awtc_next_neighbours.hxx File Reference

#include <arbdb_base.h>
#include <arbtools.h>
#include <PT_global_defs.h>
#include <pos_range.h>
#include <cb.h>

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Classes
class	FamilyList
class	FamilyFinder
class	PT_FamilyFinder

Macros
#define	ff_assert(bed)   arb_assert(bed)
#define	AWAR_NN_BASE   "next_neighbours/"
#define	AWAR_NN_OLIGO_LEN   AWAR_NN_BASE "oligo_len"
#define	AWAR_NN_MISMATCHES   AWAR_NN_BASE "mismatches"
#define	AWAR_NN_FAST_MODE   AWAR_NN_BASE "fast_mode"
#define	AWAR_NN_REL_MATCHES   AWAR_NN_BASE "rel_matches"
#define	AWAR_NN_REL_SCALING   AWAR_NN_BASE "scaling"

Functions
void	AWTC_create_common_next_neighbour_vars (AW_root *aw_root, const RootCallback &awar_changed_cb)
void	AWTC_create_common_next_neighbour_fields (AW_window *aws, int scaler_length)

Macro Definition Documentation

#define ff_assert

(

bed

)

arb_assert(bed)

Definition at line 30 of file awtc_next_neighbours.hxx.

Referenced by FamilyList::insertSortedBy_matches(), FamilyList::insertSortedBy_rel_matches(), and PT_FF_comImpl::PT_FF_comImpl().

#define AWAR_NN_BASE   "next_neighbours/"

Definition at line 116 of file awtc_next_neighbours.hxx.

#define AWAR_NN_OLIGO_LEN   AWAR_NN_BASE "oligo_len"

Definition at line 118 of file awtc_next_neighbours.hxx.

Referenced by adjustOligolenAndMismatches(), AWTC_create_common_next_neighbour_fields(), AWTC_create_common_next_neighbour_vars(), awtc_nn_search(), awtc_nn_search_all_listed(), and FastAligner_start().

#define AWAR_NN_MISMATCHES   AWAR_NN_BASE "mismatches"

Definition at line 119 of file awtc_next_neighbours.hxx.

Referenced by adjustOligolenAndMismatches(), AWTC_create_common_next_neighbour_fields(), AWTC_create_common_next_neighbour_vars(), awtc_nn_search(), awtc_nn_search_all_listed(), and FastAligner_start().

#define AWAR_NN_FAST_MODE   AWAR_NN_BASE "fast_mode"

Definition at line 120 of file awtc_next_neighbours.hxx.

Referenced by AWTC_create_common_next_neighbour_fields(), AWTC_create_common_next_neighbour_vars(), awtc_nn_search(), awtc_nn_search_all_listed(), and FastAligner_start().

#define AWAR_NN_REL_MATCHES   AWAR_NN_BASE "rel_matches"

Definition at line 121 of file awtc_next_neighbours.hxx.

Referenced by AWTC_create_common_next_neighbour_fields(), AWTC_create_common_next_neighbour_vars(), awtc_nn_search(), awtc_nn_search_all_listed(), and FastAligner_start().

#define AWAR_NN_REL_SCALING   AWAR_NN_BASE "scaling"

Definition at line 122 of file awtc_next_neighbours.hxx.

Referenced by AWTC_create_common_next_neighbour_fields(), AWTC_create_common_next_neighbour_vars(), awtc_nn_search(), and awtc_nn_search_all_listed().

Function Documentation

void AWTC_create_common_next_neighbour_vars	(	AW_root *	aw_root,
		const RootCallback &	awar_changed_cb
	)

Definition at line 315 of file AWTC_next_neighbours.cxx.

References AW_awar::add_callback(), adjustOligolenAndMismatches(), AW_root::awar_int(), AWAR_NN_FAST_MODE, AWAR_NN_MISMATCHES, AWAR_NN_OLIGO_LEN, AWAR_NN_REL_MATCHES, AWAR_NN_REL_SCALING, RSS_BOTH_MIN, and AW_awar::set_minmax().

Referenced by create_next_neighbours_vars(), and FastAligner_create_variables().

void AWTC_create_common_next_neighbour_fields	(	AW_window *	aws,
		int	scaler_length
	)

Definition at line 328 of file AWTC_next_neighbours.cxx.

References AW_window::at(), AW_SCALER_EXP_LOWER, AWAR_NN_FAST_MODE, AWAR_NN_MISMATCHES, AWAR_NN_OLIGO_LEN, AWAR_NN_REL_MATCHES, AWAR_NN_REL_SCALING, AW_window::create_input_field_with_scaler(), AW_window::create_option_menu(), AW_window::insert_default_option(), AW_window::insert_option(), RSS_BOTH_MAX, RSS_BOTH_MIN, RSS_SOURCE, RSS_TARGET, and AW_window::update_option_menu().

Referenced by create_common_next_neighbour_fields(), and create_family_settings_window().