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SQ_functions.h File Reference
#include "SQ_GroupData.h"
#include <map>
#include <string>
#include <smartptr.h>
#include <arbdb_base.h>
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Classes

struct  SQ_weights
 

Typedefs

typedef SmartPtr< SQ_GroupDataSQ_GroupDataPtr
 
typedef std::map< std::string,
SQ_GroupDataPtr
SQ_GroupDataDictionary
 

Enumerations

enum  SQ_TREE_ERROR { NONE = 0, ZOMBIE = 1, MISSING_NODE = 2 }
 

Functions

GB_ERROR SQ_remove_quality_entries (GBDATA *gb_main)
 
GB_ERROR SQ_pass1_no_tree (SQ_GroupData *globalData, GBDATA *gb_main, AP_filter *filter, arb_progress &progress)
 
GB_ERROR SQ_pass2_no_tree (const SQ_GroupData *globalData, GBDATA *gb_main, AP_filter *filter, arb_progress &progress)
 
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_evaluate (GBDATA *gb_main, const SQ_weights &weights, bool marked_only)
 
GB_ERROR SQ_mark_species (GBDATA *gb_main, int condition, bool marked_only)
 
void SQ_clear_group_dictionary ()
 
SQ_TREE_ERROR SQ_check_tree_structure (TreeNode *node)
 

Typedef Documentation

Definition at line 39 of file SQ_functions.h.

Definition at line 42 of file SQ_functions.h.

Enumeration Type Documentation

Enumerator
NONE 
ZOMBIE 
MISSING_NODE 

Definition at line 80 of file SQ_functions.h.

Function Documentation

GB_ERROR SQ_remove_quality_entries ( GBDATA gb_main)
GB_ERROR SQ_pass1_no_tree ( SQ_GroupData globalData,
GBDATA gb_main,
AP_filter filter,
arb_progress progress 
)
GB_ERROR SQ_pass2_no_tree ( const SQ_GroupData globalData,
GBDATA gb_main,
AP_filter filter,
arb_progress progress 
)
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_evaluate ( GBDATA gb_main,
const SQ_weights weights,
bool  marked_only 
)
GB_ERROR SQ_mark_species ( GBDATA gb_main,
int  condition,
bool  marked_only 
)
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().

SQ_TREE_ERROR SQ_check_tree_structure ( TreeNode node)