#include "probe.h"
#include <PT_server_prototypes.h>
#include <struct_man.h>
#include "pt_split.h"
#include "probe_tree.h"
#include <arb_strbuf.h>
#include <arb_defs.h>
#include <arb_sort.h>
#include <cctype>
#include <map>

Include dependency graph for PT_match.cxx:

Classes
class	Mismatches

class	MatchRequest

struct	format_props

Functions
void	aisc_link (dll_public dll, PT_probematch match)

static int	pt_sort_compare_match (const void PT_probematch_ptr1, const void PT_probematch_ptr2, void *)

static void	pt_sort_match_list (PT_local *locs)

char *	create_reversed_probe (char *probe, int len)

CONSTEXPR_INLINE double	calc_position_wmis (int pos, int seq_len, double y1, double y2)

static void	pt_build_pos_to_weight (PT_MATCH_TYPE type, const char *sequence)

int	probe_match (PT_local *locs, aisc_string probestring)

void	set_max (const char *str, int &curr_max)

static format_props	detect_format_props (const PT_local *locs, bool show_gpos)

void	cat_internal (GBS_strstruct &memfile, int len, const char *text, int width, char spacer, bool align_left)

void	cat_spaced_left (GBS_strstruct &memfile, const char *text, int width)

void	cat_spaced_right (GBS_strstruct &memfile, const char *text, int width)

void	cat_dashed_left (GBS_strstruct &memfile, const char *text, int width)

void	cat_dashed_right (GBS_strstruct &memfile, const char *text, int width)

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)

static const char *	get_match_info_formatted (PT_probematch *ml, const format_props &format)

static const char *	get_match_hinfo_formatted (PT_probematch *ml, const format_props &format)

static void	gene_rel_2_abs (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 *)

Variables
static std::map< PT_local *, Splits >	splits_for_match_overlay

Function Documentation

void aisc_link	(	dll_public *	dll,
		PT_probematch *	match
	)

inline

Definition at line 25 of file PT_match.cxx.

Referenced by MatchRequest::add_hit(), and pt_sort_match_list().

static int pt_sort_compare_match	(	const void *	PT_probematch_ptr1,
		const void *	PT_probematch_ptr2,
		void *
	)

static

Definition at line 285 of file PT_match.cxx.

References cmp, psg, PT_MATCH_TYPE_INTEGER, and probe_struct_global::sort_by.

Referenced by pt_sort_match_list().

static void pt_sort_match_list ( PT_local * locs )

static

Definition at line 312 of file PT_match.cxx.

References aisc_link(), aisc_unlink(), ARB_calloc(), GB_sort(), NULp, psg, pt_sort_compare_match(), and probe_struct_global::sort_by.

Referenced by probe_match().

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().

CONSTEXPR_INLINE double calc_position_wmis	(	int	pos,
		int	seq_len,
		double	y1,
		double	y2
	)

Definition at line 342 of file PT_match.cxx.

Referenced by pt_build_pos_to_weight().

static void pt_build_pos_to_weight	(	PT_MATCH_TYPE	type,
		const char *	sequence
	)

static

Definition at line 346 of file PT_match.cxx.

References calc_position_wmis(), probe_struct_global::pos_to_weight, psg, and PT_MATCH_TYPE_WEIGHTED_PLUS_POS.

Referenced by get_match_overlay(), 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.

void set_max	(	const char *	str,
		int &	curr_max
	)

inline

Definition at line 454 of file PT_match.cxx.

Referenced by detect_format_props().

static format_props detect_format_props	(	const PT_local *	locs,
		bool	show_gpos
	)

static

Definition at line 461 of file PT_match.cxx.

References probe_struct_global::ecoli, format_props::ecoli_width, format(), GBS_global_string(), gene_flag, format_props::gene_or_full_width, format_props::gpos_width, info2bio(), format_props::name_width, format_props::pos_width, psg, PT_abs_2_ecoli_rel(), set_max(), format_props::show_ecoli, format_props::show_gpos, format_props::show_mismatches, virt_fullname(), and virt_name().

Referenced by match_string().

void cat_internal	(	GBS_strstruct &	memfile,
		int	len,
		const char *	text,
		int	width,
		char	spacer,
		bool	align_left
	)

inline

Definition at line 487 of file PT_match.cxx.

References GBS_strstruct::cat(), pt_assert, and GBS_strstruct::put().

Referenced by cat_dashed_left(), cat_dashed_right(), cat_spaced_left(), and cat_spaced_right().

void cat_spaced_left	(	GBS_strstruct &	memfile,
		const char *	text,
		int	width
	)

inline

Definition at line 516 of file PT_match.cxx.

References cat_internal().

Referenced by get_match_info_formatted().

void cat_spaced_right	(	GBS_strstruct &	memfile,
		const char *	text,
		int	width
	)

inline

Definition at line 517 of file PT_match.cxx.

References cat_internal().

Referenced by get_match_info_formatted().

void cat_dashed_left	(	GBS_strstruct &	memfile,
		const char *	text,
		int	width
	)

inline

Definition at line 518 of file PT_match.cxx.

References cat_internal().

Referenced by get_match_hinfo_formatted().

void cat_dashed_right	(	GBS_strstruct &	memfile,
		const char *	text,
		int	width
	)

inline

Definition at line 519 of file PT_match.cxx.

References cat_internal().

Referenced by get_match_hinfo_formatted().

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.

static const char* get_match_info_formatted	(	PT_probematch *	ml,
		const format_props &	format
	)

static

static const char* get_match_hinfo_formatted	(	PT_probematch *	ml,
		const format_props &	format
	)

static

static void gene_rel_2_abs ( PT_probematch * ml )

static

after gene probe match all positions are gene-relative. gene_rel_2_abs() makes them genome-absolute.

Definition at line 685 of file PT_match.cxx.

References probe_struct_global::data, probe_struct_global::gb_main, probe_input_data::get_geneabspos(), psg, pt_assert, and ta.

Referenced by match_string().

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.

Variable Documentation

std::map<PT_local*,Splits> splits_for_match_overlay

static

Definition at line 362 of file PT_match.cxx.

Classes

Functions

Variables

Function Documentation

Variable Documentation