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BlastNaLookupTable Struct Reference

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The basic lookup table structure for blastn searches. More...

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

+ Collaboration diagram for BlastNaLookupTable:

Public Attributes

Int4 mask
 part of index to mask off, that is, top (wordsize*charsize) bits should be discarded. More...
 
Int4 word_length
 Length in bases of the full word match required to trigger extension. More...
 
Int4 lut_word_length
 Length in bases of a word indexed by the lookup table. More...
 
Int4 scan_step
 number of bases between successive words More...
 
Int4 backbone_size
 number of cells in the backbone More...
 
Int4 longest_chain
 length of the longest chain on the backbone More...
 
NaLookupBackboneCellthick_backbone
 the "thick" backbone. More...
 
Int4overflow
 the overflow array for the compacted lookup table More...
 
Int4 overflow_size
 Number of elements in the overflow array. More...
 
PV_ARRAY_TYPEpv
 Presence vector bitfield; bit positions that are set indicate that the corresponding thick backbone cell contains hits. More...
 
void * scansub_callback
 function for scanning subject sequences More...
 
void * extend_callback
 function for extending hits More...
 
BlastSeqLocmasked_locations
 masked locations, only non-NULL for soft-masking. More...
 

Detailed Description

The basic lookup table structure for blastn searches.

Definition at line 131 of file blast_nalookup.h.

Member Data Documentation

◆ backbone_size

Int4 BlastNaLookupTable::backbone_size

number of cells in the backbone

Definition at line 139 of file blast_nalookup.h.

◆ extend_callback

void* BlastNaLookupTable::extend_callback

function for extending hits

Definition at line 154 of file blast_nalookup.h.

Referenced by BlastChooseNaExtend(), and NuclWordFinderTextFixture::setupAll().

◆ longest_chain

Int4 BlastNaLookupTable::longest_chain

length of the longest chain on the backbone

Definition at line 140 of file blast_nalookup.h.

◆ lut_word_length

Int4 BlastNaLookupTable::lut_word_length

Length in bases of a word indexed by the lookup table.

Definition at line 136 of file blast_nalookup.h.

Referenced by BlastChooseNaExtend(), BlastNaExtendJumper(), s_BlastNaExtend(), s_BlastNaExtendAligned(), and NuclWordFinderTextFixture::setupLookupTable().

◆ mask

Int4 BlastNaLookupTable::mask

part of index to mask off, that is, top (wordsize*charsize) bits should be discarded.

Definition at line 132 of file blast_nalookup.h.

◆ masked_locations

BlastSeqLoc* BlastNaLookupTable::masked_locations

masked locations, only non-NULL for soft-masking.

Definition at line 155 of file blast_nalookup.h.

Referenced by s_BlastNaExtend(), and s_BlastNaExtendAligned().

◆ overflow

Int4* BlastNaLookupTable::overflow

the overflow array for the compacted lookup table

Definition at line 147 of file blast_nalookup.h.

◆ overflow_size

Int4 BlastNaLookupTable::overflow_size

Number of elements in the overflow array.

Definition at line 149 of file blast_nalookup.h.

◆ pv

PV_ARRAY_TYPE* BlastNaLookupTable::pv

Presence vector bitfield; bit positions that are set indicate that the corresponding thick backbone cell contains hits.

Definition at line 150 of file blast_nalookup.h.

◆ scan_step

Int4 BlastNaLookupTable::scan_step

number of bases between successive words

Definition at line 138 of file blast_nalookup.h.

Referenced by BlastChooseNaExtend(), and NuclWordFinderTextFixture::setupLookupTable().

◆ scansub_callback

void* BlastNaLookupTable::scansub_callback

function for scanning subject sequences

Definition at line 153 of file blast_nalookup.h.

◆ thick_backbone

NaLookupBackboneCell* BlastNaLookupTable::thick_backbone

the "thick" backbone.

after queries are indexed, compact the backbone to put at most NA_HITS_PER_CELL hits on the backbone, otherwise point to some overflow storage

Definition at line 141 of file blast_nalookup.h.

◆ word_length

Int4 BlastNaLookupTable::word_length

Length in bases of the full word match required to trigger extension.

Definition at line 134 of file blast_nalookup.h.

Referenced by BlastChooseNaExtend(), BlastNaExtendJumper(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), and NuclWordFinderTextFixture::setupLookupTable().


The documentation for this struct was generated from the following file:
Modified on Sun May 19 04:44:24 2024 by modify_doxy.py rev. 669887