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... | |
| SShortPatternItems * | one_word_items |
| Items necessary when pattern fits in one word. More... | |
| SLongPatternItems * | multi_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.
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 |
Additional items, when pattern requires multiple words.
Definition at line 166 of file pattern.h.
Referenced by BOOST_AUTO_TEST_CASE(), s_FindHitsLong(), s_FindHitsVeryLong(), s_InitDNAPattern(), s_PackLongPattern(), s_PackVeryLongPattern(), s_PatternSearchItemsInit(), s_PHIBlastAlignPatterns(), s_PHIGetExtraLongPattern(), s_PHIGetLongPattern(), SPHIPatternSearchBlkFree(), and SPHIPatternSearchBlkNew().
◆ 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 |
Items necessary when pattern fits in one word.
Definition at line 163 of file pattern.h.
Referenced by _PHIBlastFindHitsShort(), BOOST_AUTO_TEST_CASE(), s_FindHitsShortDNA(), s_FindHitsVeryLong(), s_InitDNAPattern(), s_PatternSearchItemsInit(), s_PHIGetExtraLongPattern(), s_PHIGetShortPattern(), SPHIPatternSearchBlkFree(), and SPHIPatternSearchBlkNew().
◆ 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:
- include/algo/blast/core/pattern.h
