/* This file is generated by aisc_mkpt.
 * Any changes you make here will be overwritten later!
 */

#ifndef NT_LOCAL_PROTO_H
#define NT_LOCAL_PROTO_H

/* define ARB attributes: */
#ifndef ATTRIBUTES_H
# include <attributes.h>
#endif


/* AP_consensus.cxx */

#ifndef AW_BASE_HXX
#include <aw_base.hxx>
#endif

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);

/* AP_pos_var_pars.cxx */
AW_window *AP_create_pos_var_pars_window(AW_root *root);

/* ColumnStat_2_gnuplot.cxx */
AW_window *NT_create_colstat_2_gnuplot_window(AW_root *root);

/* NT_branchAnalysis.cxx */

class TREE_canvas;

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

/* NT_cb.cxx */

#ifndef ARBDB_BASE_H
#include <arbdb_base.h>
#endif
class TREE_canvas;

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, TREE_canvas *ntw);
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);

/* NT_concatenate.cxx */
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);

/* NT_dbrepair.cxx */
GB_ERROR NT_repair_DB(GBDATA *gb_main);
void NT_rerepair_DB(AW_window *, GBDATA *gb_main);

/* NT_edconf.cxx */
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 *, int use_species_aside, TREE_canvas *ntw);
void NT_create_config_after_import(TREE_canvas *ntw, bool imported_from_scratch);

/* NT_extern.cxx */
void NT_start_if(const char *arb_ntree_args);
void NT_exit_now_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args) __ATTR__NORETURN;
void NT_confirm_exit_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args);
void NT_confirm_exit(AW_window *aws, int exitcode);
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);

/* NT_group_search.cxx */
TREE_canvas *NT_get_canvas_showing_tree(const char *tree_name, bool forceDisplay);

/* NT_import.cxx */
void NT_import_sequences(AW_window *aww, TREE_canvas *ntw);

/* NT_join.cxx */
AW_window *NT_create_species_join_window(AW_root *root);

/* NT_main.cxx */
GB_ERROR NT_format_all_alignments(GBDATA *gb_main);

/* NT_shadeTree.cxx */
void NT_install_treeShader(TREE_canvas *ntw, GBDATA *gb_main);
void NT_configure_treeShader(void);

/* NT_sort.cxx */
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);

/* NT_split_ali.cxx */
AW_window *NT_create_splitAlignment_window(AW_root *awr);

/* NT_sync_scroll.cxx */
AW_window *NT_create_syncScroll_window(AW_root *awr, TREE_canvas *ntw);

/* NT_syncroot.cxx */
AW_window *NT_create_syncroot_window(AW_root *awr, GBDATA *gb_main);

/* NT_taxonomy.cxx */
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);

/* NT_trackAliChanges.cxx */
void NT_create_trackAliChanges_Awars(AW_root *root, AW_default properties);
AW_window *NT_create_trackAliChanges_window(AW_root *root);

/* NT_userland_fixes.cxx */
void NT_repair_userland_problems(void);

/* NT_validManual.cxx */
void NT_createValidNamesAwars(AW_root *aw_root, AW_default aw_def);
AW_window *NT_create_searchManuallyNames_window(AW_root *aw_root);

/* NT_validNames.cxx */
void NT_deleteValidNames(AW_window *);
void NT_importValidNames(AW_window *);
void NT_suggestValidNames(AW_window *);

/* ad_ext.cxx */
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);

/* ad_spec.cxx */
void NT_count_different_chars(AW_window *, GBDATA *gb_main);
void NT_create_sai_from_pfold(AW_window *aww);

/* ad_transpro.cxx */
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);

/* ad_trees.cxx */
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);

#else
#error NT_local_proto.h included twice
#endif /* NT_LOCAL_PROTO_H */