#include "seqio.hxx"#include <AP_filter.hxx>#include <xferset.h>#include <arbdbt.h>#include <gb_aci.h>#include <arb_strarray.h>#include <arb_file.h>#include <arb_diff.h>#include <arb_progress.h>#include <arb_global_defs.h>#include <xml.hxx>#include <unistd.h>
Go to the source code of this file.
Classes | |
| struct | export_format |
| class | SpeciesSelector |
| class | export_sequence_data |
Namespaces | |
| SEQIO | |
Macros | |
| #define | sio_assert(cond) arb_assert(cond) |
Enumerations | |
| enum | EXPORT_CMD { EXPORT_XML, EXPORT_INVALID, EXPORT_USING_FORM } |
Functions | |
| static EXPORT_CMD | check_internal (const char *command) |
| static GB_ERROR | read_export_format (export_format *efo, const char *file, bool load_complete_form) |
| static const char * | exported_sequence (GBDATA *gb_species, size_t *seq_len, GB_ERROR *error) |
| static GB_ERROR | XML_recursive (GBDATA *gbd, int depth) |
| static GB_ERROR | export_species_using_form (FILE *out, const char *form, const GBL_call_env &callEnv) |
| static GB_ERROR | export_write_species (GBDATA *gb_species, FILE *out, const GBL_env &env, const export_format &efo) |
| static GB_ERROR | export_format_single (const char *db_name, const char *formname, const char *outname, char **resulting_outname, RuleSetPtr ruleset) |
| static GB_ERROR | export_format_multiple (const char *dbname, const char *formname, const char *outname, bool multiple, char **resulting_outname, RuleSetPtr ruleset) |
| GB_ERROR | SEQIO::export_by_format (GBDATA *gb_main, ExportWhich which, const char *one_species, AP_filter *filter, int cut_stop_codon, int compress, const char *dbname, const char *formname, const char *field_transfer_set, const char *outname, int multiple, char **real_outname) |
| GB_ERROR | SEQIO::get_exportFormat_information (const char *eft_formname, ExportFormatInfo &info) |
| char * | SEQIO::get_exportFormat_evalForm (const char *eft_formname, GB_ERROR &error) |
Variables | |
| static const char * | internal_export_commands [] |
| static export_sequence_data * | esd = NULp |
Macro Definition Documentation
| #define sio_assert | ( | cond | ) | arb_assert(cond) |
Definition at line 29 of file seq_export.cxx.
Referenced by export_sequence_data::count_species(), export_sequence_data::detectVerticalGaps(), SEQIO::export_by_format(), export_format_single(), export_sequence_data::export_sequence_data(), export_write_species(), exported_sequence(), SEQIO::get_exportFormat_evalForm(), export_sequence_data::get_gb_main(), and XML_recursive().
Enumeration Type Documentation
| enum EXPORT_CMD |
| Enumerator | |
|---|---|
| EXPORT_XML | |
| EXPORT_INVALID | |
| EXPORT_USING_FORM | |
Definition at line 38 of file seq_export.cxx.
Function Documentation
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Definition at line 51 of file seq_export.cxx.
References EXPORT_INVALID.
Referenced by read_export_format().
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Definition at line 90 of file seq_export.cxx.
References SEQIO::appendTo(), check_internal(), export_format::description, error(), EXPORT_INVALID, export_format::export_mode, EXPORT_USING_FORM, export_format::form, GB_await_error(), GB_canonical_path(), GB_failedTo_error(), GB_IO_error(), GB_is_regularfile(), GB_path_in_ARBHOME(), GB_read_fp(), GBS_global_string(), GBS_string_eval(), NULp, export_format::pre_format, SEQIO::read_string_pair(), export_format::suffix, and export_format::system.
Referenced by export_format_single(), SEQIO::get_exportFormat_evalForm(), and SEQIO::get_exportFormat_information().
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Definition at line 479 of file seq_export.cxx.
References export_sequence_data::get_export_sequence(), and sio_assert.
Referenced by SEQIO::export_by_format(), and XML_recursive().
Definition at line 484 of file seq_export.cxx.
References error(), exported_sequence(), GB_child(), GB_DB, GB_get_father(), GB_is_container(), GB_nextChild(), GB_read_as_string(), GB_read_key_pntr(), GB_read_type(), GBT_read_char_pntr(), export_sequence_data::getAlignment(), NULp, seq, and sio_assert.
Referenced by export_write_species().
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Definition at line 543 of file seq_export.cxx.
References error(), fputs(), GB_await_error(), GBS_find_string(), GBS_string_eval_in_env(), and NULp.
Referenced by export_write_species().
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Definition at line 563 of file seq_export.cxx.
References error(), EXPORT_INVALID, export_format::export_mode, export_species_using_form(), EXPORT_USING_FORM, EXPORT_XML, export_format::form, NULp, sio_assert, and XML_recursive().
Referenced by export_format_single().
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Definition at line 583 of file seq_export.cxx.
References ARB_date_string(), arb_progress::auto_subtitles(), FieldTransfer::CLONE_ITEM_SPECIES, error(), export_format::export_mode, export_write_species(), EXPORT_XML, export_sequence_data::first_species(), GB_await_error(), GB_create_tempfile(), GB_informationf(), GB_IO_error(), GB_is_privatefile(), GB_unique_filename(), GB_unlink_or_warn(), GBK_system(), GBS_global_string_copy(), GBS_string_eval(), export_sequence_data::get_gb_main(), arb_progress::inc_and_check_user_abort(), SmartPtr< T, C >::isSet(), export_sequence_data::next_species(), NULp, export_format::pre_format, read_export_format(), FieldTransfer::RENAME_ITEM_WHILE_TEMP_CLONE_EXISTS, sio_assert, export_format::suffix, and export_format::system.
Referenced by export_format_multiple().
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Definition at line 709 of file seq_export.cxx.
References export_sequence_data::count_species(), error(), export_format_single(), export_sequence_data::first_species(), GB_append_suffix(), GB_concat_path(), GB_split_full_path(), GBS_global_string(), GBT_read_char_pntr(), export_sequence_data::next_species(), NULp, oname, and export_sequence_data::set_single_mode().
Referenced by SEQIO::export_by_format().
Variable Documentation
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Definition at line 46 of file seq_export.cxx.
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Definition at line 477 of file seq_export.cxx.
Referenced by SEQIO::export_by_format().
