121 void GBT_scan_db(StrArray& fieldNames, GBDATA *gbd, const
char *datapath);
123 void GBT_message(GBDATA *gb_main, const
char *msg);
137 GBDATA *
GBT_open(const
char *path, const
char *opent);
165 GBDATA *
GBT_find_tree(GBDATA *gb_main, const
char *tree_name);
186 #error ad_t_prot.h included twice
GBDATA * GBT_find_bottom_tree(GBDATA *gb_main)
GB_ERROR GBT_add_new_experiment_changekey(GBDATA *gb_main, const char *name, GB_TYPES type)
GB_ERROR GBT_add_new_changekey_to_keypath(GBDATA *gb_main, const char *name, GB_TYPES type, const char *keypath)
GBDATA * GBT_create_new_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created)
NOT4PERL GB_ERROR GBT_move_tree(GBDATA *gb_moved_tree, GBT_ORDER_MODE mode, GBDATA *gb_target_tree)
GBDATA * GBT_first_SAI(GBDATA *gb_main)
size_t GBT_count_leafs(const TreeNode *tree)
void GBT_compression_test(struct Unfixed_cb_parameter *, GBDATA *gb_main)
GBDATA * GBT_first_marked_species(GBDATA *gb_main)
AliDataPtr format(AliDataPtr data, const size_t wanted_len, GB_ERROR &error)
GB_ERROR GBT_write_tree_with_remark(GBDATA *gb_main, const char *tree_name, TreeNode *tree, const char *remark)
GB_ERROR GB_set_macro_error(GBDATA *gb_main, const char *curr_error)
GB_ERROR GBT_rename_species(const char *oldname, const char *newname, bool ignore_protection)
void GBT_unlink_tree(TreeNode *tree)
GBDATA * GBT_first_marked_species_rel_species_data(GBDATA *gb_species_data)
long GBT_mark_all_that(GBDATA *gb_main, int flag, bool(*condition)(GBDATA *, void *), void *cd)
GB_ERROR GBT_restore_marked_species(GBDATA *gb_main, const char *stored_marked)
GBDATA * GBT_expect_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value)
GBDATA ** GBT_gen_species_array(GBDATA *gb_main, long *speciesCountPtr)
GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest)
GBDATA * GBT_expect_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name)
int GBT_count_alignments(GBDATA *gb_main)
long GBT_mark_all(GBDATA *gb_main, int flag)
GBDATA * GBT_expect_species_rel_species_data(GBDATA *gb_species_data, const char *name)
char * GBT_complementNucSequence(const char *s, int len, char T_or_U)
GBDATA * GBT_tree_behind(GBDATA *gb_tree)
GB_ERROR GBT_check_alignment_name(const char *alignment_name)
GB_ERROR GBT_macro_execute(const char *macro_name, bool loop_marked, bool run_async)
TreeNode * GBT_remove_leafs(TreeNode *tree, GBT_TreeRemoveType mode, const GB_HASH *species_hash, int *removed, int *groups_removed)
char * GBT_tree_2_newick(const TreeNode *tree, NewickFormat format, bool compact)
GBDATA * GBT_get_alignment(GBDATA *gb_main, const char *aliname)
const char * GBT_name_of_bottom_tree(GBDATA *gb_main)
NOT4PERL GB_ERROR GBT_with_stored_species(GBDATA *gb_main, const char *stored, species_callback doit, int *clientdata)
const char * GBT_name_of_largest_tree(GBDATA *gb_main)
long GBT_get_SAI_count(GBDATA *gb_main)
void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd)
char * GBT_reverseNucSequence(const char *s, int len)
TreeNode * GBT_read_tree(GBDATA *gb_main, const char *tree_name, TreeRoot *troot)
GB_ERROR GBT_log_to_tree_remark(GBDATA *gb_tree, const char *log_entry, bool stamp)
NOT4PERL long * GBT_readOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value)
NOT4PERL GB_ERROR GBT_remote_action_with_timeout(GBDATA *gb_main, const char *application, const char *action_name, const class ARB_timeout *timeout, bool verbose)
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname)
static char * alignment_name
const char * GBT_existing_tree(GBDATA *gb_main, const char *tree_name)
int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef)
GBDATA * GBT_expect_SAI(GBDATA *gb_main, const char *name)
GBDATA * GBT_get_tree_data(GBDATA *gb_main)
GB_ERROR GBT_remote_read_awar(GBDATA *gb_main, const char *application, const char *awar_name)
bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name)
GB_ERROR(* species_callback)(GBDATA *gb_species, int *clientdata)
GB_ERROR GBT_link_tree(TreeNode *tree, GBDATA *gb_main, bool show_status, int *zombies, int *duplicates)
char * GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname)
GB_ERROR GBT_delete_alignment(GBDATA *gbMain, const char *source)
char * GBT_get_startup_alignment(GBDATA *gb_main)
GBDATA * GBT_open(const char *path, const char *opent)
char * GBT_get_default_helix_nr(GBDATA *)
GB_ERROR GBT_add_alignment_changekeys(GBDATA *gb_main, const char *ali)
void GBT_install_message_handler(GBDATA *gb_main)
GBDATA * GBT_first_species_rel_species_data(GBDATA *gb_species_data)
const char * GBT_get_tree_name(GBDATA *gb_tree)
NOT4PERL float * GBT_read_float(GBDATA *gb_container, const char *fieldpath)
GB_ERROR GBT_write_tree_remark(GBDATA *gb_main, const char *tree_name, const char *remark)
GBDATA * GBT_find_SAI(GBDATA *gb_main, const char *name)
NOT4PERL GBDATA * GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()")
GB_ERROR GBT_add_new_species_changekey(GBDATA *gb_main, const char *name, GB_TYPES type)
GB_ERROR GBT_convert_changekey(GBDATA *gb_main, const char *name, GB_TYPES target_type)
NOT4PERL long * GBT_read_int(GBDATA *gb_container, const char *fieldpath)
char * GBT_read_string(GBDATA *gb_container, const char *fieldpath)
GB_ERROR GBT_overwrite_tree(GBDATA *gb_tree, TreeNode *tree)
NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U)
GB_ERROR GBT_check_tree_name(const char *tree_name)
GBDATA * GBT_find_next_tree(GBDATA *gb_tree)
const char * GBT_tree_info_string(GBDATA *gb_main, const char *tree_name, int maxTreeNameLen)
GB_ERROR GBT_begin_rename_session(GBDATA *gb_main, int all_flag)
GBDATA * GBT_find_top_tree(GBDATA *gb_main)
GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name)
GB_ERROR GBT_add_new_gene_changekey(GBDATA *gb_main, const char *name, GB_TYPES type)
GB_ERROR GBT_write_tree(GBDATA *gb_main, const char *tree_name, TreeNode *tree)
GB_ERROR GBT_write_group_name(GBDATA *gb_group_name, const char *new_group_name, bool pedantic)
GBDATA * GBT_expect_species(GBDATA *gb_main, const char *name)
char * GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name)
GB_ERROR GBT_copy_alignment(GBDATA *gbMain, const char *source, const char *dest)
static char const * macro_name
GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len)
#define __ATTR__DEPRECATED_TODO(reason)
GB_ERROR GBT_write_float_converted(GBDATA *gb_float_writable, const char *data)
char * GBT_readOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value)
GBDATA * GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated)
GBDATA * GBT_next_marked_species(GBDATA *gb_species)
GB_ERROR GBT_copy_tree(GBDATA *gb_main, const char *source_name, const char *dest_name)
void GBT_scan_db(StrArray &fieldNames, GBDATA *gbd, const char *datapath)
GB_ERROR GBT_rename_tree(GBDATA *gb_main, const char *source_name, const char *dest_name)
TreeNode * GBT_read_tree_and_size(GBDATA *gb_main, const char *tree_name, TreeRoot *troot, int *tree_size)
GBDATA * GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data)
GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname)
const char * GBT_relativeMacroname(const char *macro_name)
GBDATA * GBT_find_species_rel_species_data(GBDATA *gb_species_data, const char *name)
long GBT_size_of_tree(GBDATA *gb_main, const char *tree_name)
GB_ERROR GBT_remote_action(GBDATA *gb_main, const char *application, const char *action_name)
char * GBT_get_default_ref(GBDATA *)
GB_TYPES GBT_get_type_of_changekey(GBDATA *gb_main, const char *field_name, const char *change_key_path)
NOT4PERL float * GBT_readOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value)
GBDATA * GBT_find_sequence(GBDATA *gb_species, const char *aliname)
char * GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator)
GB_ERROR GBT_abort_rename_session(void)
GB_ERROR GBT_commit_rename_session(void) __ATTR__USERESULT
long GBT_count_marked_species(GBDATA *gb_main)
const char * GBT_readOrCreate_char_pntr(GBDATA *gb_container, const char *fieldpath, const char *default_value)
GB_ERROR GBT_add_new_changekey(GBDATA *gb_main, const char *name, int type) __ATTR__DEPRECATED_TODO("obsolete. use GBT_add_new_species_changekey() instead")
GB_ERROR GBT_write_byte(GBDATA *gb_container, const char *fieldpath, unsigned char content)
GBDATA * GBT_searchOrCreate_itemfield_according_to_changekey(GBDATA *gb_item, const char *field_name, const char *change_key_path)
GBDATA * GBT_next_SAI(GBDATA *gb_sai)
GB_ERROR GBT_remote_awar(GBDATA *gb_main, const char *application, const char *awar_name, const char *value)
GB_ERROR GBT_is_invalid(const TreeNode *tree)
GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content)
GBDATA * GBT_get_changekey(GBDATA *gb_main, const char *key, const char *change_key_path)
#define __ATTR__USERESULT
GB_ERROR GBT_write_float(GBDATA *gb_container, const char *fieldpath, float content)
GBDATA * GBT_create(GBDATA *father, const char *key, long delete_level)
GBDATA * GBT_find_or_create(GBDATA *father, const char *key, long delete_level)
GBDATA * GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name)
GBDATA * GBT_first_species(GBDATA *gb_main)
char * GBT_read_as_string(GBDATA *gb_container, const char *fieldpath)
void GBT_get_tree_names(ConstStrArray &names, GBDATA *gb_main, bool sorted)
void GBT_message(GBDATA *gb_main, const char *msg)
GB_ERROR GBT_compress_sequence_tree2(GBDATA *gbd, const char *tree_name, const char *ali_name) __ATTR__USERESULT
GB_ERROR GBT_log_to_named_trees_remark(GBDATA *gb_main, const char *tree_name, const char *log_entry, bool stamp)
char * GBT_get_default_helix(GBDATA *)
GB_ERROR GB_clear_macro_error(GBDATA *gb_main)
GBDATA * GBT_find_or_create_species(GBDATA *gb_main, const char *name, bool markCreated)
GBDATA * GBT_next_species(GBDATA *gb_species)
GB_ERROR GBT_write_name_to_groupData(GBDATA *gb_group, bool createNameEntry, const char *new_group_name, bool pedantic)
GBDATA * GBT_find_species(GBDATA *gb_main, const char *name)
GB_ERROR GBT_set_startup_alignment(GBDATA *gb_main, const char *alignment_name)
GB_CSTR * GBT_get_names_of_species_in_tree(const TreeNode *tree, size_t *count)
NOT4PERL GBDATA * GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write)
char * GBT_get_default_alignment(GBDATA *gb_main)
const char * GBT_get_name(GBDATA *gb_item)
GBDATA * GBT_find_SAI_rel_SAI_data(GBDATA *gb_sai_data, const char *name)
char * GBT_store_marked_species(GBDATA *gb_main, bool unmark_all)
GBDATA * GBT_find_or_create_SAI(GBDATA *gb_main, const char *name)
long GBT_get_species_count(GBDATA *gb_main)
GBDATA * GBT_find_item_rel_item_data(GBDATA *gb_item_data, const char *id_field, const char *id_value)
GBDATA * GBT_find_tree(GBDATA *gb_main, const char *tree_name)
GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content)
NOT4PERL char * GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length)
GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name)
GBDATA * GBT_get_presets(GBDATA *gb_main)
GBDATA * GBT_get_SAI_data(GBDATA *gb_main)
GB_CSTR GBT_get_name_or_description(GBDATA *gb_item)
GB_ERROR GBT_write_int_converted(GBDATA *gb_int_writable, const char *data, size_t *rounded)
GB_ERROR GB_get_macro_error(GBDATA *gb_main)
const char * GBT_read_char_pntr(GBDATA *gb_container, const char *fieldpath)
GBDATA * GBT_find_or_create_item_rel_item_data(GBDATA *gb_item_data, const char *itemname, const char *id_field, const char *id, bool markCreated)
static const char * action_name[]
GBDATA * GBT_create_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type) __ATTR__DEPRECATED_TODO("better use GBT_create_new_alignment()")
GBDATA * GBT_tree_infrontof(GBDATA *gb_tree)
NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target)
NOT4PERL GB_CSTR GBT_read_name(GBDATA *gb_item) __ATTR__DEPRECATED_TODO("please use GBT_get_name or GBT_get_name_or_description()")
GBDATA * GBT_get_species_data(GBDATA *gb_main)
GB_write_int const char s