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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/kmer__unit__test_8cpp_source.html below:

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

53 #define NCBI_BOOST_NO_AUTO_TEST_MAIN 59 #ifndef SKIP_DOXYGEN_PROCESSING 73  data

.resize(sequence.length());

74  for

(

size_t i

=0;

i

< sequence.length();

i

++) {

77

bioseq->

SetInst

().SetLength((

unsigned int

)sequence.length());

80

bioseq->

SetId

().clear();

86 template

<

class

TKmerCounts>

97

counts.Reset(seqloc, *scope);

105  const string

seq1 =

"AAAAAAAAA"

;

106  const string

seq2 =

"BBBBBBBBBB"

;

109  for

(

int i

=3;

i

< 6;

i

++) {

110  for

(

int

j=15;j <= 20;j++) {

120

BOOST_CHECK_EQUAL(counts.

GetNumCounts

(), seq1.length()

138  const string

seq_x =

"AXAXAXAXAXAXAX"

;

139  const string

seq_xonly =

"XXXXXXXXXXXXX"

;

143  for

(

int i

=3;

i

< 6;

i

++) {

151

BOOST_CHECK_EQUAL((

int

)counts_xonly.

GetNumCounts

(), 0);

154  const string

seq_short =

"ABC"

;

193  const int

kKmerLen = 4;

198

vector< CRef<CSeq_loc> > seqs;

199

vector<CSparseKmerCounts> counts_vect;

200

TKMethods::TDistMatrix dmat;

203

BOOST_REQUIRE_EQUAL(status, 0);

204

BOOST_REQUIRE(seqs.size() > 0);

205

BOOST_REQUIRE(!scope.

Empty

());

208

BOOST_CHECK_THROW(TKMethods::ComputeCounts(vector<

CRef<CSeq_loc>

>(),

209

*scope, counts_vect),

219

TKMethods::ComputeCounts(seqs, *scope, counts_vect);

220

BOOST_REQUIRE_EQUAL(counts_vect.size(), seqs.size());

222

TKMethods::ComputeDistMatrix(counts_vect,

223

TKMethods::eFractionCommonKmersGlobal, dmat);

225

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

226

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

228

TKMethods::ComputeDistMatrix(counts_vect,

229

TKMethods::eFractionCommonKmersLocal, dmat);

231

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

232

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

238

TKMethods::ComputeCounts(seqs, *scope, counts_vect);

239

BOOST_REQUIRE_EQUAL(counts_vect.size(), seqs.size());

241

TKMethods::ComputeDistMatrix(counts_vect,

242

TKMethods::eFractionCommonKmersGlobal, dmat);

244

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

245

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

247

TKMethods::ComputeDistMatrix(counts_vect,

248

TKMethods::eFractionCommonKmersLocal, dmat);

250

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

251

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

256

TKMethods::ComputeCounts(seqs, *scope, counts_vect);

257

BOOST_REQUIRE_EQUAL(counts_vect.size(), seqs.size());

259

TKMethods::ComputeDistMatrix(counts_vect,

260

TKMethods::eFractionCommonKmersGlobal, dmat);

262

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

263

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

265

TKMethods::ComputeDistMatrix(counts_vect,

266

TKMethods::eFractionCommonKmersLocal, dmat);

268

BOOST_REQUIRE_EQUAL(dmat.GetRows(), seqs.size());

269

BOOST_CHECK_CLOSE(dmat(0, 1), 0.0, 1e-6);

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

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

Exception class for Kmer counts.

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector.

static unsigned int GetKmerLength(void)

Get default kmer length.

static void SetUseCompressed(bool use_comp)

Set default option for using compressed alphabet.

static void SetAlphabetSize(unsigned size)

Set Default alphabet size.

unsigned int GetNumCounts(void) const

Get number of all k-mers found in the sequence.

static unsigned int CountCommonKmers(const CSparseKmerCounts &v1, const CSparseKmerCounts &v2, bool repetitions=true)

Copmute number of common kmers between two count vectors.

static void SetKmerLength(unsigned len)

Set default k-mer length.

static vector< Uint1 > & SetTransTable(void)

Set default compressed alphabet letter translation table.

Interface for computing and manipulating k-mer counts vectors that allows for different implementatio...

int ReadFastaQueries(const string &filename, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, bool parse_deflines, objects::CSeqIdGenerator *id_generator)

const Uint1 AMINOACID_TO_NCBISTDAA[]

Translates between ncbieaa and ncbistdaa.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

bool Empty(void) const THROWS_NONE

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

virtual void SetParams()

Called at the beginning of Run, before creating thread pool.

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

TNcbistdaa & SetNcbistdaa(void)

Select the variant.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

BOOST_AUTO_TEST_CASE(TestSparseKmerCounts)

static CRef< CBioseq > s_CreateBioseq(const string &sequence, int id)

static void s_CreateKmerCounts(const string &seq, TKmerCounts &counts)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

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

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