SQ_functions.cxx File Reference

#include "SQ_ambiguities.h"
#include "SQ_helix.h"
#include "SQ_physical_layout.h"
#include "SQ_functions.h"
#include <aw_preset.hxx>
#include <arb_progress.h>
#include <TreeNode.h>

Include dependency graph for SQ_functions.cxx:

Go to the source code of this file.

Typedefs
typedef GBDATA *(*	species_iterator )(GBDATA *)

Enumerations
enum	{ CS_CLEAR, CS_PASS1 }

Functions
void	SQ_clear_group_dictionary ()
static GB_ERROR	no_data_error (GBDATA *gb_species, const char *ali_name)
static int	sq_round (double value)
GB_ERROR	SQ_remove_quality_entries (GBDATA *gb_main)
GB_ERROR	SQ_add_changekeys (GBDATA *gb_main, const char *alignment_name)
GB_ERROR	SQ_evaluate (GBDATA *gb_main, const SQ_weights &weights, bool marked_only)
static char *	SQ_fetch_filtered_sequence (GBDATA *read_sequence, AP_filter *filter)
static GB_ERROR	SQ_pass1 (SQ_GroupData *globalData, GBDATA *gb_main, TreeNode *node, AP_filter *filter)
GB_ERROR	SQ_pass1_no_tree (SQ_GroupData *globalData, GBDATA *gb_main, AP_filter *filter, arb_progress &progress)
static GB_ERROR	SQ_pass2 (const SQ_GroupData *globalData, GBDATA *gb_main, TreeNode *node, AP_filter *filter)
GB_ERROR	SQ_pass2_no_tree (const SQ_GroupData *globalData, GBDATA *gb_main, AP_filter *filter, arb_progress &progress)
static void	create_multi_level_consensus (TreeNode *node, SQ_GroupData *data)
GB_ERROR	SQ_pass1_on_tree (TreeNode *node, GBDATA *gb_main, SQ_GroupData *data, AP_filter *filter, arb_progress &progress)
GB_ERROR	SQ_pass2_on_tree (TreeNode *node, GBDATA *gb_main, const SQ_GroupData *data, AP_filter *filter, arb_progress &progress)
GB_ERROR	SQ_mark_species (GBDATA *gb_main, int condition, bool marked_only)
SQ_TREE_ERROR	SQ_check_tree_structure (TreeNode *node)

Variables
static SQ_GroupDataDictionary	group_dict

Typedef Documentation

typedef GBDATA*(* species_iterator)(GBDATA *)

Definition at line 26 of file SQ_functions.cxx.

Enumeration Type Documentation

anonymous enum

Enumerator
CS_CLEAR
CS_PASS1

Definition at line 30 of file SQ_functions.cxx.

Function Documentation

void SQ_clear_group_dictionary

(

)

Definition at line 34 of file SQ_functions.cxx.

References group_dict, and swap().

Referenced by sq_calc_seq_quality_cb().

static GB_ERROR no_data_error ( GBDATA *  gb_species, const char *  ali_name  )

static

Definition at line 39 of file SQ_functions.cxx.

References GB_entry(), GB_read_char_pntr(), and GBS_global_string().

Referenced by SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), and SQ_pass2_no_tree().

static int sq_round ( double  value )

static

Definition at line 45 of file SQ_functions.cxx.

Referenced by SQ_evaluate(), SQ_pass2(), and SQ_pass2_no_tree().

GB_ERROR SQ_remove_quality_entries

(

GBDATA *

gb_main

)

Definition at line 53 of file SQ_functions.cxx.

References GB_transaction::close(), error(), GB_delete(), GB_FIND, GB_search(), GBT_first_species(), GBT_next_species(), NULp, and ta.

Referenced by sq_remove_quality_entries_cb().

GB_ERROR SQ_add_changekeys	(	GBDATA *	gb_main,
		const char *	alignment_name
	)

Definition at line 69 of file SQ_functions.cxx.

References error(), GB_FLOAT, GB_INT, GB_NONE, GB_STRING, GBS_global_string(), GBT_add_new_species_changekey(), NULp, and type.

Referenced by SQ_evaluate().

GB_ERROR SQ_evaluate	(	GBDATA *	gb_main,
		const SQ_weights &	weights,
		bool	marked_only
	)

Definition at line 115 of file SQ_functions.cxx.

References abs, alignment_name, SQ_weights::bases, SQ_weights::consensus, SQ_weights::diff_from_average, error(), GB_entry(), GB_get_error(), GB_INT, GB_read_int(), GB_search(), GB_write_int(), GBS_global_string(), GBT_first_marked_species(), GBT_first_species(), GBT_get_default_alignment(), GBT_next_marked_species(), GBT_next_species(), SQ_weights::gc, SQ_weights::helix, SQ_weights::iupac, NULp, result, seq_assert, SQ_add_changekeys(), and sq_round().

Referenced by sq_calc_seq_quality_cb().

static char* SQ_fetch_filtered_sequence ( GBDATA *  read_sequence, AP_filter *  filter  )

static

Definition at line 225 of file SQ_functions.cxx.

References ARB_alloc(), GB_read_char_pntr(), AP_filter::get_filtered_length(), AP_filter::get_filterpos_2_seqpos(), NULp, and UNCOVERED.

Referenced by SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), and SQ_pass2_no_tree().

static GB_ERROR SQ_pass1 ( SQ_GroupData *  globalData, GBDATA *  gb_main, TreeNode *  node, AP_filter *  filter  )

static

Definition at line 245 of file SQ_functions.cxx.

References alignment_name, error(), GB_CREATE_CONTAINER, GB_entry(), GB_get_error(), TreeNode::gb_node, GB_search(), GBT_get_default_alignment(), AP_filter::get_filtered_length(), SQ_GroupData::getSize(), no_data_error(), NULp, seq_assert, SQ_GroupData::SQ_add_sequence(), SQ_helix::SQ_calc_helix_layout(), SQ_physical_layout::SQ_calc_physical_layout(), SQ_ambiguities::SQ_count_ambiguities(), SQ_GroupData::SQ_count_sequences(), SQ_fetch_filtered_sequence(), SQ_physical_layout::SQ_get_gc_proportion(), SQ_physical_layout::SQ_get_number_of_bases(), SQ_GroupData::SQ_init_consensus(), SQ_GroupData::SQ_is_initialized(), SQ_GroupData::SQ_set_avg_bases(), and SQ_GroupData::SQ_set_avg_gc().

Referenced by SQ_pass1_on_tree().

GB_ERROR SQ_pass1_no_tree	(	SQ_GroupData *	globalData,
		GBDATA *	gb_main,
		AP_filter *	filter,
		arb_progress &	progress
	)

Definition at line 318 of file SQ_functions.cxx.

References alignment_name, error(), GB_CREATE_CONTAINER, GB_entry(), GB_get_error(), GB_search(), GBT_first_species(), GBT_get_default_alignment(), GBT_next_species(), AP_filter::get_filtered_length(), arb_progress::inc_and_check_user_abort(), no_data_error(), NULp, seq_assert, SQ_GroupData::SQ_add_sequence(), SQ_helix::SQ_calc_helix_layout(), SQ_physical_layout::SQ_calc_physical_layout(), SQ_ambiguities::SQ_count_ambiguities(), SQ_GroupData::SQ_count_sequences(), SQ_fetch_filtered_sequence(), SQ_physical_layout::SQ_get_gc_proportion(), SQ_physical_layout::SQ_get_number_of_bases(), SQ_GroupData::SQ_init_consensus(), SQ_GroupData::SQ_is_initialized(), SQ_GroupData::SQ_set_avg_bases(), and SQ_GroupData::SQ_set_avg_gc().

Referenced by sq_calc_seq_quality_cb().

static GB_ERROR SQ_pass2 ( const SQ_GroupData *  globalData, GBDATA *  gb_main, TreeNode *  node, AP_filter *  filter  )

static

Definition at line 391 of file SQ_functions.cxx.

References alignment_name, consensus_result::conformity, consensus_result::deviation, diff(), error(), TreeNode::father, GB_CREATE_CONTAINER, GB_entry(), GB_FLOAT, GB_get_error(), GB_INT, TreeNode::gb_node, GB_read_float(), GB_read_int(), GB_search(), GB_STRING, GB_write_float(), GB_write_int(), GB_write_string(), GBT_get_default_alignment(), group_dict, TreeNode::name, no_data_error(), NULp, seq_assert, SQ_fetch_filtered_sequence(), SQ_GroupData::SQ_get_avg_bases(), SQ_GroupData::SQ_get_avg_gc(), and sq_round().

Referenced by SQ_pass2_on_tree().

GB_ERROR SQ_pass2_no_tree	(	const SQ_GroupData *	globalData,
		GBDATA *	gb_main,
		AP_filter *	filter,
		arb_progress &	progress
	)

Definition at line 552 of file SQ_functions.cxx.

References alignment_name, consensus_result::conformity, consensus_result::deviation, diff(), error(), GB_CREATE_CONTAINER, GB_entry(), GB_FLOAT, GB_get_error(), GB_INT, GB_read_float(), GB_read_int(), GB_search(), GB_STRING, GB_write_float(), GB_write_int(), GB_write_string(), GBT_first_species(), GBT_get_default_alignment(), GBT_next_species(), arb_progress::inc_and_check_user_abort(), no_data_error(), NULp, seq_assert, SQ_GroupData::SQ_calc_consensus(), SQ_fetch_filtered_sequence(), SQ_GroupData::SQ_get_avg_bases(), SQ_GroupData::SQ_get_avg_gc(), SQ_GroupData::SQ_get_nr_sequences(), and sq_round().

Referenced by sq_calc_seq_quality_cb().

static void create_multi_level_consensus ( TreeNode *  node, SQ_GroupData *  data  )

static

Definition at line 701 of file SQ_functions.cxx.

References SQ_GroupData::clone(), group_dict, and TreeNode::name.

Referenced by SQ_pass1_on_tree().

GB_ERROR SQ_pass1_on_tree	(	TreeNode *	node,
		GBDATA *	gb_main,
		SQ_GroupData *	data,
		AP_filter *	filter,
		arb_progress &	progress
	)

Definition at line 707 of file SQ_functions.cxx.

References SQ_GroupData::clone(), create_multi_level_consensus(), error(), TreeNode::gb_node, SQ_GroupData::getSize(), arb_progress::inc(), TreeNode::is_leaf(), TreeNode::name, NULp, seq_assert, SQ_GroupData::SQ_add(), SQ_pass1(), and SQ_pass1_on_tree().

Referenced by sq_calc_seq_quality_cb(), and SQ_pass1_on_tree().

GB_ERROR SQ_pass2_on_tree	(	TreeNode *	node,
		GBDATA *	gb_main,
		const SQ_GroupData *	data,
		AP_filter *	filter,
		arb_progress &	progress
	)

Definition at line 759 of file SQ_functions.cxx.

References error(), gb_main, TreeNode::gb_node, arb_progress::inc(), TreeNode::is_leaf(), NULp, SQ_pass2(), and SQ_pass2_on_tree().

Referenced by sq_calc_seq_quality_cb(), and SQ_pass2_on_tree().

GB_ERROR SQ_mark_species	(	GBDATA *	gb_main,
		int	condition,
		bool	marked_only
	)

Definition at line 778 of file SQ_functions.cxx.

References alignment_name, error(), GB_CREATE_CONTAINER, GB_entry(), GB_INT, GB_read_flag(), GB_read_int(), GB_search(), GB_write_flag(), GBT_first_marked_species(), GBT_first_species(), GBT_get_default_alignment(), GBT_next_marked_species(), GBT_next_species(), NULp, result, and seq_assert.

Referenced by sq_calc_seq_quality_cb().

SQ_TREE_ERROR SQ_check_tree_structure

(

TreeNode *

node

)

Definition at line 825 of file SQ_functions.cxx.

References TreeNode::gb_node, TreeNode::is_leaf(), MISSING_NODE, NONE, SQ_check_tree_structure(), and ZOMBIE.

Referenced by sq_calc_seq_quality_cb(), and SQ_check_tree_structure().

Variable Documentation

SQ_GroupDataDictionary group_dict

static

Definition at line 28 of file SQ_functions.cxx.

Referenced by create_multi_level_consensus(), SQ_clear_group_dictionary(), and SQ_pass2().