#include <aw_base.hxx>
#include <arb_error.h>
#include <pos_range.h>
#include <string>

Include dependency graph for fast_aligner.hxx:

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

Classes
struct	AlignDataAccess

Macros
#define	INTEGRATED_ALIGNERS_TITLE "Integrated Aligners"

Typedefs
typedef char (	Aligner_get_consensus_func )(const char *species_name, PosRange range)

typedef bool(*	Aligner_get_selected_range )(PosRange &range)

typedef GBDATA (	Aligner_get_first_selected_species )(int *total_no_of_selected_species)

typedef GBDATA (	Aligner_get_next_selected_species )(void)

typedef char (	Aligner_get_helix_string )(GBDATA gb_main, const char alignment_name)

Functions
AW_window *	FastAligner_create_window (AW_root awr, const AlignDataAccess data_access)

void	FastAligner_create_variables (AW_root *root, AW_default db1)

void	FastAligner_set_align_current (AW_root *root, AW_default db1)

void	FastAligner_set_reference_species (AW_root *root)

void	FastAligner_start (AW_window aw, const AlignDataAccess data_access)

ARB_ERROR	FastAligner_delete_temp_entries (GBDATA gb_main, const char alignment)

Macro Definition Documentation

#define INTEGRATED_ALIGNERS_TITLE "Integrated Aligners"

Definition at line 28 of file fast_aligner.hxx.

Referenced by FastAligner_create_window(), and ED4_root::generate_window().

Typedef Documentation

typedef char*(* Aligner_get_consensus_func)(const char *species_name, PosRange range)

Definition at line 30 of file fast_aligner.hxx.

typedef bool(* Aligner_get_selected_range)(PosRange &range)

Definition at line 31 of file fast_aligner.hxx.

typedef GBDATA*(* Aligner_get_first_selected_species)(int *total_no_of_selected_species)

Definition at line 32 of file fast_aligner.hxx.

typedef GBDATA*(* Aligner_get_next_selected_species)(void)

Definition at line 33 of file fast_aligner.hxx.

typedef char*(* Aligner_get_helix_string)(GBDATA *gb_main, const char *alignment_name)

Definition at line 34 of file fast_aligner.hxx.

Function Documentation

AW_window* FastAligner_create_window	(	AW_root *	awr,
		const AlignDataAccess *	data_access
	)

Definition at line 2636 of file fast_aligner.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_PT_SERVER, AWAR_SPECIES_NAME, AWM_ALL, AWM_EXP, awt_create_PTSERVER_selection_button(), awt_create_SAI_selection_button(), AWT_insert_config_manager(), build_reverse_complement(), create_family_settings_window(), create_island_hopping_window(), FA_AROUND_CURSOR, FA_AWAR_ACTION_ON_ERROR, FA_AWAR_AROUND, FA_AWAR_CONTINUE_ON_ERROR, FA_AWAR_MIRROR, FA_AWAR_NEXT_RELATIVES, FA_AWAR_PROTECTION, FA_AWAR_PT_SERVER_ALIGNMENT, FA_AWAR_RANGE, FA_AWAR_REFERENCE, FA_AWAR_REFERENCE_NAME, FA_AWAR_RELATIVE_RANGE, FA_AWAR_REPORT, FA_AWAR_SAI_RANGE_CHARS, FA_AWAR_SAI_RANGE_NAME, FA_AWAR_SHOW_GAPS_MESSAGES, FA_AWAR_TO_ALIGN, FA_AWAR_USE_ISLAND_HOPPING, FA_CURRENT, FA_MARK_ALIGNED, FA_MARK_FAILED, FA_MARKED, FA_NO_ACTION, FA_NO_REPORT, FA_REF_CONSENSUS, FA_REF_EXPLICIT, FA_REF_RELATIVES, FA_REPORT, FA_SAI_MULTI_RANGE, FA_SELECTED, FA_SELECTED_RANGE, FA_TEMP_REPORT, FA_TURN_ALWAYS, FA_TURN_INTERACTIVE, FA_TURN_NEVER, FA_WHOLE_SEQUENCE, FastAligner_set_reference_species(), FastAligner_start(), AlignDataAccess::gb_main, INTEGRATED_ALIGNERS_TITLE, AW_window::load_xfig(), makeHelpCallback(), NULp, and RootAsWindowCallback::simple().

Referenced by ED4_create_faligner_window().

void FastAligner_create_variables	(	AW_root *	root,
		AW_default	db1
	)

Definition at line 2413 of file fast_aligner.cxx.

References ARB_in_novice_mode(), AW_root::awar(), AWAR_DEFAULT_ALIGNMENT, AW_root::awar_float(), AW_root::awar_int(), AWAR_PT_SERVER, AW_root::awar_string(), AWTC_create_common_next_neighbour_vars(), FA_AWAR_ACTION_ON_ERROR, FA_AWAR_AROUND, FA_AWAR_BASE_FREQ_A, FA_AWAR_BASE_FREQ_C, FA_AWAR_BASE_FREQ_G, FA_AWAR_BASE_FREQ_T, FA_AWAR_CONTINUE_ON_ERROR, FA_AWAR_ESTIMATE_BASE_FREQ, FA_AWAR_EXPECTED_DISTANCE, FA_AWAR_GAP_A, FA_AWAR_GAP_B, FA_AWAR_GAP_C, FA_AWAR_MIRROR, FA_AWAR_NEXT_RELATIVES, FA_AWAR_PROTECTION, FA_AWAR_PT_SERVER_ALIGNMENT, FA_AWAR_RANGE, FA_AWAR_REFERENCE, FA_AWAR_REFERENCE_NAME, FA_AWAR_RELATIVE_RANGE, FA_AWAR_REPORT, FA_AWAR_SAI_RANGE_CHARS, FA_AWAR_SAI_RANGE_NAME, FA_AWAR_SHOW_GAPS_MESSAGES, FA_AWAR_STRUCTURE_SUPPLEMENT, FA_AWAR_SUBST_PARA_AC, FA_AWAR_SUBST_PARA_AG, FA_AWAR_SUBST_PARA_AT, FA_AWAR_SUBST_PARA_CG, FA_AWAR_SUBST_PARA_CT, FA_AWAR_SUBST_PARA_GT, FA_AWAR_THRESHOLD, FA_AWAR_TO_ALIGN, FA_AWAR_USE_ISLAND_HOPPING, FA_AWAR_USE_SECONDARY, FA_CURRENT, FA_NO_ACTION, FA_NO_REPORT, FA_REF_EXPLICIT, FA_TURN_INTERACTIVE, FA_WHOLE_SEQUENCE, nullcb(), AW_awar::read_char_pntr(), AW_awar::set_minmax(), and AW_awar::write_int().

Referenced by ED4_root::generate_window().

void FastAligner_set_align_current	(	AW_root *	root,
		AW_default	db1
	)

Definition at line 2470 of file fast_aligner.cxx.

References AW_root::awar_int(), FA_AWAR_TO_ALIGN, and FA_CURRENT.

void FastAligner_set_reference_species ( AW_root * root )

Definition at line 2474 of file fast_aligner.cxx.

References AW_root::awar(), AWAR_SPECIES_NAME, FA_AWAR_REFERENCE_NAME, AW_awar::read_string(), and AW_awar::write_string().

Referenced by FastAligner_create_window(), and ED4_root::generate_window().

void FastAligner_start	(	AW_window *	aw,
		const AlignDataAccess *	data_access
	)

Definition at line 2160 of file fast_aligner.cxx.

References RangeList::add(), AlignDataAccess::alignment_name, alignment_name, arb_progress::allow_title_reuse(), aw_message_if(), AW_root::awar(), AWAR_CURSOR_POSITION_LOCAL, AWAR_NN_FAST_MODE, AWAR_NN_MISMATCHES, AWAR_NN_OLIGO_LEN, AWAR_NN_REL_MATCHES, AWAR_PT_SERVER, AWAR_SPECIES_NAME, RangeList::begin(), build_RangeList_from_string(), AlignDataAccess::do_refresh, RangeList::end(), PosRange::end(), error(), FA_AROUND_CURSOR, fa_assert(), FA_AWAR_ACTION_ON_ERROR, FA_AWAR_AROUND, FA_AWAR_BASE_FREQ_A, FA_AWAR_BASE_FREQ_C, FA_AWAR_BASE_FREQ_T, FA_AWAR_CONTINUE_ON_ERROR, FA_AWAR_ESTIMATE_BASE_FREQ, FA_AWAR_EXPECTED_DISTANCE, FA_AWAR_GAP_A, FA_AWAR_GAP_B, FA_AWAR_GAP_C, FA_AWAR_MIRROR, FA_AWAR_NEXT_RELATIVES, FA_AWAR_PROTECTION, FA_AWAR_PT_SERVER_ALIGNMENT, FA_AWAR_RANGE, FA_AWAR_REFERENCE, FA_AWAR_REFERENCE_NAME, FA_AWAR_RELATIVE_RANGE, FA_AWAR_REPORT, FA_AWAR_SAI_RANGE_CHARS, FA_AWAR_SAI_RANGE_NAME, FA_AWAR_SHOW_GAPS_MESSAGES, FA_AWAR_STRUCTURE_SUPPLEMENT, FA_AWAR_SUBST_PARA_AC, FA_AWAR_SUBST_PARA_AG, FA_AWAR_SUBST_PARA_AT, FA_AWAR_SUBST_PARA_CG, FA_AWAR_SUBST_PARA_CT, FA_AWAR_SUBST_PARA_GT, FA_AWAR_THRESHOLD, FA_AWAR_TO_ALIGN, FA_AWAR_USE_ISLAND_HOPPING, FA_AWAR_USE_SECONDARY, FA_CURRENT, FA_MARKED, FA_REF_CONSENSUS, FA_REF_EXPLICIT, FA_REF_RELATIVES, FA_SAI_MULTI_RANGE, FA_SELECTED, FA_SELECTED_RANGE, FA_WHOLE_SEQUENCE, GB_await_error(), GB_have_error(), gb_main, AlignDataAccess::gb_main, GB_read_string(), GBS_global_string(), GBT_expect_SAI(), GBT_find_sequence(), GBT_get_alignment_len(), GBT_get_default_alignment(), AlignDataAccess::get_first_selected_species, get_first_selected_species(), AlignDataAccess::get_group_consensus, AlignDataAccess::get_next_selected_species, get_next_selected_species(), AW_window::get_root(), AlignDataAccess::get_selected_range, SearchRelativeParams::getFamilyFinder(), AlignDataAccess::getHelixString(), PosRange::is_part(), island_hopper, NULp, AW_awar::read_char_pntr(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), AlignDataAccess::refresh_display, FamilyFinder::restrict_2_region(), RSS_BOTH_MIN, PosRange::start(), ta, PosRange::whole(), and AW_awar::write_as_string().

Referenced by FastAligner_create_window().

ARB_ERROR FastAligner_delete_temp_entries	(	GBDATA *	gb_main,
		const char *	alignment
	)

Definition at line 1238 of file fast_aligner.cxx.

References error(), fa_assert(), GB_delete(), GB_FIND, GB_search(), GBT_get_name_or_description(), INSERTS_NAME, NULp, and QUALITY_NAME.

Referenced by ED4_delete_temp_entries().

Classes

Macros

Typedefs

Functions

Macro Definition Documentation

Typedef Documentation

Function Documentation