adali.cxx File Reference

#include <arbdbt.h>
#include <adGene.h>
#include "gb_local.h"
#include <arb_strarray.h>
#include <arb_str.h>
#include <arb_global_defs.h>

Include dependency graph for adali.cxx:

Go to the source code of this file.

Classes
struct	gene_part_pos

Enumerations
enum	CopyMoveDelMode { COPY, MOVE, DELETE }

Functions
static void	check_for_species_without_data (const char *species_name, long value, void *counterPtr)
GBDATA *	GBT_get_presets (GBDATA *gb_main)
int	GBT_count_alignments (GBDATA *gb_main)
static GB_ERROR	GBT_check_alignment (GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash)
GB_ERROR	GBT_check_data (GBDATA *Main, const char *alignment_name)
void	GBT_get_alignment_names (ConstStrArray &names, GBDATA *gbd)
static char *	gbt_nonexisting_alignment (GBDATA *gbMain)
GB_ERROR	GBT_check_alignment_name (const char *alignment_name)
static GB_ERROR	create_ali_strEntry (GBDATA *gb_ali, const char *field, const char *strval, long write_protection)
static GB_ERROR	create_ali_intEntry (GBDATA *gb_ali, const char *field, int intval, long write_protection)
GBDATA *	GBT_create_alignment (GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created)
static GB_ERROR	gbt_rename_alignment_of_item (GBDATA *gb_item_container, const char *item_name, const char *item_entry_name, const char *source, const char *dest, CopyMoveDelMode mode)
static GB_ERROR	copy_move_del_alignment (GBDATA *gbMain, const char *source, const char *dest, CopyMoveDelMode mode)
GB_ERROR	GBT_copy_alignment (GBDATA *gbMain, const char *source, const char *dest)
GB_ERROR	GBT_rename_alignment (GBDATA *gbMain, const char *source, const char *dest)
GB_ERROR	GBT_delete_alignment (GBDATA *gbMain, const char *source)
NOT4PERL GBDATA *	GBT_add_data (GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)
NOT4PERL GBDATA *	GBT_create_sequence_data (GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write)
GBDATA *	GBT_gen_accession_number (GBDATA *gb_species, const char *ali_name)
int	GBT_is_partial (GBDATA *gb_species, int default_value, bool define_if_undef)
GBDATA *	GBT_find_sequence (GBDATA *gb_species, const char *aliname)
static char *	get_default_alignment (GBDATA *gb_main, bool use_startup_ali)
char *	GBT_get_default_alignment (GBDATA *gb_main)
char *	GBT_get_startup_alignment (GBDATA *gb_main)
GB_ERROR	GBT_set_default_alignment (GBDATA *gb_main, const char *alignment_name)
GB_ERROR	GBT_set_startup_alignment (GBDATA *gb_main, const char *alignment_name)
GBDATA *	GBT_get_alignment (GBDATA *gb_main, const char *aliname)
long	GBT_get_alignment_len (GBDATA *gb_main, const char *aliname)
GB_ERROR	GBT_set_alignment_len (GBDATA *gb_main, const char *aliname, long new_len)
char *	GBT_get_alignment_type_string (GBDATA *gb_main, const char *aliname)
GB_alignment_type	GBT_get_alignment_type (GBDATA *gb_main, const char *aliname)
bool	GBT_is_alignment_protein (GBDATA *gb_main, const char *alignment_name)
static const char *	gb_cache_genome (GBDATA *gb_genome)
static void	init_gpp (int parts)
static void	getPartPositions (const GEN_position *pos, int part, size_t *startPos, size_t *stopPos)
NOT4PERL char *	GBT_read_gene_sequence_and_length (GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length)
char *	GBT_read_gene_sequence (GBDATA *gb_gene, bool use_revComplement, char partSeparator)

Variables
static gene_part_pos *	gpp = NULp

Enumeration Type Documentation

enum CopyMoveDelMode

Enumerator
COPY
MOVE
DELETE

Definition at line 452 of file adali.cxx.

Function Documentation

static void check_for_species_without_data ( const char *  species_name, long  value, void *  counterPtr  )

static

Definition at line 20 of file adali.cxx.

References GB_warningf().

Referenced by GBT_check_data().

GBDATA* GBT_get_presets

(

GBDATA *

gb_main

)

Definition at line 30 of file adali.cxx.

References GBT_find_or_create().

Referenced by apply_command_to_alignment(), arb_prm_read(), concatenateAlignments(), copy_move_del_alignment(), GBT_check_data(), GBT_count_alignments(), GBT_create_alignment(), GBT_get_alignment(), GBT_get_alignment_names(), get_global_alignments(), MG_copy_and_check_alignments(), NT_format_all_alignments(), and PV_WriteTranslatedSequenceToDB().

int GBT_count_alignments

(

GBDATA *

gb_main

)

Definition at line 34 of file adali.cxx.

References GB_entry(), GB_nextEntry(), and GBT_get_presets().

Referenced by NT_format_all_alignments().

static GB_ERROR GBT_check_alignment ( GBDATA *  gb_main, GBDATA *  preset_alignment, GB_HASH *  species_name_hash  )

static

Definition at line 46 of file adali.cxx.

References error(), gb_assert, GB_BITS, GB_child(), GB_DB, GB_delete(), GB_entry(), GB_nextChild(), GB_read_char_pntr(), GB_read_count(), GB_read_int(), GB_read_key_pntr(), GB_read_string_count(), GB_read_type(), gb_species_data, GB_STRING, GB_warningf(), GB_write_int(), GB_write_security_delete(), GB_write_security_write(), GBS_global_string(), GBS_read_hash(), GBS_write_hash(), GBT_create_unique_species_name(), GBT_first_SAI_rel_SAI_data(), GBT_first_species_rel_species_data(), GBT_get_SAI_data(), GBT_get_species_data(), GBT_next_SAI(), GBT_next_species(), GBT_read_string(), GBT_write_int(), GBT_write_string(), NULp, and type.

Referenced by GBT_check_data().

GB_ERROR GBT_check_data	(	GBDATA *	Main,
		const char *	alignment_name
	)

Definition at line 218 of file adali.cxx.

References check_for_species_without_data(), error(), GB_entry(), GB_find_string(), GB_IGNORE_CASE, GB_nextEntry(), GB_read_char_pntr(), GB_warningf(), GBS_create_hash(), GBS_free_hash(), GBS_global_string(), GBS_hash_do_const_loop(), GBS_incr_hash(), GBS_read_hash(), GBT_check_alignment(), GBT_first_species_rel_species_data(), GBT_get_name(), GBT_get_presets(), GBT_get_SAI_data(), GBT_get_species_count(), GBT_get_species_data(), GBT_get_tree_data(), GBT_next_species(), GBT_write_string(), NULp, and SEARCH_GRANDCHILD.

Referenced by ali_checklen_cb(), ALI_realign_marked(), ARB_format_alignment(), concatenateAlignments(), ArbImporter::import_data(), insdel_event(), insdel_sai_event(), MG_save_cb(), MG_save_quick_result_cb(), NT_database_optimization(), NT_format_all_alignments(), PV_WriteTranslatedSequenceToDB(), and transpro_event().

void GBT_get_alignment_names	(	ConstStrArray &	names,
		GBDATA *	gbd
	)

Definition at line 317 of file adali.cxx.

References GB_entry(), GB_nextEntry(), GB_read_char_pntr(), GBT_get_presets(), and ConstStrArray::put().

Referenced by ARB_main(), concatenateFieldsCreateNewSpecies(), get_global_alignments(), MG_copy_and_check_alignments(), MG_equal_alignments(), MG_remaps::MG_remaps(), NT_database_optimization(), and NT_del_mark_move_REF().

static char* gbt_nonexisting_alignment ( GBDATA *  gbMain )

static

Definition at line 330 of file adali.cxx.

References GB_clear_error(), GBS_global_string_copy(), GBT_get_alignment(), and NULp.

Referenced by copy_move_del_alignment().

GB_ERROR GBT_check_alignment_name

(

const char *

alignment_name

)

Definition at line 343 of file adali.cxx.

References ARB_strBeginsWith(), error(), GB_check_key(), and GBS_global_string().

Referenced by concatenateAlignments(), copy_move_del_alignment(), GBT_create_alignment(), gene_extract_handler(), and ArbImporter::import_data().

static GB_ERROR create_ali_strEntry ( GBDATA *  gb_ali, const char *  field, const char *  strval, long  write_protection  )

static

Definition at line 351 of file adali.cxx.

References error(), GB_await_error(), GB_create(), GB_STRING, GB_write_security_delete(), GB_write_security_write(), GB_write_string(), GBS_global_string(), and NULp.

Referenced by GBT_create_alignment().

static GB_ERROR create_ali_intEntry ( GBDATA *  gb_ali, const char *  field, int  intval, long  write_protection  )

static

Definition at line 369 of file adali.cxx.

References error(), GB_await_error(), GB_create(), GB_INT, GB_write_int(), GB_write_security_delete(), GB_write_security_write(), GBS_global_string(), and NULp.

Referenced by GBT_create_alignment().

GBDATA* GBT_create_alignment	(	GBDATA *	gb_main,
		const char *	name,
		long	len,
		long	aligned,
		long	security,
		const char *	type,
		const char *	why_created
	)

Definition at line 388 of file adali.cxx.

References ARB_date_string(), create_ali_intEntry(), create_ali_strEntry(), error(), gb_assert, GB_await_error(), GB_create_container(), GB_export_errorf(), GB_find_string(), GB_IGNORE_CASE, GB_write_security_delete(), GBS_global_string(), GBS_global_string_copy(), GBT_check_alignment_name(), GBT_get_presets(), NULp, result, and SEARCH_GRANDCHILD.

Referenced by ALI_translate_marked(), concatenateAlignments(), create_ali_handler(), gene_extract_handler(), ArbImporter::import_data(), PV_WriteTranslatedSequenceToDB(), and split_alignment().

static GB_ERROR gbt_rename_alignment_of_item ( GBDATA *  gb_item_container, const char *  item_name, const char *  item_entry_name, const char *  source, const char *  dest, CopyMoveDelMode  mode  )

static

Definition at line 454 of file adali.cxx.

References COPY, DELETE, error(), GB_await_error(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_delete(), GB_entry(), GB_nextEntry(), GBS_global_string(), GBT_get_name_or_description(), NULp, and UNCOVERED.

Referenced by copy_move_del_alignment().

static GB_ERROR copy_move_del_alignment ( GBDATA *  gbMain, const char *  source, const char *  dest, CopyMoveDelMode  mode  )

static

Definition at line 489 of file adali.cxx.

References GB_transaction::close(), COPY, DELETE, error(), gb_assert, GB_await_error(), GB_clear_error(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_delete(), GB_have_error(), gb_species_data, GBS_global_string(), GBT_check_alignment_name(), GBT_get_alignment(), GBT_get_presets(), GBT_get_SAI_data(), GBT_get_species_data(), gbt_nonexisting_alignment(), gbt_rename_alignment_of_item(), GBT_write_string(), MOVE, NULp, and ta.

Referenced by GBT_copy_alignment(), GBT_delete_alignment(), and GBT_rename_alignment().

GB_ERROR GBT_copy_alignment	(	GBDATA *	gbMain,
		const char *	source,
		const char *	dest
	)

Definition at line 584 of file adali.cxx.

References COPY, and copy_move_del_alignment().

Referenced by copy_rename_handler().

GB_ERROR GBT_rename_alignment	(	GBDATA *	gbMain,
		const char *	source,
		const char *	dest
	)

Definition at line 587 of file adali.cxx.

References copy_move_del_alignment(), and MOVE.

Referenced by copy_rename_handler(), and MG_equal_alignments().

GB_ERROR GBT_delete_alignment	(	GBDATA *	gbMain,
		const char *	source
	)

Definition at line 590 of file adali.cxx.

References copy_move_del_alignment(), DELETE, and NULp.

Referenced by delete_ali_cb(), and split_alignment().

NOT4PERL GBDATA* GBT_add_data	(	GBDATA *	species,
		const char *	ali_name,
		const char *	key,
		GB_TYPES	type
	)

Definition at line 597 of file adali.cxx.

References error(), GB_check_hkey(), GB_check_key(), GB_create_container(), GB_entry(), GB_export_error(), GB_FIND, GB_search(), GB_STRING, GB_write_string(), GBS_global_string(), and NULp.

Referenced by ALI_translate_marked(), alignCompactedTo(), CON_calc_max_freq(), CON_export(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), create_concatInfo_SAI(), export_to_DB(), GBT_create_sequence_data(), gen_extract_gene_2_pseudoSpecies(), NT_count_different_chars(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), ALI_ARBDB::put_SAI(), PV_WriteTranslatedSequenceToDB(), st_ml_add_quality_string_to_species(), DBwriter::writeSequence(), and writeToArb().

NOT4PERL GBDATA* GBT_create_sequence_data	(	GBDATA *	species,
		const char *	ali_name,
		const char *	key,
		GB_TYPES	type,
		int	security_write
	)

Definition at line 643 of file adali.cxx.

References error(), GB_export_error(), GB_write_security_write(), GBT_add_data(), and NULp.

Referenced by copy_field_into_partial_alignments(), SequenceHandler::create(), ArbImporter::read_data(), and split_data_into_parts().

GBDATA* GBT_gen_accession_number	(	GBDATA *	gb_species,
		const char *	ali_name
	)

Definition at line 655 of file adali.cxx.

References error(), GB_entry(), GB_export_error(), GB_read_char_pntr(), GBS_checksum(), GBS_global_string(), GBT_find_sequence(), and GBT_write_string().

Referenced by AWTC_pars_names(), AWTC_recreate_name(), and NT_create_sai_from_pfold().

int GBT_is_partial	(	GBDATA *	gb_species,
		int	default_value,
		bool	define_if_undef
	)

Definition at line 672 of file adali.cxx.

References error(), GB_entry(), GB_export_error(), GB_read_int(), GBT_write_int(), NULp, and result.

Referenced by count_partial_and_full(), nt_add_partial(), nt_best_partial_match_rec(), and sequence_is_partial().

GBDATA* GBT_find_sequence	(	GBDATA *	gb_species,
		const char *	aliname
	)

Definition at line 708 of file adali.cxx.

References GB_entry(), and NULp.

Referenced by adaptCopiedAlignment(), alignTo(), alignToNextRelative(), ARB_main(), awtc_nn_search(), awtc_nn_search_all_listed(), AP_sequence::bind_to_species(), calculateEndPosition(), Candidate::Candidate(), compress_sequence_tree(), CON_export(), CON_insertSequences(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), ImportTestData::countSpeciesAndData(), dot_missing_bases(), ED4_get_marked_from_menu(), ED4_pfold_set_SAI(), export_to_DB(), FastAligner_start(), g_b_create_master(), gbl_sequence(), GBT_gen_accession_number(), GBT_read_gene_sequence_and_length(), GEN_root::GEN_root(), GEN_update_GENE_CONTENT(), GEN_write_position(), get_helix_string(), export_sequence_data::get_seq_data(), BI_helix::init(), BI_ecoli_ref::init(), init_indices_and_count_sons(), insert_genes_of_organism(), insert_new_species_terminal(), FilterDefinition::make_filter(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_remap(), modsai_cb(), nt_add_partial(), pd_get_the_gene_names(), pd_get_the_names(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), PT_init_input_data(), PV_WriteTranslatedSequenceToDB(), ReadArbdb(), readCompactedSequence(), reverseComplement(), SEC_seq_data::SEC_seq_data(), species_has_alignment(), split_alignment(), trackAlignmentChanges(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), and update_RangeList().

static char* get_default_alignment ( GBDATA *  gb_main, bool  use_startup_ali  )

static

behavior

See also

GBT_get_default_alignment.

Parameters

use_startup_ali

if 'true' -> always return the value seen when first called with 'true' + make calls with 'false' always return an error. The intention is to be able to force that an applications sticks with the alignment found at startup and ignores if alignment is changed in arb_ntree.

Definition at line 713 of file adali.cxx.

References ARB_strBeginsWith(), ARB_strdup(), gb_assert, GB_DEFAULT_ALIGNMENT, GB_export_error(), GB_export_errorf(), GB_have_error(), GBT_read_string(), NO_ALI_SELECTED, and NULp.

Referenced by GBT_get_default_alignment(), and GBT_get_startup_alignment().

char* GBT_get_default_alignment

(

GBDATA *

gb_main

)

Returns

default alignment returns

• the alignment that was selected in ARB alignment admin, when GBT_get_startup_alignment was called first OR
• the alignment currently selected in ARB alignment admin OR
• NULp if NO (valid) alignment selected. An error is exported in that case!

Definition at line 747 of file adali.cxx.

References get_default_alignment().

Referenced by AP_calc_pos_var_pars(), AP_create_consensus_var(), ARB_main(), AWTC_pars_names(), AWTC_recreate_name(), calculateEndPosition(), CON_calc_max_freq_cb(), create_splitAlignment_awars(), DI_create_matrix_variables(), edit_SAI_description(), export_seq_data(), export_sequence_data::export_sequence_data(), FastAligner_start(), Structure3D::FindTypeOfRNA(), FINAL_TYPE< SEQTYPE >::finish(), gbl_ali_name(), gbl_read_seq_sai_or_species(), gbl_sequence(), gbl_sequence_type(), GBT_set_startup_alignment(), gde_filter_weights(), getArbFilter(), BI_helix::init(), BI_ecoli_ref::init(), main(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_gene_species_using_current_alignment(), mark_nontree_cb(), mark_tree_cb(), modify_target_string(), NA_Alignment::NA_Alignment(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_createConcatenationAwars(), NT_import_sequences(), NT_mark_all_cb(), ALI_ARBDB::open(), pars_create_all_awars(), pd_export_pt_server(), pd_get_the_names(), PH_create_filter_variables(), predef_prg(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), pt_init_main_struct(), PT_prepare_data(), resolve_IUPAC_target_string(), SEC_db_interface::SEC_db_interface(), show_count(), split_ali_cb(), sq_calc_seq_quality_cb(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), StaticData::track_ali(), track_ali_change_cb(), and translateSAItoColors().

char* GBT_get_startup_alignment

(

GBDATA *

gb_main

)

same interface as GBT_get_default_alignment. When this was called once w/o error, calls to GBT_get_default_alignment always return the alignment which was default then.

Definition at line 757 of file adali.cxx.

References get_default_alignment().

Referenced by GBT_set_startup_alignment(), ED4_root::init_alignment(), and propertyName().

GB_ERROR GBT_set_default_alignment	(	GBDATA *	gb_main,
		const char *	alignment_name
	)

Definition at line 765 of file adali.cxx.

References GB_DEFAULT_ALIGNMENT, and GBT_write_string().

Referenced by ARB_main(), and GBT_set_startup_alignment().

GB_ERROR GBT_set_startup_alignment	(	GBDATA *	gb_main,
		const char *	alignment_name
	)

Definition at line 768 of file adali.cxx.

References ARB_strdup(), error(), GB_await_error(), GB_clear_error(), GBS_global_string(), GBT_get_default_alignment(), GBT_get_startup_alignment(), GBT_set_default_alignment(), NO_ALI_SELECTED, and NULp.

Referenced by pars_start_cb(), and startup_sequence_cb().

GBDATA* GBT_get_alignment	(	GBDATA *	gb_main,
		const char *	aliname
	)

Returns

global alignment container for alignment 'aliname' or NULp if alignment not found (error exported in that case)

Definition at line 808 of file adali.cxx.

References gb_assert, GB_export_error(), GB_export_errorf(), GB_find_string(), GB_get_father(), GB_have_error(), GB_IGNORE_CASE, GBT_get_presets(), NO_ALI_SELECTED, NULp, and SEARCH_GRANDCHILD.

Referenced by ALI_realign_marked(), ALI_translate_marked(), alignment_vars_callback(), AWTI_import_set_ali_and_type(), ED4_terminal::changed_by_database(), concatenateAlignments(), copy_move_del_alignment(), export_seq_data(), GBT_get_alignment_len(), GBT_get_alignment_type_string(), gbt_nonexisting_alignment(), GBT_set_alignment_len(), gene_extract_handler(), ED4_root::init_alignment(), MG_copy_and_check_alignments(), pd_export_pt_server(), PV_WriteTranslatedSequenceToDB(), SEC_db_interface::SEC_db_interface(), and split_alignment().

long GBT_get_alignment_len	(	GBDATA *	gb_main,
		const char *	aliname
	)

Returns

length (>0) of alignment 'aliname' or -1 if alignment not found (error exported in that case) 0 if alignment length is zero (=invalid; error exported in that case)

Definition at line 833 of file adali.cxx.

References gb_assert, GB_export_errorf(), GB_have_error(), GBT_get_alignment(), and GBT_read_int().

Referenced by ALI_realign_marked(), ALI_translate_marked(), ARB_main(), awt_create_select_filter_window_aw_cb(), awt_get_filter(), ST_ML::calc_st_ml(), ColumnStat::calculate(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), compress_sequence_tree(), CON_calc_max_freq(), CON_calculate(), concatenateAlignments(), create_concatInfo_SAI(), di_autodetect_callback(), di_calculate_matrix(), export_seq_data(), export_sequence_data::export_sequence_data(), export_to_DB(), FastAligner_start(), FINAL_TYPE< SEQTYPE >::finish(), BI_helix::init(), BI_ecoli_ref::init(), DI_MATRIX::load(), PHDATA::load(), NT_count_different_chars(), pars_check_size(), PARS_tree_init(), PH_create_filter_variables(), PT_prepare_data(), PV_WriteTranslatedSequenceToDB(), PVP_calculate(), ReadArbdb(), realign_event(), Aligner::run(), SEC_db_interface::SEC_db_interface(), split_alignment(), valid_alignment_selected(), write_sequence_autoinc_alisize(), and writeToArb().

GB_ERROR GBT_set_alignment_len	(	GBDATA *	gb_main,
		const char *	aliname,
		long	new_len
	)

Definition at line 848 of file adali.cxx.

References error(), GB_await_error(), GBT_get_alignment(), GBT_write_int(), and NULp.

Referenced by realign_event(), and write_sequence_autoinc_alisize().

char* GBT_get_alignment_type_string	(	GBDATA *	gb_main,
		const char *	aliname
	)

Returns

type-string of alignment 'aliname' or NULp if alignment not found (error exported in that case)

Definition at line 863 of file adali.cxx.

References gb_assert, GB_export_errorf(), GB_have_error(), GBT_get_alignment(), GBT_read_string(), NULp, and result.

Referenced by gbl_sequence_type(), GBT_get_alignment_type(), MG_copy_and_check_alignments(), MG_equal_alignments(), NT_createConcatenationAwars(), NT_import_sequences(), and propertyName().

GB_alignment_type GBT_get_alignment_type	(	GBDATA *	gb_main,
		const char *	aliname
	)

Returns

type of alignment as enum type (GB_alignment_type). GB_AT_UNKNOWN if alignment not found (error exported in that case)

Definition at line 878 of file adali.cxx.

References gb_assert, GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_AT_UNKNOWN, and GBT_get_alignment_type_string().

Referenced by ALI_realign_marked(), CON_calc_max_freq(), CON_calculate(), export_sequence_data::export_sequence_data(), export_to_DB(), GBT_is_alignment_protein(), ED4_root::init_alignment(), InsertDatainGDE(), modify_target_string(), NA_Alignment::NA_Alignment(), pd_export_pt_server(), PVP_calculate(), resolve_IUPAC_target_string(), reverseComplement(), Aligner::run(), sq_calc_seq_quality_cb(), and track_ali_change_cb().

bool GBT_is_alignment_protein	(	GBDATA *	gb_main,
		const char *	alignment_name
	)

Definition at line 898 of file adali.cxx.

References gb_assert, GB_AT_AA, GB_AT_UNKNOWN, and GBT_get_alignment_type().

Referenced by calculate_clusters(), PH_filter::calculate_column_homology(), ArbParsimony::generate_tree(), DI_MATRIX::load(), and NT_count_different_chars().

static const char* gb_cache_genome ( GBDATA *  gb_genome )

static

Definition at line 907 of file adali.cxx.

References GB_read_string(), and NULp.

Referenced by GBT_read_gene_sequence_and_length().

static void init_gpp ( int  parts )

static

Definition at line 929 of file adali.cxx.

References ARB_alloc(), gene_part_pos::certain, NULp, gene_part_pos::offset, and gene_part_pos::parts.

Referenced by GBT_read_gene_sequence_and_length().

static void getPartPositions ( const GEN_position *  pos, int  part, size_t *  startPos, size_t *  stopPos  )

static

Definition at line 953 of file adali.cxx.

References gene_part_pos::certain, gb_assert, gene_part_pos::offset, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by GBT_read_gene_sequence_and_length().

NOT4PERL char* GBT_read_gene_sequence_and_length	(	GBDATA *	gb_gene,
		bool	use_revComplement,
		char	partSeparator,
		size_t *	gene_length
	)

Definition at line 960 of file adali.cxx.

References ARB_alloc(), GEN_position::complement, error(), gb_assert, GB_AT_DNA, GB_await_error(), gb_cache_genome(), GB_export_errorf(), GB_get_grandfather(), GB_read_count(), GBS_global_string(), GBT_determine_T_or_U(), GBT_find_sequence(), GBT_reverseComplementNucSequence(), GEN_free_position(), GEN_global_gene_identifier(), GEN_read_position(), GEN_sortAndMergeLocationParts(), getPartPositions(), init_gpp(), NULp, GEN_position::parts, result, and start.

Referenced by GBT_read_gene_sequence(), primer_design_event_init(), and translate_gene_sequence().

char* GBT_read_gene_sequence	(	GBDATA *	gb_gene,
		bool	use_revComplement,
		char	partSeparator
	)

Definition at line 1062 of file adali.cxx.

References GBT_read_gene_sequence_and_length(), and NULp.

Referenced by gbl_sequence(), gen_extract_gene_2_pseudoSpecies(), GEN_update_GENE_CONTENT(), and pd_get_the_gene_names().

Variable Documentation

gene_part_pos* gpp = NULp

static

Definition at line 927 of file adali.cxx.