NCBI C++ ToolKit
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SPHIPatternSearchBlk Struct Reference

Search Toolkit Book for SPHIPatternSearchBlk

Structure containing all auxiliary information needed in a pattern search. More...

#include <algo/blast/core/pattern.h>

+ Collaboration diagram for SPHIPatternSearchBlk:

Public Attributes

EPatternType flagPatternLength
 Indicates if the whole pattern fits in 1 word, each of several parts of the pattern fit in a word, or some parts of the pattern are too long to fit in a word. More...
 
double patternProbability
 Probability of this letter combination. More...
 
Int4 minPatternMatchLength
 Minimum length of string to match this pattern. More...
 
SShortPatternItemsone_word_items
 Items necessary when pattern fits in one word. More...
 
SLongPatternItemsmulti_word_items
 Additional items, when pattern requires multiple words. More...
 
Int4 num_patterns_db
 Number of patterns actually found during the database search. More...
 
char * pattern
 Pattern used, saved here for error reporting. More...
 

Detailed Description

Structure containing all auxiliary information needed in a pattern search.

Definition at line 155 of file pattern.h.

Member Data Documentation

◆ flagPatternLength

EPatternType SPHIPatternSearchBlk::flagPatternLength

Indicates if the whole pattern fits in 1 word, each of several parts of the pattern fit in a word, or some parts of the pattern are too long to fit in a word.

Definition at line 159 of file pattern.h.

Referenced by BOOST_AUTO_TEST_CASE(), FindPatternHits(), s_InitDNAPattern(), s_PatternSearchItemsInit(), s_PHIBlastAlignPatterns(), SPHIPatternSearchBlkFree(), and SPHIPatternSearchBlkNew().

◆ minPatternMatchLength

Int4 SPHIPatternSearchBlk::minPatternMatchLength

Minimum length of string to match this pattern.

Definition at line 161 of file pattern.h.

Referenced by Blast_SetPHIPatternInfo(), BOOST_AUTO_TEST_CASE(), s_PatternSearchItemsInit(), and SPHIPatternSearchBlkNew().

◆ multi_word_items

SLongPatternItems* SPHIPatternSearchBlk::multi_word_items

◆ num_patterns_db

Int4 SPHIPatternSearchBlk::num_patterns_db

Number of patterns actually found during the database search.

Definition at line 168 of file pattern.h.

Referenced by Blast_RunFullSearch(), BOOST_AUTO_TEST_CASE(), CBlastTracebackSearch::Run(), CBlastTracebackSearch::RunSimple(), and s_HSPPHIGetEvalue().

◆ one_word_items

SShortPatternItems* SPHIPatternSearchBlk::one_word_items

◆ pattern

char* SPHIPatternSearchBlk::pattern

Pattern used, saved here for error reporting.

Definition at line 170 of file pattern.h.

Referenced by Blast_SetPHIPatternInfo(), SPHIPatternSearchBlkFree(), and SPHIPatternSearchBlkNew().

◆ patternProbability

double SPHIPatternSearchBlk::patternProbability

Probability of this letter combination.

Definition at line 160 of file pattern.h.

Referenced by Blast_SetPHIPatternInfo(), BOOST_AUTO_TEST_CASE(), s_PatternSearchItemsInit(), and SPHIPatternSearchBlkNew().


The documentation for this struct was generated from the following file:
Modified on Tue Apr 23 07:40:38 2024 by modify_doxy.py rev. 669887