ARB
Classes | Macros | Functions | Variables
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 charname_only (const char *fullpath)
 
GB_ERROR not_in_match_error (const char *cmd)
 
bool wants_import_genome (AW_root *awr)
 
static charencode_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)
 
GBDATAAWTI_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 ArbImporterimporter = 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
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
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
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
static string expandSetVariables ( const SetVariables variables,
const string source,
bool &  error_occurred,
const import_format ifo 
)
static
bool contains_wildcards ( const char mask)
inline

Definition at line 1022 of file AWTI_import.cxx.

References NULp.

Referenced by no_files_found_error().

static GB_ERROR no_files_found_error ( const char mask)
static
bool is_dynamic ( const char field)
inline

Definition at line 1316 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 
)
static void genom_flag_changed ( AW_root awr)
static
void AWTI_cleanup_importer ( )
static void import_window_close_cb ( AW_window aww,
bool *  doExit 
)
static

Definition at line 1424 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 1435 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
static void update_format_description ( const char ift)
static
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 
)
static
void AWTI_open_import_window ( AW_root awr,
const char def_importname,
bool  do_exit,
GBDATA gb_main,
const RootCallback &  after_import_cb 
)

Variable Documentation

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

Definition at line 1519 of file AWTI_import.cxx.