NT_concatenate.cxx File Reference

#include "NT_local.h"
#include <items.h>
#include <item_sel_list.h>
#include <awt_sel_boxes.hxx>
#include <AW_rename.hxx>
#include <aw_question.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <arb_progress.h>
#include <arb_strbuf.h>
#include <arb_strarray.h>
#include <awt_modules.hxx>
#include <arb_global_defs.h>

Include dependency graph for NT_concatenate.cxx:

Go to the source code of this file.

Classes
struct	SpeciesConcatenateList

Macros
#define	AWAR_CON_SEQUENCE_TYPE   "tmp/concat/sequence_type"
#define	AWAR_CON_NEW_ALIGNMENT_NAME   "tmp/concat/new_alignment_name"
#define	AWAR_CON_ALIGNMENT_SEPARATOR   "tmp/concat/alignment_separator"
#define	AWAR_CON_SELECTED_ALI   "tmp/concat/database_alignments"
#define	AWAR_CON_MERGE_FIELD   "tmp/concat/merge_field"
#define	AWAR_CON_STORE_SIM_SP_NO   "tmp/concat/store_sim_sp_no"
#define	AWAR_CON_ALLOW_OVERWRITE_ALI   "tmp/concat/overwrite"
#define	AWAR_CON_INSGAPS_FOR_MISS_ALIS   "tmp/concat/insgaps"
#define	MOVE_DOWN   0
#define	MOVE_UP   1

Enumerations
enum	MergeSpeciesType { MERGE_SPECIES_SIMPLE, MERGE_SPECIES_AND_CONCAT_ALI }

Functions
void	NT_createConcatenationAwars (AW_root *aw_root, AW_default aw_def, GBDATA *gb_main)
char *	get_alitype_eval (AW_root *aw_root)
static void	alitype_changed_cb (AW_root *aw_root, AW_DB_selection *db_sel)
static AW_DB_selection *	createSelectionList (GBDATA *gb_main, AW_window *aws, const char *awarName)
static GB_ERROR	create_concatInfo_SAI (GBDATA *gb_main, const char *new_ali_name, const char *ali_separator, const StrArray &ali_names)
static void	concatenateAlignments (AW_window *aws, AW_selection *selected_alis)
static void	addSpeciesToConcatenateList (SpeciesConcatenateList **sclp, GB_CSTR species_name)
static void	freeSpeciesConcatenateList (SpeciesConcatenateList *scl)
static GB_ERROR	checkAndMergeFields (GBDATA *gb_new_species, GB_ERROR error, SpeciesConcatenateList *scl)
static GBDATA *	concatenateFieldsCreateNewSpecies (AW_window *, GBDATA *gb_species, SpeciesConcatenateList *scl)
static void	mergeSimilarSpecies (AW_window *aws, MergeSpeciesType mergeType, AW_selection *selected_alis)
static AW_window *	createMergeSimilarSpeciesWindow (AW_root *aw_root, MergeSpeciesType mergeType, AW_selection *selected_alis)
AW_window *	NT_createMergeSimilarSpeciesWindow (AW_root *aw_root)
static AW_window *	NT_createMergeSimilarSpeciesAndConcatenateWindow (AW_root *aw_root, AW_selection *selected_alis)
static void	useSelectedAlignment (AW_window *aww)
AW_window *	NT_createConcatenationWindow (AW_root *aw_root)

Macro Definition Documentation

#define AWAR_CON_SEQUENCE_TYPE   "tmp/concat/sequence_type"

Definition at line 31 of file NT_concatenate.cxx.

Referenced by concatenateAlignments(), get_alitype_eval(), NT_createConcatenationAwars(), and NT_createConcatenationWindow().

#define AWAR_CON_NEW_ALIGNMENT_NAME   "tmp/concat/new_alignment_name"

Definition at line 32 of file NT_concatenate.cxx.

Referenced by concatenateAlignments(), NT_createConcatenationAwars(), NT_createConcatenationWindow(), and useSelectedAlignment().

#define AWAR_CON_ALIGNMENT_SEPARATOR   "tmp/concat/alignment_separator"

Definition at line 33 of file NT_concatenate.cxx.

Referenced by concatenateAlignments(), NT_createConcatenationAwars(), and NT_createConcatenationWindow().

#define AWAR_CON_SELECTED_ALI   "tmp/concat/database_alignments"

Definition at line 34 of file NT_concatenate.cxx.

Referenced by NT_createConcatenationAwars(), NT_createConcatenationWindow(), and useSelectedAlignment().

#define AWAR_CON_MERGE_FIELD   "tmp/concat/merge_field"

Definition at line 35 of file NT_concatenate.cxx.

Referenced by createMergeSimilarSpeciesWindow(), mergeSimilarSpecies(), and NT_createConcatenationAwars().

#define AWAR_CON_STORE_SIM_SP_NO   "tmp/concat/store_sim_sp_no"

Definition at line 36 of file NT_concatenate.cxx.

Referenced by createMergeSimilarSpeciesWindow(), mergeSimilarSpecies(), and NT_createConcatenationAwars().

#define AWAR_CON_ALLOW_OVERWRITE_ALI   "tmp/concat/overwrite"

Definition at line 38 of file NT_concatenate.cxx.

Referenced by concatenateAlignments(), NT_createConcatenationAwars(), and NT_createConcatenationWindow().

#define AWAR_CON_INSGAPS_FOR_MISS_ALIS   "tmp/concat/insgaps"

Definition at line 39 of file NT_concatenate.cxx.

Referenced by concatenateAlignments(), NT_createConcatenationAwars(), and NT_createConcatenationWindow().

#define MOVE_DOWN   0

Definition at line 41 of file NT_concatenate.cxx.

#define MOVE_UP   1

Definition at line 42 of file NT_concatenate.cxx.

Enumeration Type Documentation

enum MergeSpeciesType

Enumerator
MERGE_SPECIES_SIMPLE
MERGE_SPECIES_AND_CONCAT_ALI

Definition at line 590 of file NT_concatenate.cxx.

Function Documentation

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

Definition at line 52 of file NT_concatenate.cxx.

References ARB_strdup(), aw_message(), AWAR_CON_ALIGNMENT_SEPARATOR, AWAR_CON_ALLOW_OVERWRITE_ALI, AWAR_CON_INSGAPS_FOR_MISS_ALIS, AWAR_CON_MERGE_FIELD, AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SELECTED_ALI, AWAR_CON_SEQUENCE_TYPE, AWAR_CON_STORE_SIM_SP_NO, AW_root::awar_int(), AW_root::awar_string(), GB_await_error(), GB_clear_error(), GBS_global_string(), GBT_get_alignment_type_string(), GBT_get_default_alignment(), NULp, AW_awar::set_srt(), SRT_AUTOCORRECT_ALINAME, and ta.

Referenced by nt_create_all_awars().

char* get_alitype_eval ( AW_root *  aw_root )

inline

Definition at line 88 of file NT_concatenate.cxx.

References AW_root::awar(), AWAR_CON_SEQUENCE_TYPE, GBS_global_string_copy(), and AW_awar::read_char_pntr().

Referenced by alitype_changed_cb(), and createSelectionList().

static void alitype_changed_cb ( AW_root *  aw_root, AW_DB_selection *  db_sel  )

static

Definition at line 92 of file NT_concatenate.cxx.

References awt_reconfigure_ALI_selection_list(), and get_alitype_eval().

Referenced by NT_createConcatenationWindow().

static AW_DB_selection* createSelectionList ( GBDATA *  gb_main, AW_window *  aws, const char *  awarName  )

static

Definition at line 98 of file NT_concatenate.cxx.

References awt_create_ALI_selection_list(), get_alitype_eval(), AW_window::get_root(), and nt_assert.

Referenced by NT_createConcatenationWindow().

static GB_ERROR create_concatInfo_SAI ( GBDATA *  gb_main, const char *  new_ali_name, const char *  ali_separator, const StrArray &  ali_names  )

static

Definition at line 116 of file NT_concatenate.cxx.

References error(), GB_await_error(), GB_STRING, GB_write_string(), GBT_add_data(), GBT_find_or_create_SAI(), GBT_get_alignment_len(), info, nt_assert, NULp, and offset.

Referenced by concatenateAlignments().

static void concatenateAlignments ( AW_window *  aws, AW_selection *  selected_alis  )

static

Definition at line 179 of file NT_concatenate.cxx.

References aw_message(), AW_root::awar(), AWAR_CON_ALIGNMENT_SEPARATOR, AWAR_CON_ALLOW_OVERWRITE_ALI, AWAR_CON_INSGAPS_FOR_MISS_ALIS, AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SEQUENCE_TYPE, GBS_strstruct::cat(), create_concatInfo_SAI(), arb_progress::done(), error(), GB_await_error(), GB_end_transaction_show_error(), GB_find_string(), GB_IGNORE_CASE, NT_global::gb_main, GB_push_transaction(), GB_read_char_pntr(), GB_STRING, GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBT_add_alignment_changekeys(), GBT_add_data(), GBT_check_alignment_name(), GBT_check_data(), GBT_count_marked_species(), GBT_create_alignment(), GBT_find_sequence(), GBT_first_marked_species(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_name_or_description(), GBT_get_presets(), GBT_join_strings(), GBT_next_marked_species(), GBS_strstruct::get_data(), AW_window::get_root(), AW_selection::get_values(), GLOBAL, arb_progress::inc_and_check_user_abort(), GBS_strstruct::nput(), nt_assert, NULp, AW_awar::read_int(), AW_awar::read_string(), and SEARCH_GRANDCHILD.

Referenced by mergeSimilarSpecies(), and NT_createConcatenationWindow().

static void addSpeciesToConcatenateList ( SpeciesConcatenateList **  sclp, GB_CSTR  species_name  )

static

Definition at line 314 of file NT_concatenate.cxx.

References ARB_strdup(), NT_global::gb_main, gb_species_data, GBT_find_species_rel_species_data(), GBT_get_species_data(), GLOBAL, SpeciesConcatenateList::next, SpeciesConcatenateList::species, and SpeciesConcatenateList::species_name.

Referenced by mergeSimilarSpecies().

static void freeSpeciesConcatenateList ( SpeciesConcatenateList *  scl )

static

Definition at line 329 of file NT_concatenate.cxx.

References SpeciesConcatenateList::next, and SpeciesConcatenateList::species_name.

Referenced by mergeSimilarSpecies().

static GB_ERROR checkAndMergeFields ( GBDATA *  gb_new_species, GB_ERROR  error, SpeciesConcatenateList *  scl  )

static

Definition at line 338 of file NT_concatenate.cxx.

References add(), ARB_strdup(), error(), GB_FIND, GB_get_subfields(), GB_read_as_string(), GB_read_type(), GB_search(), GB_STRING, GBT_write_string(), SpeciesConcatenateList::next, nt_assert, NULp, SpeciesConcatenateList::species, SpeciesConcatenateList::species_name, and type.

Referenced by concatenateFieldsCreateNewSpecies().

static GBDATA* concatenateFieldsCreateNewSpecies ( AW_window *  , GBDATA *  gb_species, SpeciesConcatenateList *  scl  )

static

Definition at line 497 of file NT_concatenate.cxx.

References AW_get_nameserver_addid(), aw_message(), AWTC_generate_one_name(), AWTC_makeUniqueShortName(), checkAndMergeFields(), error(), GB_await_error(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_end_transaction(), GB_entry(), GB_export_errorf(), NT_global::gb_main, GB_push_transaction(), GB_read_as_string(), GB_read_char_pntr(), gb_species_data, GB_STRING, GB_write_string(), GBS_checksum(), GBS_global_string_copy(), GBT_add_data(), GBT_find_sequence(), GBT_find_species_rel_species_data(), GBT_get_alignment_names(), GBT_get_species_data(), GBT_read_string(), GBT_write_string(), GLOBAL, SpeciesConcatenateList::next, and NULp.

Referenced by mergeSimilarSpecies().

static void mergeSimilarSpecies ( AW_window *  aws, MergeSpeciesType  mergeType, AW_selection *  selected_alis  )

static

Definition at line 595 of file NT_concatenate.cxx.

References addSpeciesToConcatenateList(), arb_progress::auto_subtitles(), aw_message(), AW_root::awar(), AWAR_CON_MERGE_FIELD, AWAR_CON_STORE_SIM_SP_NO, concatenateAlignments(), concatenateFieldsCreateNewSpecies(), error(), FIF_NAME_SELECTED, freeSpeciesConcatenateList(), GB_await_error(), GB_begin_transaction(), GB_end_transaction_show_error(), GB_entry(), GB_incur_error_if(), NT_global::gb_main, GB_read_as_string(), GB_write_flag(), GB_write_lossless_int(), GBS_global_string(), GBT_count_marked_species(), GBT_first_marked_species(), GBT_get_name_or_description(), GBT_mark_all(), GBT_next_marked_species(), GBT_searchOrCreate_itemfield_according_to_changekey(), AW_window::get_root(), GLOBAL, arb_progress::inc_and_check_user_abort(), MERGE_SPECIES_AND_CONCAT_ALI, SpeciesConcatenateList::next, NO_FIELD_SELECTED, nt_assert, NULp, prepare_and_get_selected_itemfield(), AW_awar::read_string(), SpeciesConcatenateList::species, and SPECIES_get_selector().

Referenced by createMergeSimilarSpeciesWindow().

static AW_window* createMergeSimilarSpeciesWindow ( AW_root *  aw_root, MergeSpeciesType  mergeType, AW_selection *  selected_alis  )

static

Definition at line 712 of file NT_concatenate.cxx.

References AW_POPDOWN(), AWAR_CON_MERGE_FIELD, AWAR_CON_STORE_SIM_SP_NO, create_itemfield_selection_button(), FIELD_FILTER_INT_WRITEABLE, FIELD_FILTER_STRING_READABLE, NT_global::gb_main, GBS_global_string_copy(), GLOBAL, makeHelpCallback(), MERGE_SPECIES_AND_CONCAT_ALI, MERGE_SPECIES_SIMPLE, mergeSimilarSpecies(), NULp, SF_ALLOW_NEW, and SPECIES_get_selector().

Referenced by NT_createMergeSimilarSpeciesAndConcatenateWindow(), and NT_createMergeSimilarSpeciesWindow().

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().

static AW_window* NT_createMergeSimilarSpeciesAndConcatenateWindow ( AW_root *  aw_root, AW_selection *  selected_alis  )

static

Definition at line 759 of file NT_concatenate.cxx.

References createMergeSimilarSpeciesWindow(), MERGE_SPECIES_AND_CONCAT_ALI, nt_assert, and NULp.

Referenced by NT_createConcatenationWindow().

static void useSelectedAlignment ( AW_window *  aww )

static

Definition at line 777 of file NT_concatenate.cxx.

References aw_message(), AW_root::awar(), AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SELECTED_ALI, AW_window::get_root(), NO_ALI_SELECTED, AW_awar::read_char_pntr(), and AW_awar::write_string().

Referenced by NT_createConcatenationWindow().

AW_window* NT_createConcatenationWindow

(

AW_root *

aw_root

)

Definition at line 789 of file NT_concatenate.cxx.

References AW_awar::add_callback(), alitype_changed_cb(), AW_POPDOWN(), AW_root::awar(), AWAR_CON_ALIGNMENT_SEPARATOR, AWAR_CON_ALLOW_OVERWRITE_ALI, AWAR_CON_INSGAPS_FOR_MISS_ALIS, AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SELECTED_ALI, AWAR_CON_SEQUENCE_TYPE, awt_create_subset_selection_list(), concatenateAlignments(), createSelectionList(), NT_global::gb_main, AW_selection::get_sellist(), GLOBAL, AW_window::load_xfig(), makeHelpCallback(), NT_createMergeSimilarSpeciesAndConcatenateWindow(), NT_createMergeSimilarSpeciesWindow(), and useSelectedAlignment().

Referenced by popup_new_main_window().