pt_prototypes.h File Reference

#include <attributes.h>

Include dependency graph for pt_prototypes.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Functions
long	PTD_save_lower_tree (FILE *out, POS_TREE1 *node, long pos, ARB_ERROR &error)
long	PTD_save_upper_tree (FILE *out, POS_TREE1 *&node, long pos, long &node_pos, ARB_ERROR &error)
ARB_ERROR	enter_stage_1_build_tree (PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT
ARB_ERROR	enter_stage_2_load_tree (PT_main *, const char *tname) __ATTR__USERESULT
void	PT_dump_tree_statistics (const char *indexfilename)
template<typename PT >
void	PT_dump_POS_TREE_recursive (PT *pt, const char *prefix, FILE *out)
void	PT_dump_POS_TREE (POS_TREE1 *IF_DEBUG(node), FILE *IF_DEBUG(out))
int	PT_index_dump (const PT_main *main)
void	pt_export_error (PT_local *locs, const char *error)
void	pt_export_error_if (PT_local *locs, ARB_ERROR &error)
const char *	virt_name (const PT_probematch *ml)
const char *	virt_fullname (const PT_probematch *ml)
char *	ptpd_read_names (PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR &error)
bytestring *	PT_unknown_names (const PT_pdc *pdc)
int	find_family (PT_family *ffinder, bytestring *species)
int	PT_find_exProb (PT_exProb *pep, int dummy_1x)
int	compress_data (char *probestring)
ARB_ERROR	probe_read_data_base (const char *name, bool readOnly) __ATTR__USERESULT
size_t	probe_compress_sequence (char *seq, size_t seqsize)
char *	readable_probe (const char *compressed_probe, size_t len, char T_or_U)
GB_ERROR	PT_prepare_data (GBDATA *gb_main)
GB_ERROR	PT_init_input_data (void)
void	PT_build_species_hash (void)
long	PT_abs_2_ecoli_rel (long pos)
void	PT_init_psg (void)
void	PT_exit_psg (void)
int	server_shutdown (PT_main *, aisc_string passwd)
int	broadcast (PT_main *main, int dummy_1x)
int	ARB_main (int argc, char *argv[])
char *	create_reversed_probe (char *probe, int len)
int	probe_match (PT_local *locs, aisc_string probestring)
const char *	get_match_overlay (const PT_probematch *ml)
const char *	get_match_acc (const PT_probematch *ml)
int	get_match_start (const PT_probematch *ml)
int	get_match_stop (const PT_probematch *ml)
bytestring *	match_string (const PT_local *locs)
bytestring *	MP_match_string (const PT_local *locs)
bytestring *	MP_all_species_string (const PT_local *)
int	MP_count_all_species (const PT_local *)
int	pt_init_bond_matrix (PT_local *THIS)
char *	get_design_info (const PT_tprobes *tprobe)
char *	get_design_hinfo (const PT_pdc *pdc)
int	PT_start_design (PT_pdc *pdc, int dummy_1x)
template<typename CHAINITER >
bool	PT_chain_has_valid_entries (const typename CHAINITER::POS_TREE_TYPE *const node)
void	PT_init_cache_sizes (Stage stage)
void	PT_add_to_chain (POS_TREE1 *node, const DataLoc &loc)
POS_TREE1 *	PT_change_leaf_to_node (POS_TREE1 *node)
POS_TREE1 *	PT_leaf_to_chain (POS_TREE1 *node)
POS_TREE1 *	PT_create_leaf (POS_TREE1 **pfather, PT_base base, const DataLoc &loc)
void	PTD_put_longlong (FILE *out, ULONG i)
void	PTD_put_int (FILE *out, ULONG i)
void	PTD_put_short (FILE *out, ULONG i)
void	PTD_put_byte (FILE *out, ULONG i)
void	PTD_debug_nodes (void)
void	PTD_delete_saved_node (POS_TREE1 *&node)
long	PTD_write_leafs_to_disk (FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR &error)
ARB_ERROR	PTD_read_leafs_from_disk (const char *fname, POS_TREE2 *&root_ptr) __ATTR__USERESULT
const char *	get_blocksize_description (int blocksize)
template<typename T >
int	PT_forwhole_chain (POS_TREE1 *node, T &func)
template<typename T >
int	PT_forwhole_chain (POS_TREE2 *node, T &func)

Function Documentation

long PTD_save_lower_tree	(	FILE *	out,
		POS_TREE1 *	node,
		long	pos,
		ARB_ERROR &	error
	)

Definition at line 237 of file PT_buildtree.cxx.

References check_tree_was_saved(), and save_lower_subtree().

Referenced by enter_stage_1_build_tree().

long PTD_save_upper_tree	(	FILE *	out,
		POS_TREE1 *&	node,
		long	pos,
		long &	node_pos,
		ARB_ERROR &	error
	)

Definition at line 243 of file PT_buildtree.cxx.

References check_tree_was_saved(), has_unsaved_sons(), pt_assert, PTD_delete_saved_node(), and save_upper_tree().

Referenced by enter_stage_1_build_tree().

ARB_ERROR enter_stage_1_build_tree	(	PT_main *	,
		const char *	tname,
		ULONG	ARM_size_kb
	)

Definition at line 395 of file PT_buildtree.cxx.

References ARB_strdup(), build_pos_tree(), probe_struct_global::char_count, Partition::contains(), probe_statistic_struct::cut_offs, probe_struct_global::data, probe_struct_global::data_count, decide_passes_to_use(), arb_progress::done(), Partition::done(), probe_struct_global::enter_stage(), error(), Partition::estimate_max_probes_for_any_pass(), fflush_all(), fputc(), fputs(), GB_abort_transaction(), GB_await_error(), GB_begin_transaction(), GB_commit_transaction(), GB_get_usable_memory(), GB_getenv(), probe_struct_global::gb_main, GB_move_file(), GB_set_mode_of_file(), GB_size_of_file(), GB_unlink(), GB_warning(), GB_warningf(), GBK_system(), GBK_terminate(), GBS_add_ptserver_logentry(), GBS_global_string(), GBS_global_string_copy(), GBS_readable_size(), probe_input_data::get_abspos(), probe_input_data::get_dataPtr(), probe_input_data::get_size(), Partition::next(), NULp, Partition::number_of_passes(), probe_input_data::preload_rel2abs(), psg, pt_assert, PT_change_leaf_to_node(), PT_create_leaf(), PT_init_cache_sizes(), PT_N, PT_SERVER_MAGIC, PT_SERVER_VERSION, PTD_debug_nodes(), PTD_put_byte(), PTD_put_int(), PTD_put_longlong(), PTD_put_short(), PTD_save_lower_tree(), PTD_save_upper_tree(), PTSERVER_BIN_MB, seq, DataLoc::set_position(), STAGE1, and probe_struct_global::stat.

Referenced by run_command().

ARB_ERROR enter_stage_2_load_tree	(	PT_main *	,
		const char *	tname
	)

Definition at line 590 of file PT_buildtree.cxx.

References probe_struct_global::enter_stage(), error(), GB_IO_error(), GB_size_of_file(), GBS_readable_size(), psg, PT_init_cache_sizes(), PTD_read_leafs_from_disk(), STAGE2, and probe_struct_global::TREE_ROOT2().

Referenced by run_command(), and start_pt_server().

void PT_dump_tree_statistics

(

const char *

indexfilename

)

Definition at line 326 of file PT_debug.cxx.

References PT_statistic::analyse(), PT_statistic::dump(), GB_size_of_file(), psg, and probe_struct_global::TREE_ROOT2().

Referenced by run_command().

template<typename PT >

void PT_dump_POS_TREE_recursive	(	PT *	pt,
		const char *	prefix,
		FILE *	out
	)

Definition at line 369 of file PT_debug.cxx.

References base_2_readable(), dump_POS_TREE_special(), GBS_global_string_copy(), PT_BASES, PT_dump_POS_TREE_recursive(), PT_forwhole_chain(), and PT_QU.

Referenced by check_tree_was_saved(), PT_dump_POS_TREE_recursive(), and PT_dump_POS_TREE_to_file().

void PT_dump_POS_TREE	(	POS_TREE1 *	IF_DEBUGnode,
		FILE *	IF_DEBUGout
	)

Definition at line 399 of file PT_debug.cxx.

References fflush_all(), fputs(), AbsLoc::get_abs_pos(), AbsLoc::get_name(), DataLoc::get_rel_pos(), PT1_CHAIN, PT1_LEAF, PT1_NODE, PT1_SAVED, PT1_UNDEF, PT_BASES, PT_forwhole_chain(), and PT_read_son().

int PT_index_dump

(

const PT_main *

main

)

Definition at line 450 of file PT_debug.cxx.

References PT_dump_POS_TREE_to_file().

void pt_export_error	(	PT_local *	locs,
		const char *	error
	)

Definition at line 19 of file PT_etc.cxx.

Referenced by probe_match(), and pt_export_error_if().

void pt_export_error_if	(	PT_local *	locs,
		ARB_ERROR &	error
	)

Definition at line 22 of file PT_etc.cxx.

References ARB_ERROR::deliver(), ARB_ERROR::expect_no_error(), and pt_export_error().

Referenced by PT_start_design().

const char* virt_name

(

const PT_probematch *

ml

)

Definition at line 57 of file PT_etc.cxx.

References probe_struct_global::data, gene_flag, gene_struct::get_arb_species_name(), get_gene_struct_by_internal_gene_name(), probe_input_data::get_shortname(), psg, and pt_assert.

Referenced by detect_format_props(), get_match_info_formatted(), match_string(), and MP_match_string().

const char* virt_fullname

(

const PT_probematch *

ml

)

Definition at line 69 of file PT_etc.cxx.

References probe_struct_global::data, gene_flag, gene_struct::get_arb_gene_name(), probe_input_data::get_fullname(), get_gene_struct_by_internal_gene_name(), probe_input_data::get_shortname(), and psg.

Referenced by detect_format_props(), and get_match_info_formatted().

char* ptpd_read_names	(	PT_local *	locs,
		const char *	names_list,
		const char *	checksums,
		ARB_ERROR &	error
	)

Definition at line 120 of file PT_etc.cxx.

References arb2internal_name(), GBS_strstruct::cat(), probe_struct_global::data, probe_struct_global::data_count, GBS_global_string(), GBS_read_hash(), gene_flag, probe_input_data::get_checksum(), get_list_part(), probe_struct_global::namehash, NULp, psg, pt_assert, GBS_strstruct::put(), GBS_strstruct::release(), result, and probe_input_data::set_group_state().

Referenced by PT_start_design().

bytestring* PT_unknown_names

(

const PT_pdc *

pdc

)

Definition at line 204 of file PT_etc.cxx.

References locs, and NULp.

int find_family	(	PT_family *	ffinder,
		bytestring *	species
	)

make sorted list of family members of species

Definition at line 389 of file PT_family.cxx.

References OligoRegistry::add(), OligoRegistry::begin(), FamilyStat::calc_rel_matches(), complement_probe(), contains_ambiguities(), bytestring::data, probe_struct_global::data_count, OligoRegistry::end(), FF_COMPLEMENT, FF_FORWARD, FF_REVERSE, FF_REVERSE_COMPLEMENT, FamilyStat::limit_hits_for_next_traversal(), make_PT_family_list(), PT_Traversal::mark_matching(), probe_compress_sequence(), psg, PT_A, PT_Traversal::restrictMatchesToRegion(), reverse_probe(), s, seq, bytestring::size, probe_struct_global::TREE_ROOT2(), and PT_Traversal::unrestrictMatchesToRegion().

int PT_find_exProb	(	PT_exProb *	pep,
		int	dummy_1x
	)

Definition at line 108 of file PT_findEx.cxx.

References GBS_strstruct::cat(), compress_data(), findLeftmostProbe(), findNextProbe(), psg, pt_assert, GBS_strstruct::put(), arb_test::readable(), readable_probe(), GBS_strstruct::release_memfriendly(), and probe_struct_global::TREE_ROOT2().

int compress_data

(

char *

probestring

)

change a sequence with normal bases the PT_? format and delete all other signs

Definition at line 21 of file PT_io.cxx.

References PT_A, PT_C, PT_G, PT_N, PT_QU, and PT_T.

Referenced by probe_match(), and PT_find_exProb().

ARB_ERROR probe_read_data_base	(	const char *	name,
		bool	readOnly
	)

Definition at line 50 of file PT_io.cxx.

References error(), GB_await_error(), GB_begin_transaction(), GB_end_transaction(), GB_is_writeablefile(), gb_main, probe_struct_global::gb_main, GB_open(), GB_set_verbose(), probe_struct_global::gb_shell, GBS_global_string(), and psg.

Referenced by pt_init_main_struct(), and run_command().

size_t probe_compress_sequence	(	char *	seq,
		size_t	seqsize
	)

Definition at line 78 of file PT_io.cxx.

References PT_compressed::createFrom(), PT_compressed::get_seq(), PT_compressed::get_size(), and pt_assert.

Referenced by find_family(), and PT_start_design().

char* readable_probe	(	const char *	compressed_probe,
		size_t	len,
		char	T_or_U
	)

Definition at line 91 of file PT_io.cxx.

References ARB_alloc(), NULp, PT_A, PT_B_UNDEF, PT_C, PT_G, PT_N, PT_QU, PT_T, result, safeCharIndex(), SmartMallocPtr, and tab().

Referenced by ProbeIterator::dump(), and PT_find_exProb().

GB_ERROR PT_prepare_data

(

GBDATA *

gb_main

)

Definition at line 203 of file PT_io.cxx.

References arb_progress::done(), error(), fflush_all(), GB_await_error(), GB_begin_transaction(), GB_delete(), GB_end_transaction(), GB_FIND, GB_number_of_subentries(), GB_search(), gb_species_data, GB_SYSTEM_FOLDER, GBS_global_string_copy(), GBT_first_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_default_alignment(), GBT_get_species_data(), GBT_next_species(), arb_progress::inc(), pt_assert, and PT_prepare_species_sequence().

Referenced by run_command().

GB_ERROR PT_init_input_data

(

void

)

Definition at line 269 of file PT_io.cxx.

References probe_struct_global::alignment_name, probe_struct_global::data, probe_struct_global::data_count, arb_progress::done(), probe_struct_global::ecoli, error(), fflush_all(), GB_begin_transaction(), GB_commit_transaction(), probe_struct_global::gb_main, GB_number_of_subentries(), GB_read_string(), gb_species_data, GBT_find_SAI_rel_SAI_data(), GBT_find_sequence(), GBT_first_species_rel_species_data(), GBT_get_default_ref(), GBT_get_SAI_data(), GBT_get_species_data(), GBT_next_species(), arb_progress::inc(), probe_input_data::init(), NULp, and psg.

Referenced by pt_init_main_struct().

void PT_build_species_hash

(

void

)

Definition at line 325 of file PT_io.cxx.

References probe_struct_global::bi_ecoli, probe_struct_global::char_count, probe_struct_global::data, probe_struct_global::data_count, probe_struct_global::ecoli, GB_MIND_CASE, GBS_create_hash(), GBS_write_hash(), probe_input_data::get_shortname(), probe_input_data::get_size(), BI_ecoli_ref::init(), max, probe_struct_global::max_size, probe_struct_global::namehash, and psg.

Referenced by pt_init_main_struct().

long PT_abs_2_ecoli_rel

(

long

pos

)

Definition at line 347 of file PT_io.cxx.

References BasePosition::abs_2_rel(), probe_struct_global::bi_ecoli, probe_struct_global::ecoli, and psg.

Referenced by detect_format_props(), get_match_info_formatted(), remove_tprobes_outside_ecoli_range(), and shown_ecoli().

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().

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	dummy_1x
	)

Definition at line 190 of file PT_main.cxx.

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

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

Definition at line 1545 of file mkptypes.cxx.

char* create_reversed_probe	(	char *	probe,
		int	len
	)

reverse order of bases in a probe

Definition at line 335 of file PT_match.cxx.

References ARB_strduplen(), and reverse_probe().

Referenced by get_design_info(), and probe_match().

int probe_match	(	PT_local *	locs,
		aisc_string	probestring
	)

find out where a given probe matches

Definition at line 364 of file PT_match.cxx.

References MatchRequest::allowed_mismatches(), ARB_strdup(), MatchRequest::collect_hits_for(), complement_probe(), compress_data(), create_reversed_probe(), GBS_global_string(), locs, probe_struct_global::main_probe, MIN_PROBE_LENGTH, psg, pt_assert, pt_build_pos_to_weight(), pt_export_error(), pt_sort_match_list(), probe_struct_global::reversed, probe_struct_global::TREE_ROOT2(), and y.

const char* get_match_overlay

(

const PT_probematch *

ml

)

Definition at line 521 of file PT_match.cxx.

References base_2_readable(), Splits::check(), probe_struct_global::data, probe_input_data::get_dataPtr(), probe_input_data::get_size(), is_std_base(), locs, NULp, psg, pt_build_pos_to_weight(), result, and seq.

Referenced by get_match_info_formatted().

const char* get_match_acc

(

const PT_probematch *

ml

)

Definition at line 606 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_acc(), and psg.

int get_match_start

(

const PT_probematch *

ml

)

Definition at line 609 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_start(), and psg.

int get_match_stop

(

const PT_probematch *

ml

)

Definition at line 612 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_stop(), and psg.

bytestring* match_string

(

const PT_local *

locs

)

Create list of species where probe matches.

header^1name^1info^1name^1info....^0 (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MATCH_STRING'

Definition at line 705 of file PT_match.cxx.

References GBS_strstruct::cat(), bytestring::data, detect_format_props(), format(), gene_flag, gene_rel_2_abs(), get_match_hinfo_formatted(), get_match_info_formatted(), GBS_strstruct::get_position(), NULp, GBS_strstruct::put(), GBS_strstruct::release(), bytestring::size, and virt_name().

bytestring* MP_match_string

(

const PT_local *

locs

)

Create list of species where probe matches and append number of mismatches and weighted mismatches (used by multiprobe)

Format: "header^1name^1#mismatches^1#wmismatches^1name^1#mismatches^1#wmismatches....^0" (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MP_MATCH_STRING'

Definition at line 741 of file PT_match.cxx.

References GBS_strstruct::cat(), bytestring::data, GBS_strstruct::erase(), GBS_strstruct::get_data(), GBS_strstruct::get_position(), GBS_strstruct::nprintf(), NULp, GBS_strstruct::put(), bytestring::size, and virt_name().

bytestring* MP_all_species_string

(

const PT_local *

)

Create list of all species known to PT server

Format: ^1name^1name....^0 (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MP_ALL_SPECIES_STRING'

Definition at line 769 of file PT_match.cxx.

References GBS_strstruct::cat(), bytestring::data, probe_struct_global::data, probe_struct_global::data_count, GBS_strstruct::erase(), GBS_strstruct::get_data(), GBS_strstruct::get_position(), probe_input_data::get_shortname(), NULp, psg, GBS_strstruct::put(), and bytestring::size.

int MP_count_all_species

(

const PT_local *

)

Definition at line 792 of file PT_match.cxx.

References probe_struct_global::data_count, and psg.

int pt_init_bond_matrix

(

PT_local *

THIS

)

Definition at line 50 of file PT_new_design.cxx.

char* get_design_info

(

const PT_tprobes *

tprobe

)

Definition at line 524 of file PT_new_design.cxx.

References abs, buffer, BUFFERSIZE, complement_probe(), create_reversed_probe(), erase_formatter(), GB_give_buffer(), GB_give_buffer2(), get_formatter(), hitgroup_idx2char(), probe_2_readable(), pt_assert, pt_get_gc_content(), pt_get_temperature(), shown_apos(), shown_ecoli(), and shown_qual().

char* get_design_hinfo

(

const PT_pdc *

pdc

)

Definition at line 605 of file PT_new_design.cxx.

References ARB_strdup(), buffer, BUFFERSIZE, erase_formatter(), GB_give_buffer(), GBS_global_string_copy(), PD_formatter::get_apos_width(), PD_formatter::get_ecol_width(), get_formatter(), PD_formatter::get_grps_width(), PD_formatter::get_max_designed_len(), get_max_probelen(), PD_formatter::get_qual_width(), NULp, pt_assert, and s.

int PT_start_design	(	PT_pdc *	pdc,
		int	dummy_1x
	)

Definition at line 1426 of file PT_new_design.cxx.

References OutgroupMatcher::calculate_outgroup_matches(), clip_tprobes(), ProbeCandidates::create_tprobes(), DUMP_TPROBES, erase_formatter(), error(), fputs(), GBS_global_string(), GBT_splitNdestroy_string(), gene_flag, DesignTargets::generate(), DesignTargets::get_added_count(), DesignTargets::get_count(), DesignTargets::get_error(), get_max_probelen(), locs, MIN_DESIGN_PROBE_LENGTH, names, probe_compress_sequence(), PSM_QUALITY, PSM_SEQUENCE, pt_assert, pt_export_error_if(), ptpd_read_names(), remove_tprobes_outside_ecoli_range(), remove_tprobes_with_too_many_mishits(), seq, CharPtrArray::size(), sort_tprobes_by(), SPLIT_DROPEMPTY, tprobes_calculate_bonds(), and tprobes_sumup_perc_and_calc_quality().

template<typename CHAINITER >

bool PT_chain_has_valid_entries

(

const typename CHAINITER::POS_TREE_TYPE *const

node

)

Definition at line 51 of file PT_prefixtree.cxx.

References locs_in_chain_order(), and pt_assert.

void PT_init_cache_sizes

(

Stage

stage

)

Definition at line 126 of file PT_prefixtree.cxx.

References CACHE_SEQ_PERCENT, probe_struct_global::data_count, psg, pt_assert, probe_input_data::set_cache_sizes(), and STAGE1.

Referenced by enter_stage_1_build_tree(), and enter_stage_2_load_tree().

void PT_add_to_chain	(	POS_TREE1 *	node,
		const DataLoc &	loc
	)

Definition at line 199 of file PT_prefixtree.cxx.

References PT_short_chain_header::abspos, ChainEntryBuffer::add(), PT_long_chain_header::entries, PT_long_chain_header::entrymem, POS_TREE1::flags, Memory::get(), AbsLoc::get_abs_pos(), ChainEntryBuffer::get_lastname(), ChainEntryBuffer::get_mem(), AbsLoc::get_name(), ChainEntryBuffer::get_refabspos(), ChainEntryBuffer::get_size(), PT_long_chain_header::lastname, max, MEM, PT_long_chain_header::memsize, PT_long_chain_header::memused, PT_short_chain_header::name, NULp, pt_assert, pt_assert_stage, PTM_MIN_SIZE, Memory::put(), PT_long_chain_header::refabspos, SHORT_CHAIN_HEADER_ELEMS, SHORT_CHAIN_HEADER_FLAG_BIT, SHORT_CHAIN_HEADER_SIZE_MASK, STAGE1, and POS_TREE1::udata().

Referenced by build_pos_tree(), and PT_leaf_to_chain().

POS_TREE1* PT_change_leaf_to_node

(

POS_TREE1 *

node

)

Definition at line 278 of file PT_prefixtree.cxx.

References father, Memory::get(), POS_TREE1::get_father(), POS_TREE1::is_leaf(), MEM, PT1_EMPTY_NODE_SIZE, PT1_LEAF_SIZE, PT1_NODE, pt_assert, pt_assert_stage, PT_change_link_in_father(), Memory::put(), POS_TREE1::set_father(), POS_TREE1::set_type(), and STAGE1.

Referenced by build_pos_tree(), and enter_stage_1_build_tree().

POS_TREE1* PT_leaf_to_chain

(

POS_TREE1 *

node

)

Definition at line 293 of file PT_prefixtree.cxx.

References father, POS_TREE1::flags, Memory::get(), POS_TREE1::get_father(), POS_TREE1::is_leaf(), MEM, PT1_CHAIN, PT1_LEAF_SIZE, PT_add_to_chain(), pt_assert, pt_assert_stage, PT_change_link_in_father(), Memory::put(), POS_TREE1::set_father(), POS_TREE1::set_type(), SHORT_CHAIN_HEADER_FLAG_BIT, SHORT_CHAIN_HEADER_SIZE_MASK, and STAGE1.

Referenced by build_pos_tree(), and PT_create_leaf().

POS_TREE1* PT_create_leaf	(	POS_TREE1 **	pfather,
		PT_base	base,
		const DataLoc &	loc
	)

Definition at line 318 of file PT_prefixtree.cxx.

References father, FLAG_FREE_BITS, POS_TREE1::flags, Memory::get(), AbsLoc::get_abs_pos(), POS_TREE1::get_father(), AbsLoc::get_name(), DataLoc::get_rel_pos(), POS_TREE1::is_saved(), MEM, PT1_EMPTY_LEAF_SIZE, PT1_LEAF, PT1_NODE, PT1_NODE_SIZE, pt_assert, pt_assert_stage, PT_BASES, PT_change_link_in_father(), PT_leaf_to_chain(), PT_QU, PT_SHORT_SIZE, PT_write_int(), PT_write_pointer(), PT_write_short(), Memory::put(), POS_TREE1::set_father(), POS_TREE1::set_type(), STAGE1, and POS_TREE1::udata().

Referenced by build_pos_tree(), and enter_stage_1_build_tree().

void PTD_put_longlong	(	FILE *	out,
		ULONG	i
	)

Referenced by enter_stage_1_build_tree(), and PTD_write_node_to_disk().

void PTD_put_int	(	FILE *	out,
		ULONG	i
	)

Definition at line 433 of file PT_prefixtree.cxx.

References ASSERT_RESULT, pt_assert, PT_write_int(), SIZE, and STATIC_ASSERT().

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

void PTD_put_short	(	FILE *	out,
		ULONG	i
	)

Definition at line 444 of file PT_prefixtree.cxx.

References ASSERT_RESULT, pt_assert, PT_write_short(), and SIZE.

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

void PTD_put_byte	(	FILE *	out,
		ULONG	i
	)

Definition at line 452 of file PT_prefixtree.cxx.

References fputc(), pt_assert, and PT_write_char().

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

void PTD_debug_nodes

(

void

)

Referenced by enter_stage_1_build_tree().

void PTD_delete_saved_node

(

POS_TREE1 *&

node

)

Definition at line 619 of file PT_prefixtree.cxx.

References get_memsize_of_saved(), MEM, NULp, and Memory::put().

Referenced by PTD_save_upper_tree().

long PTD_write_leafs_to_disk	(	FILE *	out,
		POS_TREE1 *const	node,
		long	pos,
		long *	node_pos,
		ARB_ERROR &	error
	)

Definition at line 781 of file PT_prefixtree.cxx.

References error(), POS_TREE1::father, POS_TREE1::get_type(), POS_TREE1::is_saved(), PT1_CHAIN, PT1_LEAF, PT1_NODE, PT1_SAVED, PT1_UNDEF, pt_assert, pt_assert_stage, PT_BASES, PT_QU, PT_read_big(), PT_read_son(), PTD_write_chain_to_disk(), PTD_write_leafs_to_disk(), PTD_write_node_to_disk(), PTD_write_tip_to_disk(), and STAGE1.

Referenced by PTD_write_leafs_to_disk(), and write_subtree().

ARB_ERROR PTD_read_leafs_from_disk	(	const char *	fname,
		POS_TREE2 *&	root_ptr
	)

Definition at line 829 of file PT_prefixtree.cxx.

References probe_struct_global::big_db, buffer, error(), GB_await_error(), GB_map_file(), GB_size_of_file(), GBS_global_string(), main(), NULp, psg, pt_assert, pt_assert_stage, PT_read_big(), PT_read_char(), PT_read_int(), PT_read_short(), PT_SERVER_MAGIC, PT_SERVER_VERSION, STAGE2, and STATIC_ASSERT().

Referenced by enter_stage_2_load_tree().

const char* get_blocksize_description

(

int

blocksize

)

template<typename T >

int PT_forwhole_chain	(	POS_TREE1 *	node,
		T &	func
	)

Definition at line 693 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE1.

template<typename T >

int PT_forwhole_chain	(	POS_TREE2 *	node,
		T &	func
	)

Definition at line 702 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE2.