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NCBI C++ ToolKit: src/algo/cobalt/unit_test/options_unit_test.cpp Source File

BOOST_CHECK_THROW(opts.

(

BOOST_CHECK_NO_THROW(opts->

());

vector<CMultiAlignerOptions::SConstraint>& constr

constr[0].seq1_start = 1;

constr[0].seq1_stop = 5;

constr[0].seq2_start = 3;

constr[0].seq2_stop = 1;

User-defined methods of the data storage class.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

Options and parameters for multiple alignement.

void SetDomainHitlistSize(int size)

Set hitlist size (per sequence) for domain search.

void SetKmerAlphabet(TKMethods::ECompressedAlphabet alph)

Set alphabet for creating word count vectors.

void SetKmerLength(int len)

Set word size for creating word count vectors in query clustering.

bool Validate(void)

Validate parameter values.

void SetBlastpEvalue(double evalue)

Set e-value for accepting Blastp hits.

void SetUseQueryClusters(bool use)

Set use of query clustering option.

bool IsStandardMode(void) const

Check whether parameter values belong to any of the standard modes.

void SetDomainHits(CConstRef< objects::CBlast4_archive > archive)

Set pre-computed domain hits.

CConstRef< objects::CBlast4_archive > GetDomainHits(void) const

Get pre-computed domain hits.

TMode GetMode(void) const

Get options mode.

const vector< string > & GetMessages(void)

Get warning messages.

const vector< CPattern > & GetCddPatterns(void) const

Get regular expression patterns for identification of conserved domains.

void SetRpsDb(const string &dbname)

Use RPS Blast with given database.

bool CanGetDomainHits(void) const

Are pre-computed domain hits set.

TConstraints & SetUserConstraints(void)

Set user constraints.

static const TMode kDefaultMode

Default options mode.

vector< CPattern > & SetCddPatterns(void)

Set regular expression patterns for identification of conserved domains.

@ fNoPatterns

Do not use conserved domain patterns.

@ fNoRpsBlast

Do not use RPS Blast.

@ fNonStandard

Not used as input, indicates that.

void SetRpsEvalue(double evalue)

Set e-value threshold for accepting RPS Blast hits.

Interface for CMultiAligner.

#define MSerial_AsnText

I/O stream manipulators –.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

BOOST_AUTO_TEST_CASE(TestOptionsModes)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

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

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