ARB
Classes | Macros | Typedefs | Enumerations | Functions | Variables
MG_species.cxx File Reference
#include "merge.hxx"
#include "MG_adapt_ali.hxx"
#include <AW_rename.hxx>
#include <db_query.h>
#include <db_scanner.hxx>
#include <item_sel_list.h>
#include <xfergui.h>
#include <xferset.h>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <arb_str.h>
#include <arb_strbuf.h>
#include <arb_global_defs.h>
Include dependency graph for MG_species.cxx:

Go to the source code of this file.

Classes

class  ScopedTransporter
 
class  AdaptedAlignmentTransporter
 
class  ViaFtsTransporter
 
struct  MergeFieldScanner
 

Macros

#define AWAR_SPECIES_SRC   AWAR_MERGE_TMP_SRC "name"
 
#define AWAR_FIELD_SRC   AWAR_MERGE_TMP_SRC "field"
 
#define AWAR_TAG_SRC   AWAR_MERGE_TMP_SRC "tag"
 
#define AWAR_SPECIES_DST   AWAR_MERGE_TMP_DST "name"
 
#define AWAR_FIELD_DST   AWAR_MERGE_TMP_DST "field"
 
#define AWAR_TAG_DST   AWAR_MERGE_TMP_DST "tag"
 
#define AWAR_TAG_DEL   AWAR_MERGE_TMP "tagdel"
 
#define AWAR_APPEND   AWAR_MERGE_TMP "append"
 
#define AWAR_SPECIES_XFER_TYPE   AWAR_MERGE_SAV "xferType"
 
#define AWAR_SPECIES_XFER_SCOPE   AWAR_MERGE_SAV "xferScope"
 
#define AWAR_SPECIES_XFER_FTS   AWAR_MERGE_SAV "fts"
 

Typedefs

typedef SmartPtr< MG_remapsMG_remapsPtr
 

Enumerations

enum  SpeciesXferType { SXT_WHOLE_SPECIES, SXT_SINGLE_FIELD, SXT_USING_FTS }
 
enum  SpeciesXferScope { SXS_SELECTED_SPECIES, SXS_LISTED_SPECIES }
 

Functions

const charMG_left_AWAR_SPECIES_NAME ()
 
void MG_create_species_awars (AW_root *aw_root, AW_default aw_def)
 
static void MG_map_species (AW_root *aw_root, DbSel db)
 
static GB_ERROR MG_transfer_fields_info (char *fieldname=NULp)
 
static GB_ERROR MG_transfer_one_species (AW_root *aw_root, MG_remaps &remap, GBDATA *gb_src_species, GBDATA *gb_dst_species_data, bool src_is_genome, bool dst_is_genome, GB_HASH *source_organism_hash, GB_HASH *dest_species_hash, GB_HASH *error_suppressor)
 
static const charget_reference_species_names (AW_root *awr)
 
static bool adaption_enabled (AW_root *awr)
 
static void mg_transfer_selected_species (AW_window *aww)
 
static void mg_transfer_listed_species (AW_window *aww)
 
static GB_ERROR transfer_single_field (GBDATA *const gb_src_species, GBDATA *const gb_dst_species, const char *const field, GBDATA *const gb_src_field, const bool append, const bool transfer_of_alignment, const MG_remaps &rm)
 
bool fieldContainsAlignment (const char *field)
 
static void transfer_field_of_listed_cb (AW_window *aww)
 
static void transfer_field_of_selected_cb (AW_window *aww)
 
static void popup_single_field_transfer_window (AW_root *aw_root, SpeciesXferScope scope)
 
static void MG_merge_tagged_field_cb (AW_window *aww)
 
static AW_windowcreate_mg_merge_tagged_fields_window (AW_root *aw_root)
 
static GB_ERROR MG_equal_alignments (bool autoselect_equal_alignment_name)
 
GB_ERROR MERGE_sequences_simple (AW_root *awr)
 
static void mg_select_species1 (GBDATA *, AW_root *aw_root, const char *item_name)
 
static void mg_select_species2 (GBDATA *, AW_root *aw_root, const char *item_name)
 
static GBDATAmg_get_first_species_data1 (GBDATA *, AW_root *, QUERY_RANGE)
 
static GBDATAmg_get_first_species_data2 (GBDATA *, AW_root *, QUERY_RANGE)
 
static GBDATAmg_get_selected_species1 (GBDATA *, AW_root *aw_root)
 
static GBDATAmg_get_selected_species2 (GBDATA *, AW_root *aw_root)
 
static void mg_initialize_species_selectors ()
 
static void mg_xfer_via_fts (AW_root *aw_root, SpeciesXferScope scope)
 
static void MG_transfer_species (AW_window *aww)
 
AW_windowMG_create_merge_species_window (AW_root *awr, bool dst_is_new)
 

Variables

static DbScannerscanner_src = NULp
 
static DbScannerscanner_dst = NULp
 
static MutableItemSelector MG_species_selector [2]
 
static MergeFieldScanner fieldScanner
 

Macro Definition Documentation

#define AWAR_SPECIES_SRC   AWAR_MERGE_TMP_SRC "name"
#define AWAR_FIELD_SRC   AWAR_MERGE_TMP_SRC "field"
#define AWAR_TAG_SRC   AWAR_MERGE_TMP_SRC "tag"
#define AWAR_SPECIES_DST   AWAR_MERGE_TMP_DST "name"
#define AWAR_FIELD_DST   AWAR_MERGE_TMP_DST "field"
#define AWAR_TAG_DST   AWAR_MERGE_TMP_DST "tag"
#define AWAR_TAG_DEL   AWAR_MERGE_TMP "tagdel"
#define AWAR_APPEND   AWAR_MERGE_TMP "append"
#define AWAR_SPECIES_XFER_TYPE   AWAR_MERGE_SAV "xferType"
#define AWAR_SPECIES_XFER_SCOPE   AWAR_MERGE_SAV "xferScope"
#define AWAR_SPECIES_XFER_FTS   AWAR_MERGE_SAV "fts"

Typedef Documentation

Definition at line 1055 of file MG_species.cxx.

Enumeration Type Documentation

Enumerator
SXT_WHOLE_SPECIES 
SXT_SINGLE_FIELD 
SXT_USING_FTS 

Definition at line 51 of file MG_species.cxx.

Enumerator
SXS_SELECTED_SPECIES 
SXS_LISTED_SPECIES 

Definition at line 57 of file MG_species.cxx.

Function Documentation

const char* MG_left_AWAR_SPECIES_NAME ( )
void MG_create_species_awars ( AW_root aw_root,
AW_default  aw_def 
)
static void MG_map_species ( AW_root aw_root,
DbSel  db 
)
static
static GB_ERROR MG_transfer_fields_info ( char fieldname = NULp)
static
static GB_ERROR MG_transfer_one_species ( AW_root aw_root,
MG_remaps remap,
GBDATA gb_src_species,
GBDATA gb_dst_species_data,
bool  src_is_genome,
bool  dst_is_genome,
GB_HASH source_organism_hash,
GB_HASH dest_species_hash,
GB_HASH error_suppressor 
)
static
static const char* get_reference_species_names ( AW_root awr)
static
static bool adaption_enabled ( AW_root awr)
static
static void mg_transfer_selected_species ( AW_window aww)
static
static void mg_transfer_listed_species ( AW_window aww)
static
static GB_ERROR transfer_single_field ( GBDATA *const  gb_src_species,
GBDATA *const  gb_dst_species,
const char *const  field,
GBDATA *const  gb_src_field,
const bool  append,
const bool  transfer_of_alignment,
const MG_remaps rm 
)
static
bool fieldContainsAlignment ( const char field)
inline
static void transfer_field_of_listed_cb ( AW_window aww)
static
static void transfer_field_of_selected_cb ( AW_window aww)
static
static void popup_single_field_transfer_window ( AW_root aw_root,
SpeciesXferScope  scope 
)
static
static void MG_merge_tagged_field_cb ( AW_window aww)
static
static AW_window* create_mg_merge_tagged_fields_window ( AW_root aw_root)
static
static GB_ERROR MG_equal_alignments ( bool  autoselect_equal_alignment_name)
static
GB_ERROR MERGE_sequences_simple ( AW_root awr)
static void mg_select_species1 ( GBDATA ,
AW_root aw_root,
const char item_name 
)
static
static void mg_select_species2 ( GBDATA ,
AW_root aw_root,
const char item_name 
)
static
static GBDATA* mg_get_first_species_data1 ( GBDATA ,
AW_root ,
QUERY_RANGE   
)
static

Definition at line 877 of file MG_species.cxx.

References GBT_get_species_data(), and GLOBAL_gb_src.

Referenced by mg_initialize_species_selectors().

static GBDATA* mg_get_first_species_data2 ( GBDATA ,
AW_root ,
QUERY_RANGE   
)
static

Definition at line 880 of file MG_species.cxx.

References GBT_get_species_data(), and GLOBAL_gb_dst.

Referenced by mg_initialize_species_selectors().

static GBDATA* mg_get_selected_species1 ( GBDATA ,
AW_root aw_root 
)
static
static GBDATA* mg_get_selected_species2 ( GBDATA ,
AW_root aw_root 
)
static
static void mg_initialize_species_selectors ( )
static
static void mg_xfer_via_fts ( AW_root aw_root,
SpeciesXferScope  scope 
)
static
static void MG_transfer_species ( AW_window aww)
static
AW_window* MG_create_merge_species_window ( AW_root awr,
bool  dst_is_new 
)

Definition at line 1172 of file MG_species.cxx.

References AW_awar::add_callback(), AW_window::at(), aw_message(), AW_POPDOWN(), AW_root::awar(), AW_root::awar_int(), AWAR_REMAP_ENABLE, AWAR_REMAP_SPECIES_LIST, AWAR_SPECIES_DST, AWAR_SPECIES_SRC, AWAR_SPECIES_XFER_FTS, AWAR_SPECIES_XFER_SCOPE, AWAR_SPECIES_XFER_TYPE, AW_root::awar_string(), AWM_ALL, AWM_DISABLED, AW_window::button_length(), QUERY::query_spec::by_pos_fig, AW_window::callback(), QUERY::query_spec::config_pos_fig, QUERY::query_spec::count_pos_fig, DbScanner::create(), AW_window::create_autosize_button(), AW_window::create_button(), AW_window::create_menu(), create_mg_check_fields_window(), create_mg_merge_tagged_fields_window(), AW_window::create_option_menu(), QUERY::create_query_box(), AW_window::create_text_field(), AW_window::create_toggle(), DB_SCANNER, QUERY::query_spec::do_delete_pos_fig, QUERY::query_spec::do_mark_pos_fig, QUERY::query_spec::do_query_pos_fig, QUERY::query_spec::do_refresh_pos_fig, QUERY::query_spec::do_set_pos_fig, QUERY::query_spec::do_unmark_pos_fig, DST_DB, QUERY::query_spec::ere_pos_fig, error(), QUERY::query_spec::expect_hit_in_ref_list, QUERY::query_spec::gb_main, QUERY::query_spec::gb_ref, GB_USERFLAG_QUERY, QUERY::query_spec::get_queried_itemtype(), AW_window::get_root(), GLOBAL_gb_dst, GLOBAL_gb_src, AW_window_simple_menu::init(), AW_window::insert_menu_topic(), AW_window::insert_option(), QUERY::query_spec::key_pos_fig, AW_window::load_xfig(), makeHelpCallback(), MG_create_preserves_selection_window(), MG_expect_renamed(), MG_gene_species_create_field_transfer_def_window(), mg_initialize_species_selectors(), MG_map_species(), MG_transfer_species(), NULp, QUERY::query_spec::open_parser_pos_fig, QUERY::query_spec::qbox_pos_fig, QUERY::query_spec::query_pos_fig, QUERY::query_spec::result_pos_fig, QUERY::query_spec::select_bit, AW_window::sens_mask(), AW_window::sep______________(), ScopedTransporter::set_query_to_update(), AW_window::shadow_width(), QUERY::query_spec::species_name, SRC_DB, SXS_LISTED_SPECIES, SXS_SELECTED_SPECIES, SXT_SINGLE_FIELD, SXT_USING_FTS, SXT_WHOLE_SPECIES, QUERY::query_spec::tree_name, AW_window::update_option_menu(), QUERY::query_spec::use_menu, AW_awar::write_int(), and XFER_select_RuleSet().

Referenced by MERGE_create_main_window().

Variable Documentation

DbScanner* scanner_src = NULp
static

Definition at line 48 of file MG_species.cxx.

DbScanner* scanner_dst = NULp
static

Definition at line 49 of file MG_species.cxx.

Referenced by MG_map_species().

MutableItemSelector MG_species_selector[2]
static

Definition at line 901 of file MG_species.cxx.

MergeFieldScanner fieldScanner
static

Definition at line 1146 of file MG_species.cxx.