Functions for accessing hits in the protein BLAST lookup table. More...
#include <algo/blast/core/blast_aascan.h>#include <algo/blast/core/blast_aalookup.h>#include "masksubj.inl"
Include dependency graph for blast_aascan.c:
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Functions | |
| static Int4 | s_BlastAaScanSubject (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 array_size, Int4 *s_range) |
| Scans the subject sequence from "offset" to the end of the sequence. More... | |
| static Int4 | s_BlastSmallAaScanSubject (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 array_size, Int4 *s_range) |
| same function for small lookup table More... | |
| static Int4 | s_BlastCompressedAaScanSubject (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 array_size, Int4 *s_range) |
| Scans the subject sequence from "offset" to the end of the sequence, assuming a compressed protein alphabet Copies at most array_size hits. More... | |
| static void | s_AddToRPSBucket (RPSBucket *b, Uint4 q_off, Uint4 s_off) |
| Add one query-subject pair to the list of such pairs retrieved from the RPS blast lookup table. More... | |
| Int4 | BlastRPSScanSubject (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *sequence, Int4 *offset) |
| Scans the RPS query sequence from "offset" to the end of the sequence. More... | |
| void | BlastChooseProteinScanSubject (LookupTableWrap *lookup_wrap) |
| Choose the most appropriate function to scan through protein subject sequences. More... | |
Detailed Description
Functions for accessing hits in the protein BLAST lookup table.
Definition in file blast_aascan.c.
Function Documentation
◆ BlastChooseProteinScanSubject()
| void BlastChooseProteinScanSubject | ( | LookupTableWrap * | lookup_wrap | ) |
Choose the most appropriate function to scan through protein subject sequences.
- Parameters
-
lookup_wrap Structure containing lookup table [in][out]
Definition at line 553 of file blast_aascan.c.
References BlastAaLookupTable::bone_type, eAaLookupTable, eBackbone, eCompressedAaLookupTable, LookupTableWrap::lut, LookupTableWrap::lut_type, s_BlastAaScanSubject(), s_BlastCompressedAaScanSubject(), s_BlastSmallAaScanSubject(), BlastAaLookupTable::scansub_callback, and BlastCompressedAaLookupTable::scansub_callback.
Referenced by AascanTestFixture::AascanTestFixture(), CompressedAascanTestFixture::CompressedAascanTestFixture(), and s_BlastSetUpAuxStructures().
◆ BlastRPSScanSubject()
| Int4 BlastRPSScanSubject | ( | const LookupTableWrap * | lookup_wrap, |
| const BLAST_SequenceBlk * | sequence, | ||
| Int4 * | offset | ||
| ) |
Scans the RPS query sequence from "offset" to the end of the sequence.
Copies at most array_size hits. Returns the number of hits found. If there isn't enough room to copy all the hits, return early, and update "offset".
- Parameters
-
lookup_wrap the lookup table [in] sequence the subject sequence [in] offset the offset in the subject at which to begin scanning [in/out]
- Returns
- The number of hits found.
Definition at line 450 of file blast_aascan.c.
References ASSERT, ComputeTableIndex(), ComputeTableIndexIncremental(), RPSBackboneCell::entries, eRPSLookupTable, for(), i, BLAST_SequenceBlk::length, lookup(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, RPSBackboneCell::num_used, offset, PV_ARRAY_BTS, PV_ARRAY_TYPE, PV_TEST, RPS_BUCKET_SIZE, RPS_HITS_PER_CELL, s_AddToRPSBucket(), and BLAST_SequenceBlk::sequence.
Referenced by s_BlastRPSWordFinder_OneHit(), and s_BlastRPSWordFinder_TwoHit().
◆ s_AddToRPSBucket()
Add one query-subject pair to the list of such pairs retrieved from the RPS blast lookup table.
- Parameters
-
b the List in which the current pair will be placed [in/out] q_off query offset [in] s_off subject offset [in]
Definition at line 422 of file blast_aascan.c.
References b, i, BlastOffsetPair::q_off, BlastOffsetPair::qs_offsets, and BlastOffsetPair::s_off.
Referenced by BlastRPSScanSubject().
◆ s_BlastAaScanSubject()
|
static |
Scans the subject sequence from "offset" to the end of the sequence.
Copies at most array_size hits. Returns the number of hits found. If there isn't enough room to copy all the hits, return early, and update "offset".
- Parameters
-
lookup_wrap the lookup table [in] subject the subject sequence [in] offset_pairs Array to which hits will be copied [out] array_size length of the offset arrays [in]
- Returns
- The number of hits found.
Definition at line 48 of file blast_aascan.c.
References AA_HITS_PER_CELL, ASSERT, ComputeTableIndex(), ComputeTableIndexIncremental(), eAaLookupTable, eBackbone, AaLookupBackboneCell::entries, i, lookup(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, AaLookupBackboneCell::num_used, AaLookupBackboneCell::overflow_cursor, AaLookupBackboneCell::payload, PV_ARRAY_BTS, PV_ARRAY_TYPE, PV_TEST, s_DetermineScanningOffsets(), and subject.
Referenced by BlastChooseProteinScanSubject().
◆ s_BlastCompressedAaScanSubject()
|
static |
Scans the subject sequence from "offset" to the end of the sequence, assuming a compressed protein alphabet Copies at most array_size hits.
Returns the number of hits found. If there isn't enough room to copy all the hits, return early, and update "offset".
- Parameters
-
lookup_wrap the lookup table [in] subject the subject sequence [in] offset the offset in the subject at which to begin scanning [in/out] offset_pairs Array to which hits will be copied [out] array_size length of the offset arrays [in]
- Returns
- The number of hits found.
Definition at line 234 of file blast_aascan.c.
References ASSERT, COMPRESSED_HITS_CELL_MASK, COMPRESSED_HITS_PER_BACKBONE_CELL, COMPRESSED_HITS_PER_OVERFLOW_CELL, eCompressedAaLookupTable, CompressedMixedOffsets::head, i, lookup(), LookupTableWrap::lut, LookupTableWrap::lut_type, CompressedOverflowCell::next, NULL, CompressedLookupBackboneCell::num_used, CompressedLookupBackboneCell::overflow_list, CompressedLookupBackboneCell::payload, PV_ARRAY_TYPE, PV_TEST, BlastOffsetPair::q_off, BlastOffsetPair::qs_offsets, CompressedLookupBackboneCell::query_offset, CompressedMixedOffsets::query_offsets, CompressedOverflowCell::query_offsets, CompressedLookupBackboneCell::query_offsets, s_ComputeCompressedIndex(), s_DetermineScanningOffsets(), BlastOffsetPair::s_off, subject, and while().
Referenced by BlastChooseProteinScanSubject().
◆ s_BlastSmallAaScanSubject()
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static |
same function for small lookup table
Definition at line 134 of file blast_aascan.c.
References AA_HITS_PER_CELL, ASSERT, ComputeTableIndex(), ComputeTableIndexIncremental(), eAaLookupTable, AaLookupSmallboneCell::entries, eSmallbone, i, lookup(), LookupTableWrap::lut, LookupTableWrap::lut_type, NULL, AaLookupSmallboneCell::num_used, AaLookupSmallboneCell::overflow_cursor, AaLookupSmallboneCell::payload, PV_ARRAY_BTS, PV_ARRAY_TYPE, PV_TEST, s_DetermineScanningOffsets(), and subject.
Referenced by BlastChooseProteinScanSubject().
