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BlastMBLookupTable Struct Reference

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The lookup table structure used for Mega BLAST. More...

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

+ Collaboration diagram for BlastMBLookupTable:

Public Attributes

Int4 word_length
 number of exact letter matches that will trigger an ungapped extension More...
 
Int4 lut_word_length
 number of letters in a lookup table word More...
 
Int8 hashsize
 = 4^(lut_word_length) More...
 
Boolean discontiguous
 Are discontiguous words used? More...
 
Int4 template_length
 Length of the discontiguous word template. More...
 
EDiscTemplateType template_type
 Type of the discontiguous word template. More...
 
Boolean two_templates
 Use two templates simultaneously. More...
 
EDiscTemplateType second_template_type
 Type of the second discontiguous word template. More...
 
Boolean stride
 is lookup table created with a stride More...
 
Int4 scan_step
 Step size for scanning the database. More...
 
Int4hashtable
 Array of positions. More...
 
Int4hashtable2
 Array of positions for second template. More...
 
Int4next_pos
 Extra positions stored here. More...
 
Int4next_pos2
 Extra positions for the second template. More...
 
PV_ARRAY_TYPEpv_array
 Presence vector, used for quick presence check. More...
 
Int4 pv_array_bts
 The exponent of 2 by which pv_array is smaller than the backbone. More...
 
Int4 longest_chain
 Largest number of query positions for a given word. More...
 
void * scansub_callback
 function for scanning subject sequences More...
 
void * extend_callback
 function for extending hits More...
 
Int4 num_unique_pos_added
 Number of positions added to the l.t. More...
 
Int4 num_words_added
 Number of words added to the l.t. More...
 
BlastSeqLocmasked_locations
 masked locations, only non-NULL for soft-masking. More...
 

Detailed Description

The lookup table structure used for Mega BLAST.

Definition at line 238 of file blast_nalookup.h.

Member Data Documentation

◆ discontiguous

Boolean BlastMBLookupTable::discontiguous

◆ extend_callback

void* BlastMBLookupTable::extend_callback

function for extending hits

Definition at line 264 of file blast_nalookup.h.

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

◆ hashsize

Int8 BlastMBLookupTable::hashsize

◆ hashtable

Int4* BlastMBLookupTable::hashtable

◆ hashtable2

Int4* BlastMBLookupTable::hashtable2

Array of positions for second template.

Definition at line 254 of file blast_nalookup.h.

Referenced by BlastMBLookupTableDestruct(), and s_FillDiscMBTable().

◆ longest_chain

Int4 BlastMBLookupTable::longest_chain

◆ lut_word_length

Int4 BlastMBLookupTable::lut_word_length

◆ masked_locations

BlastSeqLoc* BlastMBLookupTable::masked_locations

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

Definition at line 268 of file blast_nalookup.h.

Referenced by BlastMBLookupTableDestruct(), BlastMBLookupTableNew(), s_BlastNaExtend(), and s_BlastNaExtendAligned().

◆ next_pos

Int4* BlastMBLookupTable::next_pos

Extra positions stored here.

Definition at line 255 of file blast_nalookup.h.

Referenced by BlastMBLookupTableDestruct(), s_FillContigMBTable(), s_FillDiscMBTable(), and s_MBLookup().

◆ next_pos2

Int4* BlastMBLookupTable::next_pos2

Extra positions for the second template.

Definition at line 256 of file blast_nalookup.h.

Referenced by BlastMBLookupTableDestruct(), and s_FillDiscMBTable().

◆ num_unique_pos_added

Int4 BlastMBLookupTable::num_unique_pos_added

Number of positions added to the l.t.

Definition at line 266 of file blast_nalookup.h.

Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), and s_FillDiscMBTable().

◆ num_words_added

Int4 BlastMBLookupTable::num_words_added

Number of words added to the l.t.

Definition at line 267 of file blast_nalookup.h.

Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), and s_FillDiscMBTable().

◆ pv_array

PV_ARRAY_TYPE* BlastMBLookupTable::pv_array

◆ pv_array_bts

Int4 BlastMBLookupTable::pv_array_bts

The exponent of 2 by which pv_array is smaller than the backbone.

Definition at line 259 of file blast_nalookup.h.

Referenced by BlastMBLookupTableNew(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FillPV(), s_MBCountWordsInSubject_16_1(), and s_MBLookup().

◆ scan_step

Int4 BlastMBLookupTable::scan_step

◆ scansub_callback

void* BlastMBLookupTable::scansub_callback

function for scanning subject sequences

Definition at line 263 of file blast_nalookup.h.

Referenced by TestFixture::RunScanSubject(), and s_MBChooseScanSubject().

◆ second_template_type

EDiscTemplateType BlastMBLookupTable::second_template_type

Type of the second discontiguous word template.

Definition at line 248 of file blast_nalookup.h.

Referenced by s_FillDiscMBTable(), and s_MB_DiscWordScanSubject_TwoTemplates_1().

◆ stride

Boolean BlastMBLookupTable::stride

is lookup table created with a stride

Definition at line 251 of file blast_nalookup.h.

Referenced by BlastMBLookupTableNew(), s_BlastNaExtend(), s_BlastNaExtendAligned(), and s_BlastNaExtendDirect().

◆ template_length

Int4 BlastMBLookupTable::template_length

◆ template_type

EDiscTemplateType BlastMBLookupTable::template_type

◆ two_templates

Boolean BlastMBLookupTable::two_templates

Use two templates simultaneously.

Definition at line 247 of file blast_nalookup.h.

Referenced by s_FillDiscMBTable(), and s_MBChooseScanSubject().

◆ word_length

Int4 BlastMBLookupTable::word_length

The documentation for this struct was generated from the following file:
Modified on Wed Mar 27 11:18:19 2024 by modify_doxy.py rev. 669887