ARB: PROBE/PT_io.cxx File Reference

ARB

PROBE

#include "probe.h"
#include "pt_prototypes.h"
#include "PT_compress.h"
#include <arbdbt.h>
#include <BI_basepos.hxx>
#include <arb_progress.h>
#include <arb_file.h>

Include dependency graph for PT_io.cxx:

Go to the source code of this file.

Functions
int	compress_data (char *probestring)

ARB_ERROR	probe_read_data_base (const char *name, bool readOnly)

size_t	probe_compress_sequence (char *seq, size_t seqsize)

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

GBDATA *	expect_entry (GBDATA gb_species, const char entry_name)

GB_ERROR	PT_prepare_species_sequence (GBDATA gb_species, const char alignment_name, bool &data_missing, PT_compressed &compressed)

GB_ERROR	PT_prepare_data (GBDATA *gb_main)

GB_ERROR	PT_init_input_data ()

void	PT_build_species_hash ()

long	PT_abs_2_ecoli_rel (long pos)

Function Documentation

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().

GBDATA* expect_entry	(	GBDATA *	gb_species,
		const char *	entry_name
	)

inline

Definition at line 121 of file PT_io.cxx.

References GB_entry(), GB_export_errorf(), and GBT_get_name_or_description().

Referenced by probe_input_data::init().

GB_ERROR PT_prepare_species_sequence	(	GBDATA *	gb_species,
		const char *	alignment_name,
		bool &	data_missing,
		PT_compressed &	compressed
	)

inline

Definition at line 148 of file PT_io.cxx.

References PT_compressed::createFrom(), error(), GB_await_error(), GB_BYTES, GB_checksum(), GB_create(), GB_delete(), GB_entry(), GB_INT, GB_INTS, GB_read_char_pntr(), GB_read_string_count(), GB_write_bytes(), GB_write_int(), GB_write_ints(), GBS_global_string(), GBT_get_name_or_description(), PT_compressed::get_allowed_size(), PT_compressed::get_offsets(), PT_compressed::get_seq(), PT_compressed::get_size(), NULp, and seq.

Referenced by PT_prepare_data().

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 )

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().