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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_GroupData > SQ_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)
 
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_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

typedef SmartPtr< SQ_GroupData> SQ_GroupDataPtr

Definition at line 39 of file SQ_functions.h.

typedef std::map< std::string, SQ_GroupDataPtr> SQ_GroupDataDictionary

Definition at line 42 of file SQ_functions.h.

Enumeration Type Documentation

enum SQ_TREE_ERROR
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)

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_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().

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().

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_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().

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().

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)

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().

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