AalookupTestFixture Struct Reference

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Collaboration diagram for AalookupTestFixture:

[legend]List of all members.

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Detailed Description

A general lookup table for the test.

Definition at line 65 of file aalookup_unit_test.cpp.

Public Member Functions
	AalookupTestFixture ()
	~AalookupTestFixture ()
void	GetSeqBlk (char *gid)
void	GetSeqBlk ()
void	GetSeqBlk (Int4 len)
void	FillLookupTable (bool hasNeighbor=false)
Public Attributes
BLAST_SequenceBlk *	query_blk
BlastSeqLoc *	lookup_segments
LookupTableOptions *	lookup_options
BlastScoreBlk *	sbp
LookupTableWrap *	lookup_wrap_ptr
BlastAaLookupTable *	lookup

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Constructor & Destructor Documentation

AalookupTestFixture::AalookupTestFixture (   )  [inline]

Definition at line 78 of file aalookup_unit_test.cpp. References lookup, lookup_options, lookup_segments, lookup_wrap_ptr, query_blk, and sbp.

AalookupTestFixture::~AalookupTestFixture (   )  [inline]

Definition at line 88 of file aalookup_unit_test.cpp. References BlastScoreBlkFree(), BlastSeqLocFree(), BlastSequenceBlkFree(), lookup_options, lookup_segments, lookup_wrap_ptr, LookupTableOptionsFree(), LookupTableWrapFree(), query_blk, and sbp.

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Member Function Documentation

void AalookupTestFixture::FillLookupTable (  bool  hasNeighbor = false  )  [inline]

Definition at line 162 of file aalookup_unit_test.cpp. References BLAST_FillLookupTableOptions(), BLAST_FillScoringOptions(), BLAST_GAP_EXTN_PROT, BLAST_GAP_OPEN_PROT, Blast_ScoreBlkMatrixInit(), BLASTAA_SEQ_CODE, BlastFindMatrixPath(), BlastScoreBlkNew(), BlastScoringOptionsFree(), BlastScoringOptionsNew(), eBlastTypeBlastp, FALSE, lookup, lookup_options, lookup_segments, lookup_wrap_ptr, LookupTableOptionsNew(), LookupTableWrapInit(), LookupTableWrap::lut, query_blk, and sbp.

void AalookupTestFixture::GetSeqBlk (  Int4  len  )  [inline]

Definition at line 148 of file aalookup_unit_test.cpp. References BlastSeqLocNew(), BlastSetUp_SeqBlkNew(), lookup_segments, malloc(), query_blk, and TRUE.

void AalookupTestFixture::GetSeqBlk (   )  [inline]

Definition at line 127 of file aalookup_unit_test.cpp. References BLASTAA_SIZE, BlastSeqLocNew(), BlastSetUp_SeqBlkNew(), debruijn(), iexp(), len, lookup_segments, malloc(), query_blk, and TRUE.

void AalookupTestFixture::GetSeqBlk (  char *  gid  )  [inline]

Definition at line 97 of file aalookup_unit_test.cpp. References BlastSeqBlkNew(), BlastSeqBlkSetSequence(), BlastSeqLocNew(), SBlastSequence::data, eBlastEncodingProtein, eNa_strand_unknown, eNoSentinels, GetSentinelByte(), GetSequence(), id, CTestObjMgr::Instance(), BLAST_SequenceBlk::length, SBlastSequence::length, lookup_segments, query_blk, AutoPtr< X, Del >::release(), BLAST_SequenceBlk::sequence, and BLAST_SequenceBlk::sequence_start.

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Member Data Documentation

BlastAaLookupTable* AalookupTestFixture::lookup

Definition at line 72 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), and FillLookupTable().

LookupTableOptions* AalookupTestFixture::lookup_options

Definition at line 69 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), FillLookupTable(), and ~AalookupTestFixture().

BlastSeqLoc* AalookupTestFixture::lookup_segments

Definition at line 68 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), FillLookupTable(), GetSeqBlk(), and ~AalookupTestFixture().

LookupTableWrap* AalookupTestFixture::lookup_wrap_ptr

Definition at line 71 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), FillLookupTable(), and ~AalookupTestFixture().

BLAST_SequenceBlk* AalookupTestFixture::query_blk

Definition at line 67 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), FillLookupTable(), GetSeqBlk(), and ~AalookupTestFixture().

BlastScoreBlk* AalookupTestFixture::sbp

Definition at line 70 of file aalookup_unit_test.cpp. Referenced by AalookupTestFixture(), FillLookupTable(), and ~AalookupTestFixture().

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The documentation for this struct was generated from the following file:

• src/algo/blast/unit_tests/api/aalookup_unit_test.cpp

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