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BlastNaHashLookupTable Struct Reference

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

+ Collaboration diagram for BlastNaHashLookupTable:

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...
 
NaHashLookupBackboneCellthick_backbone
 the "thick" backbone. More...
 
Int4overflow
 the overflow array for the compacted lookup table More...
 
Int4 offsets_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...
 
Int4 pv_array_bts
 power of 2 by which to divide a word to access PV_ARRAY_TYPE element in pv array More...
 
void * scansub_callback
 function for scanning subject sequences More...
 
void * hash_callback
 hash function to be used for hash table More...
 
BlastSeqLocmasked_locations
 masked locations, only non-NULL for soft-masking. More...
 

Detailed Description

Definition at line 637 of file blast_nalookup.h.

Member Data Documentation

◆ backbone_size

Int4 BlastNaHashLookupTable::backbone_size

number of cells in the backbone

Definition at line 645 of file blast_nalookup.h.

◆ hash_callback

void* BlastNaHashLookupTable::hash_callback

hash function to be used for hash table

Definition at line 662 of file blast_nalookup.h.

◆ longest_chain

Int4 BlastNaHashLookupTable::longest_chain

length of the longest chain on the backbone

Definition at line 646 of file blast_nalookup.h.

◆ lut_word_length

Int4 BlastNaHashLookupTable::lut_word_length

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

Definition at line 642 of file blast_nalookup.h.

◆ mask

Int4 BlastNaHashLookupTable::mask

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

Definition at line 638 of file blast_nalookup.h.

◆ masked_locations

BlastSeqLoc* BlastNaHashLookupTable::masked_locations

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

Definition at line 663 of file blast_nalookup.h.

◆ offsets_size

Int4 BlastNaHashLookupTable::offsets_size

Number of elements in the overflow array.

Definition at line 655 of file blast_nalookup.h.

◆ overflow

Int4* BlastNaHashLookupTable::overflow

the overflow array for the compacted lookup table

Definition at line 653 of file blast_nalookup.h.

◆ pv

PV_ARRAY_TYPE* BlastNaHashLookupTable::pv

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

Definition at line 656 of file blast_nalookup.h.

◆ pv_array_bts

Int4 BlastNaHashLookupTable::pv_array_bts

power of 2 by which to divide a word to access PV_ARRAY_TYPE element in pv array

Definition at line 659 of file blast_nalookup.h.

◆ scan_step

Int4 BlastNaHashLookupTable::scan_step

number of bases between successive words

Definition at line 644 of file blast_nalookup.h.

◆ scansub_callback

void* BlastNaHashLookupTable::scansub_callback

function for scanning subject sequences

Definition at line 661 of file blast_nalookup.h.

◆ thick_backbone

NaHashLookupBackboneCell* BlastNaHashLookupTable::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 647 of file blast_nalookup.h.

◆ word_length

Int4 BlastNaHashLookupTable::word_length

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

Definition at line 640 of file blast_nalookup.h.


The documentation for this struct was generated from the following file:
Modified on Wed May 22 11:26:44 2024 by modify_doxy.py rev. 669887