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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__mt__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/unit_tests/blast_mt/blast_mt_unit_test.cpp Source File

61 #define NCBI_BOOST_NO_AUTO_TEST_MAIN 67 using namespace ncbi

;

78  int

num_seqs = seqdb->GetNumSeqs();

79  int

kNumTestOids =

MIN

(5000, num_seqs/4);

80  while

(gis.size() <= kNumTestOids) {

81  int

oid = rand() % num_seqs;

83

seqdb->OidToGi(oid, gi);

97  int

kNumTestOids =

MIN

(5000, num_seqs/4);

98  while

(ids.size() <= kNumTestOids) {

99  int

oid = rand() % num_seqs;

100

list<CRef<CSeq_id> >

t

= seqdb->

GetSeqIDs

(oid);

118

m_gis(gis), m_db(db), m_isProtein(isProtein){ }

128  for

(

int i

=0;

i

< m_gis.size();

i

++) {

152  const int

kNumThreads=64;

153

vector<CDLTestThread*> threads;

154  for

(

int i

=0;

i

< kNumThreads;

i

++) {

157  for

(

int i

=0;

i

< kNumThreads;

i

++) {

160  for

(

int i

=0;

i

< kNumThreads;

i

++) {

161

threads[

i

]->Join();

167  string

db =

"rRNA_typestrains/16S_ribosomal_RNA"

;

168  bool

isProtein =

false

;

174  string

db =

"refseq_select_prot"

;

175  bool

isProtein =

true

;

184

m_gis(gis), m_dataloader(ld){ }

190  for

(

int i

=0;

i

< m_gis.size();

i

++) {

216  const int

kNumThreads=64;

217

vector<CDLTest2Thread*> threads;

218  for

(

int i

=0;

i

< kNumThreads;

i

++) {

221  for

(

int i

=0;

i

< kNumThreads;

i

++) {

224  for

(

int i

=0;

i

< kNumThreads;

i

++) {

225

threads[

i

]->Join();

233  string

db =

"rRNA_typestrains/16S_ribosomal_RNA"

;

234  bool

isProtein =

false

;

242  string

db =

"refseq_select_prot"

;

243  bool

isProtein =

true

;

253

m_db(db), m_isProtein(isProtein), m_Ids(ids){}

257  for

(

int i

=0;

i

< m_Ids.size();

i

++) {

276  int

kNumTestOids =

MIN

(5000, num_seqs/4);

280  const int

kNumThreads=64;

281

vector<CSeqDBTestThread*> threads;

282  for

(

int i

=0;

i

< kNumThreads;

i

++) {

285  for

(

int i

=0;

i

< kNumThreads;

i

++) {

288  for

(

int i

=0;

i

< kNumThreads;

i

++) {

289

threads[

i

]->Join();

298  bool

isProtein =

true

;

307  bool

isProtein =

false

;

319

m_db(db), m_isProtein(isProtein), m_Oids(oids){ }

323  for

(

int i

=0;

i

< m_Oids.size();

i

++) {

338  const int

kNumThreads=64;

339  const int

kNumTestOids = 5000;

340

vector<CSeqDBTest2Thread*> threads;

345  for

(

int i

=0;

i

< kNumTestOids;

i

++) {

346  int

oid = rand() % num_seqs;

350  for

(

int i

=0;

i

< kNumThreads;

i

++) {

353  for

(

int i

=0;

i

< kNumThreads;

i

++) {

356  for

(

int i

=0;

i

< kNumThreads;

i

++) {

357

threads[

i

]->Join();

366  bool

isProtein =

true

;

375

m_SeqDB(seqdb), m_Oids(oids){ }

378  for

(

int i

=0;

i

< m_Oids.size();

i

++) {

380

m_SeqDB->GetSequence(m_Oids[

i

], &

buf

);

382

m_SeqDB->RetSequence(&

buf

);

394  const int

kNumThreads=64;

395  const int

kNumTestOids = 5000;

396

vector<CSeqDBTest3Thread*> threads;

402  for

(

int i

=0;

i

< kNumTestOids;

i

++) {

403  int

oid = rand() % num_seqs;

407  for

(

int i

=0;

i

< kNumThreads;

i

++) {

410  for

(

int i

=0;

i

< kNumThreads;

i

++) {

413  for

(

int i

=0;

i

< kNumThreads;

i

++) {

414

threads[

i

]->Join();

423  bool

isProtein =

false

;

Produce formatted blast output for command line applications.

void s_GenerateGiList(CRef< CSeqDB > &seqdb, vector< TGi > &gis)

void s_MTSeqDBTest2(string &db, bool isProtein)

void s_MTDataLoaderTest(string &db, bool isProtein)

void s_MTSeqDBTest(string &db, bool isProtein)

BOOST_AUTO_TEST_CASE(MT_DataLoaderForEachThread_16S)

void s_MTSeqDBTest3(string &db, bool isProtein)

void s_GenerateAccsList(CRef< CSeqDB > &seqdb, vector< string > &ids)

void s_MTDataLoaderTest2(string &db, bool isProtein)

Declares the CBlastNucleotideOptionsHandle class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

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

build_archive declarations

static const int kSubjectsDataLoaderPriority

The default priority for subjects, should be used for subjects/databases.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static string GetLoaderNameFromArgs(CConstRef< CSeqDB > db_handle)

CDLTest2Thread(vector< TGi > &gis, string &ld)

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CDLTestThread(vector< TGi > &gis, string &db, bool isProtein)

CSeqDBTest2Thread(string &db, bool isProtein, vector< int > &oids)

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CSeqDBTest3Thread(CRef< CSeqDB > seqdb, vector< int > &oids)

CSeqDBTestThread(string &db, bool isProtein, vector< string > &ids)

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

void GetSequenceAsString(int oid, CSeqUtil::ECoding coding, string &output, TSeqRange range=TSeqRange()) const

Get a sequence in a given encoding.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

int GetNumSeqs() const

Returns the number of sequences available.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

void AccessionToOids(const string &acc, vector< int > &oids) const

Translate an Accession to a list of OIDs.

void SetNumberOfThreads(int num_threads, bool force_mt=false)

Setting the number of threads.

static SQLCHAR output[256]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

void AddDataLoader(const string &loader_name, TPriority pri=kPriority_Default)

Add data loader by name.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TId

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const TId & GetId(void) const

@ e_Gi

GenInfo Integrated Database.

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

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

#define MIN(a, b)

returns smaller of a and b.

Defines NCBI C++ exception handling.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

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

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