ST_window.cxx File Reference

#include "st_ml.hxx"
#include "st_quality.hxx"
#include <gui_aliview.hxx>
#include <ColumnStat.hxx>
#include <item_sel_list.h>
#include <awt_filter.hxx>
#include <awt_config_manager.hxx>
#include <aw_awars.hxx>
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <arbdbt.h>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <arb_strbuf.h>

Include dependency graph for ST_window.cxx:

Go to the source code of this file.

Classes
struct	st_check_cb_data

Macros
#define	ST_ML_AWAR   "tmp/st_ml/"
#define	ST_ML_AWAR_COLSTAT_PREFIX   ST_ML_AWAR "colstat/"
#define	ST_ML_AWAR_COLSTAT_NAME   ST_ML_AWAR_COLSTAT_PREFIX "name"
#define	ST_ML_AWAR_FILTER_PREFIX   ST_ML_AWAR "filter/"
#define	ST_ML_AWAR_FILTER_ALIGNMENT   ST_ML_AWAR_FILTER_PREFIX "alignment"
#define	ST_ML_AWAR_FILTER_NAME   ST_ML_AWAR_FILTER_PREFIX "name"
#define	ST_ML_AWAR_FILTER_FILTER   ST_ML_AWAR_FILTER_PREFIX "filter"
#define	ST_ML_AWAR_FILTER_SIMPLIFY   ST_ML_AWAR_FILTER_PREFIX "simplify"
#define	ST_ML_AWAR_CQ_BUCKET_SIZE   ST_ML_AWAR "bucket_size"
#define	ST_ML_AWAR_CQ_MARKED_ONLY   ST_ML_AWAR "marked_only"
#define	ST_ML_AWAR_CQ_DEST_FIELD   ST_ML_AWAR "dest_field"
#define	ST_ML_AWAR_CQ_REPORT   ST_ML_AWAR "report"
#define	ST_ML_AWAR_CQ_KEEP_REPORTS   ST_ML_AWAR "keep_reports"

Functions
static void	st_ok_cb (AW_window *aww, ST_ML *st_ml)
void	STAT_set_postcalc_callback (ST_ML *st_ml, WindowCallbackSimple postcalc_cb, AW_window *cb_win)
AW_window *	STAT_create_main_window (AW_root *root, ST_ML *st_ml)
ST_ML *	STAT_create_ST_ML (GBDATA *gb_main)
void	STAT_destroy_ST_ML (ST_ML *&st_ml)
ST_ML_Color *	STAT_get_color_string (ST_ML *st_ml, char *species_name, AP_tree *node, int start_ali_pos, int end_ali_pos)
bool	STAT_update_ml_likelihood (ST_ML *st_ml, char *result[4], int &latest_update, const char *species_name, AP_tree *node)
AP_tree *	STAT_find_node_by_name (ST_ML *st_ml, const char *species_name)
static GB_ERROR	st_remove_entries (AW_root *awr, GBDATA *gb_main, bool verbose)
static void	st_remove_entries_cb (AW_window *aww, GBDATA *gb_main)
static void	st_check_cb (AW_window *aww, st_check_cb_data *data)
static void	STAT_create_awars (AW_root *root, GBDATA *gb_main)
AW_window *	STAT_create_chimera_check_window (AW_root *root, GBDATA *gb_main)

Variables
static AWT_config_mapping_def	chimera_config_mapping []

Macro Definition Documentation

#define ST_ML_AWAR   "tmp/st_ml/"

Definition at line 30 of file ST_window.cxx.

#define ST_ML_AWAR_COLSTAT_PREFIX   ST_ML_AWAR "colstat/"

Definition at line 32 of file ST_window.cxx.

#define ST_ML_AWAR_COLSTAT_NAME   ST_ML_AWAR_COLSTAT_PREFIX "name"

Definition at line 33 of file ST_window.cxx.

Referenced by STAT_create_awars(), STAT_create_chimera_check_window(), and STAT_create_main_window().

#define ST_ML_AWAR_FILTER_PREFIX   ST_ML_AWAR "filter/"

Definition at line 35 of file ST_window.cxx.

#define ST_ML_AWAR_FILTER_ALIGNMENT   ST_ML_AWAR_FILTER_PREFIX "alignment"

Definition at line 36 of file ST_window.cxx.

Referenced by st_check_cb(), st_remove_entries(), and STAT_create_awars().

#define ST_ML_AWAR_FILTER_NAME   ST_ML_AWAR_FILTER_PREFIX "name"

Definition at line 37 of file ST_window.cxx.

Referenced by STAT_create_awars(), and STAT_create_chimera_check_window().

#define ST_ML_AWAR_FILTER_FILTER   ST_ML_AWAR_FILTER_PREFIX "filter"

Definition at line 38 of file ST_window.cxx.

Referenced by STAT_create_awars().

#define ST_ML_AWAR_FILTER_SIMPLIFY   ST_ML_AWAR_FILTER_PREFIX "simplify"

Definition at line 39 of file ST_window.cxx.

Referenced by STAT_create_awars().

#define ST_ML_AWAR_CQ_BUCKET_SIZE   ST_ML_AWAR "bucket_size"

Definition at line 41 of file ST_window.cxx.

Referenced by st_check_cb(), STAT_create_awars(), and STAT_create_chimera_check_window().

#define ST_ML_AWAR_CQ_MARKED_ONLY   ST_ML_AWAR "marked_only"

Definition at line 42 of file ST_window.cxx.

Referenced by st_check_cb(), st_ok_cb(), STAT_create_awars(), STAT_create_chimera_check_window(), and STAT_create_main_window().

#define ST_ML_AWAR_CQ_DEST_FIELD   ST_ML_AWAR "dest_field"

Definition at line 43 of file ST_window.cxx.

Referenced by st_check_cb(), st_remove_entries(), STAT_create_awars(), and STAT_create_chimera_check_window().

#define ST_ML_AWAR_CQ_REPORT   ST_ML_AWAR "report"

Definition at line 44 of file ST_window.cxx.

Referenced by st_check_cb(), STAT_create_awars(), and STAT_create_chimera_check_window().

#define ST_ML_AWAR_CQ_KEEP_REPORTS   ST_ML_AWAR "keep_reports"

Definition at line 45 of file ST_window.cxx.

Referenced by st_check_cb(), STAT_create_awars(), and STAT_create_chimera_check_window().

Function Documentation

static void st_ok_cb ( AW_window *  aww, ST_ML *  st_ml  )

static

Definition at line 47 of file ST_window.cxx.

References alignment_name, AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE, ST_ML::calc_st_ml(), ST_ML::do_postcalc_callback(), error(), GB_end_transaction(), GB_push_transaction(), ST_ML::get_column_statistic(), ST_ML::get_gb_main(), AW_window::get_root(), AW_window::hide_or_notify(), NULp, AW_awar::read_int(), and ST_ML_AWAR_CQ_MARKED_ONLY.

Referenced by STAT_create_main_window().

void STAT_set_postcalc_callback	(	ST_ML *	st_ml,
		WindowCallbackSimple	postcalc_cb,
		AW_window *	cb_win
	)

Definition at line 66 of file ST_window.cxx.

References ST_ML::set_postcalc_callback().

Referenced by configureColumnStat().

AW_window* STAT_create_main_window	(	AW_root *	root,
		ST_ML *	st_ml
	)

Definition at line 70 of file ST_window.cxx.

References AW_POPDOWN(), AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE, COLSTAT_create_selection_window(), ST_ML::create_column_statistic(), ST_ML::get_column_statistic(), ST_ML::get_gb_main(), AW_window::load_xfig(), makeHelpCallback(), ST_ML_AWAR_COLSTAT_NAME, ST_ML_AWAR_CQ_MARKED_ONLY, and st_ok_cb().

Referenced by configureColumnStat().

ST_ML* STAT_create_ST_ML

(

GBDATA *

gb_main

)

Definition at line 110 of file ST_window.cxx.

Referenced by ARB_main().

void STAT_destroy_ST_ML

(

ST_ML *&

st_ml

)

Definition at line 113 of file ST_window.cxx.

References NULp, and st_ml.

Referenced by ED4_root::~ED4_root().

ST_ML_Color* STAT_get_color_string	(	ST_ML *	st_ml,
		char *	species_name,
		AP_tree *	node,
		int	start_ali_pos,
		int	end_ali_pos
	)

Definition at line 118 of file ST_window.cxx.

References ST_ML::get_color_string().

bool STAT_update_ml_likelihood	(	ST_ML *	st_ml,
		char *	result[4],
		int &	latest_update,
		const char *	species_name,
		AP_tree *	node
	)

See also

ST_ML::update_ml_likelihood()

Definition at line 122 of file ST_window.cxx.

References ST_ML::update_ml_likelihood().

AP_tree* STAT_find_node_by_name	(	ST_ML *	st_ml,
		const char *	species_name
	)

Definition at line 127 of file ST_window.cxx.

References ST_ML::find_node_by_name().

Referenced by ED4_toggle_detailed_column_stats(), and st_ml_add_sequence_part_to_stat().

static GB_ERROR st_remove_entries ( AW_root *  awr, GBDATA *  gb_main, bool  verbose  )

static

Definition at line 143 of file ST_window.cxx.

References aw_message(), AW_root::awar(), GBS_strstruct::cat(), error(), GB_delete(), GB_entry(), GBT_first_species(), GBT_get_species_count(), GBT_next_species(), GBS_strstruct::get_data(), arb_progress::inc_and_check_user_abort(), NO_FIELD_SELECTED, GBS_strstruct::nprintf(), NULp, AW_awar::read_string(), ST_ML_AWAR_CQ_DEST_FIELD, ST_ML_AWAR_FILTER_ALIGNMENT, and ta.

Referenced by st_check_cb(), and st_remove_entries_cb().

static void st_remove_entries_cb ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 202 of file ST_window.cxx.

References aw_message_if(), gb_main, AW_window::get_root(), and st_remove_entries().

Referenced by STAT_create_chimera_check_window().

static void st_check_cb ( AW_window *  aww, st_check_cb_data *  data  )

static

Definition at line 206 of file ST_window.cxx.

References aw_message(), AW_root::awar(), AWAR_TREE, GB_transaction::close(), st_check_cb_data::colstat, error(), st_check_cb_data::filter, GB_await_error(), st_check_cb_data::gb_main, AW_window::get_root(), NULp, prepare_and_get_selected_itemfield(), AW_awar::read_int(), AW_awar::read_string(), SPECIES_get_selector(), ST_ML_AWAR_CQ_BUCKET_SIZE, ST_ML_AWAR_CQ_DEST_FIELD, ST_ML_AWAR_CQ_KEEP_REPORTS, ST_ML_AWAR_CQ_MARKED_ONLY, ST_ML_AWAR_CQ_REPORT, ST_ML_AWAR_FILTER_ALIGNMENT, st_ml_check_sequence_quality(), st_remove_entries(), and ta.

Referenced by STAT_create_chimera_check_window().

static void STAT_create_awars ( AW_root *  root, GBDATA *  gb_main  )

static

Definition at line 238 of file ST_window.cxx.

References AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE, AW_awar::map(), ST_ML_AWAR_COLSTAT_NAME, ST_ML_AWAR_CQ_BUCKET_SIZE, ST_ML_AWAR_CQ_DEST_FIELD, ST_ML_AWAR_CQ_KEEP_REPORTS, ST_ML_AWAR_CQ_MARKED_ONLY, ST_ML_AWAR_CQ_REPORT, ST_ML_AWAR_FILTER_ALIGNMENT, ST_ML_AWAR_FILTER_FILTER, ST_ML_AWAR_FILTER_NAME, and ST_ML_AWAR_FILTER_SIMPLIFY.

Referenced by STAT_create_chimera_check_window().

AW_window* STAT_create_chimera_check_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 270 of file ST_window.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_DEFAULT_ALIGNMENT, AW_root::awar_string(), awt_create_select_filter_win(), AWT_insert_config_manager(), st_check_cb_data::colstat, COLSTAT_create_selection_window(), create_itemfield_selection_button(), FIELD_FILTER_STRING_WRITEABLE, st_check_cb_data::filter, WeightedFilter::get_adfiltercbstruct(), makeHelpCallback(), NULp, SF_ALLOW_NEW, SPECIES_get_selector(), st_check_cb(), ST_ML_AWAR_COLSTAT_NAME, ST_ML_AWAR_CQ_BUCKET_SIZE, ST_ML_AWAR_CQ_DEST_FIELD, ST_ML_AWAR_CQ_KEEP_REPORTS, ST_ML_AWAR_CQ_MARKED_ONLY, ST_ML_AWAR_CQ_REPORT, ST_ML_AWAR_FILTER_NAME, st_remove_entries_cb(), and STAT_create_awars().

Referenced by popup_new_main_window().

Variable Documentation

AWT_config_mapping_def chimera_config_mapping[]

static

Initial value:

= {
    { ST_ML_AWAR_CQ_MARKED_ONLY,  "marked_only" },
    { ST_ML_AWAR_COLSTAT_NAME,    "colstat" },
    { ST_ML_AWAR_FILTER_NAME,     "filter" },
    { ST_ML_AWAR_CQ_BUCKET_SIZE,  "bucketsize" },
    { ST_ML_AWAR_CQ_DEST_FIELD,   "destfield" }, 
    { ST_ML_AWAR_CQ_REPORT,       "report" },
    { ST_ML_AWAR_CQ_KEEP_REPORTS, "keepold" },

    { NULp, NULp }
}

Definition at line 258 of file ST_window.cxx.