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Typedefs | Enumerations | Functions | Variables
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_evaluate (GBDATA *gb_main, const SQ_weights &weights, bool marked_only)
 
static charSQ_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)
 
void SQ_calc_and_apply_group_data (TreeNode *node, GBDATA *gb_main, SQ_GroupData *data, AP_filter *filter, arb_progress &progress)
 
void SQ_calc_and_apply_group_data2 (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
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)
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
static GB_ERROR SQ_pass1 ( SQ_GroupData globalData,
GBDATA gb_main,
TreeNode node,
AP_filter filter 
)
static
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 
)
static
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 
)
static

Definition at line 845 of file SQ_functions.cxx.

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

Referenced by SQ_calc_and_apply_group_data().

void SQ_calc_and_apply_group_data ( TreeNode node,
GBDATA gb_main,
SQ_GroupData data,
AP_filter filter,
arb_progress progress 
)
void SQ_calc_and_apply_group_data2 ( 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)

Variable Documentation

SQ_GroupDataDictionary group_dict
static