SExtraLongPatternItems Struct Reference

Search Toolkit Book for SExtraLongPatternItems

Auxiliary items needed for a PHI BLAST search with pattern that contains pieces longer than a word. More...

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

Public Attributes
Int4	numPlacesInWord [100]
	When pattern has more than 7 words, keep track of how many places of pattern in each word of the representation;. More...
Int4	spacing [100]
	Spaces until next word due to wildcard. More...
Int4	highestPlace
	Number of places in pattern representation as computed in input_pattern. More...
Int4	whichMostSpecific
	Which word in an extra long pattern has the lowest probability of a match. More...

Detailed Description

Auxiliary items needed for a PHI BLAST search with pattern that contains pieces longer than a word.

Definition at line 105 of file pattern.h.

Member Data Documentation

highestPlace

Int4 SExtraLongPatternItems::highestPlace

Number of places in pattern representation as computed in input_pattern.

Definition at line 111 of file pattern.h.

Referenced by s_PHIBlastAlignPatterns(), and SPHIPatternSearchBlkNew().

numPlacesInWord

Int4 SExtraLongPatternItems::numPlacesInWord[100]

When pattern has more than 7 words, keep track of how many places of pattern in each word of the representation;.

Definition at line 108 of file pattern.h.

Referenced by s_FindHitsVeryLong(), s_PackVeryLongPattern(), s_PHIBlastAlignPatterns(), and s_PHIGetExtraLongPattern().

spacing

Int4 SExtraLongPatternItems::spacing[100]

Spaces until next word due to wildcard.

Definition at line 110 of file pattern.h.

Referenced by s_FindHitsVeryLong(), s_PackVeryLongPattern(), and s_PHIGetExtraLongPattern().

whichMostSpecific

Int4 SExtraLongPatternItems::whichMostSpecific

Which word in an extra long pattern has the lowest probability of a match.

Definition at line 113 of file pattern.h.

Referenced by s_FindHitsVeryLong(), and s_PackVeryLongPattern().

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The documentation for this struct was generated from the following file:

• include/algo/blast/core/pattern.h