#include <attributes.h>
#include <aw_base.hxx>
#include <arbdb_base.h>

Include dependency graph for NT_local_proto.h:

This graph shows which files directly or indirectly include this file:

Functions
void	AP_create_consensus_var (AW_root *aw_root, AW_default aw_def)

AW_window *	AP_create_con_expert_window (AW_root *aw_root)

AW_window *	AP_create_max_freq_window (AW_root *aw_root)

AW_window *	AP_create_pos_var_pars_window (AW_root *root)

AW_window *	NT_create_colstat_2_gnuplot_window (AW_root *root)

AW_window *	NT_create_branch_analysis_window (AW_root aw_root, TREE_canvas ntw)

void	NT_delete_mark_all_cb (AW_window , TREE_canvas ntw)

AW_window *	NT_create_select_tree_window (AW_root awr, const char awar_tree)

void	NT_select_bottom_tree (AW_window aww, const char awar_tree)

void	NT_create_alignment_vars (AW_root aw_root, AW_default aw_def, GBDATA gb_main)

AW_window *	NT_create_alignment_admin_window (AW_root root, AW_window aw_popmedown)

AW_window *	NT_create_select_alignment_window (AW_root *awr)

void	NT_createConcatenationAwars (AW_root aw_root, AW_default aw_def, GBDATA gb_main)

AW_window *	NT_createMergeSimilarSpeciesWindow (AW_root *aw_root)

AW_window *	NT_createConcatenationWindow (AW_root *aw_root)

GB_ERROR	NT_repair_DB (GBDATA *gb_main)

void	NT_rerepair_DB (AW_window , GBDATA gb_main)

void	NT_activate_configMarkers_display (TREE_canvas *ntw)

void	NT_popup_configuration_admin (AW_window aw_main, TREE_canvas ntw)

AW_window *	NT_create_startEditorOnOldConfiguration_window (AW_root *awr)

void	NT_start_editor_on_tree (AW_window aww, int use_species_aside, TREE_canvas ntw)

void	NT_create_config_after_import (TREE_canvas *ntw, bool imported_from_scratch)

void	NT_start (const char *arb_ntree_args, bool restart_with_new_ARB_PID)

void	NT_exit (AW_window *aws, int exitcode)

void	NT_restart (AW_root aw_root, const char arb_ntree_args)

TreeNode *	NT_get_tree_root_of_canvas (TREE_canvas *ntw)

TREE_canvas *	NT_get_canvas_by_index (int idx)

void	NT_fill_canvas_selection_list (class AW_selection_list sellst, TREE_canvas to_skip)

void	NT_deselect_group (AW_root *awr)

TREE_canvas *	NT_create_main_window (AW_root *aw_root)

TREE_canvas *	NT_get_canvas_showing_tree (const char *tree_name, bool forceDisplay)

void	NT_import_sequences (AW_window aww, TREE_canvas ntw)

AW_window *	NT_create_species_join_window (AW_root *root)

GB_ERROR	NT_format_all_alignments (GBDATA *gb_main)

void	NT_install_treeShader (TREE_canvas ntw, GBDATA gb_main)

void	NT_configure_treeShader (void)

void	NT_resort_data_by_phylogeny (AW_window , TREE_canvas ntw)

void	NT_create_resort_awars (AW_root *awr, AW_default aw_def)

AW_window *	NT_create_resort_window (AW_root *awr)

AW_window *	NT_create_splitAlignment_window (AW_root *awr)

AW_window *	NT_create_syncScroll_window (AW_root awr, TREE_canvas ntw)

AW_window *	NT_create_syncroot_window (AW_root awr, GBDATA gb_main)

void	NT_create_compare_taxonomy_awars (AW_root *aw_root, AW_default props)

AW_window *	NT_create_compare_taxonomy_window (AW_root aw_root, TREE_canvas ntw)

void	NT_create_trackAliChanges_Awars (AW_root *root, AW_default properties)

AW_window *	NT_create_trackAliChanges_window (AW_root *root)

void	NT_repair_userland_problems (void)

void	NT_createValidNamesAwars (AW_root *aw_root, AW_default aw_def)

AW_window *	NT_create_searchManuallyNames_window (AW_root *aw_root)

void	NT_deleteValidNames (AW_window *)

void	NT_importValidNames (AW_window *)

void	NT_suggestValidNames (AW_window *)

void	NT_create_extendeds_vars (AW_root aw_root, AW_default aw_def, GBDATA gb_main)

AW_window *	NT_create_extendeds_window (AW_root *aw_root)

void	NT_count_different_chars (AW_window , GBDATA gb_main)

void	NT_create_sai_from_pfold (AW_window *aww)

AW_window *	NT_create_dna_2_pro_window (AW_root *root)

AW_window *	NT_create_realign_dna_window (AW_root *root)

void	NT_create_transpro_variables (AW_root *root, AW_default props)

void	NT_create_twoTreeSelection (AW_window *aws)

AW_window *	NT_create_compareTopologies_window (AW_root *root)

AW_window *	NT_create_moveGroupInfo_window (AW_root *root)

AW_window *	NT_create_consense_window (AW_root *aw_root)

AW_window *	NT_create_sort_tree_by_other_tree_window (AW_root aw_root, TREE_canvas ntw)

void	NT_create_multifurcate_tree_awars (AW_root *aw_root, AW_default props)

AW_window *	NT_create_multifurcate_tree_window (AW_root aw_root, TREE_canvas ntw)

Function Documentation

void AP_create_consensus_var	(	AW_root *	aw_root,
		AW_default	aw_def
	)

AW_window* AP_create_con_expert_window ( AW_root * aw_root )

AW_window* AP_create_max_freq_window ( AW_root * aw_root )

Definition at line 468 of file AP_consensus.cxx.

References AW_POPDOWN(), AWAR_MAX_FREQ_IGNORE_GAPS, AWAR_MAX_FREQ_SAI_NAME, awt_create_SAI_selection_list(), CON_calc_max_freq_cb(), NT_global::gb_main, GB_pop_transaction(), GB_push_transaction(), GLOBAL, AW_window::load_xfig(), and makeHelpCallback().

Referenced by popup_new_main_window().

AW_window* AP_create_pos_var_pars_window ( AW_root * root )

Definition at line 48 of file AP_pos_var_pars.cxx.

References AP_calc_pos_var_pars(), AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_PVP_SAI, AWAR_PVP_TREE, AW_root::awar_string(), awt_create_SAI_selection_list(), awt_create_TREE_selection_list(), AWT_registerTreeAwarSimple(), NT_global::gb_main, GBT_name_of_largest_tree(), GLOBAL, makeHelpCallback(), NO_TREE_SELECTED, ta, and AW_awar::write_string().

Referenced by popup_new_main_window().

AW_window* NT_create_colstat_2_gnuplot_window ( AW_root * root )

Definition at line 588 of file ColumnStat_2_gnuplot.cxx.

References AW_awar::add_callback(), AW_create_fileselection_awars(), AW_create_standard_fileselection(), AW_HORIZONTAL, AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_CS2GP, AWAR_CS2GP_FILTER_NAME, AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX, AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX, AWAR_CS2GP_NAME, AWAR_CS2GP_SMOOTH_GNUPLOT, AWAR_CS2GP_SMOOTH_VALUES, AWAR_CS2GP_SUFFIX, AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), awt_create_filter_awars(), awt_create_select_filter(), awt_create_select_filter_win(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), COLSTAT_create_selection_list(), adfiltercbstruct::def_alignment, NT_global::gb_main, GLOBAL, AW_selection_list::insert(), AW_selection_list::insert_default(), makeHelpCallback(), PLOT, PLOT_AND_VIEW, PLOT_CLEANUP, PT_PLOT_TYPES, ta, AW_awar::touch(), and AW_selection_list::update().

Referenced by popup_new_main_window().

AW_window* NT_create_branch_analysis_window	(	AW_root *	aw_root,
		TREE_canvas *	ntw
	)

Definition at line 307 of file NT_branchAnalysis.cxx.

References TREE_canvas::get_index(), BranchWindow::get_window(), and nt_assert.

Referenced by popup_new_main_window().

void NT_delete_mark_all_cb	(	AW_window *	,
		TREE_canvas *	ntw
	)

Definition at line 31 of file NT_cb.cxx.

References aw_ask_sure(), aw_message(), GB_transaction::close(), error(), GB_delete(), AWT_canvas::gb_main, GBT_first_marked_species(), GBT_next_marked_species(), NULp, AWT_canvas::request_refresh(), and ta.

Referenced by popup_new_main_window().

AW_window* NT_create_select_tree_window	(	AW_root *	awr,
		const char *	awar_tree
	)

Definition at line 60 of file NT_cb.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), awt_auto_popdown_cb(), awt_create_TREE_selection_list(), NT_global::gb_main, GBS_global_string(), GLOBAL, nt_assert, and popup_tree_admin_window().

Referenced by popup_new_main_window().

void NT_select_bottom_tree	(	AW_window *	aww,
		const char *	awar_tree
	)

Definition at line 92 of file NT_cb.cxx.

References AW_root::awar(), NT_global::gb_main, GBT_name_of_bottom_tree(), AW_window::get_root(), GLOBAL, ta, and AW_awar::write_string().

Referenced by popup_new_main_window().

void NT_create_alignment_vars	(	AW_root *	aw_root,
		AW_default	aw_def,
		GBDATA *	gb_main
	)

Definition at line 98 of file NT_cb.cxx.

References AWAR_DEFAULT_ALIGNMENT, AW_root::awar_string(), GB_DEFAULT_ALIGNMENT, GB_search(), GB_STRING, AW_awar::map(), and ta.

Referenced by nt_create_all_awars().

AW_window* NT_create_alignment_admin_window	(	AW_root *	root,
		AW_window *	aw_popmedown
	)

Definition at line 109 of file NT_cb.cxx.

References ALI_create_admin_window(), AWAR_DEFAULT_ALIGNMENT, NT_global::gb_main, GLOBAL, AW_window::hide(), MAIN_ADMIN, and NULp.

Referenced by NT_create_select_alignment_window(), and popup_new_main_window().

AW_window* NT_create_select_alignment_window ( AW_root * awr )

Definition at line 119 of file NT_cb.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_DEFAULT_ALIGNMENT, awt_auto_popdown_cb(), awt_create_ALI_selection_list(), NT_global::gb_main, GLOBAL, NT_create_alignment_admin_window(), and NULp.

Referenced by popup_new_main_window().

void NT_createConcatenationAwars	(	AW_root *	aw_root,
		AW_default	aw_def,
		GBDATA *	gb_main
	)

AW_window* NT_createMergeSimilarSpeciesWindow ( AW_root * aw_root )

Definition at line 753 of file NT_concatenate.cxx.

References createMergeSimilarSpeciesWindow(), MERGE_SPECIES_SIMPLE, and NULp.

Referenced by NT_createConcatenationWindow(), and popup_new_main_window().

AW_window* NT_createConcatenationWindow ( AW_root * aw_root )

GB_ERROR NT_repair_DB ( GBDATA * gb_main )

Definition at line 1015 of file NT_dbrepair.cxx.

References GEN_is_genome_db(), NT_convert_gene_locations(), NT_del_mark_move_REF(), NT_fix_dict_compress(), NT_fix_gene_data(), NULp, CheckedConsistencies::perform_check(), CheckedConsistencies::perform_item_checks(), CheckedConsistencies::register_item_check(), remove_dup_colors(), and ta.

Referenced by nt_check_database_consistency(), and NT_rerepair_DB().

void NT_rerepair_DB	(	AW_window *	,
		GBDATA *	gb_main
	)

Definition at line 1040 of file NT_dbrepair.cxx.

References aw_message(), CheckedConsistencies::forgetDoneChecks(), NT_repair_DB(), and NULp.

Referenced by popup_new_main_window().

void NT_activate_configMarkers_display ( TREE_canvas * ntw )

Definition at line 254 of file NT_edconf.cxx.

References AW_awar::add_callback(), AWAR_CL_DISPLAY_CONFIG_MARKERS, AWAR_CL_SELECTED_CONFIGS, AW_root::awar_int(), AW_root::awar_string(), AWT_canvas::awr, gb_main, AWT_canvas::gb_main, GBS_global_string(), TREE_canvas::get_index(), install_config_change_callbacks(), selected_configs_awar_changed_cb(), selected_configs_display_awar_changed_cb(), and AW_awar::touch().

Referenced by popup_new_main_window().

void NT_popup_configuration_admin	(	AW_window *	aw_main,
		TREE_canvas *	ntw
	)

Definition at line 1253 of file NT_edconf.cxx.

References create_configuration_admin_window(), and AW_window::get_root().

Referenced by popup_new_main_window().

AW_window* NT_create_startEditorOnOldConfiguration_window ( AW_root * awr )

Definition at line 1271 of file NT_edconf.cxx.

References AW_POPDOWN(), AWAR_CONFIGURATION, awt_create_CONFIG_selection_list(), NT_global::gb_main, GLOBAL, init_config_awars(), nt_start_editor_on_configuration(), and NULp.

Referenced by popup_new_main_window().

void NT_start_editor_on_tree	(	AW_window *	aww,
		int	use_species_aside,
		TREE_canvas *	ntw
	)

Definition at line 1294 of file NT_edconf.cxx.

References aw_message_if(), BY_CALLING_THE_EDITOR, DEFAULT_CONFIGURATION, error(), GBK_system(), AW_window::get_root(), init_config_awars(), nt_create_configuration(), and NT_get_tree_root_of_canvas().

Referenced by popup_new_main_window().

void NT_create_config_after_import	(	TREE_canvas *	ntw,
		bool	imported_from_scratch
	)

create a new config after import

Parameters

imported_from_scratch if true -> DB was created from scratch, all species in DB are marked. if false -> data was imported into existing DB. Other species may be marked as well, imported species are "queried".

Definition at line 1322 of file NT_edconf.cxx.

References GB_clear_user_flag(), AWT_canvas::gb_main, GB_read_flag(), GB_user_flag(), GB_USERFLAG_QUERY, GB_USERFLAG_WASMARKED, GB_write_flag(), GB_write_user_flag(), GBT_first_species(), GBT_next_species(), nt_create_config_after_import(), and ta.

Referenced by nt_seq_load_cb(), and start_main_window_after_import().

void NT_start	(	const char *	arb_ntree_args,
		bool	restart_with_new_ARB_PID
	)

Definition at line 397 of file NT_extern.cxx.

References command, GBS_global_string_copy(), and nt_run().

Referenced by exit_from_merge(), NT_restart(), and nt_start_2nd_arb().

void NT_exit	(	AW_window *	aws,
		int	exitcode
	)

Definition at line 410 of file NT_extern.cxx.

References AWTI_cleanup_importer(), NT_global::gb_main, GB_read_clients(), AW_window::get_root(), GLOBAL, nt_disconnect_from_db(), really_exit(), and shutdown_macro_recording().

Referenced by nt_create_intro_window(), and popup_new_main_window().

void NT_restart	(	AW_root *	aw_root,
		const char *	arb_ntree_args
	)

Definition at line 419 of file NT_extern.cxx.

References EXIT_SUCCESS, NT_global::gb_main, GB_read_clients(), GLOBAL, nt_disconnect_from_db(), NT_start(), and really_exit().

Referenced by exit_from_merge(), nt_intro_start_merge(), and nt_start_2nd_arb().

TreeNode* NT_get_tree_root_of_canvas ( TREE_canvas * ntw )

Definition at line 858 of file NT_extern.cxx.

References AWT_TREE, AWT_graphic_tree::get_root_node(), and NULp.

Referenced by nt_create_config_after_import(), NT_resort_data_by_phylogeny(), NT_start_editor_on_tree(), and nt_store_configuration().

TREE_canvas* NT_get_canvas_by_index ( int idx )

return canvas with index 'idx' [0...MAX_NT_WINDOWS-1]

Definition at line 978 of file NT_extern.cxx.

References TREE_canvas_registry::get_canvas(), TREE_canvas_registry::instance(), MAX_NT_WINDOWS, and nt_assert.

Referenced by CanvasRef::get_canvas(), NT_get_canvas_showing_tree(), and sync_changed_cb().

void NT_fill_canvas_selection_list	(	class AW_selection_list *	sellst,
		TREE_canvas *	to_skip
	)

insert canvases into selection list (using canvas-indices as values)

Definition at line 999 of file NT_extern.cxx.

References GBS_global_string(), TREE_canvas::get_awar_tree(), TREE_canvas_registry::get_canvas(), TREE_canvas_registry::get_count(), AW_selection_list::insert(), TREE_canvas_registry::instance(), nt_assert, and AW_awar::read_char_pntr().

Referenced by refill_syncWithList_cb().

void NT_deselect_group ( AW_root * awr )

Definition at line 1021 of file NT_extern.cxx.

References AW_root::awar(), AWAR_GROUP, NULp, and AW_awar::write_pointer().

Referenced by ad_move_tree_info().

TREE_canvas* NT_create_main_window ( AW_root * aw_root )

Definition at line 1856 of file NT_extern.cxx.

References aw_message(), error(), NT_global::gb_main, GB_request_undo_type(), GB_UNDO_NONE, GB_UNDO_UNDO, GLOBAL, nt_create_all_awars(), NT_install_treeShader(), NULp, popup_new_main_window(), and AW_window::show().

Referenced by startup_mainwindow_and_dbserver().

TREE_canvas* NT_get_canvas_showing_tree	(	const char *	tree_name,
		bool	forceDisplay
	)

Definition at line 369 of file NT_group_search.cxx.

References AW_window::activate(), AWT_canvas::aww, TREE_canvas::get_awar_tree(), AWT_canvas::is_shown(), MAX_NT_WINDOWS, nt_assert, NT_get_canvas_by_index(), NULp, AW_awar::read_char_pntr(), and AW_awar::write_string().

Referenced by ad_move_tree_info(), and get_canvas_able_to_show().

void NT_import_sequences	(	AW_window *	aww,
		TREE_canvas *	ntw
	)

Opens the "Import Sequences" dialog from the ARB main window (ARB_NTREE)

Definition at line 48 of file NT_import.cxx.

References aw_message(), AW_root::awar(), AWAR_IMPORT_GENOM_DB, AWTI_import_set_ali_and_type(), AWTI_open_import_window(), AWTI_set_importDB_pointer(), GB_await_error(), NT_global::gb_main, GBT_get_alignment_type_string(), GBT_get_default_alignment(), GEN_is_genome_db(), AW_window::get_root(), GLOBAL, GLOBAL_gb_src, got_macro_ability(), IF_ASSERTION_USED, IMP_GENOME_FLATFILE, IMP_PLAIN_SEQUENCE, nt_assert, nt_seq_load_cb(), NULp, ta, and AW_awar::write_int().

Referenced by popup_new_main_window().

AW_window* NT_create_species_join_window ( AW_root * root )

Definition at line 143 of file NT_join.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_SPECIES_JOIN_FIELD, AWAR_SPECIES_JOIN_SEP, AWAR_SPECIES_JOIN_SEP2, AW_root::awar_string(), create_itemfield_selection_button(), FIELD_FILTER_STRING_READABLE, NT_global::gb_main, GLOBAL, makeHelpCallback(), NULp, SPECIES_get_selector(), and species_rename_join().

Referenced by popup_new_main_window().

GB_ERROR NT_format_all_alignments ( GBDATA * gb_main )

Definition at line 54 of file NT_main.cxx.

References ARB_format_alignment(), GB_transaction::close(), arb_progress::done(), GB_entry(), GB_INT, GB_nextEntry(), GB_read_char_pntr(), GB_read_int(), GB_search(), GB_write_int(), GBS_global_string_copy(), GBT_check_data(), GBT_count_alignments(), GBT_get_presets(), GBT_write_int(), GENOM_ALIGNMENT, arb_progress::inc_and_check_user_abort(), NULp, and ta.

Referenced by nt_check_database_consistency(), and nt_seq_load_cb().

void NT_install_treeShader	(	TREE_canvas *	ntw,
		GBDATA *	gb_main
	)

Definition at line 145 of file NT_shadeTree.cxx.

References AP_tree::set_tree_shader().

Referenced by NT_create_main_window().

void NT_configure_treeShader ( void )

Definition at line 149 of file NT_shadeTree.cxx.

References DOWNCAST, AP_tree::get_tree_shader(), and nt_assert.

Referenced by popup_new_main_window().

void NT_resort_data_by_phylogeny	(	AW_window *	,
		TREE_canvas *	ntw
	)

Definition at line 167 of file NT_sort.cxx.

References aw_message(), error(), NT_global::gb_main, GLOBAL, NT_get_tree_root_of_canvas(), NULp, and resort_data_base().

Referenced by popup_new_main_window().

void NT_create_resort_awars	(	AW_root *	awr,
		AW_default	aw_def
	)

Definition at line 199 of file NT_sort.cxx.

References AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE_REV1, AWAR_TREE_REV2, AWAR_TREE_REV3, AWAR_TREE_SORT1, AWAR_TREE_SORT2, AWAR_TREE_SORT3, and NO_FIELD_SELECTED.

Referenced by nt_create_all_awars().

AW_window* NT_create_resort_window ( AW_root * awr )

Definition at line 209 of file NT_sort.cxx.

References AW_POPDOWN(), AWAR_TREE_REV1, AWAR_TREE_REV2, AWAR_TREE_REV3, AWAR_TREE_SORT1, AWAR_TREE_SORT2, AWAR_TREE_SORT3, create_itemfield_selection_button(), FIELD_FILTER_RESORT, NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), NT_resort_data_by_user_criteria(), and SPECIES_get_selector().

Referenced by popup_new_main_window().

AW_window* NT_create_splitAlignment_window ( AW_root * awr )

Definition at line 549 of file NT_split_ali.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_RANGE, AWAR_SPLIT_ALI_MARKED, AWAR_SPLIT_ALI_OVERWRITE, AWAR_SPLIT_ALI_POSITIONS, AWAR_SPLIT_ALI_TARGET, create_splitAlignment_awars(), NT_global::gb_main, GLOBAL, makeHelpCallback(), NULp, split_ali_cb(), and use_editor_range_cb().

Referenced by popup_new_main_window().

AW_window* NT_create_syncScroll_window	(	AW_root *	awr,
		TREE_canvas *	ntw
	)

AW_window* NT_create_syncroot_window	(	AW_root *	awr,
		GBDATA *	gb_main
	)

Definition at line 220 of file NT_syncroot.cxx.

References AW_POPDOWN(), AWAR_TREE_SYNCROOT_SELECTED, awt_create_subset_selection_list(), awt_create_TREE_selection_list(), create_syncroot_awars(), AW_selection::get_sellist(), makeHelpCallback(), multiroot_sync_subsetTrees(), NULp, and rootsync_subsetTrees_vs_selected().

Referenced by popup_new_main_window().

void NT_create_compare_taxonomy_awars	(	AW_root *	aw_root,
		AW_default	props
	)

Definition at line 335 of file NT_taxonomy.cxx.

References AW_root::awar(), AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE_COMPARE_ACTION, AWAR_TREE_COMPARE_MIN_TAX_LEVELS, AWAR_TREE_COMPARE_WRITE_FIELD, AWAR_TREE_NAME, MARK, NO_FIELD_SELECTED, and AW_awar::read_string().

Referenced by nt_create_all_awars().

AW_window* NT_create_compare_taxonomy_window	(	AW_root *	aw_root,
		TREE_canvas *	ntw
	)

Definition at line 345 of file NT_taxonomy.cxx.

References ALL, AW_POPDOWN(), AWAR_TREE_COMPARE_ACTION, AWAR_TREE_COMPARE_MIN_TAX_LEVELS, AWAR_TREE_COMPARE_WRITE_FIELD, COMMON, create_itemfield_selection_button(), FIELD_FILTER_INT_WRITEABLE, AWT_canvas::gb_main, INVERT, AW_window::load_xfig(), makeHelpCallback(), MARK, mark_action(), MISSING_LEFT, MISSING_RIGHT, NT_create_twoTreeSelection(), SF_ALLOW_NEW, SPECIES_get_selector(), TAX, and UNMARK.

Referenced by popup_new_main_window().

void NT_create_trackAliChanges_Awars	(	AW_root *	root,
		AW_default	properties
	)

Definition at line 152 of file NT_trackAliChanges.cxx.

References AW_root::awar_string(), AWAR_TRACK_ALI, AWAR_TRACK_INITIALS, GB_getenvUSER(), NT_global::gb_main, and GLOBAL.

Referenced by nt_create_all_awars().

AW_window* NT_create_trackAliChanges_window ( AW_root * root )

Definition at line 157 of file NT_trackAliChanges.cxx.

References AW_POPDOWN(), AWAR_TRACK_ALI, AWAR_TRACK_INITIALS, awt_create_ALI_selection_list(), NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), and trackAlignmentChanges().

Referenced by popup_new_main_window().

void NT_repair_userland_problems ( void )

Definition at line 54 of file NT_userland_fixes.cxx.

References UserlandCheck::Run().

Referenced by startup_mainwindow_and_dbserver().

void NT_createValidNamesAwars	(	AW_root *	aw_root,
		AW_default	aw_def
	)

Definition at line 36 of file NT_validManual.cxx.

References AWAR_INPUT_INITIALS, AWAR_SELECTED_VALNAME, and AW_root::awar_string().

Referenced by nt_create_all_awars().

AW_window* NT_create_searchManuallyNames_window ( AW_root * aw_root )

Definition at line 154 of file NT_validManual.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_INPUT_INITIALS, AWAR_SELECTED_VALNAME, createValNameList(), NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), selectValidNameFromList(), and updateValNameList().

Referenced by popup_new_main_window().

void NT_deleteValidNames ( AW_window * )

Definition at line 28 of file NT_validNames.cxx.

References aw_message(), error(), GB_begin_transaction(), GB_commit_transaction(), GB_CREATE_CONTAINER, GB_delete(), NT_global::gb_main, GB_search(), GB_write_security_delete(), and GLOBAL.

Referenced by popup_new_main_window().

void NT_importValidNames ( AW_window * )

Definition at line 49 of file NT_validNames.cxx.

References aw_message(), validNames::determineType(), error(), GB_await_error(), GB_begin_transaction(), GB_create_container(), GB_end_transaction(), GB_entry(), NT_global::gb_main, GB_path_in_ARBLIB(), GBT_write_string(), GLOBAL, nt_assert, NULp, and string().

Referenced by popup_new_main_window().

void NT_suggestValidNames ( AW_window * )

Definition at line 162 of file NT_validNames.cxx.

References aw_message(), GB_await_error(), GB_begin_transaction(), GB_CREATE_CONTAINER, GB_end_transaction_show_error(), GB_entry(), NT_global::gb_main, GB_nextEntry(), GB_read_string(), GB_search(), GBT_first_species(), GBT_next_species(), GBT_read_string(), GBT_write_string(), GLOBAL, nt_assert, and NULp.

Referenced by popup_new_main_window().

void NT_create_extendeds_vars	(	AW_root *	aw_root,
		AW_default	aw_def,
		GBDATA *	gb_main
	)

Definition at line 286 of file ad_ext.cxx.

References AW_awar::add_callback(), AW_root::awar(), AW_root::awar_int(), AWAR_SAI_GROUP, AWAR_SAI_NAME, AWAR_SAI_REFRESH_GROUPS, AW_root::awar_string(), get_SAI_group(), AW_awar::read_char_pntr(), refresh_group_cb(), refresh_SAI_groups_cb(), and set_SAI_group_cb().

Referenced by nt_create_all_awars().

AW_window* NT_create_extendeds_window ( AW_root * aw_root )

Definition at line 318 of file ad_ext.cxx.

References AW_POPDOWN(), AWAR_SAI_NAME, AWAR_TOPAREA_SAIS, awt_create_SAI_selection_list(), copy_SAI_cb(), copy_SAI_to_species_cb(), DbScanner::create(), create_SAI_group_window(), DB_SCANNER, delete_SAI_cb(), edit_SAI_description(), NT_global::gb_main, GLOBAL, makeHelpCallback(), map_SAI_to_scanner(), NULp, rename_SAI_cb(), and SAI_get_selector().

Referenced by NT_create_sai_from_pfold(), and popup_new_main_window().

void NT_count_different_chars	(	AW_window *	,
		GBDATA *	gb_main
	)

void NT_create_sai_from_pfold ( AW_window * aww )

Creates an SAI from protein secondary structure of a selected species.

Parameters

[in] aww AW_window

The function takes the currently selected species and searches for the field "sec_struct". A new SAI is created using the data in this field. A simple input window allows the user to change the default name ([species name]_pfold) for the new SAI.

Note: The import filter "dssp_all.ift" allows for importing the amino acid sequence as well as the protein secondary structure from a dssp file and the structure is stored in the field "sec_struct". That way, secondary structure can be aligned along with the sequence manually and can later be extracted to create an SAI.

Attention: The import filter "dssp_2nd_struct.ift" extracts only the protein secondary structure which is stored as alignment data. SAIs can simply be created from these species via move_species_to_extended().

Definition at line 127 of file ad_spec.cxx.

References AW_window::activate(), aw_input(), aw_message(), AW_root::awar(), AWAR_SAI_NAME, AWAR_SPECIES_NAME, error(), GB_await_error(), GB_begin_transaction(), GB_child(), GB_copy_dropProtectMarksAndTempstate(), GB_CREATE_CONTAINER, GB_create_container(), GB_delete(), GB_end_transaction_show_error(), GB_entry(), GB_FIND, NT_global::gb_main, GB_nextChild(), GB_read_key(), GB_read_string(), GB_read_type(), GB_search(), GB_write_string(), GBS_global_string_copy(), GBT_find_SAI_rel_SAI_data(), GBT_find_species(), GBT_gen_accession_number(), GBT_get_default_alignment(), GBT_get_SAI_data(), GBT_write_string(), AW_window::get_root(), GLOBAL, NT_create_extendeds_window(), NULp, AW_awar::read_string(), and AW_awar::write_string().