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BLAST_SequenceBlk Struct Reference

Search Toolkit Book for BLAST_SequenceBlk

Structure to hold a sequence. More...

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

+ Collaboration diagram for BLAST_SequenceBlk:

Public Attributes

Uint1sequence
 Sequence used for search (could be translation). More...
 
Uint1sequence_start
 Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte. More...
 
Int4 length
 Length of sequence. More...
 
Int2 frame
 Frame of the query, needed for translated searches. More...
 
Int2 subject_strand
 Strand of the subject sequence for translated searches. More...
 
Int4 oid
 The ordinal id of the current sequence. More...
 
Boolean sequence_allocated
 TRUE if memory has been allocated for sequence. More...
 
Boolean sequence_start_allocated
 TRUE if memory has been allocated for sequence_start. More...
 
Uint1sequence_start_nomask
 Query sequence without masking. More...
 
Uint1sequence_nomask
 Start of query sequence without masking. More...
 
Boolean nomask_allocated
 If false the two above are just pointers to sequence and sequence_start. More...
 
Uint1oof_sequence
 Mixed-frame protein representation of a nucleotide sequence for out-of-frame alignment. More...
 
Boolean oof_sequence_allocated
 TRUE if memory has been allocated for oof_sequence. More...
 
Uint1compressed_nuc_seq
 4-to-1 compressed version of sequence More...
 
Uint1compressed_nuc_seq_start
 start of compressed_nuc_seq More...
 
BlastMaskLoclcase_mask
 Locations to be masked from operations on this sequence: lookup table for query; scanning for subject. More...
 
Boolean lcase_mask_allocated
 TRUE if memory has been allocated for lcase_mask. More...
 
Int4 chunk
 Used for indexing only: the chunk number within the subject sequence. More...
 
Uint1gen_code_string
 for nucleotide subject sequences (tblast[nx]), the genetic code used to create a translated protein sequence (NULL if not applicable). More...
 
SSeqRangeseq_ranges
 Ranges of the sequence to search. More...
 
Uint4 num_seq_ranges
 Number of elements in seq_ranges. More...
 
Boolean seq_ranges_allocated
 TRUE if memory has been allocated for seq_ranges. More...
 
ESubjectMaskingType mask_type
 type of subject masking More...
 
Uint1 bases_offset
 

Detailed Description

Structure to hold a sequence.

Definition at line 242 of file blast_def.h.

Member Data Documentation

◆ bases_offset

Uint1 BLAST_SequenceBlk::bases_offset

Definition at line 287 of file blast_def.h.

Referenced by BLAST_PreliminarySearchEngine(), and s_VDBSRC_GetSequence().

◆ chunk

Int4 BLAST_SequenceBlk::chunk

Used for indexing only: the chunk number within the subject sequence.

Definition at line 270 of file blast_def.h.

◆ compressed_nuc_seq

Uint1* BLAST_SequenceBlk::compressed_nuc_seq

4-to-1 compressed version of sequence

Definition at line 263 of file blast_def.h.

Referenced by BlastCompressBlastnaSequence().

◆ compressed_nuc_seq_start

Uint1* BLAST_SequenceBlk::compressed_nuc_seq_start

start of compressed_nuc_seq

Definition at line 264 of file blast_def.h.

Referenced by BlastCompressBlastnaSequence(), and BlastSequenceBlkFree().

◆ frame

Int2 BLAST_SequenceBlk::frame

Frame of the query, needed for translated searches.

Definition at line 247 of file blast_def.h.

Referenced by s_BlastProtGappedAlignment().

◆ gen_code_string

Uint1* BLAST_SequenceBlk::gen_code_string

for nucleotide subject sequences (tblast[nx]), the genetic code used to create a translated protein sequence (NULL if not applicable).

This field is NOT owned by this data structure, it's owned by the genetic code singleton.

See also
gencode_singleton.h

Definition at line 272 of file blast_def.h.

Referenced by BLAST_ComputeTraceback_MT(), BLAST_PreliminarySearchEngine(), s_MatchingSequenceInitialize(), s_SequenceGetTranslatedRange(), and SetupSubjects_OMF().

◆ lcase_mask

BlastMaskLoc* BLAST_SequenceBlk::lcase_mask

Locations to be masked from operations on this sequence: lookup table for query; scanning for subject.

Definition at line 265 of file blast_def.h.

Referenced by BlastSequenceBlkFree(), BOOST_AUTO_TEST_CASE(), s_GetFilteringLocationsForOneContext(), s_MultiSeqGetSequence(), s_QueryFactoryGetSequence(), CBlastSetupTestFixture::s_TestSingleSubjectNuclMask(), and SetupSubjects_OMF().

◆ lcase_mask_allocated

Boolean BLAST_SequenceBlk::lcase_mask_allocated

TRUE if memory has been allocated for lcase_mask.

Definition at line 268 of file blast_def.h.

Referenced by BlastSequenceBlkFree(), s_MultiSeqGetSequence(), s_QueryFactoryGetSequence(), CBlastSetupTestFixture::s_TestSingleSubjectNuclMask(), and SetupSubjects_OMF().

◆ length

Int4 BLAST_SequenceBlk::length

Length of sequence.

Definition at line 246 of file blast_def.h.

Referenced by AascanTestFixture::AascanTestFixture(), BLAST_ComputeTraceback_MT(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPGetTargetTranslation(), Blast_MaskUnsupportedAA(), BLAST_PreliminarySearchEngine(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastCompressBlastnaSequence(), BlastRPSScanSubject(), BlastSeqBlkSetSeqRanges(), BlastSeqBlkSetSequence(), BlastTargetTranslationNew(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CBLAST_SequenceBlk::DebugDump(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), InitializeBlastScoreBlk(), PHIBlastScanSubject(), PsiBlastComputePssmScores(), CPsiBlastValidate::QueryFactory(), s_BlastDynProgNtGappedAlignment(), s_BlastProtGappedAlignment(), s_checkDbSeqSrcFunctions(), s_MatrixInfoInit(), s_MBCountWordsInSubject_16_1(), s_NaHashLookupCountWordsInSubject_16_1(), s_PHIGappedAlignment(), s_PHITracebackFromHSPList(), s_RPSComputeTraceback(), s_SetUpLocalBlastSequenceBlk(), s_SetupQueryInfoForReevaluateTest(), CBlastSetupTestFixture::s_ValidateProtein130912(), s_VDBSRC_GetSequence(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), NuclWordFinderTextFixture::setupExtendWord(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), TestFixture::SetUpSubject(), SetupSubjects_OMF(), and TestFixture::SkipMaskedRangesCore().

◆ mask_type

ESubjectMaskingType BLAST_SequenceBlk::mask_type

type of subject masking

Definition at line 284 of file blast_def.h.

Referenced by BlastSeqBlkSetSeqRanges().

◆ nomask_allocated

Boolean BLAST_SequenceBlk::nomask_allocated

If false the two above are just pointers to sequence and sequence_start.

Definition at line 257 of file blast_def.h.

Referenced by BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), and BlastSetUp_MaskQuery().

◆ num_seq_ranges

Uint4 BLAST_SequenceBlk::num_seq_ranges

◆ oid

Int4 BLAST_SequenceBlk::oid

◆ oof_sequence

Uint1* BLAST_SequenceBlk::oof_sequence

◆ oof_sequence_allocated

Boolean BLAST_SequenceBlk::oof_sequence_allocated

TRUE if memory has been allocated for oof_sequence.

Definition at line 261 of file blast_def.h.

Referenced by BLAST_CreateMixedFrameDNATranslation(), BlastSequenceBlkClean(), and BlastTargetTranslationNew().

◆ seq_ranges

SSeqRange* BLAST_SequenceBlk::seq_ranges

Ranges of the sequence to search.

Definition at line 280 of file blast_def.h.

Referenced by BlastSeqBlkSetSeqRanges(), s_BlastSequenceBlkFreeSeqRanges(), and CBlastSetupTestFixture::s_TestSingleSubjectNuclMask().

◆ seq_ranges_allocated

Boolean BLAST_SequenceBlk::seq_ranges_allocated

TRUE if memory has been allocated for seq_ranges.

Definition at line 282 of file blast_def.h.

Referenced by BlastSeqBlkSetSeqRanges(), and s_BlastSequenceBlkFreeSeqRanges().

◆ sequence

Uint1* BLAST_SequenceBlk::sequence

Sequence used for search (could be translation).

Definition at line 243 of file blast_def.h.

Referenced by AascanTestFixture::AascanTestFixture(), BLAST_CreateMixedFrameDNATranslation(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), Blast_HSPGetTargetTranslation(), Blast_HSPListReevaluateUngapped(), Blast_MaskUnsupportedAA(), Blast_RedoAlignmentCore_MT(), Blast_TracebackFromHSPList(), BlastCompressBlastnaSequence(), BlastRPSScanSubject(), BlastSeqBlkSetCompressedSequence(), BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), BlastSetUp_MaskQuery(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), CBLAST_SequenceBlk::DebugDump(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), InitializeBlastScoreBlk(), PHIBlastScanSubject(), PsiBlastComputePssmScores(), CSeedTop::Run(), s_BlastDynProgNtGappedAlignment(), s_BlastProtGappedAlignment(), s_checkDbSeqSrcFunctions(), s_ComputeNumIdentities(), s_FindAdapters(), s_FindPolyATails(), s_FindSpliceJunctions(), s_GetFilteringLocationsForOneContext(), s_MatrixInfoInit(), s_MBCountWordsInSubject_16_1(), s_MultiSeqGetSequence(), s_NaHashLookupCountWordsInSubject_16_1(), s_PHIGappedAlignment(), s_PHITracebackFromHSPList(), s_QueryFactoryGetSequence(), s_RPSComputeTraceback(), s_SeqDbGetSequence(), s_SeqDbReleaseSequence(), s_SequenceGetProteinRange(), s_SetUpLocalBlastSequenceBlk(), s_SubjectIndexNewCleanup(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), CBlastSetupTestFixture::s_ValidateProtein130912(), s_VDBSRC_GetSequence(), s_VDBSRC_ReleaseSequence(), TestFixture::ScanCheckHitsCore(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputTblastn(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), CBlastExtendTestFixture::setupStructures(), TestFixture::SetUpSubject(), SubjectIndexNew(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CSplitQueryTestFixture::x_TestCContextTranslator(), CSequenceDataTester::x_TestLocalStrand(), and CSequenceDataTester::x_TestSingleProtein_Local().

◆ sequence_allocated

Boolean BLAST_SequenceBlk::sequence_allocated

◆ sequence_nomask

Uint1* BLAST_SequenceBlk::sequence_nomask

Start of query sequence without masking.

Definition at line 256 of file blast_def.h.

Referenced by Blast_HSPListReevaluateUngapped(), Blast_TracebackFromHSPList(), BlastSeqBlkSetSequence(), BlastSetUp_MaskQuery(), and s_ComputeNumIdentities().

◆ sequence_start

Uint1* BLAST_SequenceBlk::sequence_start

◆ sequence_start_allocated

Boolean BLAST_SequenceBlk::sequence_start_allocated

◆ sequence_start_nomask

Uint1* BLAST_SequenceBlk::sequence_start_nomask

Query sequence without masking.

Definition at line 255 of file blast_def.h.

Referenced by BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), and BlastSetUp_MaskQuery().

◆ subject_strand

Int2 BLAST_SequenceBlk::subject_strand

Strand of the subject sequence for translated searches.

Uses the same values as ENa_strand.

Definition at line 248 of file blast_def.h.


The documentation for this struct was generated from the following file:
Modified on Sat Feb 24 07:49:58 2024 by modify_doxy.py rev. 669887