TranslateRealign.h File Reference

#include <arbdb_base.h>

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Macros
#define	AUTODETECT_STARTPOS   3

Functions
GB_ERROR	ALI_translate_marked (GBDATA *gb_main, bool use_entries, bool save_entries, int selected_startpos, bool translate_all, const char *ali_source, const char *ali_dest)
GB_ERROR	ALI_realign_marked (GBDATA *gb_main, const char *ali_source, const char *ali_dest, size_t &neededLength, bool unmark_succeeded, bool cutoff_dna)

Macro Definition Documentation

#define AUTODETECT_STARTPOS   3

Definition at line 18 of file TranslateRealign.h.

Referenced by ALI_translate_marked(), NT_create_dna_2_pro_window(), and nt_trans_cursorpos_changed().

Function Documentation

GB_ERROR ALI_translate_marked	(	GBDATA *	gb_main,
		bool	use_entries,
		bool	save_entries,
		int	selected_startpos,
		bool	translate_all,
		const char *	ali_source,
		const char *	ali_dest
	)

Definition at line 81 of file TranslateRealign.cxx.

References ali_assert, ARB_strdup(), AUTODETECT_STARTPOS, aw_ask_sure(), AWAR_PROTEIN_TYPE, AWT_CODON_TABLES, error(), GB_await_error(), GB_clear_error(), GB_entry(), GB_print_error(), GB_read_string(), GB_read_string_count(), GB_STRING, GB_warning(), GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBT_add_alignment_changekeys(), GBT_add_data(), GBT_count_marked_species(), GBT_create_alignment(), GBT_first_marked_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_next_marked_species(), GBT_read_int(), arb_progress::inc_and_check_user_abort(), legal_ORF_pos(), NULp, translate_getInfo(), translate_nuc2aa(), translate_saveInfo(), and TTIT_arb2embl().

Referenced by transpro_event().

GB_ERROR ALI_realign_marked	(	GBDATA *	gb_main,
		const char *	ali_source,
		const char *	ali_dest,
		size_t &	neededLength,
		bool	unmark_succeeded,
		bool	cutoff_dna
	)

realigns DNA alignment of marked sequences according to their protein alignment

Parameters

ali_source	protein source alignment
ali_dest	modified DNA alignment
neededLength	result: minimum alignment length needed in ali_dest (if too short) or 0 if long enough
unmark_succeeded	unmark all species that were successfully realigned

Definition at line 1004 of file TranslateRealign.cxx.

References ali_assert, TransTables::any(), AP_initialize_codon_tables(), arb_progress::auto_subtitles(), buffer, Realigner::clear_failure(), Data::data, arb_progress::done(), error(), Data::error, TransTables::explicit_table(), Realigner::failure(), TransTables::forbidAllBut(), GB_append_exportedError(), GB_AT_AA, GB_AT_DNA, Data::gb_data, GB_get_transaction_level(), GB_warning(), GB_warningf(), GB_write_flag(), GB_write_string(), GBS_global_string(), GBT_check_data(), GBT_count_marked_species(), GBT_first_marked_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_alignment_type(), GBT_get_name_or_description(), GBT_next_marked_species(), Realigner::get_needed_dest_alilen(), arb_progress::inc_and_check_user_abort(), Data::len, NULp, Realigner::realign_seq(), Realigner::set_failure(), ta, translate_getInfo(), and translate_saveInfo().

Referenced by realign_event().