NT_local_proto.h File Reference
#include <attributes.h>
#include <aw_base.hxx>
#include <arbdb_base.h>
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void AP_create_consensus_var (AW_root *aw_root, AW_default aw_def)
AW_windowAP_create_con_expert_window (AW_root *aw_root)
AW_windowAP_create_max_freq_window (AW_root *aw_root)
AW_windowAP_create_pos_var_pars_window (AW_root *root)
AW_windowNT_create_colstat_2_gnuplot_window (AW_root *root)
AW_windowNT_create_branch_analysis_window (AW_root *aw_root, TREE_canvas *ntw)
void NT_delete_mark_all_cb (AW_window *, TREE_canvas *ntw)
AW_windowNT_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_windowNT_create_alignment_admin_window (AW_root *root, AW_window *aw_popmedown)
AW_windowNT_create_select_alignment_window (AW_root *awr)
void NT_createConcatenationAwars (AW_root *aw_root, AW_default aw_def, GBDATA *gb_main)
AW_windowNT_createMergeSimilarSpeciesWindow (AW_root *aw_root)
AW_windowNT_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_windowNT_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)
TreeNodeNT_get_tree_root_of_canvas (TREE_canvas *ntw)
TREE_canvasNT_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_canvasNT_create_main_window (AW_root *aw_root)
TREE_canvasNT_get_canvas_showing_tree (const char *tree_name, bool forceDisplay)
void NT_import_sequences (AW_window *aww, TREE_canvas *ntw)
AW_windowNT_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_windowNT_create_resort_window (AW_root *awr)
AW_windowNT_create_splitAlignment_window (AW_root *awr)
AW_windowNT_create_syncScroll_window (AW_root *awr, TREE_canvas *ntw)
AW_windowNT_create_syncroot_window (AW_root *awr, GBDATA *gb_main)
void NT_create_compare_taxonomy_awars (AW_root *aw_root, AW_default props)
AW_windowNT_create_compare_taxonomy_window (AW_root *aw_root, TREE_canvas *ntw)
void NT_create_trackAliChanges_Awars (AW_root *root, AW_default properties)
AW_windowNT_create_trackAliChanges_window (AW_root *root)
void NT_repair_userland_problems (void)
void NT_createValidNamesAwars (AW_root *aw_root, AW_default aw_def)
AW_windowNT_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_windowNT_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_windowNT_create_dna_2_pro_window (AW_root *root)
AW_windowNT_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_windowNT_create_compareTopologies_window (AW_root *root)
AW_windowNT_create_moveGroupInfo_window (AW_root *root)
AW_windowNT_create_consense_window (AW_root *aw_root)
AW_windowNT_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_windowNT_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)
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 

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)
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 

create a new config after import

imported_from_scratchif 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 
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)

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 
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)
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 

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 
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  )

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 
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)

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


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.

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.
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().

Referenced by popup_new_main_window().

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