ARB
Functions
arb_main.cxx File Reference
#include <arb_main.h>
Include dependency graph for arb_main.cxx:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions

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

Function Documentation

int ARB_main ( int  argc,
char argv[] 
)

Definition at line 1545 of file mkptypes.cxx.

References PARS_commands::add_marked, PARS_commands::add_selected, AW_root::add_timed_callback(), addExcludedSymParts(), addRequiredSymParts(), aisc_accept_calls(), aisc_close(), aisc_core_on_error, AISC_MAGIC_NUMBER, aisc_main, aisc_nput(), aisc_open(), aisc_server_shutdown(), ali_error(), ali_fatal_error(), ali_message(), ali_warning(), ED4_root::alignment_name, arb_prm_struct::alignment_names, ED4_root::alignment_type, AN_global, anerror, APPEARS_IN_HEADER, ALI_PREALIGNER::approximation(), arb_assert, ARB_init_global_awars(), arb_prm_menu(), arb_prm_primer(), arb_prm_read(), ARB_redirect_handlers_to(), ARB_sleep(), ARB_strdup(), arb_trace_argv(), ALI_GLOBAL::arbdb, ask_for_conversion_params(), aw_initstatus(), aw_message(), aw_popup_exit(), aw_popup_ok(), NT_global::aw_root, ED4_root::aw_root, AW_ROOT_DEFAULT, AW_root::awar(), AWAR_GDE_EXPORT_FILTER, AWAR_PHYLO_ALIGNMENT, AWT_create_root(), AWT_initTreeAwarRegistry(), AWT_install_cb_guards(), AWT_install_postcb_cb(), AWT_show_file(), ALI_ARBDB::begin_transaction(), ALI_PROFILE::borders_sequence(), build_consensus_tree(), PARS_commands::calc_bootstrap, PARS_commands::calc_branch_lengths, ALI_TLIST< T >::cardinality(), CATSCALE, ALI_PROFILE::cheapest_sequence(), check_base_invariance(), AN_gl_struct::cl_link, AN_gl_struct::cl_main, cleanup(), closeArb(), com, command, command_line_conversion(), ALI_ARBDB::commit_transaction(), configure_macro_recording(), convert_for_back_write(), count_elements(), ed_key::create_awars(), ED4_root::create_first_window(), ED4_root::create_hierarchy(), create_pars_init_window(), create_phyl_main_window(), create_select_alignment_window(), create_variables(), createOriginRNS(), ED4_root::database, arb_params::db_server, DEBUG_PRINT, DEFAULT_CONFIGURATION, arb_params::default_file, ARB_ERROR::deliver(), destroy(), DI_create_matrix_variables(), DI_create_matrix_window(), DI_timer(), do_conversion(), dot(), dumpDepths(), e4_assert, ed4_bind_mainDB_awar_callbacks(), ed4_create_all_awars(), ED4_G_SEQUENCES, ED4_pfold_set_SAI(), ED4_postcbcb(), ED4_root::edk, CharPtrArray::empty(), error(), estimate_loops(), execute(), GBT_config::exists(), EXIT_FAILURE, EXIT_SUCCESS, ARB_ERROR::expect_no_error(), Helpfile::extractInternalLinks(), fail_if_error(), FALSE, fflush(), fflush_all(), arb_params::field, arb_params::field_default, ALI_TLIST< T >::first(), ED4_root::first_window, fontsize, fputc(), fputs(), free_arb_params(), freeExcludedSymParts(), freeRequiredSymParts(), freeTree(), freextip, GB_abort_transaction(), GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_await_error(), GB_begin_transaction(), GB_close(), GB_commit_transaction(), GB_copy_dropMarksAndTempstate(), GB_create_container(), GB_delete(), GB_end_transaction(), GB_FIND, GB_get_supported_compression_flags(), GB_get_usable_memory(), GB_install_pid(), GB_IO_error(), arb_prm_struct::gb_main, gb_main, GB_open(), GB_pop_transaction(), GB_print_error(), GB_push_transaction(), GB_read_file(), GB_read_string(), GB_request_undo_type(), GB_save(), GB_save_as(), GB_search(), GB_set_next_main_idx(), GB_set_verbose(), GB_size_of_file(), gb_species_data, GB_STRING, GB_time_of_file(), GB_UNDO_NONE, GB_write_string(), GBK_singlequote(), GBK_system(), GBS_chrcat(), GBS_free_hash(), GBS_global_string(), GBS_global_string_copy(), GBS_nameserver_tag(), GBS_read_arb_tcp(), GBS_readable_size(), GBS_readable_timediff(), GBS_strcat(), GBS_strclose(), GBS_string_eval(), GBS_stropen(), GBT_compress_sequence_tree2(), GBT_count_leafs(), GBT_create(), GBT_find_SAI(), GBT_find_sequence(), GBT_first_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_alignment_names(), GBT_get_default_alignment(), GBT_get_species_count(), GBT_get_species_data(), GBT_message(), GBT_next_species(), GBT_open(), GBT_read_string(), GBT_set_default_alignment(), GBT_write_string(), GENOM_ALIGNMENT, Convaln_exception::get_code(), GBT_config::get_definition(), AP_main::get_gb_main(), PH_root::get_gb_main(), Convaln_exception::get_msg(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), get_species(), getArbFilter(), getdecl(), getinput(), gp_assert, h2x_assert, ED4_WinContext::have_context(), HEIGHT, ED4_root::helix, help(), ALI_GLOBAL::init(), BI_helix::init(), ED4_root::init_alignment(), ED4_objspec::init_object_specs(), initBaseLookups(), ali_prealigner_approx_element::ins_marker, insert_genes_of_organism(), ALI_TLIST< T >::is_empty(), ALI_PROFILE::length(), linenum, linkxarray(), long, LPR_COMMAND, LPR_OPT, lpr_opt, AW_root::main_loop(), make_alnum(), EDB_root_bact::make_string(), EDB_root_bact::make_top_bot_string(), makeUserRates(), ali_prealigner_approx_element::map, MARGIN, ALI_GLOBAL::mark_species_flag, MAX_TRY, MAXNODES, GBT_config::MIDDLE_AREA, MIO, MissingArgumentFor(), Test::name, NAME_SERVER_SLEEP, NAME_SERVER_TIMEOUT, names, need_macro_ability(), NEWBUFSIZ, tree::nodep, NUL, NULp, old_pages, AP_main::open(), PH_root::open(), open_aisc_server(), openArb(), arb_prm_struct::out, arb_prm_struct::outname, page_height, page_width, pages, pars_create_all_awars(), NtreeCommandLine::parse(), parseCommandLine(), PH_display::ph_display, PH_used_windows::phylo_main_window, PIXELS_INCH, ALI_GLOBAL::preali_context, ALI_SUB_SOLUTION::print(), print_file(), NtreeCommandLine::print_help(), print_man(), print_prologue(), arb_prm_struct::prmanz, ALI_GLOBAL::prof_context, ED4_root::protstruct, ED4_root::protstruct_len, PT_exit(), PT_init_psg(), ConstStrArray::put(), ALI_ARBDB::put_SAI(), ALI_ARBDB::put_sequence_string(), PV_CallBackFunction(), PARS_commands::quit, Helpfile::readHelp(), readSimCfg(), result, RETRY_SLEEP, run_command(), run_server(), run_test(), runtests(), save_tree_as_newick(), saveArb(), SEC, SECOND, seq, seq_colors_changed_cb(), ALI_MAP::sequence(), ALI_PROFILE::sequence(), ALI_PREALIGNER::sequence(), ED4_root::sequence_colors, ALI_PROFILE::sequence_length(), ALI_PREALIGNER::sequence_without_inserts(), AN_gl_struct::server_communication, server_load(), server_save(), set_empty_addids(), set_global_option(), set_positional_option(), setupnodex(), sheets, sheetside, AW_window::show(), show_error_and_warnings(), show_help(), show_usage(), show_warnings(), shutdown_macro_recording(), ALI_PREALIGNER::solution(), ALI_GLOBAL::species_name, splitRNS(), ED4_root::st_ml, startTime, startup_gui(), startup_sequence_cb(), STAT_create_ST_ML(), ALI_SEQUENCE::string(), string(), string_comparator(), ta, arb_params::tcp, test, timeSteps, GBT_config::TOP_AREA, topo, unattached_message(), UNCOVERED, UnknownOption(), usage(), Usage(), usedxtip, Version(), NtreeCommandLine::wants_help(), wantSTDIN(), warning(), weight, WIDTH, AW_root::window_hide(), PH_used_windows::windowList, AW_awar::write_string(), writeToArb(), and Helpfile::writeXML().

Referenced by main().

int main ( int  argc,
char **  argv 
)

Definition at line 6 of file arb_main.cxx.

References ARB_main(), and start_of_main().