#include "NT_local.h"
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <aw_awar.hxx>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_defs.h>
#include <arb_progress.h>
#include <awt_config_manager.hxx>
#include <awt_misc.hxx>
#include <awt_sel_boxes.hxx>
#include <consensus.h>
#include <consensus_config.h>
#include <chartable.h>

Include dependency graph for AP_consensus.cxx:

Macros
#define	AWAR_MAX_FREQ_PREFIX "tmp/CON_MAX_FREQ/"

#define	AWAR_CONSENSUS_PREFIX "consensus/"

#define	AWAR_CONSENSUS_PREFIX_TMP "tmp/" AWAR_CONSENSUS_PREFIX

#define	AWAR_MAX_FREQ_IGNORE_GAPS AWAR_MAX_FREQ_PREFIX "no_gaps"

#define	AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ_PREFIX "sai_name"

#define	AWAR_CONSENSUS_MARKED_ONLY AWAR_CONSENSUS_PREFIX_TMP "marked_only"

#define	AWAR_CONSENSUS_ALIGNMENT AWAR_CONSENSUS_PREFIX_TMP "alignment"

#define	AWAR_CONSENSUS_COUNTGAPS AWAR_CONSENSUS_PREFIX "countgaps"

#define	AWAR_CONSENSUS_GAPBOUND AWAR_CONSENSUS_PREFIX "gapbound"

#define	AWAR_CONSENSUS_GROUP AWAR_CONSENSUS_PREFIX "group"

#define	AWAR_CONSENSUS_CONSIDBOUND AWAR_CONSENSUS_PREFIX "considbound"

#define	AWAR_CONSENSUS_UPPER AWAR_CONSENSUS_PREFIX "upper"

#define	AWAR_CONSENSUS_LOWER AWAR_CONSENSUS_PREFIX "lower"

#define	AWAR_CONSENSUS_NAME AWAR_CONSENSUS_PREFIX_TMP "name"

#define	CONSENSUS_AWAR_SOURCE CAS_NTREE

Functions
static int	CON_insertSequences (GBDATA gb_main, const char aliname, long maxalignlen, bool onlymarked, BaseFrequencies &freqs)

static GB_ERROR	CON_export (GBDATA gb_main, const char savename, const char align, const char result, bool onlymarked, long nrofspecies, const ConsensusBuildParams &BK)

static GB_ERROR	CON_calculate (GBDATA gb_main, const ConsensusBuildParams &BK, const char aliname, bool onlymarked, const char *sainame)

static void	CON_calculate_cb (AW_window *aw)

static void	consensus_upper_lower_changed_cb (AW_root *awr, bool upper_changed)

void	AP_create_consensus_var (AW_root *aw_root, AW_default aw_def)

AW_window *	AP_create_con_expert_window (AW_root *aw_root)

static GB_ERROR	CON_calc_max_freq (GBDATA gb_main, bool ignore_gaps, const char savename, const char *aliname)

static void	CON_calc_max_freq_cb (AW_window *aw)

AW_window *	AP_create_max_freq_window (AW_root *aw_root)

Variables
static AWT_config_mapping_def	consensus_config_mapping []

Macro Definition Documentation

#define AWAR_MAX_FREQ_PREFIX "tmp/CON_MAX_FREQ/"

Definition at line 30 of file AP_consensus.cxx.

#define AWAR_CONSENSUS_PREFIX "consensus/"

Definition at line 31 of file AP_consensus.cxx.

#define AWAR_CONSENSUS_PREFIX_TMP "tmp/" AWAR_CONSENSUS_PREFIX

Definition at line 32 of file AP_consensus.cxx.

#define AWAR_MAX_FREQ_IGNORE_GAPS AWAR_MAX_FREQ_PREFIX "no_gaps"

Definition at line 34 of file AP_consensus.cxx.

Referenced by AP_create_consensus_var(), AP_create_max_freq_window(), and CON_calc_max_freq_cb().

#define AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ_PREFIX "sai_name"

Definition at line 35 of file AP_consensus.cxx.

Referenced by AP_create_consensus_var(), AP_create_max_freq_window(), and CON_calc_max_freq_cb().

#define AWAR_CONSENSUS_MARKED_ONLY AWAR_CONSENSUS_PREFIX_TMP "marked_only"

Definition at line 37 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), AP_create_consensus_var(), and CON_calculate_cb().

#define AWAR_CONSENSUS_ALIGNMENT AWAR_CONSENSUS_PREFIX_TMP "alignment"

Definition at line 38 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), AP_create_consensus_var(), and CON_calculate_cb().

#define AWAR_CONSENSUS_COUNTGAPS AWAR_CONSENSUS_PREFIX "countgaps"

Definition at line 39 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), and AP_create_consensus_var().

#define AWAR_CONSENSUS_GAPBOUND AWAR_CONSENSUS_PREFIX "gapbound"

Definition at line 40 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), and AP_create_consensus_var().

#define AWAR_CONSENSUS_GROUP AWAR_CONSENSUS_PREFIX "group"

Definition at line 41 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), and AP_create_consensus_var().

#define AWAR_CONSENSUS_CONSIDBOUND AWAR_CONSENSUS_PREFIX "considbound"

Definition at line 42 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), and AP_create_consensus_var().

#define AWAR_CONSENSUS_UPPER AWAR_CONSENSUS_PREFIX "upper"

Definition at line 43 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), AP_create_consensus_var(), and consensus_upper_lower_changed_cb().

#define AWAR_CONSENSUS_LOWER AWAR_CONSENSUS_PREFIX "lower"

Definition at line 44 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), AP_create_consensus_var(), and consensus_upper_lower_changed_cb().

#define AWAR_CONSENSUS_NAME AWAR_CONSENSUS_PREFIX_TMP "name"

Definition at line 45 of file AP_consensus.cxx.

Referenced by AP_create_con_expert_window(), AP_create_consensus_var(), and CON_calculate_cb().

#define CONSENSUS_AWAR_SOURCE CAS_NTREE

Definition at line 47 of file AP_consensus.cxx.

Function Documentation

static int CON_insertSequences	(	GBDATA *	gb_main,
		const char *	aliname,
		long	maxalignlen,
		bool	onlymarked,
		BaseFrequencies &	freqs
	)

static

read sequence data and fill into 'freqs'

Parameters

gb_main	database
aliname	name of alignment
maxalignlen	length of alignment
onlymarked	true -> marked only
freqs	sequences are inserted here (has to be empty)

Returns: number of inserted sequences

Definition at line 52 of file AP_consensus.cxx.

References BaseFrequencies::added_sequences(), arb_progress::auto_subtitles(), arb_progress::done(), GB_read_char_pntr(), GB_read_string_count(), GBS_global_string(), GBT_count_marked_species(), GBT_find_sequence(), GBT_first_marked_species(), GBT_first_species(), GBT_get_species_count(), GBT_message(), GBT_next_marked_species(), GBT_next_species(), length, and nt_assert.

Referenced by CON_calc_max_freq(), and CON_calculate().

static GB_ERROR CON_export	(	GBDATA *	gb_main,
		const char *	savename,
		const char *	align,
		const char *	result,
		bool	onlymarked,
		long	nrofspecies,
		const ConsensusBuildParams &	BK
	)

static

writes consensus SAI to DB

Parameters

gb_main	database
savename	name of SAI to save to
align	alignment name
result	SAI data to write
onlymarked	true -> was calculated on marked only (used for SAI comment)
nrofspecies	number of used sequences (used for SAI comment; if less than 20 -> add an explicit list to field '_SPECIES')
BK	parameters used for consensus calculation (used for SAI comment)

Returns: error if something goes wrong

Definition at line 90 of file AP_consensus.cxx.

References buffer, GBS_strstruct::cat(), ConsensusBuildParams::considbound, ConsensusBuildParams::countgaps, ConsensusBuildParams::gapbound, GB_delete(), GB_FIND, GB_get_father(), GB_read_char_pntr(), GB_search(), GB_STRING, GB_write_string(), GBS_global_string(), GBT_add_data(), GBT_find_or_create_SAI(), GBT_find_sequence(), GBT_first_marked_species(), GBT_first_species(), GBT_next_marked_species(), GBT_next_species(), GBT_write_string(), GBS_strstruct::get_data(), ConsensusBuildParams::group, ConsensusBuildParams::lower, GBS_strstruct::put(), and ConsensusBuildParams::upper.

Referenced by CON_calculate().

static GB_ERROR CON_calculate	(	GBDATA *	gb_main,
		const ConsensusBuildParams &	BK,
		const char *	aliname,
		bool	onlymarked,
		const char *	sainame
	)

static

calculates the consensus and writes it to SAI 'sainame' Description how consensus is calculated: ../HELP_SOURCE/source/consensus_def.hlp

Parameters

gb_main	database
BK	parameters for consensus calculation
aliname	alignment name
onlymarked	true -> use marked sequences only
sainame	name of destination SAI

Returns: error if something goes wrong

Definition at line 168 of file AP_consensus.cxx.

References arb_assert, BaseFrequencies::build_consensus_string(), CON_export(), CON_insertSequences(), error(), GB_append_exportedError(), GB_AT_UNKNOWN, GB_await_error(), GB_end_transaction(), GB_push_transaction(), GBT_get_alignment_len(), GBT_get_alignment_type(), ConsensusBuildParams::lower, NULp, result, BaseFrequencies::setup(), and ConsensusBuildParams::upper.

Referenced by CON_calculate_cb().

static void CON_calculate_cb ( AW_window * aw )

static

Definition at line 212 of file AP_consensus.cxx.

References aw_message_if(), AW_root::awar(), AWAR_CONSENSUS_ALIGNMENT, AWAR_CONSENSUS_MARKED_ONLY, AWAR_CONSENSUS_NAME, CON_calculate(), AW_awar::deny_read, AW_awar::deny_write, error(), NT_global::gb_main, AW_window::get_root(), GLOBAL, AW_awar::read_int(), AW_awar::read_string(), and ta.

Referenced by AP_create_con_expert_window().

static void consensus_upper_lower_changed_cb	(	AW_root *	awr,
		bool	upper_changed
	)

static

Definition at line 235 of file AP_consensus.cxx.

References AW_root::awar(), AWAR_CONSENSUS_LOWER, AWAR_CONSENSUS_UPPER, AW_awar::read_int(), and AW_awar::write_int().

Referenced by AP_create_consensus_var().

void AP_create_consensus_var	(	AW_root *	aw_root,
		AW_default	aw_def
	)

AW_window* AP_create_con_expert_window ( AW_root * aw_root )

static GB_ERROR CON_calc_max_freq	(	GBDATA *	gb_main,
		bool	ignore_gaps,
		const char *	savename,
		const char *	aliname
	)

static

calculates the maximum frequency for each column and write to SAI

Parameters

gb_main	database
ignore_gaps	true -> ignore gaps; see ../HELP_SOURCE/source/max_freq.hlp
savename	name of destination SAI
aliname	name of alignment to use

Returns: error if something goes wrong

Definition at line 368 of file AP_consensus.cxx.

References arb_assert, GB_transaction::close(), CON_insertSequences(), error(), GB_append_exportedError(), GB_AT_UNKNOWN, GB_await_error(), GB_have_error(), GB_STRING, GB_write_string(), GBS_global_string(), GBT_add_data(), GBT_find_or_create_SAI(), GBT_get_alignment_len(), GBT_get_alignment_type(), BaseFrequencies::max_frequency_at(), NULp, BaseFrequencies::setup(), ta, and type.

Referenced by CON_calc_max_freq_cb().

static void CON_calc_max_freq_cb ( AW_window * aw )

static

Definition at line 450 of file AP_consensus.cxx.

References aw_message_if(), AW_root::awar(), AWAR_MAX_FREQ_IGNORE_GAPS, AWAR_MAX_FREQ_SAI_NAME, CON_calc_max_freq(), error(), GB_await_error(), NT_global::gb_main, GBT_get_default_alignment(), AW_window::get_root(), GLOBAL, AW_awar::read_char_pntr(), and AW_awar::read_int().

Referenced by AP_create_max_freq_window().

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().

Variable Documentation

AWT_config_mapping_def consensus_config_mapping[]

static

Initial value:

= {
    { AWAR_CONSENSUS_COUNTGAPS,   CONSENSUS_CONFIG_COUNTGAPS },
    { AWAR_CONSENSUS_GAPBOUND,    CONSENSUS_CONFIG_GAPBOUND },
    { AWAR_CONSENSUS_GROUP,       CONSENSUS_CONFIG_GROUP },
    { AWAR_CONSENSUS_CONSIDBOUND, CONSENSUS_CONFIG_CONSIDBOUND },
    { AWAR_CONSENSUS_UPPER,       CONSENSUS_CONFIG_UPPER },
    { AWAR_CONSENSUS_LOWER,       CONSENSUS_CONFIG_LOWER },
    
    
    { AWAR_CONSENSUS_MARKED_ONLY, "marked_only" },
    { AWAR_CONSENSUS_NAME,        "name" },
    { NULp, NULp }
}

Definition at line 272 of file AP_consensus.cxx.

Macros

Functions

Variables

Macro Definition Documentation

Function Documentation

Variable Documentation