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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/optionshandle_unit_test.cpp Source File

<

BC,

T>

(BC::*mutator)(

),

(BC::*accessor)(

)

,

BOOST_REQUIRE_EQUAL(expected_value, actual_value);

;

VerifyMutatorAccessor<CBlastOptionsHandle, bool>

VerifyMutatorAccessor<CBlastOptionsHandle, double>

VerifyMutatorAccessor<CBlastOptionsHandle, double>

VerifyMutatorAccessor<CBlastOptionsHandle, int>

VerifyMutatorAccessor<CBlastOptionsHandle, int>

= -10.5;

VerifyMutatorAccessor<CBlastOptionsHandle, double>

VerifyMutatorAccessor<CBlastOptionsHandle, int>

VerifyMutatorAccessor<CBlastOptionsHandle, double>

VerifyMutatorAccessor<CBlastOptionsHandle, bool>

VerifyMutatorAccessor<CBlastOptionsHandle, int>

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts ==

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

BOOST_REQUIRE(opts !=

);

VerifyMutatorAccessor<CBlastProteinOptionsHandle, double>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, int>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, int>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, double>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, double>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, Int8>

= 0x1<<16;

VerifyMutatorAccessor<CBlastProteinOptionsHandle, unsigned int>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, Int8>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, bool>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, int>

m_OptsHandle->SetSegFiltering(

);

= m_OptsHandle->GetSegFilteringWindow();

BOOST_REQUIRE(

< 0);

VerifyMutatorAccessor<CBlastProteinOptionsHandle, double>

m_OptsHandle->SetSegFiltering(

);

= m_OptsHandle->GetSegFilteringLocut();

BOOST_REQUIRE(

< 0);

VerifyMutatorAccessor<CBlastProteinOptionsHandle, double>

m_OptsHandle->SetSegFiltering(

);

= m_OptsHandle->GetSegFilteringHicut();

BOOST_REQUIRE(

< 0);

*

=

;

VerifyMutatorAccessor<CBlastProteinOptionsHandle, const char*>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, int>

VerifyMutatorAccessor<CBlastProteinOptionsHandle, int>

VerifyMutatorAccessor<CPSIBlastOptionsHandle, double>

VerifyMutatorAccessor<CPSIBlastOptionsHandle, double>

VerifyMutatorAccessor<CPSIBlastOptionsHandle, bool>

VerifyMutatorAccessor<CPSIBlastOptionsHandle, int>

VerifyMutatorAccessor<CBlastAdvancedProteinOptionsHandle, bool>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, ELookupTableType>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

m_OptsHandle->SetStrandOption(

);

BOOST_REQUIRE_EQUAL((

)

, (

)actual_value);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, double>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, double>

kGapOpen = 7;

kGapExtend = 3;

m_OptsHandle->SetGapOpeningCost(kGapOpen);

m_OptsHandle->SetGapExtensionCost(kGapExtend);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, EBlastPrelimGapExt>

BOOST_REQUIRE_EQUAL(kGapOpen, m_OptsHandle->GetGapOpeningCost());

BOOST_REQUIRE_EQUAL(kGapExtend, m_OptsHandle->GetGapExtensionCost());

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, EBlastPrelimGapExt>

BOOST_REQUIRE_EQUAL(kGapOpen, m_OptsHandle->GetGapOpeningCost());

BOOST_REQUIRE_EQUAL(kGapExtend, m_OptsHandle->GetGapExtensionCost());

kGapOpen = 7;

kGapExtend = 3;

m_OptsHandle->SetGapOpeningCost(kGapOpen);

m_OptsHandle->SetGapExtensionCost(kGapExtend);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, EBlastTbackExt>

BOOST_REQUIRE_EQUAL(kGapOpen, m_OptsHandle->GetGapOpeningCost());

BOOST_REQUIRE_EQUAL(kGapExtend, m_OptsHandle->GetGapExtensionCost());

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

*

=

;

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, const char*>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, Int8>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, bool>

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

m_OptsHandle->SetDustFiltering(

);

= m_OptsHandle->GetDustFilteringLevel();

BOOST_REQUIRE(

< 0);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

m_OptsHandle->SetDustFiltering(

);

= m_OptsHandle->GetDustFilteringWindow();

BOOST_REQUIRE(

< 0);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, int>

m_OptsHandle->SetDustFiltering(

);

= m_OptsHandle->GetDustFilteringLinker();

BOOST_REQUIRE(

< 0);

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, bool>

* db =

;

VerifyMutatorAccessor<CBlastNucleotideOptionsHandle, const char*>

= 18;

VerifyMutatorAccessor<CDiscNucleotideOptionsHandle, unsigned char>

= 1;

VerifyMutatorAccessor<CDiscNucleotideOptionsHandle, unsigned char>

VerifyMutatorAccessor<CDiscNucleotideOptionsHandle, int>

m_OptsHandle->SetWordSize(

);

BOOST_REQUIRE(!

(

, exptn.

().c_str()));

= m_OptsHandle->GetQueryCovHspPerc();

BOOST_REQUIRE(

== 0);

m_OptsHandle->SetQueryCovHspPerc(52);

= m_OptsHandle->GetQueryCovHspPerc();

BOOST_REQUIRE(

== 52);

Declares the CBlastAdvancedProteinOptionsHandle class.

Definitions used throughout BLAST.

Declares the CBlastNucleotideOptionsHandle class.

EBlastPrelimGapExt

The algorithm to be used for preliminary gapped extensions.

@ eDynProgScoreOnly

standard affine gapping

@ eGreedyScoreOnly

Greedy extension (megaBlast)

#define BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6

#define BLAST_WORD_THRESHOLD_BLASTP_FAST

#define BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7

#define BLAST_WORD_THRESHOLD_BLASTP

neighboring word score thresholds; a threshold of zero means that only query and subject words that m...

EBlastTbackExt

The algorithm to be used for final gapped extensions with traceback.

@ eDynProgTbck

standard affine gapping

ELookupTableType

Types of the lookup table.

@ eNaLookupTable

blastn lookup table

@ eAaLookupTable

standard protein (blastp) lookup table

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Declares the CBlastProteinOptionsHandle class.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eBlastProgramMax

Undefined program.

Declares the CBlastpKmerOptionsHandle class.

Declares the CBlastxOptionsHandle class.

Handle to the Advanced BLASTP options.

Defines BLAST error codes (user errors included)

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

Handle to the protein-protein options to the BLAST algorithm.

Handle to the KMER BLASTP options.

Handle to the translated nucleotide-protein options to the BLAST algorithm.

Handle to the nucleotide-nucleotide options to the discontiguous BLAST algorithm.

Handle to the protein-protein options to the BLAST algorithm.

Handle to the protein-translated nucleotide options to the BLAST algorithm.

Handle to the translated nucleotide-translated nucleotide options to the BLAST algorithm.

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

@ eNoCompositionBasedStats

Don't use composition based statistics.

Declares the CDiscNucleotideOptionsHandle class.

int GetDustFilteringLinker() const

Get linker parameter for dust.

void SetGapExtensionCost(int e)

Sets GapExtensionCost.

double GetXDropoff() const

Returns XDropoff.

void SetLookupTableType(ELookupTableType type)

Sets LookupTableType.

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

int GetGapExtensionCost() const

Returns GapExtensionCost.

Int8 GetEffectiveSearchSpace() const

Returns EffectiveSearchSpace.

EBlastPrelimGapExt GetGapExtnAlgorithm() const

Returns GapExtnAlgorithm.

void SetWordThreshold(double wt)

Sets WordThreshold.

void SetDustFilteringWindow(int window)

Set window parameter for dust.

double GetGapTrigger() const

Returns GapTrigger.

bool GetSegFiltering() const

Is SEG filtering enabled?

EBlastTbackExt GetGapTracebackAlgorithm() const

Returns GapTracebackAlgorithm.

bool GetDustFiltering() const

Is dust filtering enabled?

void SetDbLength(Int8 len)

Sets DbLength.

bool GetSmithWatermanMode() const

Returns this mode, specifying that smith waterman rather than the normal blast heuristic should be us...

void SetWordSize(int ws)

Sets WordSize.

int GetWordSize() const

Returns WordSize.

void SetMatchReward(int r)

Sets MatchReward.

unsigned char GetTemplateType() const

Returns TemplateType.

void SetDbSeqNum(unsigned int num)

Sets DbSeqNum.

void SetGapTrigger(double g)

Sets GapTrigger.

int GetCandidateSeqs() const

Gets the max number of candidate matches to process with BLAST.

void SetSmithWatermanMode(bool m=false)

Sets this mode, specifying that smith waterman rather than the normal blast heuristic should be used ...

double GetInclusionThreshold() const

Returns InclusionThreshold.

double GetGapXDropoffFinal() const

Returns GapXDropoffFinal.

Int8 GetDbLength() const

Returns DbLength.

int GetMatchReward() const

Returns MatchReward.

void SetGapExtnAlgorithm(EBlastPrelimGapExt algo)

Sets GapExtnAlgorithm.

void SetDustFilteringLinker(int linker)

Set linker parameter for dust.

int GetSegFilteringWindow() const

Get window parameter for seg.

int GetMinHits() const

Returns the number of hits to initiate calculation of Jaccard distance.

void SetEffectiveSearchSpace(Int8 eff)

Sets EffectiveSearchSpace.

void SetGapOpeningCost(int g)

Sets GapOpeningCost.

const char * GetMatrixName() const

Returns MatrixName.

void SetCompositionBasedStats(ECompoAdjustModes mode)

Sets this mode, which mostly specifies whether composition of db sequence is taken into account when ...

double GetXDropoff() const

Returns XDropoff.

unsigned int GetDbSeqNum() const

Returns DbSeqNum.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

int GetDustFilteringLevel() const

Get level parameter for dust.

void SetGapTracebackAlgorithm(EBlastTbackExt algo)

Sets GapTracebackAlgorithm.

double GetWordThreshold() const

Returns WordThreshold.

bool GetGappedMode() const

Returns GappedMode.

double GetSegFilteringHicut() const

Get hicut parameter for seg.

void SetMismatchPenalty(int p)

Sets MismatchPenalty.

double GetPercentIdentity() const

Returns PercentIdentity.

void SetMatrixName(const char *matrix)

Sets MatrixName.

void SetRepeatFilteringDB(const char *db)

Enable repeat filtering.

void SetHitlistSize(int s)

Sets HitlistSize.

const char * GetMatrixName() const

Returns MatrixName.

int GetGapExtensionCost() const

Returns GapExtensionCost.

int GetWordSize() const

Returns WordSize.

ECompoAdjustModes GetCompositionBasedStats() const

Returns this mode, which mostly specifies whether composition of db sequence is taken into account wh...

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

void SetXDropoff(double x)

Sets XDropoff.

void SetWindowSize(int ws)

Sets WindowSize.

int GetMaxNumHspPerSequence() const

Returns MaxNumHspPerSequence.

bool GetMaskAtHash() const

Returns whether masking should only be done for lookup table creation.

void SetMatrixName(const char *matrix)

Sets MatrixName.

void SetRepeatFiltering(bool val)

Enable repeat filtering.

bool GetRepeatFiltering() const

Is repeat filtering enabled?

double GetWordThreshold() const

Returns WordThreshold.

void SetWordSize(int ws)

Sets WordSize.

void SetTemplateType(unsigned char type)

Sets TemplateType.

void SetGapXDropoffFinal(double x)

Sets GapXDropoffFinal.

int GetCutoffScore() const

Returns CutoffScore.

int GetDustFilteringWindow() const

Get window parameter for dust.

void SetXDropoff(double x)

Sets XDropoff.

void SetCullingLimit(int s)

Sets Culling limit.

void SetGapExtensionCost(int e)

Sets GapExtensionCost.

int GetGapOpeningCost() const

Returns GapOpeningCost.

void SetGapXDropoff(double x)

Sets GapXDropoff.

void SetMaskAtHash(bool m=true)

Sets MaskAtHash.

double GetGapXDropoff() const

Returns GapXDropoff.

const char * GetRepeatFilteringDB() const

Get the repeat filtering database.

ELookupTableType GetLookupTableType() const

Returns LookupTableType.

unsigned char GetTemplateLength() const

Returns TemplateLength.

void SetWordSize(int ws)

Sets WordSize.

ELookupTableType GetLookupTableType() const

int GetGapOpeningCost() const

Returns GapOpeningCost.

void SetSegFilteringWindow(int window)

Set window parameter for seg.

void SetDustFiltering(bool val)

Enable dust filtering.

int GetWindowSize() const

Returns WindowSize.

int GetMismatchPenalty() const

Returns MismatchPenalty.

int GetHitlistSize() const

Returns HitlistSize.

void SetMaxNumHspPerSequence(int m)

Sets MaxNumHspPerSequence.

void SetGappedMode(bool m=true)

Sets GappedMode.

void SetSegFiltering(bool val)

Enable SEG filtering.

void SetTemplateLength(unsigned char length)

Sets TemplateLength.

void SetPercentIdentity(double p)

Sets PercentIdentity.

double GetSegFilteringLocut() const

Get locut parameter for seg.

void SetCutoffScore(int s)

Sets CutoffScore.

void SetDustFilteringLevel(int level)

Set level parameter for dust.

const char * GetMatrixName() const

void SetGapOpeningCost(int g)

Sets GapOpeningCost.

void SetSegFilteringLocut(double locut)

Set locut parameter for seg.

void SetInclusionThreshold(double incthr)

Sets InclusionThreshold.

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested task,...

void SetSegFilteringHicut(double hicut)

Set hicut parameter for seg.

double GetEvalueThreshold() const

Returns EvalueThreshold.

int GetCullingLimit() const

Returns Culling limit.

const string & GetMsg(void) const

Get message string.

int64_t Int8

8-byte (64-bit) signed integer

ENa_strand

strand of nucleic acid

unsigned int

A callback function used to compare two keys in a database.

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

int strcmp(const char *str1, const char *str2)

void VerifyMutatorAccessor(BC &obj, void(BC::*mutator)(T), T(BC::*accessor)(void) const, T &expected_value)

BOOST_FIXTURE_TEST_CASE(Set_Get_MaskAtHash_Universal, UniversalOptiosHandleFixture)

#define CALL_MEMBER_FUNCTION(obj, membFnPtr)

BOOST_AUTO_TEST_CASE(BlastnTest)

Declares the CPSIBlastOptionsHandle class.

~AdvancedProteinOptionsHandleFixture()

AdvancedProteinOptionsHandleFixture()

CBlastAdvancedProteinOptionsHandle * m_OptsHandle

BlastNuclOptionsHandleFixture()

~BlastNuclOptionsHandleFixture()

CBlastNucleotideOptionsHandle * m_OptsHandle

DiscNucleotideOptionsHandleFixture()

CDiscNucleotideOptionsHandle * m_OptsHandle

~DiscNucleotideOptionsHandleFixture()

PSIBlastOptiosHandleFixture()

CPSIBlastOptionsHandle * m_OptsHandle

~PSIBlastOptiosHandleFixture()

ProteinOptiosHandleFixture()

~ProteinOptiosHandleFixture()

CBlastProteinOptionsHandle * m_OptsHandle

UniversalOptiosHandleFixture()

CBlastOptionsHandle * m_OptsHandle

~UniversalOptiosHandleFixture()

Declares the CTBlastnOptionsHandle class.

Declares the CTBlastxOptionsHandle class.

Utility stuff for more convenient using of Boost.Test library.

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