_GLOBAL::preali_context |
Definition at line 44 of file ali_global.hxx.
Referenced by ARB_main(), and init().
The documentation for this class was generated from the following files:
- NALIGNER/ali_global.hxx
- NALIGNER/ali_global.cxx
