#include "st_quality.hxx"#include "st_ml.hxx"#include "MostLikelySeq.hxx"#include <ColumnStat.hxx>#include <BI_helix.hxx>#include <AP_filter.hxx>#include <arb_progress.h>#include <arbdbt.h>#include <arb_strbuf.h>#include <cctype>#include <cmath>#include <items.h>
Go to the source code of this file.
Functions | |
| static void | st_ml_add_sequence_part_to_stat (ST_ML *st_ml, ColumnStat *, const char *species_name, int seq_len, int bucket_size, GB_HASH *species_to_info_hash, int start, int end) |
| static GB_ERROR | st_ml_add_quality_string_to_species (GBDATA *gb_main, const AP_filter *filter, const char *alignment_name, const char *species_name, size_t bucket_size, GB_HASH *species_to_info_hash, st_report_enum report, const char *dest_field) |
| static void | destroy_ColumnQualityInfo (long cl_info) |
| GB_ERROR | st_ml_check_sequence_quality (GBDATA *gb_main, const char *tree_name, const char *alignment_name, ColumnStat *colstat, const WeightedFilter *weighted_filter, int bucket_size, int marked_only, st_report_enum report, const char *dest_field) |
Function Documentation
|
static |
Definition at line 110 of file ST_quality.cxx.
References LikelihoodRanges::add_relative(), ST_base_vector::b, DNA_Table::char_to_enum(), dna_table, GB_read_char_pntr(), GB_read_string_count(), GBS_read_hash(), GBS_write_hash(), MostLikelySeq::get_bound_species_data(), ST_ML::get_ml_vectors(), info, max, ST_base_vector::max_frequency(), NULp, ST_GAP, ST_UNKNOWN, start, STAT_find_node_by_name(), ColumnQualityInfo::stat_five, ColumnQualityInfo::stat_half, ColumnQualityInfo::stat_user, and MostLikelySeq::tmp_out.
Referenced by st_ml_check_sequence_quality().
|
static |
Definition at line 157 of file ST_quality.cxx.
References AP_filter::blowup_string(), buffer, GBS_strstruct::cat(), error(), GB_await_error(), GB_set_temporary(), GB_STRING, GB_write_string(), GBS_global_string(), GBS_read_hash(), GBT_add_data(), GBT_find_species(), GBT_searchOrCreate_itemfield_according_to_changekey(), LikelihoodRanges::generate_string(), GBS_strstruct::get_data(), AP_filter::get_filtered_length(), Sampler::get_median(), Sampler::get_sum(), info, GBS_strstruct::nprintf(), NULp, ColumnQualityInfo::overall_range_count(), GBS_strstruct::put(), SPECIES_get_selector(), ST_QUALITY_REPORT_TEMP, ColumnQualityInfo::stat_five, ColumnQualityInfo::stat_half, and ColumnQualityInfo::stat_user.
Referenced by st_ml_check_sequence_quality().
|
static |
Definition at line 232 of file ST_quality.cxx.
References info.
Referenced by st_ml_check_sequence_quality().
| GB_ERROR st_ml_check_sequence_quality | ( | GBDATA * | gb_main, |
| const char * | tree_name, | ||
| const char * | alignment_name, | ||
| ColumnStat * | colstat, | ||
| const WeightedFilter * | weighted_filter, | ||
| int | bucket_size, | ||
| int | marked_only, | ||
| st_report_enum | report, | ||
| const char * | dest_field | ||
| ) |
Definition at line 237 of file ST_quality.cxx.
References ST_ML::calc_st_ml(), destroy_ColumnQualityInfo(), error(), GB_IGNORE_CASE, GBS_create_dynaval_hash(), GBS_free_hash(), GBT_get_names_of_species_in_tree(), GBT_get_species_count(), ST_ML::get_filter(), ST_ML::get_filtered_length(), ST_ML::get_gbt_tree(), arb_progress::inc_and_check_user_abort(), NULp, ST_MAX_SEQ_PART, st_ml, st_ml_add_quality_string_to_species(), and st_ml_add_sequence_part_to_stat().
Referenced by st_check_cb().
