Search Toolkit Book for BlastNaLookupTable
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... | |
| NaLookupBackboneCell * | thick_backbone |
| the "thick" backbone. More... | |
| Int4 * | overflow |
| the overflow array for the compacted lookup table More... | |
| Int4 | overflow_size |
| Number of elements in the overflow array. More... | |
| PV_ARRAY_TYPE * | pv |
| 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... | |
| BlastSeqLoc * | masked_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:
- include/algo/blast/core/blast_nalookup.h
