#include <attributes.h>
Go to the source code of this file.
Function Documentation
Definition at line 16 of file adChangeKey.cxx.
References CHANGEKEY_NAME, GB_CREATE_CONTAINER, GB_find_string(), GB_get_father(), GB_IGNORE_CASE, GB_search(), NULp, and SEARCH_GRANDCHILD.
Referenced by field_delete_cb(), GBT_add_new_changekey_to_keypath(), GBT_convert_changekey(), GBT_get_type_of_changekey(), gbt_set_type_of_changekey(), RegFieldSelection::get_keytype(), hide_field_cb(), reorder_keys(), and reorder_up_down().
| GB_TYPES GBT_get_type_of_changekey | ( | GBDATA * | gb_main, |
| const char * | field_name, | ||
| const char * | change_key_path | ||
| ) |
Definition at line 33 of file adChangeKey.cxx.
References CHANGEKEY_TYPE, GB_NONE, GBT_get_changekey(), GBT_read_int(), and type.
Referenced by awt_string_handler::awar_changed(), awtc_nn_search_all_listed(), field_convert_update_typesel_cb(), GBT_searchOrCreate_itemfield_according_to_changekey(), hits_sort_params::hits_sort_params(), modify_fields_of_queried_cb(), and SpeciesFlag::prepare_itemfield().
| GBDATA* GBT_searchOrCreate_itemfield_according_to_changekey | ( | GBDATA * | gb_item, |
| const char * | field_name, | ||
| const char * | change_key_path | ||
| ) |
search or create an item entry. If the entry exists, the result is identical to GB_search(gb_item, field_name, GB_FIND). If the entry does not exist, an entry with the type stored in the changekey-table will be created.
- Returns
- created itemfield or NULp in case of error (which is exported in that case)
Definition at line 61 of file adChangeKey.cxx.
References gb_assert, GB_clear_error(), GB_export_errorf(), GB_FIND, GB_get_root(), GB_have_error(), GB_NONE, GB_search(), GBT_get_type_of_changekey(), and type.
Referenced by calc_and_update_alignment_errors_cb(), mark_action(), mergeSimilarSpecies(), set_field_of_queried_cb(), and st_ml_add_quality_string_to_species().
| GB_ERROR GBT_add_new_changekey_to_keypath | ( | GBDATA * | gb_main, |
| const char * | name, | ||
| GB_TYPES | type, | ||
| const char * | keypath | ||
| ) |
Add a new or check an existing changekey for items using 'keypath'
- Parameters
-
gb_main database name name of changekey. may be hierarchical (e.g. 'ali_16s/data') type field type of the key (yields error on mismatch!) keypath location in database where changekeys are stored.
- Returns
- error
Definition at line 86 of file adChangeKey.cxx.
References ARB_strdup(), CHANGEKEY, CHANGEKEY_NAME, CHANGEKEY_TYPE, error(), gb_assert, GB_await_error(), GB_CREATE_CONTAINER, GB_create_container(), GB_DB, GB_first_non_key_char(), GB_search(), GBS_global_string(), GBT_get_changekey(), GBT_read_int(), GBT_write_int(), GBT_write_string(), and NULp.
Referenced by awt_string_handler::awar_changed(), field_create_cb(), GBT_add_new_experiment_changekey(), GBT_add_new_gene_changekey(), GBT_add_new_species_changekey(), prepare_and_get_selected_itemfield(), and SpeciesFlag::prepare_itemfield().
Definition at line 133 of file adChangeKey.cxx.
References CHANGE_KEY_PATH, and GBT_add_new_changekey_to_keypath().
Referenced by GBT_add_alignment_changekeys(), GBT_add_new_changekey(), MG_transfer_fields_info(), nt_add_partial(), species_field_selection_list_rescan(), and SQ_add_changekeys().
Definition at line 137 of file adChangeKey.cxx.
References CHANGE_KEY_PATH_GENES, and GBT_add_new_changekey_to_keypath().
Referenced by gene_field_selection_list_rescan().
Definition at line 141 of file adChangeKey.cxx.
References CHANGE_KEY_PATH_EXPERIMENTS, and GBT_add_new_changekey_to_keypath().
Referenced by experiment_field_selection_list_rescan().
Definition at line 145 of file adChangeKey.cxx.
References GBT_add_new_species_changekey().
add changekeys for alignment 'ali'
Definition at line 155 of file adChangeKey.cxx.
References error(), GB_STRING, GBS_global_string_copy(), and GBT_add_new_species_changekey().
Referenced by ALI_translate_marked(), concatenateAlignments(), copy_rename_handler(), create_ali_handler(), gene_extract_handler(), MG_copy_and_check_alignments(), MG_equal_alignments(), PV_WriteTranslatedSequenceToDB(), and split_alignment().
Definition at line 224 of file adChangeKey.cxx.
References write_int_converted().
Referenced by GBT_convert_changekey().
Definition at line 228 of file adChangeKey.cxx.
References write_float_converted().
Referenced by GBT_convert_changekey().
Definition at line 233 of file adChangeKey.cxx.
References CHANGE_KEY_PATH, CHANGEKEY_TYPE, error(), GB_await_error(), GB_create(), GB_delete(), GB_end_transaction(), GB_entry(), GB_FLOAT, GB_INT, GB_push_transaction(), GB_read_as_string(), GB_STRING, GB_warningf(), GB_write_string(), GBS_global_string(), GBT_first_species(), GBT_get_changekey(), GBT_get_name_or_description(), GBT_next_species(), GBT_read_int(), gbt_set_type_of_changekey(), GBT_write_float_converted(), GBT_write_int_converted(), and NO_FIELD_SELECTED.
Referenced by field_convert_commit_cb().
Definition at line 66 of file adRevCompl.cxx.
Referenced by revcomp_op::operate(), and SearchTree::SearchTree().
Definition at line 78 of file adRevCompl.cxx.
References GBT_complementNucleotide().
Referenced by modify_target_string(), revcomp_op::operate(), PV_ComplementarySequence(), and SearchTree::SearchTree().
| NOT4PERL GB_ERROR GBT_determine_T_or_U | ( | GB_alignment_type | alignment_type, |
| char * | T_or_U, | ||
| const char * | supposed_target | ||
| ) |
Definition at line 90 of file adRevCompl.cxx.
References GB_AT_DNA, GB_AT_RNA, GBS_global_string(), and NULp.
Referenced by alignToNextRelative(), GBT_read_gene_sequence_and_length(), modify_target_string(), PV_ComplementarySequence(), revcomp_op::revcomp_op(), reverseComplement(), SearchTree::SearchTree(), and track_ali_change_cb().
Definition at line 102 of file adRevCompl.cxx.
References GBT_complementNucleotide().
Referenced by alignToNextRelative(), GBT_read_gene_sequence_and_length(), modify_target_string(), mp_file2list(), ProbeMatchParser::ProbeMatchParser(), and reverseComplement().
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().
Definition at line 34 of file adali.cxx.
References GB_entry(), GB_nextEntry(), and GBT_get_presets().
Referenced by NT_format_all_alignments().
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().
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().
| 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().
Definition at line 584 of file adali.cxx.
References COPY, and copy_move_del_alignment().
Referenced by copy_rename_handler().
Definition at line 587 of file adali.cxx.
References copy_move_del_alignment(), and MOVE.
Referenced by copy_rename_handler(), and MG_equal_alignments().
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().
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().
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().
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().
- 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().
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().
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().
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().
- 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().
- 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().
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().
- 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().
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().
| 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().
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().
| 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 | ||
| ) |
Search for an existing or create a new, named item.
- Parameters
-
gb_item_data item container itemname description of itemtype (for error messages) id_field item-field containing ID (e.g. "name") id the ID itself (compare is case-insensitive) markCreated true -> mark item if it was created
- Returns
- found/created item or NULp if an error occurs (which is exported in that case)
Definition at line 18 of file aditem.cxx.
References error(), GB_await_error(), GB_create_container(), GB_end_transaction(), GB_export_errorf(), GB_push_transaction(), GB_write_flag(), GBT_find_item_rel_item_data(), GBT_write_string(), and NULp.
Referenced by EXP_find_or_create_experiment_rel_exp_data(), GBT_find_or_create_colorset(), GBT_find_or_create_SAI(), and GBT_find_or_create_species_rel_species_data().
| GBDATA* GBT_find_or_create_species_rel_species_data | ( | GBDATA * | gb_species_data, |
| const char * | name, | ||
| bool | markCreated | ||
| ) |
Definition at line 57 of file aditem.cxx.
References GBT_find_or_create_item_rel_item_data().
Referenced by export_to_DB(), GBT_find_or_create_species(), MG_merge_tagged_field_cb(), and species_create_handler().
Definition at line 61 of file aditem.cxx.
References GBT_find_or_create_species_rel_species_data(), and GBT_get_species_data().
Referenced by create_new_species(), and gen_extract_gene_2_pseudoSpecies().
Search for an SAI, when SAI does not exist, create it
Definition at line 65 of file aditem.cxx.
References GBT_find_or_create_item_rel_item_data(), and GBT_get_SAI_data().
Referenced by CON_calc_max_freq(), CON_export(), create_concatInfo_SAI(), create_next_SAI(), export_to_DB(), NT_count_different_chars(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), ALI_ARBDB::put_SAI(), and AP_pos_var::save_aliEntry_to_SAI().
| GBDATA* GBT_find_item_rel_item_data | ( | GBDATA * | gb_item_data, |
| const char * | id_field, | ||
| const char * | id_value | ||
| ) |
search for items starting at item container
- Parameters
-
'gb_item_data' is a container containing items 'id_field' is a field containing a unique identifier for each item (e.g. 'name' for species) 'id_value' expected value of 'id_field'
- Returns
- a pointer to an item with 'id_field' containing 'id_value' or NULp (in this case an error MAY be exported)
Note: If you expect the item to exist, use GBT_expect_item_rel_item_data()
Definition at line 74 of file aditem.cxx.
References GB_find_string(), GB_get_father(), GB_IGNORE_CASE, NULp, and SEARCH_GRANDCHILD.
Referenced by EXP_find_experiment_rel_exp_data(), GBT_create_unique_item_identifier(), GBT_expect_item_rel_item_data(), GBT_find_colorset(), GBT_find_or_create_item_rel_item_data(), GBT_find_SAI(), GBT_find_SAI_rel_SAI_data(), GBT_find_species(), GBT_find_species_rel_species_data(), and GEN_find_gene_rel_gene_data().
| GBDATA* GBT_expect_item_rel_item_data | ( | GBDATA * | gb_item_data, |
| const char * | id_field, | ||
| const char * | id_value | ||
| ) |
like GBT_find_item_rel_item_data(), but also exports an error if the item is not present
Definition at line 91 of file aditem.cxx.
References GB_export_errorf(), GB_find(), GB_get_father(), GB_have_error(), GB_read_key_pntr(), GBT_find_item_rel_item_data(), and SEARCH_GRANDCHILD.
Referenced by GBT_expect_SAI(), GBT_expect_SAI_rel_SAI_data(), GBT_expect_species(), GBT_expect_species_rel_species_data(), and GEN_expect_gene().
Definition at line 105 of file aditem.cxx.
References GBT_find_or_create().
Referenced by addSpeciesToConcatenateList(), AP_tree_root::AP_tree_root(), ARB_main(), calc_and_update_alignment_errors_cb(), compress_sequence_tree(), concatenateFieldsCreateNewSpecies(), copy_move_del_alignment(), copy_SAI_to_species_cb(), create_new_species(), DI_create_matrix_variables(), experiment_field_selection_list_rescan(), export_to_DB(), gbl_findacc(), gbl_findspec(), GBT_begin_rename_session(), GBT_check_alignment(), GBT_check_data(), GBT_count_marked_species(), GBT_create_unique_species_name(), GBT_expect_species(), GBT_find_or_create_species(), GBT_find_species(), GBT_first_marked_species(), GBT_first_species(), GBT_gen_species_array(), GBT_mark_all(), gene_extract_handler(), gene_field_selection_list_rescan(), get_first_species_data(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), ArbImporter::import_data(), launch_MapViewer_cb(), DI_MATRIX::load(), mark_action(), MERGE_sequences_simple(), mg_check_field_cb(), mg_get_first_species_data1(), mg_get_first_species_data2(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), mg_transfer_selected_species(), GroupSearch::perform_search(), popup_new_main_window(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), ArbImporter::read_data(), ReadArbdb(), resort_data_base(), Aligner::run(), QUERY::search_duplicated_field_content(), species_create_handler(), species_field_selection_list_rescan(), transfer_field_of_listed_cb(), and ScopedTransporter::transferAllIn().
Definition at line 109 of file aditem.cxx.
References GB_first_marked().
Referenced by get_first_species(), DI_MATRIX::load(), probe_match_event(), and ReadArbdb().
Definition at line 113 of file aditem.cxx.
References GB_first_marked(), and GBT_get_species_data().
Referenced by aed_start_naligning(), ALI_realign_marked(), ALI_translate_marked(), arb_prm_read(), brute_force_find_next_species(), build_reverse_complement(), CON_export(), CON_insertSequences(), concatenateAlignments(), ED4_get_marked_from_menu(), export_nds_cb(), MO_Liste::fill_marked_bakts(), GBT_create_marked_species_hash(), GBT_store_marked_species(), GEN_first_marked_organism(), GEN_first_marked_pseudo_species(), PHDATA::load(), mergeSimilarSpecies(), nt_add_partial(), nt_build_conf_marked(), NT_count_different_chars(), NT_delete_mark_all_cb(), pd_get_the_names(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), SpeciesSelector::select_first(), sina_start(), species_rename_join(), split_alignment(), SQ_evaluate(), and SQ_mark_species().
Definition at line 116 of file aditem.cxx.
References gb_assert, GB_has_key(), and GB_next_marked().
Referenced by aed_start_naligning(), ALI_realign_marked(), ALI_translate_marked(), arb_prm_read(), brute_force_find_next_species(), build_reverse_complement(), CON_export(), CON_insertSequences(), concatenateAlignments(), ED4_get_marked_from_menu(), export_nds_cb(), MO_Liste::fill_marked_bakts(), GBT_create_marked_species_hash(), GBT_store_marked_species(), GEN_next_marked_organism(), GEN_next_marked_pseudo_species(), get_next_species(), DI_MATRIX::load(), PHDATA::load(), mergeSimilarSpecies(), nt_add_partial(), nt_build_conf_marked(), NT_count_different_chars(), NT_delete_mark_all_cb(), pd_get_the_names(), probe_match_event(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), ReadArbdb(), SpeciesSelector::select_next(), sina_start(), species_rename_join(), split_alignment(), SQ_evaluate(), and SQ_mark_species().
Definition at line 121 of file aditem.cxx.
References GB_entry().
Referenced by ARB_main(), compress_sequence_tree(), GBT_check_alignment(), GBT_check_data(), GBT_gen_species_array(), get_first_species(), DI_MATRIX::load(), mg_check_field_cb(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), and ReadArbdb().
Definition at line 124 of file aditem.cxx.
References GB_entry(), and GBT_get_species_data().
Referenced by awtc_mark_hits(), awtc_nn_search_all_listed(), AWTC_pars_names(), brute_force_find_next_species(), CON_export(), CON_insertSequences(), QUERY::copy_selection_list_2_query_box(), ImportTestData::countSpeciesAndData(), create_ref_hash(), di_mark_by_distance(), EXP_get_first_experiment_data(), find_species_candidates(), GBT_convert_changekey(), GBT_create_species_hash_sized(), GBT_mark_all(), GBT_mark_all_that(), GEN_first_organism(), GEN_first_pseudo_species(), main(), mg_count_queried(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), MP_mark_probes_in_tree(), NT_create_config_after_import(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_suggestValidNames(), ImportTestData::refill_species_list(), rerun_importTest_cb(), SpeciesSelector::select_first(), set_marks_of(), split_alignment(), SQ_evaluate(), SQ_mark_species(), SQ_pass1_no_tree(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_remove_entries(), trackAlignmentChanges(), transfer_field_of_listed_cb(), ScopedTransporter::transferAllIn(), QUERY::unquery_all(), and FilteredExport::write_fasta().
Definition at line 128 of file aditem.cxx.
References gb_assert, GB_has_key(), and GB_nextEntry().
Referenced by ARB_main(), awtc_mark_hits(), awtc_nn_search_all_listed(), AWTC_pars_names(), brute_force_find_next_species(), compress_sequence_tree(), CON_export(), CON_insertSequences(), QUERY::copy_selection_list_2_query_box(), ImportTestData::countSpeciesAndData(), create_ref_hash(), di_mark_by_distance(), EXP_get_next_experiment_data(), find_species_candidates(), GBT_check_alignment(), GBT_check_data(), GBT_convert_changekey(), GBT_create_species_hash_sized(), GBT_gen_species_array(), GBT_mark_all(), GBT_mark_all_that(), GEN_next_organism(), GEN_next_pseudo_species(), get_next_species(), DI_MATRIX::load(), main(), mg_check_field_cb(), mg_count_queried(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), MP_mark_probes_in_tree(), NT_create_config_after_import(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_suggestValidNames(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), ReadArbdb(), ImportTestData::refill_species_list(), SpeciesSelector::select_next(), set_marks_of(), split_alignment(), SQ_evaluate(), SQ_mark_species(), SQ_pass1_no_tree(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_remove_entries(), trackAlignmentChanges(), transfer_field_of_listed_cb(), ScopedTransporter::transferAllIn(), QUERY::unquery_all(), and FilteredExport::write_fasta().
Definition at line 133 of file aditem.cxx.
References GBT_find_item_rel_item_data().
Referenced by add_species_to_merge_list(), addSpeciesToConcatenateList(), calc_and_update_alignment_errors_cb(), concatenateFieldsCreateNewSpecies(), copy_SAI_to_species_cb(), create_new_species(), export_to_DB(), GBT_rename_species(), GEN_find_origin_organism(), mark_action(), MG_transfer_one_species(), mg_transfer_selected_species(), nameIsUnique(), probe_match_event(), readACC(), DI_MATRIX::save(), and species_create_handler().
Definition at line 136 of file aditem.cxx.
References GBT_expect_item_rel_item_data().
Definition at line 139 of file aditem.cxx.
References GBT_find_item_rel_item_data(), and GBT_get_species_data().
Referenced by alignToNextRelative(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_openDefaultURL_on_selected_species(), awtc_nn_search(), AWTC_recreate_name(), build_reverse_complement(), calculateEndPosition(), create_primer_design_window(), EXP_item_type_species_selector::current(), FINAL_TYPE< SEQTYPE >::current(), GEN_item_type_species_selector::current(), di_mark_by_distance(), do_sth_with_species(), ed_submit_info_event(), EXP_get_first_experiment_data(), expect_species_selected(), EDB_root_bact::fill_data(), find_species_by_id(), gbl_read_seq_sai_or_species(), GBT_with_stored_species(), GEN_find_organism(), GEN_get_current_organism(), GEN_get_local_gene_data(), GEN_root::GEN_root(), GEN_species_name_changed_cb(), MO_Liste::get_all_species(), get_selected_imported_species(), get_selected_species(), insert_new_species_terminal(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_remap(), mg_get_selected_species1(), mg_get_selected_species2(), MG_map_species(), MG_update_example(), move_species_to_extended(), nt_add(), NT_create_sai_from_pfold(), nt_extract_configuration(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), PV_WriteTranslatedSequenceToDB(), rerun_importTest_cb(), SpeciesSelector::select_first(), selectValidNameFromList(), st_ml_add_quality_string_to_species(), transfer_field_of_selected_cb(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), and update_exportTest_result_cb().
Definition at line 146 of file aditem.cxx.
References GBT_expect_item_rel_item_data(), and GBT_get_species_data().
Referenced by GetDisplayInfo().
Definition at line 154 of file aditem.cxx.
References GBT_find_or_create().
Referenced by awt_create_select_filter(), copy_move_del_alignment(), copy_SAI_cb(), extended_rename_handler(), GBT_check_alignment(), GBT_check_data(), GBT_expect_SAI(), GBT_find_or_create_SAI(), GBT_find_SAI(), GBT_first_SAI(), GBT_open(), get_first_SAI_data(), ALI_ARBDB::get_SAI(), BI_helix::init(), mg_get_first_sai_data1(), mg_get_first_sai_data2(), MG_transfer_extended(), move_species_to_extended(), nt_build_sai_string(), NT_create_sai_from_pfold(), PT_init_input_data(), and ED4_root::refresh_all_windows().
Definition at line 159 of file aditem.cxx.
References GB_entry().
Referenced by GBT_check_alignment(), get_first_SAI(), and nt_build_sai_string().
Definition at line 162 of file aditem.cxx.
References GB_entry(), and GBT_get_SAI_data().
Referenced by awt_create_select_filter_window_gb_cb(), ED4_pfold_select_SAI_and_update_option_menu(), SAI_selection::fill(), find_SAI_candidates(), GBT_create_SAI_hash(), get_SAI_groups(), NT_del_mark_move_REF(), and split_alignment().
Definition at line 166 of file aditem.cxx.
References gb_assert, GB_has_key(), and GB_nextEntry().
Referenced by awt_create_select_filter_window_gb_cb(), ED4_pfold_select_SAI_and_update_option_menu(), SAI_selection::fill(), find_SAI_candidates(), GBT_check_alignment(), GBT_create_SAI_hash(), get_next_SAI(), get_SAI_groups(), nt_build_sai_string(), NT_del_mark_move_REF(), and split_alignment().
Definition at line 171 of file aditem.cxx.
References GBT_find_item_rel_item_data().
Referenced by copy_SAI_cb(), extended_rename_handler(), BI_helix::init(), MG_transfer_extended(), move_species_to_extended(), nt_build_sai_string(), NT_create_sai_from_pfold(), and PT_init_input_data().
Definition at line 174 of file aditem.cxx.
References GBT_expect_item_rel_item_data().
Referenced by saiHasDataInAli().
Definition at line 177 of file aditem.cxx.
References GBT_find_item_rel_item_data(), and GBT_get_SAI_data().
Referenced by ARB_main(), awt_create_select_filter_window_aw_cb(), awt_set_awar_to_valid_filter_good_for_tree_methods(), ColumnStat::calculate(), copy_SAI_to_species_cb(), create_next_SAI(), AP_pos_var::delete_aliEntry_from_SAI(), delete_SAI_cb(), ED4_getSaiColorString(), ED4_pfold_set_SAI(), edit_SAI_description(), EDB_root_bact::fill_data(), find_SAI_by_id(), Structure3D::FindTypeOfRNA(), gbl_read_seq_sai_or_species(), get_helix_string(), get_SAI_group(), get_selected_SAI(), BI_ecoli_ref::init(), insert_new_species_terminal(), map_extended(), map_SAI_to_scanner(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_remap(), MG_extended_delete_cb(), mg_get_selected_sai1(), mg_get_selected_sai2(), MG_transfer_extended(), modsai_cb(), NT_del_mark_move_REF(), rename_SAI_cb(), saiChanged_callback(), set_SAI_group(), and translateSAItoColors().
Definition at line 184 of file aditem.cxx.
References GBT_expect_item_rel_item_data(), and GBT_get_SAI_data().
Referenced by dot_missing_bases(), FastAligner_start(), FilterDefinition::make_filter(), and update_RangeList().
Definition at line 207 of file aditem.cxx.
References GBT_get_item_count().
Referenced by ARB_main(), AWTC_pars_names(), ST_ML::calc_st_ml(), CheckedConsistencies::CheckedConsistencies(), CON_insertSequences(), create_ref_hash(), di_mark_by_distance(), GBT_begin_rename_session(), GBT_check_data(), GBT_create_marked_species_hash(), GBT_create_species_hash(), GEN_create_pseudo_species_hash(), get_load_count(), nt_add_partial(), nt_create_configuration(), sq_calc_seq_quality_cb(), st_ml_check_sequence_quality(), st_remove_entries(), trackAlignmentChanges(), and FilteredExport::write_fasta().
Definition at line 211 of file aditem.cxx.
References GBT_get_item_count().
Referenced by CheckedConsistencies::CheckedConsistencies(), and GBT_create_SAI_hash().
Definition at line 287 of file aditem.cxx.
References GBT_create_unique_item_identifier(), and GBT_get_species_data().
Referenced by GBT_check_alignment(), and write_entry().
Definition at line 295 of file aditem.cxx.
References gb_assert, GB_number_of_marked_subentries(), GB_pop_transaction(), GB_push_transaction(), GB_read_flag(), gb_species_data, GB_write_flag(), GBT_first_species(), GBT_get_species_data(), and GBT_next_species().
Referenced by FINAL_TYPE< SEQTYPE >::AwtiExportWriter(), ED4_menu_highlight(), GBT_restore_marked_species(), ArbImporter::import_data(), mark_clusters(), mark_gene_species(), mark_organisms(), mark_referred_species(), GroupUIdata::mark_species(), MERGE_create_main_window(), mergeSimilarSpecies(), nt_extract_configuration(), NT_mark_all_cb(), and Aligner::run().
| long GBT_mark_all_that | ( | GBDATA * | gb_main, |
| int | flag, | ||
| bool(*)(GBDATA *, void *) | condition, | ||
| void * | cd | ||
| ) |
Definition at line 334 of file aditem.cxx.
References gb_assert, GB_pop_transaction(), GB_push_transaction(), GB_read_flag(), GB_write_flag(), GBT_first_species(), and GBT_next_species().
Referenced by mark_nontree_cb(), and NT_mark_all_cb().
Definition at line 372 of file aditem.cxx.
References GB_number_of_marked_subentries(), GBT_get_species_data(), and ta.
Referenced by ALI_realign_marked(), ALI_translate_marked(), arb_prm_read(), CON_insertSequences(), concatenateAlignments(), ED4_get_marked_from_menu(), export_nds_cb(), MO_Liste::fill_marked_bakts(), get_load_count(), mergeSimilarSpecies(), NT_count_different_chars(), NT_update_marked_counter(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), PV_PrintMissingDBentryInformation(), and species_rename_join().
stores the currently marked species in a string
- Parameters
-
gb_main database unmark_all if true -> unmark species
- Returns
- ';'-separated list of species names
Note: a faster (but less robust) way to temporarily store species marks, is to use the flag GB_USERFLAG_WASMARKED together with GB_write_user_flag
Definition at line 377 of file aditem.cxx.
References GBS_strstruct::cat(), GBS_strstruct::cut_tail(), GB_write_flag(), GBT_first_marked_species(), GBT_get_name(), GBT_next_marked_species(), GBS_strstruct::put(), and GBS_strstruct::release_memfriendly().
Referenced by EXP_get_first_experiment_data(), and GEN_get_first_gene_data().
| NOT4PERL GB_ERROR GBT_with_stored_species | ( | GBDATA * | gb_main, |
| const char * | stored, | ||
| species_callback | doit, | ||
| int * | clientdata | ||
| ) |
call a function with each species of a list
- Parameters
-
gb_main database stored ';'-separated list of species names doit function to call with each species in 'stored' clientdata is passed to 'doit'
- Returns
- error if sth goes wrong (or if 'doit' reports error)
Definition at line 404 of file aditem.cxx.
References error(), gb_assert, GBT_find_species(), MAX_NAME_LEN, and NULp.
Referenced by EXP_get_first_experiment_data(), GBT_restore_marked_species(), and GEN_get_first_gene_data().
restores marked species.
- Parameters
-
gb_main database stored_marked contains a ';'-separated list of species names to mark (as returned by GBT_store_marked_species)
- Returns
- error if sth goes wrong
Definition at line 446 of file aditem.cxx.
References GBT_mark_all(), GBT_with_stored_species(), NULp, and restore_mark().
Referenced by exp_restore_old_species_marks(), and gen_restore_old_species_marks().
returns the value of the "name" field of any database item or "<unnamed_item>" or similar.
- See also
- GBT_get_name
Definition at line 459 of file aditem.cxx.
References GB_read_key_pntr(), GBS_global_string(), GBT_read_char_pntr(), and result.
Referenced by adaptCopiedAlignment(), aed_start_naligning(), ALI_realign_marked(), alignToNextRelative(), appendNameAndUsedBasePositions(), are_not_in_tree(), auto_select_pseudo_species(), awt_add_sequences_to_list(), awtc_mark_hits(), AP_sequence::bind_to_species(), concatenateAlignments(), QUERY::copy_selection_list_2_query_box(), AP_sequence::do_lazy_load(), dot_sequence_by_consensus(), ED4_get_marked_from_menu(), ED4_pfold_select_SAI_and_update_option_menu(), EXP_get_experiment_id(), expect_entry(), FastAligner_delete_temp_entries(), SAI_selection::fill(), MO_Liste::fill_marked_bakts(), filter_columnstat_SAIs(), find_SAI_candidates(), find_species_candidates(), gbl_findgene(), GBT_convert_changekey(), GBT_read_name(), gbt_rename_alignment_of_item(), gde_filter_weights(), gen_extract_gene_2_pseudoSpecies(), gen_get_gene_id(), GEN_global_gene_identifier(), GEN_organism_not_found(), gene_requires(), get_SAI_description(), export_sequence_data::get_seq_data(), launch_MapViewer_cb(), ListDisplayRow::ListDisplayRow(), PHDATA::load(), mergeSimilarSpecies(), mg_check_field_cb(), MG_export_fields(), MP_mark_probes_in_tree(), nt_add_partial(), NT_fix_gene_data(), perform_query_cb(), PT_prepare_species_sequence(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), readCompactedSequence(), reverseComplement(), set_marks_of(), species_requires(), ScopedTransporter::transferAllIn(), translate_getInfo(), FilteredExport::write_fasta(), and writeStringToAlignment().
returns the value of the "name" field of any database item or NULp.
- See also
- GBT_get_name_or_description
Definition at line 468 of file aditem.cxx.
References GB_entry(), GB_read_char_pntr(), and NULp.
Referenced by build_taxonomy_rek(), ED4_terminal::event_sent_by_parent(), filter_loadable_SAIs(), GroupBuilder::find_best_matching_subtree(), GBT_add_item_to_hash(), GBT_check_data(), GBT_get_colorset_names(), GBT_store_marked_species(), insert_genes_of_organism(), MG_transfer_one_species(), PARS_map_viewer(), read_name(), ImportTestData::refill_species_list(), rerun_importTest_cb(), select_representative(), TopologyShader::shade(), species_rename_handler(), and transfer_field_of_listed_cb().
Definition at line 477 of file aditem.cxx.
References GBT_get_name_or_description().
Definition at line 485 of file aditem.cxx.
References ARB_alloc(), gb_species_data, GBT_first_species_rel_species_data(), GBT_get_species_data(), GBT_next_species(), NULp, and result.
Referenced by resort_data_base().
Definition at line 37 of file adname.cxx.
References all_flag, error(), gb_main, GB_MIND_CASE, GB_push_transaction(), GBS_create_dynaval_hash(), GBS_dynaval_free(), GBT_create_species_hash(), GBT_get_species_count(), GBT_get_species_data(), hash_size(), NameSession, and NULp.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
Definition at line 65 of file adname.cxx.
References gbt_renamed::data, error(), gb_assert, GB_entry(), GB_write_string(), GBS_global_string(), GBS_read_hash(), GBS_write_hash(), GBT_find_species_rel_species_data(), NameSession, and NULp.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
| GB_ERROR GBT_abort_rename_session | ( | void | ) |
Definition at line 127 of file adname.cxx.
References GB_abort_transaction(), gbt_free_rename_session_data(), and NameSession.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
| GB_ERROR GBT_commit_rename_session | ( | void | ) |
Definition at line 166 of file adname.cxx.
References arb_progress::allow_title_reuse(), GBT_config_item::append_to_config_string(), CI_END_OF_CONFIG, CI_SPECIES, gbt_renamed::data, destroy(), CharPtrArray::empty(), error(), GB_await_error(), GB_end_transaction(), GB_entry(), GB_read_char_pntr(), GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBS_read_hash(), GBT_colorset_root(), GBT_find_colorset(), gbt_free_rename_session_data(), GBT_get_colorset_names(), GBT_get_configuration_names(), GBT_get_tree_names(), GBT_load_colorset(), GBT_message(), GBT_read_tree(), gbt_rename_tree_rek(), GBT_save_colorset(), GBT_write_tree(), GEN_first_pseudo_species(), GEN_is_genome_db(), GEN_next_pseudo_species(), arb_progress::inc_and_check_user_abort(), GBT_config::MIDDLE_AREA, GBT_config_item::name, NameSession, GBT_config_parser::nextItem(), NULp, GBS_strstruct::release_memfriendly(), CharPtrArray::remove(), ConstStrArray::replace(), GBT_config::save(), GBT_config::set_definition(), CharPtrArray::size(), GBT_config::TOP_AREA, and GBT_config_item::type.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
| GB_ERROR GBT_compress_sequence_tree2 | ( | GBDATA * | gbd, |
| const char * | tree_name, | ||
| const char * | ali_name | ||
| ) |
Definition at line 889 of file adseqcompr.cxx.
References ASSERT_NO_ERROR, GB_transaction::close(), compress_sequence_tree(), destroy(), DOWNCAST, error(), GB_await_error(), GB_disable_quicksave(), GB_get_requested_undo_type(), GB_internal_error(), gb_main, GB_MAIN(), GB_request_undo_type(), GB_UNDO_KILL, GBT_link_tree(), GBT_name_of_largest_tree(), GBT_read_tree(), GB_MAIN_TYPE::get_transaction_level(), NULp, GB_transaction::ok(), GB_MAIN_TYPE::root_container, and ta.
Referenced by ARB_main(), and NT_database_optimization().
| void GBT_compression_test | ( | struct Unfixed_cb_parameter * | , |
| GBDATA * | gb_main | ||
| ) |
Referenced by popup_new_main_window().
Definition at line 26 of file adtools.cxx.
References error(), gb_assert, GB_create_container(), GB_export_error(), GB_have_error(), GB_write_security_delete(), and NULp.
Referenced by ARB_main(), and GBT_find_or_create().
Definition at line 42 of file adtools.cxx.
References gb_assert, GB_entry(), GB_have_error(), and GBT_create().
Referenced by AliApplicable::apply_to_alignment(), GBT_get_presets(), GBT_get_SAI_data(), GBT_get_species_data(), GBT_get_tree_data(), get_DB_state(), and set_DB_state().
Definition at line 64 of file adtools.cxx.
References ARB_strdup().
Referenced by get_helix_string(), BI_helix::init(), and NT_del_mark_move_REF().
Definition at line 66 of file adtools.cxx.
References ARB_strdup().
Referenced by BI_ecoli_ref::init(), and PT_init_input_data().
scan CONTAINER for existing sub-keys
recurses completely downwards the DB tree
- Parameters
-
fieldNames gets filled with result strings - each string is the path to a node beyond (any child container of) gbd
- every string exists only once
- the first character of a string is the type of the entry
- the strings are sorted alphabetically
gbd node where search starts datapath if not NULp -> only keys with prefix datapath are scanned and the prefix is removed from the resulting key_names.
Note: this function is incredibly slow when called from clients
Warning: avoid to add new callers for this function: the interface is really weird
Definition at line 162 of file adtools.cxx.
References GBS_hash_do_const_loop(), gbs_scan_db_compare(), gbs_scan_db_insert(), gbt_scan_db_start(), GB_DbScanner::hash_table, and NULp.
Referenced by experiment_field_selection_list_rescan(), gene_field_selection_list_rescan(), and species_field_selection_list_rescan().
| void GBT_install_message_handler | ( | GBDATA * | gb_main | ) |
Definition at line 223 of file adtools.cxx.
References find_or_create_error_container(), GB_add_callback(), gb_assert, GB_CB_SON_CREATED, GB_get_root(), GB_pop_transaction(), GB_push_transaction(), GBS_global_string(), GBT_message(), and new_gbt_message_created_cb().
Referenced by GB_login().
When called in client(or server) this causes the DB server to show the message. Message is shown via GB_warning (which uses aw_message in GUIs)
Note: The message is not shown before the transaction ends. If the transaction is aborted, the message is never shown!
see also : GB_warning()
Definition at line 238 of file adtools.cxx.
References error(), find_or_create_error_container(), gb_assert, GB_await_error(), GB_create(), GB_end_transaction(), GB_push_transaction(), GB_STRING, GB_write_string(), and NULp.
Referenced by ARB_main(), CON_insertSequences(), GBT_commit_rename_session(), GBT_install_message_handler(), gbt_read_tree_rek(), DI_MATRIX::load(), main(), mark_as_macro_executor(), nt_add(), nt_add_partial(), GroupSearch::perform_search(), read_tree_and_size_internal(), GBT_config::saveAsOver(), set_marks_of(), show_message(), transform_gbd_to_leaf(), and TREE_load_to_db().
Read value from database field (of type GB_STRING)
- Parameters
-
gb_container where to start search for field fieldpath relative path from gb_container
- Returns
- NULp in case of error (use GB_await_error()) or when field does not exist. otherwise returns a heap copy.
other functions return a pointer to a temporary variable (invalidated by next call)
Definition at line 267 of file adtools.cxx.
References GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_read_string(), GB_search(), NULp, and result.
Referenced by ARB_main(), collectKeysRegisteredInDatabase(), concatenateFieldsCreateNewSpecies(), DI_ENTRY::DI_ENTRY(), ED4_get_and_jump_to_current(), ED4_jump_to_current_species(), ED4_selected_SAI_changed_cb(), ED4_selected_species_changed_cb(), edit_SAI_description(), ALI_selection::fill(), GBT_check_alignment(), GBT_config::GBT_config(), GBT_get_alignment_type_string(), GBT_load_colorset(), get_default_alignment(), getArbFilter(), PHDATA::load(), MG_merge_tagged_field_cb(), nt_build_conf_marked(), NT_suggestValidNames(), pars_generate_aliview(), and relink_pseudo_species_to_organisms().
like GBT_read_string()
but
- field may be of any type (result gets converted to reasonable char*)
Definition at line 290 of file adtools.cxx.
References GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_read_as_string(), GB_search(), NULp, and result.
Referenced by compare_hits(), QUERY::DbQuery_update_list(), and gbl_readdb().
like GBT_read_string()
but
- result is not a heap-copy and may be invalidated by further DB access (especially by overwriting that fields)
Note: Under no circumstances you may modify the result!
Definition at line 307 of file adtools.cxx.
References GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_read_char_pntr(), GB_search(), NULp, and result.
Referenced by compare_hits(), delete_unused_changekeys(), export_format_multiple(), GBT_get_configuration_names(), GBT_get_name_or_description(), GBT_log_to_tree_remark(), gen_extract_gene_2_pseudoSpecies(), get_SAI_group(), get_SAI_groups(), set_field_of_queried_cb(), set_SAI_group(), and XML_recursive().
similar to GBT_read_string()
but
- for fields of type GB_INT
- result gets invalidated by next call
Definition at line 327 of file adtools.cxx.
References GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_read_int(), GB_search(), NULp, and result.
Referenced by ALI_translate_marked(), collectKeysRegisteredInDatabase(), compare_hits(), delete_unused_changekeys(), Itemfield_Selection::fill(), find_largest_tree(), GBT_add_new_changekey_to_keypath(), GBT_convert_changekey(), GBT_get_alignment_len(), GBT_get_type_of_changekey(), RegFieldSelection::get_keytype(), and NodeTextBuilder::init().
similar to GBT_read_string()
but
- for fields of type GB_FLOAT
- result gets invalidated by next call
Definition at line 349 of file adtools.cxx.
References GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_read_float(), GB_search(), NULp, and result.
Referenced by compare_hits().
| char* GBT_readOrCreate_string | ( | GBDATA * | gb_container, |
| const char * | fieldpath, | ||
| const char * | default_value | ||
| ) |
like GBT_read_string(),
but if field does not exist, it will be created and initialized with 'default_value'
Definition at line 371 of file adtools.cxx.
References GB_pop_transaction(), GB_push_transaction(), GB_read_string(), GB_searchOrCreate_string(), NULp, and result.
Referenced by check_for_remote_command(), MG_merge_tagged_field_cb(), and nt_add().
| const char* GBT_readOrCreate_char_pntr | ( | GBDATA * | gb_container, |
| const char * | fieldpath, | ||
| const char * | default_value | ||
| ) |
like GBT_read_char_pntr(),
but if field does not exist, it will be created and initialized with 'default_value'
Definition at line 386 of file adtools.cxx.
References GB_pop_transaction(), GB_push_transaction(), GB_read_char_pntr(), GB_searchOrCreate_string(), NULp, and result.
Referenced by awt_create_select_filter_window_gb_cb(), and ArbImporter::read_data().
| NOT4PERL long* GBT_readOrCreate_int | ( | GBDATA * | gb_container, |
| const char * | fieldpath, | ||
| long | default_value | ||
| ) |
like GBT_read_int(),
but if field does not exist, it will be created and initialized with 'default_value'
Definition at line 402 of file adtools.cxx.
References GB_pop_transaction(), GB_push_transaction(), GB_read_int(), GB_searchOrCreate_int(), NULp, and result.
Referenced by check_for_remote_command(), gb_load_single_key_data(), get_DB_state(), NodeTextBuilder::init(), AWT_graphic_tree::show_ruler(), and tree_vars_callback().
| NOT4PERL float* GBT_readOrCreate_float | ( | GBDATA * | gb_container, |
| const char * | fieldpath, | ||
| float | default_value | ||
| ) |
like GBT_read_float(),
but if field does not exist, it will be created and initialized with 'default_value'
Definition at line 422 of file adtools.cxx.
References gb_assert, GB_pop_transaction(), GB_push_transaction(), GB_read_float(), GB_searchOrCreate_float(), NULp, and result.
Referenced by AWT_graphic_tree::show_ruler().
Write content to database field of type GB_STRING
if field exists, it will be overwritten. if field does not exist, it will be created.
The field should be unique, i.e. it should not exist twice or more in it's parent container
- Returns
- GB_ERROR on failure
Definition at line 451 of file adtools.cxx.
References error(), gb_assert, GB_await_error(), GB_end_transaction(), GB_nextEntry(), GB_push_transaction(), GB_search(), GB_STRING, and GB_write_string().
Referenced by alignToNextRelative(), ARB_main(), check_for_remote_command(), checkAndMergeFields(), CON_export(), concatenateFieldsCreateNewSpecies(), config_comment_changed_cb(), copy_move_del_alignment(), copy_SAI_cb(), copy_SAI_to_species_cb(), create_data_entry(), create_new_species(), create_split_gene(), edit_SAI_description(), experiment_copy_handler(), extended_rename_handler(), findOrCreate_configuration(), GBT_add_new_changekey_to_keypath(), GBT_check_alignment(), GBT_check_data(), GBT_find_or_create_item_rel_item_data(), GBT_gen_accession_number(), GBT_get_configuration_names(), GBT_remote_awar(), GBT_remote_read_awar(), GBT_save_colorset(), GBT_set_default_alignment(), gbt_write_tree(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_or_create_gene_rel_gene_data(), gene_copy_handler(), InsertDatainGDE(), MERGE_sequences_simple(), mg_check_field_cb(), MG_export_fields(), MG_merge_tagged_field_cb(), NT_create_sai_from_pfold(), NT_importValidNames(), NT_suggestValidNames(), remove_redundant_translation(), rename_SAI_cb(), AP_pos_var::save_aliEntry_to_SAI(), GBT_config::saveAsOver(), selectValidNameFromList(), set_addid(), set_SAI_group(), species_copy_cb(), trace_termChange_in_global_awar(), transfer_field_of_listed_cb(), translate_getInfo(), translate_saveInfo(), write_tree_remark(), and writeHistory().
like GBT_write_string(),
but for fields of type GB_INT
Definition at line 471 of file adtools.cxx.
References error(), gb_assert, GB_await_error(), GB_end_transaction(), GB_INT, GB_nextEntry(), GB_push_transaction(), GB_search(), and GB_write_int().
Referenced by create_gene_species(), Itemfield_Selection::fill(), GBT_add_new_changekey_to_keypath(), GBT_check_alignment(), GBT_is_partial(), GBT_set_alignment_len(), GBT_set_color_group(), gbt_set_type_of_changekey(), gbt_write_tree(), gbt_write_tree_nodes(), hide_field_cb(), NT_format_all_alignments(), and GroupBuilder::update_group().
like GBT_write_string(),
but for fields of type GB_BYTE
Definition at line 486 of file adtools.cxx.
References error(), gb_assert, GB_await_error(), GB_BYTE, GB_end_transaction(), GB_nextEntry(), GB_push_transaction(), GB_search(), and GB_write_byte().
Referenced by remove_redundant_translation().
like GBT_write_string(),
but for fields of type GB_FLOAT
Definition at line 502 of file adtools.cxx.
References error(), gb_assert, GB_await_error(), GB_end_transaction(), GB_FLOAT, GB_nextEntry(), GB_push_transaction(), GB_search(), and GB_write_float().
Referenced by tree_write_float().
Open a database (as GB_open does) Additionally:
- disable saving in the PT_SERVER directory,
- create an index for species and extended names (server only!),
- Parameters
-
path filename of the DB opent see GB_login()
- Returns
- database handle (or NULp in which case an error is exported)
- See also
- GB_open()
Definition at line 524 of file adtools.cxx.
References error(), gb_assert, GB_close(), GB_create_index(), GB_disable_path(), GB_export_error(), GB_FIND, GB_have_error(), GB_IGNORE_CASE, GB_number_of_subentries(), GB_open(), GB_path_in_ARBLIB(), GB_search(), GBT_get_SAI_data(), GBT_SAI_INDEX_SIZE, GBT_SPECIES_INDEX_SIZE, hash_size(), max, NULp, and ta.
Referenced by ARB_main(), load_and_startup_main_window(), main(), and SelectedDatabase::open_db_for_merge().
Definition at line 670 of file adtools.cxx.
References error(), GB_read_char_pntr(), GB_searchOrCreate_string(), GB_write_string(), GBS_global_string(), MACRO_TRIGGER_ERROR, NULp, and ta.
Referenced by check_for_remote_command(), and BoundActionTracker::set_recording().
Definition at line 687 of file adtools.cxx.
References error(), GB_await_error(), GB_FIND, GB_read_char_pntr(), GB_search(), GBS_global_string(), MACRO_TRIGGER_ERROR, NULp, and ta.
Referenced by check_for_remote_command(), macro_terminated(), and start_remote_command_for_application().
Definition at line 699 of file adtools.cxx.
References error(), GB_FIND, GB_search(), GB_write_string(), MACRO_TRIGGER_ERROR, NULp, and ta.
Referenced by check_for_remote_command(), and macro_terminated().
| 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 | ||
| ) |
Definition at line 792 of file adtools.cxx.
References remote_awars::action(), error(), GB_begin_transaction(), GB_end_transaction(), GB_write_string(), gbt_wait_for_remote_action(), NULp, remote_awars::result(), start_remote_command_for_application(), and wait_for_dbentry().
Referenced by AWT_trigger_remote_action(), and GBT_remote_action().
Definition at line 809 of file adtools.cxx.
References GBT_remote_action_with_timeout(), mark_as_macro_executor(), and NULp.
| GB_ERROR GBT_remote_awar | ( | GBDATA * | gb_main, |
| const char * | application, | ||
| const char * | awar_name, | ||
| const char * | value | ||
| ) |
Definition at line 815 of file adtools.cxx.
References remote_awars::awar(), error(), GB_begin_transaction(), GB_end_transaction(), GB_write_string(), gbt_wait_for_remote_action(), GBT_write_string(), mark_as_macro_executor(), NULp, remote_awars::result(), start_remote_command_for_application(), remote_awars::value(), and wait_for_dbentry().
| GB_ERROR GBT_remote_read_awar | ( | GBDATA * | gb_main, |
| const char * | application, | ||
| const char * | awar_name | ||
| ) |
Definition at line 834 of file adtools.cxx.
References remote_awars::action(), remote_awars::awar(), error(), GB_begin_transaction(), GB_end_transaction(), GB_write_string(), gbt_wait_for_remote_action(), GBT_write_string(), mark_as_macro_executor(), NULp, start_remote_command_for_application(), remote_awars::value(), and wait_for_dbentry().
make macro_name relative if it is located in or below ARBMACROHOME or ARBMACRO. Inverse function of fullMacroname()
- Returns
- pointer into macro_name (relative part) or macro_name itself (if macro is located somewhere else)
Definition at line 907 of file adtools.cxx.
References GB_getenvARBMACRO(), GB_getenvARBMACROHOME(), macro_name, relative_inside(), and result.
Referenced by RecordingMacro::write_action().
simply execute a macro
In doubt: do not use this function, instead use ../SL/MACROS/macros.hxx
- Parameters
-
macro_name contains the macro filename (either with full path or relative to directories pointed to by ARBMACRO or ARBMACROHOME) loop_marked if true -> call macro once for each marked species run_async if true -> run perl asynchronously (will not detect perl failure in that case!)
Definition at line 919 of file adtools.cxx.
References error(), fullMacroname(), GB_await_error(), GB_path_in_ARBHOME(), GBK_singlequote(), GBK_system(), GBS_global_string_copy(), and NULp.
Referenced by MacroRecorder::execute().
Definition at line 27 of file adtree.cxx.
References GBT_find_or_create().
Referenced by awt_create_TREE_selection_list(), ensure_trees_have_order(), GBT_check_data(), GBT_find_bottom_tree(), GBT_find_top_tree(), GBT_find_tree(), GBT_get_tree_names(), gbt_write_tree(), get_first_tree(), reorder_trees_cb(), and transfer_tree().
| TreeNode* GBT_remove_leafs | ( | TreeNode * | tree, |
| GBT_TreeRemoveType | mode, | ||
| const GB_HASH * | species_hash, | ||
| int * | removed, | ||
| int * | groups_removed | ||
| ) |
Remove leafs from given 'tree'.
- Parameters
-
tree tree from which species will be removed mode defines what to remove species_hash hash translation from leaf-name to species-dbnode (not needed if tree is linked; see GBT_link_tree) removed will be incremented for each removed leaf (if !NULp) groups_removed will be incremented for each removed group (if !NULp)
- Returns
- new root node
if 'species_hash' is not provided and tree is not linked, the function will silently act strange:
- GBT_REMOVE_MARKED and GBT_REMOVE_UNMARKED will remove any leaf
- GBT_REMOVE_ZOMBIES and GBT_KEEP_MARKED will remove all leafs
Definition at line 34 of file adtree.cxx.
References destroy(), TreeNode::fixDeletedSon(), TreeNode::forget_origin(), TreeNode::forget_relatives(), gb_assert, TreeNode::gb_node, GB_read_flag(), GBS_read_hash(), GBT_REMOVE_MARKED, GBT_REMOVE_UNMARKED, GBT_REMOVE_ZOMBIES, TreeNode::get_tree_root(), TreeNode::is_leaf(), TreeNode::is_root_node(), TreeNode::leftson, TreeNode::name, NULp, TreeNode::rightson, and tree.
Referenced by NT_alltree_remove_leafs(), and sq_calc_seq_quality_cb().
| GB_ERROR GBT_write_group_name | ( | GBDATA * | gb_group_name, |
| const char * | new_group_name, | ||
| bool | pedantic | ||
| ) |
Definition at line 230 of file adtree.cxx.
References GBS_strstruct::cat(), GBS_strstruct::cat_sQuoted(), error(), gb_assert, GB_GROUP_NAME_MAX, GB_read_key_pntr(), GB_warningf(), GB_write_string(), GBS_global_string(), GBS_static_string(), GBS_strstruct::get_data(), KEELED_INDICATOR, label, GBS_strstruct::nprintf(), NULp, and parse_treelabel().
Referenced by gbt_read_tree_rek(), GBT_write_name_to_groupData(), gbt_write_tree_nodes(), FoundGroup::rename_by_ACI(), and SpecSetRegistry::write_node_information().
| GB_ERROR GBT_write_name_to_groupData | ( | GBDATA * | gb_group, |
| bool | createNameEntry, | ||
| const char * | new_group_name, | ||
| bool | pedantic | ||
| ) |
Definition at line 325 of file adtree.cxx.
References GB_await_error(), GB_FIND, GB_search(), GB_STRING, and GBT_write_group_name().
Referenced by AWT_graphic_tree::toggle_group(), and GroupBuilder::update_group().
Definition at line 523 of file adtree.cxx.
References gbt_write_tree(), and NULp.
Referenced by ARB_main(), compress_sequence_tree(), di_calculate_tree_cb(), GBT_commit_rename_session(), GBT_write_tree_with_remark(), main(), NT_alltree_remove_leafs(), and AP_tree_root::saveToDB().
Definition at line 526 of file adtree.cxx.
References GB_get_root(), gbt_write_tree(), and NULp.
Referenced by adjustTreeRoot(), NTREE_move_tree_info(), and ARB_seqtree_root::saveToDB().
Definition at line 533 of file adtree.cxx.
References GBT_find_tree(), and write_tree_remark().
Referenced by di_calculate_tree_cb(), GBT_write_tree_with_remark(), and main().
append 'log_entry' to tree comment
- Parameters
-
gb_tree the tree log_entry text to append stamp true -> prefix date before 'log_entry'
- Returns
- error in case of failure
Definition at line 537 of file adtree.cxx.
References error(), GB_await_error(), GB_have_error(), GBS_log_action_to(), GBT_read_char_pntr(), NULp, and write_tree_remark().
Referenced by adjustTreeRoot(), GBT_log_to_named_trees_remark(), and NTREE_move_tree_info().
| GB_ERROR GBT_log_to_named_trees_remark | ( | GBDATA * | gb_main, |
| const char * | tree_name, | ||
| const char * | log_entry, | ||
| bool | stamp | ||
| ) |
append 'log_entry' to tree comment
- Parameters
-
gb_main database tree_name name of tree log_entry text to append stamp true -> prefix date before 'log_entry'
- Returns
- error in case of failure
Definition at line 556 of file adtree.cxx.
References GBS_global_string(), GBT_find_tree(), and GBT_log_to_tree_remark().
Referenced by di_calculate_tree_cb(), and main().
| GB_ERROR GBT_write_tree_with_remark | ( | GBDATA * | gb_main, |
| const char * | tree_name, | ||
| TreeNode * | tree, | ||
| const char * | remark | ||
| ) |
Definition at line 570 of file adtree.cxx.
References error(), GBT_write_tree(), and GBT_write_tree_remark().
Referenced by create_consense_tree_cb(), save_tree_as_newick(), and TREE_load_to_db().
| TreeNode* GBT_read_tree_and_size | ( | GBDATA * | gb_main, |
| const char * | tree_name, | ||
| TreeRoot * | troot, | ||
| int * | tree_size | ||
| ) |
Loads a tree from DB into any user defined structure.
- Parameters
-
gb_main DB root node tree_name is the name of the tree in the db troot constructs the tree-node instances tree_size if specified -> will be set to "size of tree" (aka number of leafs minus 1)
- Returns
- NULp if any error occurs (which is exported then)
- root of loaded tree (dynamic type depends on 'nodeFactory')
Definition at line 770 of file adtree.cxx.
References TreeNode::announce_tree_constructed(), TreeRoot::delete_by_node(), error(), gb_assert, GB_entry(), GB_export_errorf(), GB_FIND, GB_read_int(), GB_search(), GBT_check_tree_name(), GBT_find_tree(), TreeNode::is_normal_group(), NULp, read_tree_and_size_internal(), and tree.
Referenced by GBT_read_tree(), and MatrixOrder::MatrixOrder().
- See also
- GBT_read_tree_and_size()
Definition at line 837 of file adtree.cxx.
References GBT_read_tree_and_size(), and NULp.
Referenced by create_consense_tree_cb(), di_calculate_compressed_matrix_cb(), DI_MATRIX::extract_from_tree(), GBT_commit_rename_session(), GBT_compress_sequence_tree2(), get_cached_taxonomy(), load_and_add_tree(), ARB_seqtree_root::loadFromDB(), main(), mark_action(), NT_alltree_remove_leafs(), PVP_calculate(), sort_tree_by_other_tree(), sq_calc_seq_quality_cb(), TREE_write_Newick(), and TREE_write_XML().
Definition at line 842 of file adtree.cxx.
References TreeNode::is_leaf().
Referenced by ARB_main(), count_nodes(), DeconstructedTree::deconstruct_weighted(), export_tree_node_print_xml(), GBT_get_names_of_species_in_tree(), GBT_link_tree_using_species_hash(), get_cached_taxonomy(), and AP_pos_var::retrieve().
Definition at line 880 of file adtree.cxx.
References TreeNode::father, gbt_invalid_because(), gbt_is_invalid(), and TreeNode::is_leaf().
Referenced by di_calculate_tree_cb().
| GB_ERROR GBT_link_tree | ( | TreeNode * | tree, |
| GBDATA * | gb_main, | ||
| bool | show_status, | ||
| int * | zombies, | ||
| int * | duplicates | ||
| ) |
Link a given tree to the database. That means that for all tips the member 'gb_node' is set to the database container holding the species data.
- Parameters
-
tree which will be linked to DB gb_main DB root node show_status show a progress indicator? zombies if specified -> set to number of zombies (aka non-existing species) in tree duplicates if specified -> set to number of duplicated species in tree
- Returns
- error on failure
- See also
- GBT_unlink_tree()
Definition at line 953 of file adtree.cxx.
References error(), GBS_free_hash(), GBT_create_species_hash(), and GBT_link_tree_using_species_hash().
Referenced by ST_ML::calc_st_ml(), compress_sequence_tree(), GBT_compress_sequence_tree2(), get_cached_taxonomy(), ARB_seqtree_root::linkToDB(), PVP_calculate(), AP_tree::relink(), sq_calc_seq_quality_cb(), TREE_write_Newick(), and TREE_write_XML().
| void GBT_unlink_tree | ( | TreeNode * | tree | ) |
Definition at line 986 of file adtree.cxx.
References TreeNode::unlink_from_DB().
Referenced by ARB_seqtree_root::unlinkFromDB().
- Returns
- DB tree container associated with tree_name
- NULp if no such tree exists
Definition at line 993 of file adtree.cxx.
References GB_entry(), and GBT_get_tree_data().
Referenced by ad_tree_set_security(), adjustTreeRoot(), ARB_main(), BoundTreeAwarCallback::bind_tree_callback(), calc_pvp(), TreeAdmin::delete_tree_cb(), GBT_existing_tree(), GBT_log_to_named_trees_remark(), GBT_read_tree_and_size(), GBT_size_of_tree(), GBT_tree_info_string(), GBT_write_tree_remark(), get_cached_taxonomy(), get_source_and_check_target_tree(), ARB_seqtree_root::loadFromDB(), TreeAdmin::make_dest_treename_unique_cb(), MG_transfer_tree(), AP_tree_root::saveToDB(), transfer_tree(), TreeAdmin::tree_copy_or_rename_cb(), tree_vars_callback(), TREE_write_Newick(), and TREE_write_XML().
Definition at line 1031 of file adtree.cxx.
References ensure_trees_have_order(), GB_get_father(), get_tree_idx(), and get_tree_infrontof_idx().
Referenced by reorder_trees_cb(), and transfer_tree().
Definition at line 1036 of file adtree.cxx.
References ensure_trees_have_order(), GB_get_father(), get_tree_behind_idx(), and get_tree_idx().
Referenced by GBT_find_next_tree(), MG_transfer_tree(), reorder_trees_cb(), and transfer_tree().
Definition at line 1042 of file adtree.cxx.
References ensure_trees_have_order(), GBT_get_tree_data(), get_tree_behind_idx(), and get_tree_with_idx().
Referenced by GBT_find_next_tree(), MG_transfer_tree(), and reorder_trees_cb().
Definition at line 1050 of file adtree.cxx.
References ensure_trees_have_order(), GBT_get_tree_data(), and get_tree_infrontof_idx().
Referenced by GBT_name_of_bottom_tree(), reorder_trees_cb(), and transfer_tree().
Definition at line 1056 of file adtree.cxx.
References GBT_find_tree(), GBT_get_tree_name(), and get_first_tree().
Referenced by popup_new_main_window().
Definition at line 1063 of file adtree.cxx.
References gb_assert, GB_get_root(), GBT_find_top_tree(), GBT_tree_behind(), and NULp.
Referenced by TreeAdmin::delete_tree_cb(), and MG_transfer_tree().
Definition at line 1079 of file adtree.cxx.
References gb_assert, GB_read_key_pntr(), is_tree(), and NULp.
Referenced by TreeAdmin::delete_tree_cb(), GBT_existing_tree(), GBT_name_of_bottom_tree(), GBT_name_of_largest_tree(), and MG_transfer_tree().
Definition at line 1085 of file adtree.cxx.
References error(), GB_check_key(), GBS_global_string(), and NO_TREE_SELECTED.
Referenced by di_calculate_tree_cb(), GBT_read_tree_and_size(), gbt_write_tree(), and get_source_and_check_target_tree().
Definition at line 1103 of file adtree.cxx.
References find_largest_tree(), and GBT_get_tree_name().
Referenced by AP_create_pos_var_pars_window(), GBT_compress_sequence_tree2(), and NT_create_database_optimization_window().
Definition at line 1107 of file adtree.cxx.
References GBT_find_bottom_tree(), and GBT_get_tree_name().
Referenced by NT_select_bottom_tree().
Definition at line 1114 of file adtree.cxx.
References GB_entry(), GB_export_errorf(), GB_give_other_buffer(), GB_read_char_pntr(), GB_read_int(), GB_read_security_write(), GB_warningf(), GBS_global_string(), GBT_find_tree(), NULp, and result.
Referenced by AWT_tree_selection::fill().
Definition at line 1162 of file adtree.cxx.
References GB_entry(), GB_read_int(), and GBT_find_tree().
Referenced by pars_check_size().
| void GBT_get_tree_names | ( | ConstStrArray & | names, |
| GBDATA * | gb_main, | ||
| bool | sorted | ||
| ) |
Definition at line 1187 of file adtree.cxx.
References ensure_trees_have_order(), error(), gb_assert, GB_child(), GB_nextChild(), GB_number_of_subentries(), GB_read_key_pntr(), GBK_terminatef(), GBT_get_tree_data(), get_tree_idx(), indexed_name::idx, indexed_name::name, ConstStrArray::put(), CharPtrArray::reserve(), reserve_tree_idx(), and set_tree_idx().
Referenced by collect_searched_trees(), AWT_tree_selection::fill(), GBT_commit_rename_session(), and NT_alltree_remove_leafs().
| NOT4PERL GB_ERROR GBT_move_tree | ( | GBDATA * | gb_moved_tree, |
| GBT_ORDER_MODE | mode, | ||
| GBDATA * | gb_target_tree | ||
| ) |
Definition at line 1245 of file adtree.cxx.
References ensure_trees_have_order(), error(), gb_assert, GB_get_father(), GBT_BEHIND, get_tree_idx(), reserve_tree_idx(), and set_tree_idx().
Referenced by reorder_trees_cb(), and transfer_tree().
Definition at line 1302 of file adtree.cxx.
References copy_tree_container(), error(), GB_get_father(), get_source_and_check_target_tree(), get_tree_idx(), reserve_tree_idx(), and set_tree_idx().
Referenced by TreeAdmin::tree_copy_or_rename_cb().
Definition at line 1320 of file adtree.cxx.
References copy_tree_container(), error(), GB_delete(), GB_test_delete_possible(), GBS_global_string(), and get_source_and_check_target_tree().
Referenced by TreeAdmin::tree_copy_or_rename_cb().
Definition at line 1350 of file adtree.cxx.
References fill_species_name_array(), gb_assert, GBT_count_leafs(), IF_ASSERTION_USED, and result.
Referenced by TreeContainer::add(), mark_action(), and st_ml_check_sequence_quality().
| char* GBT_tree_2_newick | ( | const TreeNode * | tree, |
| NewickFormat | format, | ||
| bool | compact | ||
| ) |
Definition at line 1412 of file adtree.cxx.
References error(), gb_assert, GBS_regreplace(), NULp, nWRAP, GBS_strstruct::put(), GBS_strstruct::release(), result, RUNNING_TEST, and tree2newick().
