Search Toolkit Book for SLongPatternItems
Auxiliary items needed for a PHI BLAST search with pattern containing multiple words. More...
#include <algo/blast/core/pattern.h>
Collaboration diagram for SLongPatternItems:
Public Attributes | |
| Int4 | numWords |
| Number of words need to hold bit representation of pattern. More... | |
| Int4 | match_maskL [100] |
| Bit mask representation of input pattern for long patterns. More... | |
| Int4 | bitPatternByLetter [256][11] |
| Which positions can a character occur in for long patterns. More... | |
| Int4 | SLL [100][256] |
| For each letter in the alphabet and each word in the masked pattern representation, holds a bit pattern saying for which positions the letter will match. More... | |
| Int4 | inputPatternMasked [(30 *11)] |
| Masked input pattern. More... | |
| SDNALongPatternItems * | dna_items |
| Additional items necessary for a DNA pattern. More... | |
| SExtraLongPatternItems * | extra_long_items |
| Additional items necessary if pattern contains pieces longer than a word. More... | |
Detailed Description
Auxiliary items needed for a PHI BLAST search with pattern containing multiple words.
Member Data Documentation
◆ bitPatternByLetter
| Int4 SLongPatternItems::bitPatternByLetter[256][11] |
Which positions can a character occur in for long patterns.
Definition at line 137 of file pattern.h.
Referenced by s_FindHitsLong(), s_PackLongPattern(), and s_PHIGetLongPattern().
◆ dna_items
| SDNALongPatternItems* SLongPatternItems::dna_items |
Additional items necessary for a DNA pattern.
Definition at line 145 of file pattern.h.
Referenced by s_FindHitsVeryLong(), s_InitDNAPattern(), and SPHIPatternSearchBlkFree().
◆ extra_long_items
| SExtraLongPatternItems* SLongPatternItems::extra_long_items |
Additional items necessary if pattern contains pieces longer than a word.
Definition at line 147 of file pattern.h.
Referenced by BOOST_AUTO_TEST_CASE(), s_FindHitsVeryLong(), s_PackVeryLongPattern(), s_PHIBlastAlignPatterns(), s_PHIGetExtraLongPattern(), SPHIPatternSearchBlkFree(), and SPHIPatternSearchBlkNew().
◆ inputPatternMasked
| Int4 SLongPatternItems::inputPatternMasked[(30 * 11)] |
Masked input pattern.
Definition at line 143 of file pattern.h.
Referenced by s_PackLongPattern(), s_PHIBlastAlignPatterns(), and SPHIPatternSearchBlkNew().
◆ match_maskL
| Int4 SLongPatternItems::match_maskL[100] |
Bit mask representation of input pattern for long patterns.
Definition at line 134 of file pattern.h.
Referenced by s_FindHitsLong(), s_FindHitsVeryLong(), s_InitDNAPattern(), s_PackLongPattern(), s_PackVeryLongPattern(), s_PHIGetExtraLongPattern(), and s_PHIGetLongPattern().
◆ numWords
| Int4 SLongPatternItems::numWords |
Number of words need to hold bit representation of pattern.
Definition at line 132 of file pattern.h.
Referenced by BOOST_AUTO_TEST_CASE(), s_FindHitsLong(), s_FindHitsVeryLong(), s_InitDNAPattern(), s_PackLongPattern(), s_PackVeryLongPattern(), s_PHIGetExtraLongPattern(), and s_PHIGetLongPattern().
◆ SLL
| Int4 SLongPatternItems::SLL[100][256] |
For each letter in the alphabet and each word in the masked pattern representation, holds a bit pattern saying for which positions the letter will match.
Similar to whichPositionsByCharacter for many-word patterns.
Definition at line 142 of file pattern.h.
Referenced by s_FindHitsVeryLong(), s_InitDNAPattern(), s_PackVeryLongPattern(), and s_PHIGetExtraLongPattern().
The documentation for this struct was generated from the following file:
- include/algo/blast/core/pattern.h
