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 | |
| Uint1 * | sequence |
| Sequence used for search (could be translation). More... | |
| Uint1 * | sequence_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... | |
| Uint1 * | sequence_start_nomask |
| Query sequence without masking. More... | |
| Uint1 * | sequence_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... | |
| Uint1 * | oof_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... | |
| Uint1 * | compressed_nuc_seq |
| 4-to-1 compressed version of sequence More... | |
| Uint1 * | compressed_nuc_seq_start |
| start of compressed_nuc_seq More... | |
| BlastMaskLoc * | lcase_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... | |
| Uint1 * | gen_code_string |
| for nucleotide subject sequences (tblast[nx]), the genetic code used to create a translated protein sequence (NULL if not applicable). More... | |
| SSeqRange * | seq_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 |
Number of elements in seq_ranges.
Definition at line 281 of file blast_def.h.
Referenced by AascanTestFixture::AascanTestFixture(), BlastSeqBlkSetSeqRanges(), s_BlastSequenceBlkFreeSeqRanges(), CBlastSetupTestFixture::s_TestSingleSubjectNuclMask(), TestFixture::SetUpQuery(), TestFixture::SetUpSubject(), and SetupSubjects_OMF().
◆ oid
| Int4 BLAST_SequenceBlk::oid |
The ordinal id of the current sequence.
Definition at line 250 of file blast_def.h.
Referenced by Blast_GetOneQueryStructs(), Blast_HSPListReevaluateUngapped(), s_MultiSeqGetSequence(), s_QueryFactoryGetSequence(), s_SeqDbGetSequence(), and s_VDBSRC_GetSequence().
◆ oof_sequence
| Uint1* BLAST_SequenceBlk::oof_sequence |
Mixed-frame protein representation of a nucleotide sequence for out-of-frame alignment.
Definition at line 259 of file blast_def.h.
Referenced by BLAST_CreateMixedFrameDNATranslation(), Blast_TracebackFromHSPList(), BlastSeqBlkSetCompressedSequence(), BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), BlastTargetTranslationNew(), BOOST_AUTO_TEST_CASE(), s_BlastProtGappedAlignment(), s_ComputeNumIdentities(), and s_SetUpLocalBlastSequenceBlk().
◆ 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 |
TRUE if memory has been allocated for sequence.
Definition at line 251 of file blast_def.h.
Referenced by Blast_GetOneQueryStructs(), BlastSeqBlkSetCompressedSequence(), BlastSequenceBlkClean(), CBLAST_SequenceBlk::DebugDump(), InitializeBlastScoreBlk(), s_SeqDbGetSequence(), s_SeqDbReleaseSequence(), and s_VDBSRC_ReleaseSequence().
◆ 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 |
Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte.
Definition at line 244 of file blast_def.h.
Referenced by AascanTestFixture::AascanTestFixture(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPListReevaluateUngapped(), BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), BlastSetUp_MaskQuery(), BlastTargetTranslationNew(), BOOST_AUTO_TEST_CASE(), CBLAST_SequenceBlk::DebugDump(), CompressedAalookupTestFixture::GetSeqBlk(), AalookupTestFixture::GetSeqBlk(), InitializeBlastScoreBlk(), CPsiBlastValidate::QueryFactory(), CDeltaBlast::Run(), s_checkDbSeqSrcFunctions(), s_MultiSeqGetSequence(), s_MultiSeqReleaseSequence(), s_QueryFactoryGetSequence(), s_QueryFactoryReleaseSequence(), s_SeqDbGetSequence(), s_SeqDbReleaseSequence(), s_SequenceGetTranslatedRange(), s_VDBSRC_GetSequence(), s_VDBSRC_ReleaseSequence(), NtlookupTestFixture::SetUpQuery(), and TestFixture::SetUpQuery().
◆ sequence_start_allocated
| Boolean BLAST_SequenceBlk::sequence_start_allocated |
TRUE if memory has been allocated for sequence_start.
Definition at line 253 of file blast_def.h.
Referenced by BlastSeqBlkSetSequence(), BlastSequenceBlkClean(), CBLAST_SequenceBlk::DebugDump(), InitializeBlastScoreBlk(), s_MultiSeqReleaseSequence(), s_QueryFactoryReleaseSequence(), s_SeqDbReleaseSequence(), and s_VDBSRC_ReleaseSequence().
◆ 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:
- include/algo/blast/core/blast_def.h
