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Classes | Macros | Enumerations | Functions | Variables
GEN_map.cxx File Reference
#include "GEN_local.hxx"
#include "GEN_gene.hxx"
#include "GEN_graphic.hxx"
#include "GEN_nds.hxx"
#include "EXP_local.hxx"
#include <dbui.h>
#include <db_query.h>
#include <awt.hxx>
#include <awt_prompt.hxx>
#include <awt_input_mask.hxx>
#include <aw_preset.hxx>
#include <aw_awars.hxx>
#include <aw_question.hxx>
#include <AW_rename.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <adGene.h>
#include <ad_cb.h>
#include <arb_progress.h>
#include <rootAsWin.h>
#include <mode_text.h>
#include <map>
Include dependency graph for GEN_map.cxx:

Go to the source code of this file.

Classes

class  GEN_map_window
 
class  GEN_map_manager
 
struct  gene_container_changed_cb_data
 
struct  EG2PS_data
 
class  GEN_unique_param
 
struct  GEN_command_mode_param
 
struct  GEN_extract_mode_param
 
struct  GEN_item_type_species_selector
 
struct  GEN_update_info
 

Macros

#define DISPLAY_TYPE_BIT(disp_type)   (1<<(disp_type))
 
#define ALL_DISPLAY_TYPES   (DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLES)-1)
 

Enumerations

enum  GEN_PERFORM_MODE {
  GEN_PERFORM_ALL_ORGANISMS, GEN_PERFORM_CURRENT_ORGANISM, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, GEN_PERFORM_MARKED_ORGANISMS,
  GEN_PERFORM_MODES
}
 
enum  GEN_MARK_MODE {
  GEN_MARK, GEN_UNMARK, GEN_INVERT_MARKED, GEN_COUNT_MARKED,
  GEN_EXTRACT_MARKED, GEN_MARK_HIDDEN, GEN_MARK_VISIBLE, GEN_UNMARK_HIDDEN,
  GEN_UNMARK_VISIBLE
}
 
enum  GEN_HIDE_MODE {
  GEN_HIDE_ALL, GEN_UNHIDE_ALL, GEN_INVERT_HIDE_ALL, GEN_HIDE_MARKED,
  GEN_UNHIDE_MARKED, GEN_INVERT_HIDE_MARKED
}
 
enum  MarkCommand { UNMARK, MARK, INVERT, MARK_UNMARK_REST }
 

Functions

 DECLARE_CBTYPE_FVV_AND_BUILDERS (GenmapWindowCallback, void, GEN_map_window *)
 
const char * GEN_window_local_awar_name (const char *awar_name, int window_nr)
 
static void reinit_NDS_4_window (GEN_map_window *win)
 
static void GEN_NDS_changed (GBDATA *gb_viewkey)
 
static void GEN_gene_container_changed_cb (GBDATA *, gene_container_changed_cb_data *cb_data)
 
int GEN_find_windowNr_for (GEN_graphic *wanted_graphic)
 
GBDATA * GEN_get_local_gene_data (GEN_graphic *gg)
 
static void GEN_gene_container_cb_installer (CbInstallMode install, AWT_canvas *gmw, GEN_graphic *gg)
 
static void GEN_jump_cb (AW_window *aww, bool force_center_if_fits)
 
static void GEN_jump_cb_auto (AW_root *root, GEN_map_window *win, bool force_refresh, bool force_zoom_reset)
 
static void GEN_local_organism_or_gene_name_changed_cb (AW_root *awr, GEN_map_window *win)
 
static void GEN_map_window_refresh (GEN_map_window *win)
 
void GEN_refresh_all_windows ()
 
static void GEN_map_window_refresh_if_display_type (GEN_map_window *win, bool zoom_reset, int display_type_mask)
 
static void GEN_update_unlocked_organism_and_gene_awars (GEN_map_window *win, const char *organismName, const char *geneName)
 
static void GEN_organism_or_gene_changed_cb (AW_root *awr)
 
static void GEN_local_lock_changed_cb (AW_root *awr, GEN_map_window *win, bool gene_lock)
 
static void GEN_display_param_changed_cb (AW_root *, bool zoom_reset, int display_type_mask)
 
void set_display_update_callback (AW_root *awr, const char *awar_name, bool zoom_reset, int display_type_mask)
 
static void GEN_create_genemap_local_awars (AW_root *aw_root, AW_default, int window_nr)
 
static void GEN_add_local_awar_callbacks (AW_root *awr, AW_default, GEN_map_window *win)
 
static void GEN_create_genemap_global_awars (AW_root *aw_root, AW_default def, GBDATA *gb_main)
 
static void GEN_add_global_awar_callbacks (AW_root *awr)
 
static void GEN_mode_event (AW_window *aws, GEN_map_window *win, AWT_COMMAND_MODE mode)
 
static void GEN_undo_cb (AW_window *, GB_UNDO_TYPE undo_type, GBDATA *gb_main)
 
static AW_window * GEN_create_options_window (AW_root *awr)
 
static AW_window * GEN_create_gc_window (AW_root *awr, AW_gc_manager *gcman)
 
string performmode_relative_id (const char *id, GEN_PERFORM_MODE pmode)
 
bool nameIsUnique (const char *short_name, GBDATA *gb_species_data)
 
static GB_ERROR GEN_species_add_entry (GBDATA *gb_pseudo, const char *key, const char *value)
 
static const char * readACC (GBDATA *gb_species_data, const char *name)
 
static void gen_extract_gene_2_pseudoSpecies (GBDATA *gb_species, GBDATA *gb_gene, EG2PS_data *eg2ps)
 
static void do_mark_command_for_one_species (int imode, GBDATA *gb_species, AW_CL cl_user)
 
static void do_hide_command_for_one_species (int imode, GBDATA *gb_species, AW_CL)
 
static void GEN_perform_command (GBDATA *gb_main, GEN_PERFORM_MODE pmode, void(*do_command)(int cmode, GBDATA *gb_species, AW_CL cl_user), int mode, AW_CL cl_user)
 
static void GEN_hide_command (AW_window *, GEN_PERFORM_MODE perform_mode, GEN_command_mode_param *param)
 
static void GEN_mark_command (AW_window *, GEN_PERFORM_MODE perform_mode, GEN_command_mode_param *param)
 
static GB_ERROR gene_extract_handler (const char *ali, GEN_extract_mode_param *param)
 
static void gene_extract_cb (AW_window *, GEN_extract_mode_param *param)
 
static void mark_organisms (AW_window *, MarkCommand mark, GBDATA *gb_main)
 
static void mark_gene_species (AW_window *, MarkCommand mark, GBDATA *gb_main)
 
static void mark_gene_species_of_marked_genes (AW_window *, GBDATA *gb_main)
 
static void mark_organisms_with_marked_genes (AW_window *, GBDATA *gb_main)
 
static void mark_gene_species_using_current_alignment (AW_window *, GBDATA *gb_main)
 
static void mark_genes_of_marked_gene_species (AW_window *, GBDATA *gb_main)
 
static void GEN_insert_extract_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file)
 
static void GEN_insert_multi_submenu (AW_window_menu_modes *awm, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file, void(*command)(AW_window *, GEN_PERFORM_MODE, GEN_command_mode_param *), GEN_command_mode_param *command_mode)
 
static void GEN_insert_mark_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file, GEN_MARK_MODE mark_mode)
 
static void GEN_insert_hide_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, const char *macro_prefix, const char *submenu_name, const char *hot_key, const char *help_file, GEN_HIDE_MODE hide_mode)
 
static void GEN_open_mask_window (AW_window *aww, int id, GBDATA *gb_main)
 
static void GEN_create_mask_submenu (AW_window_menu_modes *awm, GBDATA *gb_main)
 
static AW_window * create_colorize_genes_window (AW_root *aw_root, GBDATA *gb_main)
 
static AW_window * create_colorize_organisms_window (AW_root *aw_root, GBDATA *gb_main)
 
static void GEN_create_organism_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, bool submenu)
 
static void GEN_create_gene_species_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, bool submenu)
 
void GEN_create_genes_submenu (AW_window_menu_modes *awm, GBDATA *gb_main, bool for_ARB_NTREE)
 
static void GEN_create_hide_submenu (AW_window_menu_modes *awm, GBDATA *gb_main)
 
static void GEN_set_display_style (AW_window *aww, GEN_DisplayStyle style)
 
static AW_window * GEN_create_map (AW_root *aw_root, GEN_create_map_param *param)
 
AW_window * GEN_create_first_map (AW_root *aw_root, GBDATA *gb_main)
 

Variables

static const char * GEN_PERFORM_MODE_id [GEN_PERFORM_MODES]
 
static AW_repeated_question * ask_about_existing_gene_species = NULp
 
static AW_repeated_question * ask_to_overwrite_alignment = NULp
 
static long gen_count_marked_genes = 0
 
static
GEN_item_type_species_selector 		item_type_gene
 

Macro Definition Documentation

#define DISPLAY_TYPE_BIT (   disp_type)    (1<<(disp_type))

Definition at line 372 of file GEN_map.cxx.

Referenced by GEN_add_global_awar_callbacks(), and GEN_map_window_refresh_if_display_type().

#define ALL_DISPLAY_TYPES   (DISPLAY_TYPE_BIT(GEN_DISPLAY_STYLES)-1)

Definition at line 373 of file GEN_map.cxx.

Referenced by GEN_add_global_awar_callbacks().

Enumeration Type Documentation

enum GEN_PERFORM_MODE
Enumerator
GEN_PERFORM_ALL_ORGANISMS 
GEN_PERFORM_CURRENT_ORGANISM 
GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM 
GEN_PERFORM_MARKED_ORGANISMS 
GEN_PERFORM_MODES 

Definition at line 640 of file GEN_map.cxx.

enum GEN_MARK_MODE
Enumerator
GEN_MARK 
GEN_UNMARK 
GEN_INVERT_MARKED 
GEN_COUNT_MARKED 
GEN_EXTRACT_MARKED 
GEN_MARK_HIDDEN 
GEN_MARK_VISIBLE 
GEN_UNMARK_HIDDEN 
GEN_UNMARK_VISIBLE 

Definition at line 660 of file GEN_map.cxx.

enum GEN_HIDE_MODE
Enumerator
GEN_HIDE_ALL 
GEN_UNHIDE_ALL 
GEN_INVERT_HIDE_ALL 
GEN_HIDE_MARKED 
GEN_UNHIDE_MARKED 
GEN_INVERT_HIDE_MARKED 

Definition at line 679 of file GEN_map.cxx.

enum MarkCommand
Enumerator
UNMARK 
MARK 
INVERT 
MARK_UNMARK_REST 

Definition at line 1177 of file GEN_map.cxx.

Function Documentation

DECLARE_CBTYPE_FVV_AND_BUILDERS ( GenmapWindowCallback  ,
void  ,
GEN_map_window *   
)
const char* GEN_window_local_awar_name ( const char *  awar_name,
int  window_nr 
)

Definition at line 167 of file GEN_map.cxx.

References GBS_global_string().

static void reinit_NDS_4_window ( GEN_map_window *  win)
static

Definition at line 171 of file GEN_map.cxx.

References GEN_map_window::get_canvas(), GEN_graphic::get_gen_root(), GEN_map_window::get_graphic(), GEN_root::reinit_NDS(), and AWT_canvas::request_refresh().

Referenced by GEN_NDS_changed().

static void GEN_NDS_changed ( GBDATA *  gb_viewkey)
static

Definition at line 177 of file GEN_map.cxx.

References GB_get_root(), GEN_make_node_text_init(), reinit_NDS_4_window(), and GEN_map_manager::with_all_mapped_windows().

Referenced by GEN_create_genemap_global_awars().

static void GEN_gene_container_changed_cb ( GBDATA *  ,
gene_container_changed_cb_data *  cb_data 
)
static

Definition at line 196 of file GEN_map.cxx.

References gene_container_changed_cb_data::canvas, gene_container_changed_cb_data::graphic, GEN_graphic::reinit_gen_root(), and AWT_canvas::request_refresh().

Referenced by GEN_gene_container_cb_installer().

int GEN_find_windowNr_for ( GEN_graphic *  wanted_graphic)

Definition at line 202 of file GEN_map.cxx.

References GEN_map_window::get_graphic(), GEN_map_manager::get_map_manager(), GEN_map_manager::get_map_window(), GEN_map_manager::initialized(), and GEN_map_manager::no_of_managed_windows().

Referenced by GEN_get_local_gene_data().

GBDATA* GEN_get_local_gene_data ( GEN_graphic *  gg)
inline

Definition at line 216 of file GEN_map.cxx.

References AW_root::awar(), AWAR_LOCAL_ORGANISM_NAME, GBT_find_species(), gen_assert, GEN_expect_gene_data(), GEN_find_windowNr_for(), GEN_graphic::get_aw_root(), GEN_graphic::get_gb_main(), NULp, and AW_awar::read_char_pntr().

Referenced by GEN_gene_container_cb_installer().

static void GEN_gene_container_cb_installer ( CbInstallMode  install,
AWT_canvas *  gmw,
GEN_graphic *  gg 
)
static

Definition at line 234 of file GEN_map.cxx.

References FORGET_CBS, GB_add_callback(), GB_CB_CHANGED_OR_DELETED, gene_container_changed_cb_data::gb_gene_data, GB_remove_callback(), gen_assert, GEN_gene_container_changed_cb(), GEN_get_local_gene_data(), GEN_graphic::get_gb_main(), INSTALL_CBS, NULp, REMOVE_CBS, and ta.

Referenced by GEN_map_window::init().

static void GEN_jump_cb ( AW_window *  aww,
bool  force_center_if_fits 
)
static

Definition at line 276 of file GEN_map.cxx.

References AW_INT, AW_screen_area::b, AW::Rectangle::bottom(), DOWNCAST, AW_device::get_area_size(), GEN_map_window::get_canvas(), GEN_graphic::get_device(), GEN_graphic::get_gen_root(), GEN_map_window::get_graphic(), GEN_map_window::get_nr(), GEN_root::get_selected_range(), AW_screen_area::l, AW::Rectangle::left(), AW_screen_area::r, AW::Rectangle::right(), AW_screen_area::t, AW::Rectangle::top(), AW_zoomable::transform(), AW::LineVector::valid(), and win.

Referenced by GEN_jump_cb_auto(), and GEN_map_window::init().

static void GEN_jump_cb_auto ( AW_root *  root,
GEN_map_window *  win,
bool  force_refresh,
bool  force_zoom_reset 
)
static

Definition at line 349 of file GEN_map.cxx.

References assert_no_auto_refresh_for, AW_root::awar(), AWAR_GENMAP_AUTO_JUMP, GEN_jump_cb(), GEN_map_window::get_canvas(), AW_awar::read_int(), AWT_canvas::request_refresh(), and AWT_canvas::request_zoom_reset().

Referenced by GEN_local_organism_or_gene_name_changed_cb(), and GEN_map_window_refresh_if_display_type().

static void GEN_local_organism_or_gene_name_changed_cb ( AW_root *  awr,
GEN_map_window *  win 
)
static

Definition at line 364 of file GEN_map.cxx.

References GEN_jump_cb_auto(), GEN_map_window::get_canvas(), GEN_map_window::get_graphic(), and GEN_graphic::reinit_gen_root().

Referenced by GEN_add_local_awar_callbacks().

static void GEN_map_window_refresh ( GEN_map_window *  win)
static

Definition at line 375 of file GEN_map.cxx.

References GEN_map_window::get_canvas(), and AWT_canvas::request_refresh().

Referenced by GEN_map_window_refresh_if_display_type(), and GEN_refresh_all_windows().

void GEN_refresh_all_windows ( )

Definition at line 379 of file GEN_map.cxx.

References GEN_map_window_refresh(), and GEN_map_manager::with_all_mapped_windows().

Referenced by refresh_displayed_genes().

static void GEN_map_window_refresh_if_display_type ( GEN_map_window *  win,
bool  zoom_reset,
int  display_type_mask 
)
static

Definition at line 383 of file GEN_map.cxx.

References DISPLAY_TYPE_BIT, GEN_jump_cb_auto(), GEN_map_window_refresh(), GEN_graphic::get_display_style(), GEN_map_window::get_graphic(), and AW_root::SINGLETON.

Referenced by GEN_display_param_changed_cb().

static void GEN_update_unlocked_organism_and_gene_awars ( GEN_map_window *  win,
const char *  organismName,
const char *  geneName 
)
static

Definition at line 395 of file GEN_map.cxx.

References AW_root::awar(), AWAR_LOCAL_GENE_LOCK, AWAR_LOCAL_GENE_NAME, AWAR_LOCAL_ORGANISM_LOCK, AWAR_LOCAL_ORGANISM_NAME, GEN_graphic::get_aw_root(), GEN_map_window::get_graphic(), GEN_map_window::get_nr(), AW_awar::read_int(), and AW_awar::write_string().

Referenced by GEN_organism_or_gene_changed_cb().

static void GEN_organism_or_gene_changed_cb ( AW_root *  awr)
static

Definition at line 406 of file GEN_map.cxx.

References AW_root::awar(), AWAR_GENE_NAME, AWAR_ORGANISM_NAME, GEN_update_unlocked_organism_and_gene_awars(), AW_awar::read_string(), and GEN_map_manager::with_all_mapped_windows().

Referenced by GEN_add_global_awar_callbacks().

static void GEN_local_lock_changed_cb ( AW_root *  awr,
GEN_map_window *  win,
bool  gene_lock 
)
static

Definition at line 417 of file GEN_map.cxx.

References AW_root::awar(), AWAR_GENE_NAME, AWAR_LOCAL_GENE_LOCK, AWAR_LOCAL_GENE_NAME, AWAR_LOCAL_ORGANISM_LOCK, AWAR_LOCAL_ORGANISM_NAME, AWAR_ORGANISM_NAME, GEN_map_window::get_nr(), AW_awar::map(), NULp, AW_awar::read_int(), AW_awar::read_string(), AW_awar::unmap(), and AW_awar::write_string().

Referenced by GEN_add_local_awar_callbacks().

static void GEN_display_param_changed_cb ( AW_root *  ,
bool  zoom_reset,
int  display_type_mask 
)
static

Definition at line 453 of file GEN_map.cxx.

References GEN_map_window_refresh_if_display_type(), and GEN_map_manager::with_all_mapped_windows().

Referenced by set_display_update_callback().

void set_display_update_callback ( AW_root *  awr,
const char *  awar_name,
bool  zoom_reset,
int  display_type_mask 
)
inline

Definition at line 456 of file GEN_map.cxx.

References AW_awar::add_callback(), AW_root::awar(), and GEN_display_param_changed_cb().

Referenced by GEN_add_global_awar_callbacks().

static void GEN_create_genemap_local_awars ( AW_root *  aw_root,
AW_default  ,
int  window_nr 
)
static

Definition at line 463 of file GEN_map.cxx.

References AWAR_GENMAP_DISPLAY_TYPE, AW_root::awar_int(), AWAR_LOCAL_GENE_LOCK, AWAR_LOCAL_GENE_NAME, AWAR_LOCAL_ORGANISM_LOCK, AWAR_LOCAL_ORGANISM_NAME, AW_root::awar_string(), and GEN_DISPLAY_STYLE_RADIAL.

Referenced by GEN_map_window::init().

static void GEN_add_local_awar_callbacks ( AW_root *  awr,
AW_default  ,
GEN_map_window *  win 
)
static

Definition at line 475 of file GEN_map.cxx.

References AW_awar::add_callback(), AW_root::awar(), AWAR_LOCAL_GENE_LOCK, AWAR_LOCAL_GENE_NAME, AWAR_LOCAL_ORGANISM_LOCK, AWAR_LOCAL_ORGANISM_NAME, GEN_local_lock_changed_cb(), GEN_local_organism_or_gene_name_changed_cb(), GEN_map_window::get_nr(), and AW_awar::touch().

Referenced by GEN_map_window::init().

static void GEN_create_genemap_global_awars ( AW_root *  aw_root,
AW_default  def,
GBDATA *  gb_main 
)
static

Definition at line 495 of file GEN_map.cxx.

References AW_root::awar_float(), AWAR_GENMAP_ARROW_SIZE, AWAR_GENMAP_AUTO_JUMP, AWAR_GENMAP_BOOK_BASES_PER_LINE, AWAR_GENMAP_BOOK_LINE_HEIGHT, AWAR_GENMAP_BOOK_LINE_SPACE, AWAR_GENMAP_BOOK_WIDTH_FACTOR, AWAR_GENMAP_RADIAL_INSIDE, AWAR_GENMAP_RADIAL_OUTSIDE, AWAR_GENMAP_SHOW_ALL_NDS, AWAR_GENMAP_SHOW_HIDDEN, AWAR_GENMAP_VERTICAL_FACTOR_X, AWAR_GENMAP_VERTICAL_FACTOR_Y, AW_root::awar_int(), GEN_create_nds_vars(), GEN_NDS_changed(), and AW_awar::set_minmax().

Referenced by GEN_create_map().

static void GEN_add_global_awar_callbacks ( AW_root *  awr)
static

Definition at line 520 of file GEN_map.cxx.

References AW_awar::add_callback(), ALL_DISPLAY_TYPES, AW_root::awar(), AWAR_GENE_NAME, AWAR_GENMAP_ARROW_SIZE, AWAR_GENMAP_BOOK_BASES_PER_LINE, AWAR_GENMAP_BOOK_LINE_HEIGHT, AWAR_GENMAP_BOOK_LINE_SPACE, AWAR_GENMAP_BOOK_WIDTH_FACTOR, AWAR_GENMAP_RADIAL_INSIDE, AWAR_GENMAP_RADIAL_OUTSIDE, AWAR_GENMAP_SHOW_ALL_NDS, AWAR_GENMAP_SHOW_HIDDEN, AWAR_GENMAP_VERTICAL_FACTOR_X, AWAR_GENMAP_VERTICAL_FACTOR_Y, AWAR_ORGANISM_NAME, DISPLAY_TYPE_BIT, GEN_DISPLAY_STYLE_BOOK, GEN_DISPLAY_STYLE_RADIAL, GEN_DISPLAY_STYLE_VERTICAL, GEN_organism_or_gene_changed_cb(), and set_display_update_callback().

Referenced by GEN_create_map().

static void GEN_mode_event ( AW_window *  aws,
GEN_map_window *  win,
AWT_COMMAND_MODE  mode 
)
static

Definition at line 545 of file GEN_map.cxx.

References AW_root::awar(), AWAR_FOOTER, AWAR_FOOTER_MAX_LEN, AWT_MODE_INFO, AWT_MODE_SELECT, AWT_MODE_ZOOM, gen_assert, GEN_map_window::get_canvas(), AW_window::get_root(), MODE_TEXT_1BUTTON, MODE_TEXT_STANDARD_ZOOMMODE, no_mode_text_defined(), NULp, AWT_canvas::request_refresh(), AWT_canvas::set_mode(), and AW_awar::write_string().

Referenced by GEN_map_window::init().

static void GEN_undo_cb ( AW_window *  ,
GB_UNDO_TYPE  undo_type,
GBDATA *  gb_main 
)
static

Definition at line 567 of file GEN_map.cxx.

References aw_message(), error(), GB_begin_transaction(), GB_commit_transaction(), and GB_undo().

Referenced by GEN_map_window::init().

static AW_window* GEN_create_options_window ( AW_root *  awr)
static

Definition at line 578 of file GEN_map.cxx.

References AW_POPDOWN(), AW_SCALER_EXP_LOWER, AWAR_GENMAP_ARROW_SIZE, AWAR_GENMAP_AUTO_JUMP, AWAR_GENMAP_BOOK_BASES_PER_LINE, AWAR_GENMAP_BOOK_LINE_HEIGHT, AWAR_GENMAP_BOOK_LINE_SPACE, AWAR_GENMAP_BOOK_WIDTH_FACTOR, AWAR_GENMAP_RADIAL_INSIDE, AWAR_GENMAP_RADIAL_OUTSIDE, AWAR_GENMAP_SHOW_ALL_NDS, AWAR_GENMAP_SHOW_HIDDEN, AWAR_GENMAP_VERTICAL_FACTOR_X, AWAR_GENMAP_VERTICAL_FACTOR_Y, makeHelpCallback(), and NULp.

Referenced by GEN_map_window::init().

static AW_window* GEN_create_gc_window ( AW_root *  awr,
AW_gc_manager *  gcman 
)
static

Definition at line 633 of file GEN_map.cxx.

References AW_create_gc_window_named(), and NULp.

Referenced by GEN_map_window::init().

string performmode_relative_id ( const char *  id,
GEN_PERFORM_MODE  pmode 
)
inline

Definition at line 656 of file GEN_map.cxx.

References GBS_global_string().

bool nameIsUnique ( const char *  short_name,
GBDATA *  gb_species_data 
)
inline

Definition at line 691 of file GEN_map.cxx.

References GBT_find_species_rel_species_data().

static GB_ERROR GEN_species_add_entry ( GBDATA *  gb_pseudo,
const char *  key,
const char *  value 
)
static

Definition at line 695 of file GEN_map.cxx.

References error(), GB_await_error(), GB_clear_error(), GB_create(), GB_entry(), GB_export_errorf(), GB_read_type(), GB_STRING, GB_write_string(), and NULp.

Referenced by gen_extract_gene_2_pseudoSpecies().

static const char* readACC ( GBDATA *  gb_species_data,
const char *  name 
)
static

Definition at line 752 of file GEN_map.cxx.

References GB_entry(), GB_read_char_pntr(), GBT_find_species_rel_species_data(), and NULp.

Referenced by gen_extract_gene_2_pseudoSpecies().

static void gen_extract_gene_2_pseudoSpecies ( GBDATA *  gb_species,
GBDATA *  gb_gene,
EG2PS_data *  eg2ps 
)
static

Definition at line 762 of file GEN_map.cxx.

References UniqueNameDetector::add_name(), EG2PS_data::ali, ARB_strdup(), aw_message(), AWTC_generate_one_name(), AWTC_generate_random_name(), EG2PS_data::duplicateSpecies, error(), EG2PS_data::existing, GB_await_error(), GB_entry(), GB_export_errorf(), GB_get_root(), GB_read_char_pntr(), EG2PS_data::gb_species_data, GB_STRING, GB_write_string(), GBS_checksum(), GBS_global_string(), GBS_global_string_copy(), GBT_add_data(), GBT_find_or_create_species(), GBT_get_name_or_description(), GBT_read_char_pntr(), GBT_read_gene_sequence(), GEN_add_pseudo_species_to_hash(), gen_assert, GEN_find_pseudo_species(), GEN_species_add_entry(), UniqueNameDetector::name_known(), EG2PS_data::nameProblem, NULp, EG2PS_data::pseudo_hash, and readACC().

Referenced by do_mark_command_for_one_species().

static void do_mark_command_for_one_species ( int  imode,
GBDATA *  gb_species,
AW_CL  cl_user 
)
static

Definition at line 938 of file GEN_map.cxx.

References ARB_HIDDEN, GB_entry(), GB_read_byte(), GB_read_flag(), GB_write_flag(), gen_assert, GEN_COUNT_MARKED, gen_count_marked_genes, gen_extract_gene_2_pseudoSpecies(), GEN_EXTRACT_MARKED, GEN_first_gene(), GEN_INVERT_MARKED, GEN_MARK, GEN_MARK_HIDDEN, GEN_MARK_VISIBLE, GEN_next_gene(), GEN_UNMARK, GEN_UNMARK_HIDDEN, GEN_UNMARK_VISIBLE, arb_progress::inc(), and EG2PS_data::progress.

Referenced by GEN_mark_command(), and gene_extract_handler().

static void do_hide_command_for_one_species ( int  imode,
GBDATA *  gb_species,
AW_CL   
)
static

Definition at line 983 of file GEN_map.cxx.

References ARB_HIDDEN, GB_BYTE, GB_create(), GB_entry(), GB_read_byte(), GB_read_flag(), GB_write_byte(), gen_assert, GEN_first_gene(), GEN_HIDE_ALL, GEN_HIDE_MARKED, GEN_INVERT_HIDE_ALL, GEN_INVERT_HIDE_MARKED, GEN_next_gene(), GEN_UNHIDE_ALL, and GEN_UNHIDE_MARKED.

Referenced by GEN_hide_command().

static void GEN_perform_command ( GBDATA *  gb_main,
GEN_PERFORM_MODE  pmode,
void(*)(int cmode, GBDATA *gb_species, AW_CL cl_user)  do_command,
int  mode,
AW_CL  cl_user 
)
static

Definition at line 1013 of file GEN_map.cxx.

References aw_message(), error(), GB_begin_transaction(), GB_end_transaction_show_error(), gen_assert, GEN_first_marked_organism(), GEN_first_organism(), GEN_get_current_organism(), GEN_next_marked_organism(), GEN_next_organism(), GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, GEN_PERFORM_ALL_ORGANISMS, GEN_PERFORM_CURRENT_ORGANISM, GEN_PERFORM_MARKED_ORGANISMS, and NULp.

Referenced by GEN_hide_command(), GEN_mark_command(), and gene_extract_handler().

static void GEN_hide_command ( AW_window *  ,
GEN_PERFORM_MODE  perform_mode,
GEN_command_mode_param *  param 
)
static

Definition at line 1098 of file GEN_map.cxx.

References do_hide_command_for_one_species(), GEN_unique_param::gb_main, GEN_perform_command(), and GEN_command_mode_param::get_command_mode().

Referenced by GEN_insert_hide_submenu().

static void GEN_mark_command ( AW_window *  ,
GEN_PERFORM_MODE  perform_mode,
GEN_command_mode_param *  param 
)
static

Definition at line 1102 of file GEN_map.cxx.

References aw_message(), do_mark_command_for_one_species(), GEN_unique_param::gb_main, GBS_global_string(), gen_assert, GEN_COUNT_MARKED, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, GEN_PERFORM_ALL_ORGANISMS, GEN_perform_command(), GEN_PERFORM_CURRENT_ORGANISM, GEN_PERFORM_MARKED_ORGANISMS, GEN_command_mode_param::get_command_mode(), and NULp.

Referenced by GEN_insert_mark_submenu().

static GB_ERROR gene_extract_handler ( const char *  ali,
GEN_extract_mode_param *  param 
)
static

Definition at line 1125 of file GEN_map.cxx.

References ask_about_existing_gene_species, ask_to_overwrite_alignment, do_mark_command_for_one_species(), error(), GB_await_error(), GB_clear_error(), GEN_unique_param::gb_main, gb_species_data, GBT_add_alignment_changekeys(), GBT_check_alignment_name(), GBT_create_new_alignment(), GBT_get_alignment(), GBT_get_species_data(), GEN_COUNT_MARKED, GEN_EXTRACT_MARKED, GEN_perform_command(), GEN_extract_mode_param::get_perform_mode(), NULp, and ta.

Referenced by gene_extract_cb().

static void gene_extract_cb ( AW_window *  ,
GEN_extract_mode_param *  param 
)
static

Definition at line 1173 of file GEN_map.cxx.

References AWT_activate_prompt(), gene_extract_handler(), and SRT_AUTOCORRECT_ALINAME.

Referenced by GEN_insert_extract_submenu().

static void mark_organisms ( AW_window *  ,
MarkCommand  mark,
GBDATA *  gb_main 
)
static

Definition at line 1184 of file GEN_map.cxx.

References GB_read_flag(), GB_write_flag(), GBT_mark_all(), GEN_first_organism(), GEN_next_organism(), INVERT, MARK, MARK_UNMARK_REST, and ta.

Referenced by GEN_create_organism_submenu().

static void mark_gene_species ( AW_window *  ,
MarkCommand  mark,
GBDATA *  gb_main 
)
static

Definition at line 1206 of file GEN_map.cxx.

References GB_read_flag(), GB_write_flag(), GBT_mark_all(), GEN_first_pseudo_species(), GEN_next_pseudo_species(), INVERT, MARK, MARK_UNMARK_REST, and ta.

Referenced by GEN_create_gene_species_submenu().

static void mark_gene_species_of_marked_genes ( AW_window *  ,
GBDATA *  gb_main 
)
static

Definition at line 1227 of file GEN_map.cxx.

References GB_read_flag(), GB_write_flag(), GBS_free_hash(), GBT_create_organism_hash(), GEN_find_origin_gene(), GEN_first_pseudo_species(), GEN_next_pseudo_species(), and ta.

Referenced by GEN_create_gene_species_submenu().

static void mark_organisms_with_marked_genes ( AW_window *  ,
GBDATA *  gb_main 
)
static

Definition at line 1246 of file GEN_map.cxx.

References GB_read_flag(), GB_write_flag(), GEN_first_gene(), GEN_first_organism(), GEN_next_gene(), GEN_next_organism(), and ta.

Referenced by GEN_create_organism_submenu().

static void mark_gene_species_using_current_alignment ( AW_window *  ,
GBDATA *  gb_main 
)
static

Definition at line 1264 of file GEN_map.cxx.

References aw_message(), GB_await_error(), GB_entry(), GB_write_flag(), GBT_get_default_alignment(), GEN_first_pseudo_species(), GEN_next_pseudo_species(), and ta.

Referenced by GEN_create_gene_species_submenu().

static void mark_genes_of_marked_gene_species ( AW_window *  ,
GBDATA *  gb_main 
)
static

Definition at line 1286 of file GEN_map.cxx.

References GB_read_flag(), GB_write_flag(), GBS_free_hash(), GBT_create_organism_hash(), GEN_find_origin_gene(), GEN_first_pseudo_species(), GEN_next_pseudo_species(), and ta.

Referenced by GEN_create_genes_submenu().

static void GEN_insert_extract_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
const char *  macro_prefix,
const char *  submenu_name,
const char *  hot_key,
const char *  help_file 
)
static

Definition at line 1303 of file GEN_map.cxx.

References AWM_ALL, AW_window::close_sub_menu(), GEN_PERFORM_ALL_ORGANISMS, GEN_PERFORM_CURRENT_ORGANISM, GEN_PERFORM_MARKED_ORGANISMS, gene_extract_cb(), GEN_extract_mode_param::get(), AW_window::insert_menu_topic(), AW_window::insert_sub_menu(), and AW_window::local_id().

Referenced by GEN_create_genes_submenu().

static void GEN_insert_multi_submenu ( AW_window_menu_modes *  awm,
const char *  macro_prefix,
const char *  submenu_name,
const char *  hot_key,
const char *  help_file,
void(*)(AW_window *, GEN_PERFORM_MODE, GEN_command_mode_param *)  command,
GEN_command_mode_param *  command_mode 
)
static

Definition at line 1320 of file GEN_map.cxx.

References AWM_ALL, AW_window::close_sub_menu(), command, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, GEN_PERFORM_ALL_ORGANISMS, GEN_PERFORM_CURRENT_ORGANISM, GEN_PERFORM_MARKED_ORGANISMS, AW_window::insert_menu_topic(), and AW_window::insert_sub_menu().

Referenced by GEN_insert_hide_submenu(), and GEN_insert_mark_submenu().

static void GEN_insert_mark_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
const char *  macro_prefix,
const char *  submenu_name,
const char *  hot_key,
const char *  help_file,
GEN_MARK_MODE  mark_mode 
)
static

Definition at line 1342 of file GEN_map.cxx.

References GEN_insert_multi_submenu(), GEN_mark_command(), and GEN_command_mode_param::get().

Referenced by GEN_create_genes_submenu().

static void GEN_insert_hide_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
const char *  macro_prefix,
const char *  submenu_name,
const char *  hot_key,
const char *  help_file,
GEN_HIDE_MODE  hide_mode 
)
static

Definition at line 1345 of file GEN_map.cxx.

References GEN_hide_command(), GEN_insert_multi_submenu(), and GEN_command_mode_param::get().

Referenced by GEN_create_hide_submenu().

static void GEN_open_mask_window ( AW_window *  aww,
int  id,
GBDATA *  gb_main 
)
static

Definition at line 1414 of file GEN_map.cxx.

References AWT_initialize_input_mask(), AWT_look_input_mask(), gb_main, gen_assert, AW_window::get_root(), and item_type_gene.

Referenced by GEN_create_mask_submenu().

static void GEN_create_mask_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main 
)
static

Definition at line 1422 of file GEN_map.cxx.

References AWT_create_mask_submenu(), AWT_IT_GENE, and GEN_open_mask_window().

Referenced by GEN_create_genes_submenu().

static AW_window* create_colorize_genes_window ( AW_root *  aw_root,
GBDATA *  gb_main 
)
static

Definition at line 1426 of file GEN_map.cxx.

References QUERY::create_colorize_items_window(), and GEN_get_selector().

Referenced by GEN_create_genes_submenu().

static AW_window* create_colorize_organisms_window ( AW_root *  aw_root,
GBDATA *  gb_main 
)
static

Definition at line 1430 of file GEN_map.cxx.

References QUERY::create_colorize_items_window(), and ORGANISM_get_selector().

Referenced by GEN_create_organism_submenu().

static void GEN_create_organism_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
bool  submenu 
)
static

Definition at line 1434 of file GEN_map.cxx.

References AWM_ALL, AW_window::close_sub_menu(), create_colorize_organisms_window(), AW_window::create_menu(), AW_window::insert_menu_topic(), AW_window::insert_sub_menu(), INVERT, AW_window::local_id(), MARK, mark_organisms(), mark_organisms_with_marked_genes(), MARK_UNMARK_REST, DBUI::popup_organism_info_window(), AW_window::sep______________(), RootAsWindowCallback::simple(), title, and UNMARK.

Referenced by GEN_create_genes_submenu(), and GEN_map_window::init().

static void GEN_create_gene_species_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
bool  submenu 
)
static

Definition at line 1458 of file GEN_map.cxx.

References AWM_ALL, AW_window::close_sub_menu(), AW_window::create_menu(), AW_window::insert_menu_topic(), AW_window::insert_sub_menu(), INVERT, MARK, mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), MARK_UNMARK_REST, AW_window::sep______________(), title, and UNMARK.

Referenced by GEN_create_genes_submenu(), and GEN_map_window::init().

void GEN_create_genes_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main,
bool  for_ARB_NTREE 
)

Definition at line 1483 of file GEN_map.cxx.

References AWM_ALL, create_colorize_genes_window(), AW_window::create_menu(), EXP_create_experiments_submenu(), GEN_COUNT_MARKED, GEN_create_first_map(), GEN_create_gene_query_window(), GEN_create_gene_species_submenu(), GEN_create_mask_submenu(), GEN_create_organism_submenu(), GEN_insert_extract_submenu(), GEN_insert_mark_submenu(), GEN_INVERT_MARKED, GEN_MARK, GEN_MARK_HIDDEN, GEN_MARK_VISIBLE, GEN_popup_gene_infowindow(), GEN_UNMARK, GEN_UNMARK_HIDDEN, GEN_UNMARK_VISIBLE, AW_window::insert_menu_topic(), AW_window::local_id(), mark_genes_of_marked_gene_species(), NULp, AW_window::sep______________(), and RootAsWindowCallback::simple().

Referenced by GEN_map_window::init(), and popup_new_main_window().

static void GEN_create_hide_submenu ( AW_window_menu_modes *  awm,
GBDATA *  gb_main 
)
static

Definition at line 1535 of file GEN_map.cxx.

References AWM_ALL, AW_window::create_menu(), GEN_HIDE_ALL, GEN_HIDE_MARKED, GEN_insert_hide_submenu(), GEN_INVERT_HIDE_ALL, GEN_INVERT_HIDE_MARKED, GEN_UNHIDE_ALL, GEN_UNHIDE_MARKED, and AW_window::sep______________().

Referenced by GEN_map_window::init().

static void GEN_set_display_style ( AW_window *  aww,
GEN_DisplayStyle  style 
)
static

Definition at line 1549 of file GEN_map.cxx.

References AW_root::awar(), AWAR_GENMAP_DISPLAY_TYPE, DOWNCAST, GEN_map_window::get_canvas(), GEN_map_window::get_graphic(), GEN_map_window::get_nr(), AW_window::get_root(), GEN_graphic::set_display_style(), win, and AW_awar::write_int().

Referenced by GEN_map_window::init().

static AW_window* GEN_create_map ( AW_root *  aw_root,
GEN_create_map_param *  param 
)
static

Definition at line 1557 of file GEN_map.cxx.

References AW_ROOT_DEFAULT, GEN_create_map_param::gb_main, GEN_add_global_awar_callbacks(), gen_assert, GEN_create_genemap_global_awars(), GEN_make_node_text_init(), GEN_map_manager::get_map_manager(), GEN_map_manager::get_map_window(), GEN_map_manager::initialize(), GEN_map_manager::initialized(), NULp, ta, and GEN_create_map_param::window_nr.

Referenced by GEN_create_first_map(), and GEN_map_window::init().

AW_window* GEN_create_first_map ( AW_root *  aw_root,
GBDATA *  gb_main 
)

Definition at line 1585 of file GEN_map.cxx.

References GEN_create_map().

Referenced by GEN_create_genes_submenu(), and popup_new_main_window().

Variable Documentation

const char* GEN_PERFORM_MODE_id[GEN_PERFORM_MODES]
static
Initial value:
= {
"org_all",
"org_current",
"org_butcur",
"org_marked",
}

Definition at line 649 of file GEN_map.cxx.

AW_repeated_question* ask_about_existing_gene_species = NULp
static

Definition at line 715 of file GEN_map.cxx.

Referenced by gene_extract_handler().

AW_repeated_question* ask_to_overwrite_alignment = NULp
static

Definition at line 716 of file GEN_map.cxx.

Referenced by gene_extract_handler().

long gen_count_marked_genes = 0
static

Definition at line 936 of file GEN_map.cxx.

Referenced by do_mark_command_for_one_species().

GEN_item_type_species_selector item_type_gene
static

Definition at line 1412 of file GEN_map.cxx.

Referenced by GEN_open_mask_window().

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