#include <awti_imp_local.hxx>
Public Member Functions | |
| ArbImporter (const RootCallback &after_import_cb_) | |
| ~ArbImporter () | |
| GB_ERROR | read_format (const char *file) |
| void | detect_format (AW_root *root) |
| const import_format * | peek_format () const |
| int | next_file () |
| char * | read_line (int tab, char *sequencestart, char *sequenceend) |
| GB_ERROR | read_data (char *ali_name, int security_write, FieldTransfer::RuleSetPtr ruleset) |
| void | set_db_4_nameserver (GBDATA *gb_main) |
| GB_ERROR | import_data (AW_root *awr, const char *mask, bool keep_found_IDs) |
| void | import_and_continueOnSuccess (AW_window *aww) |
| GBDATA * | peekImportDB () |
| GBDATA * | takeImportDB () |
| void | detectAvailableFields (StrArray &fields, FieldsToScan whatToScan) |
Detailed Description
Definition at line 141 of file awti_imp_local.hxx.
Constructor & Destructor Documentation
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inlineexplicit |
Definition at line 163 of file awti_imp_local.hxx.
References awti_assert, and GB_open().
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inline |
Definition at line 176 of file awti_imp_local.hxx.
References awti_assert, and GB_close().
Member Function Documentation
Definition at line 246 of file AWTI_import.cxx.
References ARB_strdup(), error(), GB_path_in_ARBHOME(), GBS_global_string(), IFS_VARIABLES, NULp, and read_import_format().
Referenced by detect_format(), and update_format_description().
| void ArbImporter::detect_format | ( | AW_root * | root | ) |
Definition at line 369 of file AWTI_import.cxx.
References import_format::autodetect, AW_advice(), AW_ADVICE_TOGGLE, aw_message(), AW_root::awar(), AWAR_IMPORT_FILENAME, AWAR_IMPORT_FORMATDIR, AWAR_IMPORT_FORMATNAME, awti_assert, AWTI_IMPORT_CHECK_BUFFER_SIZE, buffer, cmp_ift(), com, encode_escaped_chars(), error(), GB_MIND_CASE, GBS_global_string(), GBS_read_dir(), GBS_string_matches(), GBT_split_string(), NULp, AW_awar::read_char_pntr(), read_format(), AW_awar::read_string(), removeHiddenFiles(), CharPtrArray::size(), SPLIT_DROPEMPTY, and AW_awar::write_string().
Referenced by detect_input_format_cb().
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inline |
Definition at line 184 of file awti_imp_local.hxx.
Referenced by update_format_description().
| int ArbImporter::next_file | ( | ) |
Definition at line 483 of file AWTI_import.cxx.
References aw_message(), awti_assert, error(), GB_await_error(), GB_create_tempfile(), GB_is_privatefile(), GB_unique_filename(), GB_unlink_or_warn(), GBK_system(), GBS_global_string(), GBS_global_string_copy(), GBS_string_eval(), NULp, result, arb_progress::show_comment(), and import_format::system.
Referenced by read_line().
Definition at line 580 of file AWTI_import.cxx.
References ARB_calloc(), awti_assert, import_format::b1, import_format::b2, BUFSIZE, SEQIO::fgets_smartLF(), GB_MIND_CASE, GBS_string_matches(), next_file(), NULp, s, SEPARATOR, and tab().
Referenced by read_data().
| GB_ERROR ArbImporter::read_data | ( | char * | ali_name, |
| int | security_write, | ||
| FieldTransfer::RuleSetPtr | ruleset | ||
| ) |
Definition at line 809 of file AWTI_import.cxx.
References import_format::autocreateacc, aw_question(), awti_assert, import_format::begin, GBS_strstruct::cat(), FieldTransfer::CLONE_ITEM_SPECIES, error(), expandSetVariables(), import_format::filetag, GB_await_error(), GB_command_interpreter_in_env(), GB_create_container(), GB_export_errorf(), GB_FIND, GB_have_error(), GB_MIND_CASE, GB_search(), gb_species_data, GB_STRING, GB_write_string(), GBS_checksum(), GBS_global_string(), GBS_global_string_copy(), GBS_string_2_key(), GBS_string_eval_in_env(), GBS_string_matches(), GBT_create_sequence_data(), GBT_get_species_data(), GBT_readOrCreate_char_pntr(), FieldTransfer::ItemClonedByRuleSet::get_error(), import_format::global_variables, FieldTransfer::ItemClonedByRuleSet::has_error(), SmartPtr< T, C >::isSet(), line, import_format::match, MAX_COMMENT_LINES, NULp, read_line(), import_format::read_this_sequence_line_too, GBS_strstruct::release(), FieldTransfer::REPLACE_ITEM_BY_CLONE, s, import_format::sequenceaci, import_format::sequencecolumn, import_format::sequenceend, import_format::sequencesrt, import_format::sequencestart, SetVariables::set(), arb_progress::show_comment(), import_format::tab, and write_entry().
Referenced by import_data().
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inline |
Definition at line 190 of file awti_imp_local.hxx.
References gb_main.
Referenced by AWTI_open_import_window().
Definition at line 1066 of file AWTI_import.cxx.
References aw_message(), aw_question(), AW_select_nameserver(), AW_root::awar(), AWAR_IMPORT_ALI, AWAR_IMPORT_ALI_PROTECTION, AWAR_IMPORT_ALI_TYPE, AWAR_IMPORT_FTS, AWTC_pars_names(), awti_assert, ARB_ERROR::deliver(), error(), GB_abort_transaction(), GB_await_error(), GB_begin_transaction(), GB_commit_transaction(), GB_delete(), GB_entry(), GB_have_error(), gb_species_data, GB_warningf(), GBS_global_string(), GBS_read_dir(), GBS_string_eval(), GBT_check_alignment_name(), GBT_check_data(), GBT_create_new_alignment(), GBT_get_species_data(), GBT_mark_all(), GEN_is_genome_db(), gene_field_selection_list_rescan(), GENOM_DB_TYPE, ErrorOr< TYPE >::getError(), ErrorOr< TYPE >::getValue(), GI_importGenomeFile(), ErrorOr< TYPE >::hasError(), arb_progress::inc(), arb_progress::inc_and_check_user_abort(), no_files_found_error(), import_format::noautonames, NULp, AW_awar::read_char_pntr(), read_data(), AW_awar::read_int(), AW_awar::read_string(), RESCAN_REFRESH, species_field_selection_list_rescan(), SRT_AUTOCORRECT_ALINAME, arb_progress::subtitle(), ta, wants_import_genome(), and XFER_getFullFTS().
Referenced by import_and_continueOnSuccess(), and rerun_importTest_cb().
| void ArbImporter::import_and_continueOnSuccess | ( | AW_window * | aww | ) |
Definition at line 1303 of file AWTI_import.cxx.
References aw_message(), AW_root::awar(), AWAR_IMPORT_FILENAME, AW_window::get_root(), AW_window::hide(), import_data(), and AW_awar::read_string().
Referenced by import_and_continue_cb().
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inline |
Definition at line 195 of file awti_imp_local.hxx.
Referenced by AWTI_acquire_imported_DB_and_cleanup_importer(), AWTI_cleanup_importer(), AWTI_open_import_window(), and AWTI_set_importDB_pointer().
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inline |
Definition at line 198 of file awti_imp_local.hxx.
References NULp.
Referenced by AWTI_acquire_imported_DB_and_cleanup_importer(), and rerun_importTest_cb().
| void ArbImporter::detectAvailableFields | ( | StrArray & | fields, |
| FieldsToScan | whatToScan | ||
| ) |
Definition at line 1319 of file AWTI_import.cxx.
References ARB_strdup(), collectKeysRegisteredInDatabase(), GBS_global_string_copy(), is_dynamic(), import_match::match, NULp, SCAN_INPUT_FIELDS, SCAN_OUTPUT_FIELDS, AW_root::SINGLETON, and SPECIES_get_selector().
Referenced by ImportFieldScanner::scanFields().
The documentation for this class was generated from the following files:
- AWTI/awti_imp_local.hxx
- AWTI/AWTI_import.cxx
