AWTI_import.cxx File Reference

#include "awti_imp_local.hxx"
#include "awti_edit.hxx"
#include <seqio.hxx>
#include <awt.hxx>
#include <GenomeImport.h>
#include <GEN.hxx>
#include <FileWatch.h>
#include <item_sel_list.h>
#include <aw_advice.hxx>
#include <aw_file.hxx>
#include <AW_rename.hxx>
#include <aw_msg.hxx>
#include <aw_question.hxx>
#include <macros.hxx>
#include <adGene.h>
#include <arb_progress.h>
#include <arb_strbuf.h>
#include <arb_str.h>
#include <gb_aci.h>
#include <climits>
#include <unistd.h>
#include <db_scanner.hxx>

Include dependency graph for AWTI_import.cxx:

Go to the source code of this file.

Classes
class	AliNameAndType
class	ImportFieldScanner

Macros
#define	MAX_COMMENT_LINES   2000
#define	GLOBAL_COMMAND(cmd)   (!error && strcmp(s1, cmd) == 0)
#define	MATCH_COMMAND(cmd)   (GLOBAL_COMMAND(cmd) && (m || !(error = not_in_match_error(cmd))))

Functions
const char *	name_only (const char *fullpath)
GB_ERROR	not_in_match_error (const char *cmd)
bool	wants_import_genome (AW_root *awr)
static char *	encode_escaped_chars (char *com)
static GB_ERROR	read_import_format (const char *fullfile, import_format *ifo, bool *var_set, bool included)
static int	cmp_ift (const void *p0, const void *p1, void *)
bool	is_hidden_file (const char *file)
static void	removeHiddenFiles (StrArray &files)
static void	write_entry (GBDATA *gb_main, GBDATA *gbd, const char *key, const char *str, const char *tag, int append, GB_TYPES type)
static string	expandSetVariables (const SetVariables &variables, const string &source, bool &error_occurred, const import_format *ifo)
bool	contains_wildcards (const char *mask)
static GB_ERROR	no_files_found_error (const char *mask)
bool	is_dynamic (const char *field)
void	AWTI_import_set_ali_and_type (AW_root *awr, const char *ali_name, const char *ali_type, GBDATA *gbmain)
static void	genom_flag_changed (AW_root *awr)
void	AWTI_cleanup_importer ()
static void	import_window_close_cb (AW_window *aww, bool *doExit)
static void	import_and_continue_cb (AW_window *aww)
static void	detect_input_format_cb (AW_window *aww)
static void	update_format_description (const char *ift)
void	AWTI_set_importDB_pointer (GBDATA *&dbPtr)
GBDATA *	AWTI_acquire_imported_DB_and_cleanup_importer ()
static void	create_import_awars (AW_root *awr, const char *def_importname)
void	AWTI_open_import_window (AW_root *awr, const char *def_importname, bool do_exit, GBDATA *gb_main, const RootCallback &after_import_cb)

Variables
static AliNameAndType	last_ali ("ali_new","rna")
static ArbImporter *	importer = NULp
static ImportFieldScanner	fieldScanner

Macro Definition Documentation

#define MAX_COMMENT_LINES   2000

Definition at line 43 of file AWTI_import.cxx.

Referenced by ArbImporter::read_data().

#define GLOBAL_COMMAND

(

cmd

)

(!error && strcmp(s1, cmd) == 0)

Referenced by read_import_format().

#define MATCH_COMMAND

(

cmd

)

(GLOBAL_COMMAND(cmd) && (m || !(error = not_in_match_error(cmd))))

Referenced by read_import_format().

Function Documentation

const char* name_only ( const char *  fullpath )

inline

Definition at line 46 of file AWTI_import.cxx.

Referenced by awt_aps_go(), File_selection::fill(), read_import_format(), Helpfile::readHelp(), and TREE_load().

GB_ERROR not_in_match_error ( const char *  cmd )

inline

Definition at line 52 of file AWTI_import.cxx.

References GBS_global_string().

bool wants_import_genome ( AW_root *  awr )

inline

Definition at line 56 of file AWTI_import.cxx.

References AW_root::awar(), AWAR_IMPORT_GENOM_DB, IMP_GENOME_FLATFILE, and AW_awar::read_int().

Referenced by detect_input_format_cb(), genom_flag_changed(), and ArbImporter::import_data().

static char* encode_escaped_chars ( char *  com )

static

Definition at line 58 of file AWTI_import.cxx.

References ARB_strdup(), result, and s.

Referenced by ArbImporter::detect_format(), and read_import_format().

static GB_ERROR read_import_format ( const char *  fullfile, import_format *  ifo, bool *  var_set, bool  included  )

static

Definition at line 85 of file AWTI_import.cxx.

References import_match::aci, import_match::append, SEQIO::appendTo(), ARB_strdup(), import_format::autocreateacc, import_format::autodetect, import_format::autotag, AW_extract_directory(), awti_assert, import_format::begin, import_match::defined_at, import_format::description, encode_escaped_chars(), import_format::end, error(), import_format::filetag, GB_export_IO_error(), GB_FLOAT, GB_INT, GB_IO_error(), GB_STRING, GBS_global_string(), GBS_global_string_copy(), SetVariables::get(), GLOBAL_COMMAND, import_format::global_variables, import_match::match, import_format::match, MATCH_COMMAND, import_match::mtag, name_only(), import_format::new_format, import_format::new_format_lineno, import_match::next, import_format::noautonames, NULp, SEQIO::read_string_pair(), import_format::read_this_sequence_line_too, import_format::sequenceaci, import_format::sequencecolumn, import_format::sequenceend, import_format::sequencesrt, import_format::sequencestart, SetVariables::set(), import_match::setvar, import_match::srt, import_format::system, import_format::tab, import_match::type, import_format::variable_errors, and import_match::write.

Referenced by ArbImporter::read_format().

static int cmp_ift ( const void *  p0, const void *  p1, void *    )

static

Definition at line 351 of file AWTI_import.cxx.

References ARB_stricmp().

Referenced by ArbImporter::detect_format().

bool is_hidden_file ( const char *  file )

inline

Definition at line 355 of file AWTI_import.cxx.

Referenced by removeHiddenFiles().

static void removeHiddenFiles ( StrArray &  files )

static

Definition at line 361 of file AWTI_import.cxx.

References is_hidden_file().

Referenced by ArbImporter::detect_format().

static void write_entry ( GBDATA *  gb_main, GBDATA *  gbd, const char *  key, const char *  str, const char *  tag, int  append, GB_TYPES  type  )

static

Definition at line 677 of file AWTI_import.cxx.

References ARB_strndup(), awti_assert, GBS_strstruct::cat(), copy(), GB_atof(), GB_create(), GB_entry(), GB_FLOAT, GB_IGNORE_CASE, GB_INT, GB_read_char_pntr(), GB_STRING, GB_write_float(), GB_write_int(), GB_write_string(), GBS_string_matches(), GBT_create_unique_species_name(), GBS_strstruct::get_data(), and GBS_strstruct::put().

Referenced by ArbImporter::read_data().

static string expandSetVariables ( const SetVariables &  variables, const string &  source, bool &  error_occurred, const import_format *  ifo  )

static

Definition at line 766 of file AWTI_import.cxx.

References error(), GB_export_error(), GBS_global_string(), GBS_global_string_copy(), SetVariables::get(), NULp, and import_format::variable_errors.

Referenced by ArbImporter::read_data().

bool contains_wildcards ( const char *  mask )

inline

Definition at line 1021 of file AWTI_import.cxx.

References NULp.

Referenced by no_files_found_error().

static GB_ERROR no_files_found_error ( const char *  mask )

static

Definition at line 1023 of file AWTI_import.cxx.

References contains_wildcards(), error(), GB_await_error(), GB_have_error(), GBS_global_string(), and NULp.

Referenced by ArbImporter::import_data().

bool is_dynamic ( const char *  field )

inline

Definition at line 1317 of file AWTI_import.cxx.

References NULp.

Referenced by ArbImporter::detectAvailableFields().

void AWTI_import_set_ali_and_type	(	AW_root *	awr,
		const char *	ali_name,
		const char *	ali_type,
		GBDATA *	gbmain
	)

Definition at line 1359 of file AWTI_import.cxx.

References AW_root::awar(), AWAR_IMPORT_ALI, AWAR_IMPORT_ALI_PROTECTION, AWAR_IMPORT_ALI_TYPE, GB_clear_error(), GB_entry(), GB_read_int(), GBT_get_alignment(), GENOM_ALIGNMENT, last_ali, NULp, AW_awar::read_string(), ta, AW_awar::write_int(), and AW_awar::write_string().

Referenced by genom_flag_changed(), and NT_import_sequences().

static void genom_flag_changed ( AW_root *  awr )

static

Definition at line 1400 of file AWTI_import.cxx.

References AW_root::awar(), AWAR_IMPORT_FORMATFILTER, AWTI_import_set_ali_and_type(), GENOM_ALIGNMENT, last_ali, AliNameAndType::name(), NULp, AliNameAndType::type(), wants_import_genome(), and AW_awar::write_string().

Referenced by create_import_awars().

void AWTI_cleanup_importer

(

)

Definition at line 1415 of file AWTI_import.cxx.

References importer, NULp, and ArbImporter::peekImportDB().

Referenced by AWTI_acquire_imported_DB_and_cleanup_importer(), import_window_close_cb(), NT_exit(), and nt_seq_load_cb().

static void import_window_close_cb ( AW_window *  aww, bool *  doExit  )

static

Definition at line 1425 of file AWTI_import.cxx.

References AW_POPDOWN(), AWTI_cleanup_importer(), and EXIT_SUCCESS.

Referenced by AWTI_open_import_window().

static void import_and_continue_cb ( AW_window *  aww )

static

Definition at line 1436 of file AWTI_import.cxx.

References ArbImporter::import_and_continueOnSuccess().

Referenced by AWTI_open_import_window().

static void detect_input_format_cb ( AW_window *  aww )

static

Definition at line 1437 of file AWTI_import.cxx.

References aw_message(), ArbImporter::detect_format(), AW_window::get_root(), and wants_import_genome().

Referenced by AWTI_open_import_window().

static void update_format_description ( const char *  ift )

static

Definition at line 1446 of file AWTI_import.cxx.

References AW_root::awar(), AWAR_IMPORT_FORMAT_DESC, import_format::description, GBS_global_string(), NULp, ArbImporter::peek_format(), ArbImporter::read_format(), AW_root::SINGLETON, and AW_awar::write_string().

Referenced by AWTI_open_import_window().

void AWTI_set_importDB_pointer

(

GBDATA *&

dbPtr

)

Definition at line 1469 of file AWTI_import.cxx.

References awti_assert, and ArbImporter::peekImportDB().

Referenced by NT_import_sequences(), nt_intro_start_import(), and startup_gui().

GBDATA* AWTI_acquire_imported_DB_and_cleanup_importer

(

)

Definition at line 1476 of file AWTI_import.cxx.

References awti_assert, AWTI_cleanup_importer(), ArbImporter::peekImportDB(), and ArbImporter::takeImportDB().

Referenced by start_main_window_after_import().

static void create_import_awars ( AW_root *  awr, const char *  def_importname  )

static

Definition at line 1482 of file AWTI_import.cxx.

References AW_awar::add_callback(), AW_create_fileselection_awars(), AW_root::awar(), AWAR_IMPORT_ALI, AWAR_IMPORT_ALI_PROTECTION, AWAR_IMPORT_ALI_TYPE, AWAR_IMPORT_AUTOCONF, AWAR_IMPORT_FILEBASE, AWAR_IMPORT_FORMAT_DESC, AWAR_IMPORT_FORMATBASE, AWAR_IMPORT_FTS, AWAR_IMPORT_GENOM_DB, AW_root::awar_int(), AW_root::awar_string(), GBS_strstruct::cat(), GB_path_in_ARBLIB(), GB_path_in_arbprop(), genom_flag_changed(), GBS_strstruct::get_data(), IMP_PLAIN_SEQUENCE, and GBS_strstruct::put().

Referenced by AWTI_open_import_window().

void AWTI_open_import_window	(	AW_root *	awr,
		const char *	def_importname,
		bool	do_exit,
		GBDATA *	gb_main,
		const RootCallback &	after_import_cb
	)

Definition at line 1522 of file AWTI_import.cxx.

References AW_awar::add_callback(), ANY_DIR, AW_create_fileselection(), aw_message_if(), AW_root::awar(), AWAR_IMPORT_ALI, AWAR_IMPORT_ALI_PROTECTION, AWAR_IMPORT_ALI_TYPE, AWAR_IMPORT_AUTOCONF, AWAR_IMPORT_FILEBASE, AWAR_IMPORT_FILENAME, AWAR_IMPORT_FORMAT_DESC, AWAR_IMPORT_FORMATBASE, AWAR_IMPORT_FORMATNAME, AWAR_IMPORT_FTS, AWAR_IMPORT_GENOM_DB, AWM_ALL, AWM_EXP, AWTI_activate_import_test_window(), awti_assert, configure_macro_recording(), create_import_awars(), detect_input_format_cb(), got_macro_ability(), IMP_GENOME_FLATFILE, IMP_PLAIN_SEQUENCE, import_and_continue_cb(), import_window_close_cb(), makeHelpCallback(), MULTI_DIRS, NULp, ArbImporter::peekImportDB(), SCAN_INPUT_FIELDS, ArbImporter::set_db_4_nameserver(), update_format_description(), AW_awar::write_string(), XFER_refresh_available_fields(), and XFER_select_RuleSet().

Referenced by NT_import_sequences(), nt_intro_start_import(), and startup_gui().

Variable Documentation

AliNameAndType last_ali("ali_new","rna")

static

Referenced by AWTI_import_set_ali_and_type(), and genom_flag_changed().

ArbImporter* importer = NULp

static

Definition at line 1413 of file AWTI_import.cxx.

Referenced by AWTI_cleanup_importer(), GI_importGenomeFile(), importerWarning(), and rerun_importTest_cb().

ImportFieldScanner fieldScanner

static

Definition at line 1520 of file AWTI_import.cxx.