Search Toolkit Book for BlastNaHashLookupTable
#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... | |
| NaHashLookupBackboneCell * | thick_backbone |
| the "thick" backbone. More... | |
| Int4 * | overflow |
| the overflow array for the compacted lookup table More... | |
| Int4 | offsets_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... | |
| 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... | |
| BlastSeqLoc * | masked_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:
- include/algo/blast/core/blast_nalookup.h
