ARB
Macros | Functions | Variables
PT_main.cxx File Reference
#include "probe.h"
#include <PT_server_prototypes.h>
#include "pt_prototypes.h"
#include "PT_mem.h"
#include <BI_basepos.hxx>
#include <arbdbt.h>
#include <arb_file.h>
#include <arb_defs.h>
#include <arb_sleep.h>
#include <servercntrl.h>
#include <server.h>
#include <client.h>
#include <struct_man.h>
#include <ut_valgrinded.h>
#include <ptclean.h>
#include <unistd.h>
#include <sys/stat.h>
#include <time.h>
Include dependency graph for PT_main.cxx:

Go to the source code of this file.

Macros

#define MAX_TRY   10
 
#define TIME_OUT   1000*60*60*24
 
#define MAX_INAME_LEN   30
 
#define MAX_ONAME_LEN   30
 
#define MAX_GNAME_LEN   1024
 

Functions

void PT_init_psg ()
 
void PT_exit_psg ()
 
static void PT_exit ()
 
static ARB_ERROR pt_init_main_struct (PT_main *, const char *filename)
 
int server_shutdown (PT_main *, aisc_string passwd)
 
int broadcast (PT_main *main, int)
 
const char * find_sep (const char *str, char sep)
 
bool copy_to_buf (const char *start, const char *behindEnd, int MAXLEN, char *destBuf)
 
static __ATTR__USERESULT ARB_ERROR parse_names_into_gene_struct (const char *map_str, gene_struct_list &listOfGenes)
 
static GB_ERROR PT_init_map ()
 
static __ATTR__USERESULT ARB_ERROR start_pt_server (const char *socket_name, const char *arbdb_name, const char *pt_name, const char *exename)
 
static int get_DB_state (GBDATA *gb_main, ARB_ERROR &error)
 
static GB_ERROR set_DB_state (GBDATA *gb_main, int dbstate)
 
static __ATTR__USERESULT ARB_ERROR run_command (const char *exename, const char *command, const arb_params *params)
 
int ARB_main (int argc, char *argv[])
 

Variables

struct probe_struct_global psg
 
int gene_flag = 0
 
PT_main * aisc_main
 
static time_t startTime
 
static gene_struct_list all_gene_structs
 
gene_struct_index_arb gene_struct_arb2internal
 
gene_struct_index_internal gene_struct_internal2arb
 
Memory MEM
 
static bool psg_initialized = false
 

Macro Definition Documentation

#define MAX_TRY   10

Definition at line 33 of file PT_main.cxx.

#define TIME_OUT   1000*60*60*24

Definition at line 34 of file PT_main.cxx.

Referenced by start_pt_server().

#define MAX_INAME_LEN   30

Referenced by parse_names_into_gene_struct().

#define MAX_ONAME_LEN   30

Referenced by parse_names_into_gene_struct().

#define MAX_GNAME_LEN   1024

Referenced by parse_names_into_gene_struct().

Function Documentation

void PT_init_psg ( void  )

Definition at line 131 of file PT_main.cxx.

References psg, psg_initialized, pt_assert, and probe_struct_global::setup().

Referenced by ARB_main().

void PT_exit_psg ( void  )

Definition at line 137 of file PT_main.cxx.

References probe_struct_global::cleanup(), Memory::clear(), psg, psg_initialized, and pt_assert.

Referenced by PT_exit().

static void PT_exit ( )
static

Definition at line 146 of file PT_main.cxx.

References aisc_main, psg_initialized, and PT_exit_psg().

Referenced by ARB_main(), and server_shutdown().

static ARB_ERROR pt_init_main_struct ( PT_main *  ,
const char *  filename 
)
static

Definition at line 155 of file PT_main.cxx.

References probe_struct_global::alignment_name, error(), GB_incur_error_if(), probe_struct_global::gb_main, GBT_get_default_alignment(), probe_read_data_base(), psg, PT_build_species_hash(), PT_init_input_data(), and ta.

Referenced by run_command(), and start_pt_server().

int server_shutdown ( PT_main *  ,
aisc_string  passwd 
)

Definition at line 171 of file PT_main.cxx.

References aisc_broadcast(), aisc_server_shutdown(), probe_struct_global::com_so, EXIT_SUCCESS, fflush_all(), psg, and PT_exit().

int broadcast ( PT_main *  main,
int   
)

Definition at line 190 of file PT_main.cxx.

References aisc_broadcast(), probe_struct_global::com_so, and psg.

const char* find_sep ( const char *  str,
char  sep 
)
inline

Definition at line 198 of file PT_main.cxx.

Referenced by parse_names_into_gene_struct().

bool copy_to_buf ( const char *  start,
const char *  behindEnd,
int  MAXLEN,
char *  destBuf 
)
inline

Definition at line 212 of file PT_main.cxx.

References start.

Referenced by parse_names_into_gene_struct().

static __ATTR__USERESULT ARB_ERROR parse_names_into_gene_struct ( const char *  map_str,
gene_struct_list &  listOfGenes 
)
static

Definition at line 222 of file PT_main.cxx.

References copy_to_buf(), ARB_ERROR::deliver(), find_sep(), GBS_global_string(), GBS_unescape_string(), MAX_GNAME_LEN, MAX_INAME_LEN, MAX_ONAME_LEN, NULp, and oname.

Referenced by PT_init_map().

static GB_ERROR PT_init_map ( )
static

Definition at line 265 of file PT_main.cxx.

References all_gene_structs, ARB_ERROR::deliver(), error(), GB_end_transaction(), GB_entry(), probe_struct_global::gb_main, GB_push_transaction(), GB_read_char_pntr(), GBS_global_string(), gene_struct_arb2internal, gene_struct_internal2arb, parse_names_into_gene_struct(), and psg.

Referenced by start_pt_server().

static __ATTR__USERESULT ARB_ERROR start_pt_server ( const char *  socket_name,
const char *  arbdb_name,
const char *  pt_name,
const char *  exename 
)
static

Definition at line 309 of file PT_main.cxx.

References aisc_accept_calls(), aisc_main, aisc_server_shutdown(), ARB_sleep(), probe_struct_global::com_so, ARB_ERROR::deliver(), enter_stage_2_load_tree(), error(), fflush_all(), fputs(), GB_IO_error(), GB_size_of_file(), GBK_singlequote(), GBK_system(), GBS_global_string(), GBS_global_string_copy(), GBS_readable_timediff(), make_valgrinded_call, NULp, open_aisc_server(), psg, pt_init_main_struct(), PT_init_map(), PT_SERVER_VERSION, SEC, startTime, and TIME_OUT.

Referenced by run_command().

static int get_DB_state ( GBDATA *  gb_main,
ARB_ERROR &  error 
)
static

Definition at line 421 of file PT_main.cxx.

References GB_await_error(), GB_end_transaction(), GB_push_transaction(), GBT_find_or_create(), GBT_readOrCreate_int(), NULp, and pt_assert.

Referenced by run_command().

static GB_ERROR set_DB_state ( GBDATA *  gb_main,
int  dbstate 
)
static

Definition at line 439 of file PT_main.cxx.

References error(), GB_await_error(), GB_end_transaction(), GB_push_transaction(), GB_searchOrCreate_int(), GB_write_int(), GBT_find_or_create(), and NULp.

Referenced by run_command().

static __ATTR__USERESULT ARB_ERROR run_command ( const char *  exename,
const char *  command,
const arb_params *  params 
)
static

Definition at line 451 of file PT_main.cxx.

References aisc_close(), AISC_MAGIC_NUMBER, aisc_main, aisc_nput(), aisc_open(), ARB_strdup(), cleanup_ptserver_database(), arb_params::db_server, ARB_ERROR::deliver(), enter_stage_1_build_tree(), enter_stage_2_load_tree(), error(), fputs(), GB_await_error(), GB_is_regularfile(), probe_struct_global::gb_main, GB_mapfile(), GB_no_transaction(), GB_save_as(), GB_size_of_file(), GB_supports_mapfile(), GBK_singlequote(), GBK_system(), GBS_add_ptserver_logentry(), GBS_global_string(), GBS_global_string_copy(), GBS_read_arb_tcp(), get_DB_state(), probe_struct_global::link, probe_struct_global::main, NULp, ARB_ERROR::preserve(), probe_read_data_base(), psg, pt_assert, PT_dump_tree_statistics(), pt_init_main_struct(), PT_prepare_data(), set_DB_state(), start, start_pt_server(), and arb_params::tcp.

Referenced by ARB_main().

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

Definition at line 607 of file PT_main.cxx.

References aisc_core_on_error, aisc_main, ARB_strdup(), arb_trace_argv(), command, arb_params::db_server, ARB_ERROR::deliver(), error(), EXIT_FAILURE, EXIT_SUCCESS, fflush(), fflush_all(), free_arb_params(), GB_install_pid(), GBS_readable_timediff(), NULp, PT_exit(), PT_init_psg(), run_command(), and startTime.

Variable Documentation

struct probe_struct_global psg

Definition at line 36 of file PT_main.cxx.

Referenced by MatchRequest::add_hit(), broadcast(), FamilyStat::calc_rel_matches(), OutgroupMatcher::calculate_outgroup_matches(), count_mishits_for_all(), Mismatches::count_weighted(), detect_format_props(), PT_statistic::dump(), enter_stage_1_build_tree(), enter_stage_2_load_tree(), find_family(), findLeftmostProbe(), gene_rel_2_abs(), DesignTargets::generate(), get_match_acc(), get_match_overlay(), get_match_start(), get_match_stop(), AbsLoc::get_pid(), AbsLoc::has_valid_name(), make_PT_family_list(), MP_all_species_string(), MP_count_all_species(), ptnd_chain_count_mishits::operator()(), probe_match(), probe_read_data_base(), PT_abs_2_ecoli_rel(), pt_build_pos_to_weight(), PT_build_species_hash(), PT_dump_POS_TREE_to_file(), PT_dump_tree_statistics(), PT_exit_psg(), PT_find_exProb(), PT_init_cache_sizes(), PT_init_input_data(), pt_init_main_struct(), PT_init_map(), PT_init_psg(), pt_sort_compare_match(), pt_sort_match_list(), PTD_read_leafs_from_disk(), PTD_write_node_to_disk(), ptpd_read_names(), remove_tprobes_with_too_many_mishits(), run_command(), server_shutdown(), start_pt_server(), virt_fullname(), and virt_name().

int gene_flag = 0

Definition at line 39 of file PT_main.cxx.

Referenced by detect_format_props(), get_match_hinfo_formatted(), match_string(), probe_match_event(), PT_start_design(), ptpd_read_names(), virt_fullname(), and virt_name().

PT_main* aisc_main

Definition at line 41 of file PT_main.cxx.

Referenced by ARB_main(), names_destroy_locs(), PT_exit(), run_command(), and start_pt_server().

time_t startTime
static

Definition at line 43 of file PT_main.cxx.

Referenced by ARB_main(), and start_pt_server().

gene_struct_list all_gene_structs
static

Definition at line 45 of file PT_main.cxx.

Referenced by PT_init_map().

gene_struct_index_arb gene_struct_arb2internal

Definition at line 46 of file PT_main.cxx.

Referenced by get_gene_struct_by_arb_species_gene_name(), and PT_init_map().

gene_struct_index_internal gene_struct_internal2arb

Definition at line 47 of file PT_main.cxx.

Referenced by get_gene_struct_by_internal_gene_name(), and PT_init_map().

Memory MEM

Definition at line 128 of file PT_main.cxx.

Referenced by probe_struct_global::enter_stage(), PT_add_to_chain(), PT_change_leaf_to_node(), PT_create_leaf(), PT_leaf_to_chain(), PTD_delete_saved_node(), PTD_write_chain_to_disk(), PTD_write_node_to_disk(), and ChainEntryBuffer::~ChainEntryBuffer().

bool psg_initialized = false
static

Definition at line 130 of file PT_main.cxx.

Referenced by PT_exit(), PT_exit_psg(), and PT_init_psg().

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