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NCBI C++ ToolKit: src/objtools/data_loaders/blastdb/unit_test/local_dataloader_test.cpp Source File

BOOST_REQUIRE_EQUAL(

, loader_name);

reference_L.push_back(556);

reference_L.push_back(437);

reference_L.push_back(1512);

reference_L.push_back(2367);

reference_L.push_back(540);

reference_L.push_back(1759);

reference_L.push_back(1758);

reference_L.push_back(1758);

reference_L.push_back(422);

reference_L.push_back(410);

BOOST_REQUIRE_EQUAL(idhs.size(), reference_L.size());

BOOST_REQUIRE_EQUAL(idhs.size(), reference_T.size());

BOOST_REQUIRE_EQUAL(idhs.size(), reference_TI.size());

BOOST_REQUIRE_EQUAL(idhs.size(), test_L.size());

BOOST_REQUIRE_EQUAL(idhs.size(), test_T.size());

BOOST_REQUIRE_EQUAL(idhs.size(), test_TI.size());

BOOST_CHECK_EQUAL_COLLECTIONS(test_L.begin(), test_L.end(),

reference_L.begin(), reference_L.end());

BOOST_CHECK_EQUAL_COLLECTIONS(test_TI.begin(), test_TI.end(),

reference_TI.begin(), reference_TI.end());

BOOST_CHECK_EQUAL_COLLECTIONS(test_T.begin(), test_T.end(),

reference_T.begin(), reference_T.end());

(

);

BOOST_REQUIRE_EQUAL(

, loader_name);

BOOST_REQUIRE(handle1);

BOOST_REQUIRE_EQUAL(

, loader_name);

BOOST_REQUIRE(handle1);

BOOST_REQUIRE(!handle2);

BOOST_REQUIRE(handle3);

defline =

;

((*iter)->IsTitle()) {

defline += (*iter)->GetTitle();

BOOST_REQUIRE(defline.find(

) == 0);

BOOST_REQUIRE_EQUAL(

, loader_name);

kExpectedLength(536);

seqid1(

);

BOOST_REQUIRE(handle1);

BOOST_CHECK_EQUAL(kExpectedTaxid, scope.

(seqid1));

BOOST_REQUIRE(bioseq1.

());

BOOST_CHECK_EQUAL(kExpectedTaxid, bioseq1->

());

monkey_id(

);

BOOST_REQUIRE(monkey_handle);

BOOST_REQUIRE_EQUAL(kExpectedLength, monkey_handle.

().

());

(

=0;

< 100;

++) {

from =

.GetRand(0, length_0 -100);

to =

.GetRand(from, length_0);

from =

.GetRand(0, length_1 -100);

to =

.GetRand(from, length_1);

(

);

vector< CRef<CLocalAdapterThread> > TTesterThreads;

kNumThreads = 48;

TTesterThreads the_threads(kNumThreads);

BOOST_REQUIRE(the_threads[

].NotEmpty());

(*thread)->Join(

**

(&

));

BOOST_REQUIRE_EQUAL(0L,

);

the_threads[

].Reset();

(

);

s1(

);

s2(

);

s3(

);

s4(

);

BOOST_REQUIRE_EQUAL(t1, s1);

BOOST_REQUIRE_EQUAL(t2, s2);

BOOST_REQUIRE_EQUAL(t3, s3);

BOOST_REQUIRE_EQUAL(t4, s4);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Data loader implementation that uses the blast databases.

TTaxId GetTaxId() const

Determine the tax-id for this bioseq.

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)

@ eNucleotide

nucleotide database

@ eProtein

protein database

virtual void * Main()

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

CLocalAdapterThread(CRef< CSeqDB > seq_db)

This class allows retrieval of sequence data from locally installed BLAST databases via CSeqDB.

virtual int GetSeqLength(int oid)

@inheritDoc

virtual CRef< CSeq_data > GetSequence(int oid, int begin=0, int end=0)

@inheritDoc

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TPrim & Get(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

TLoader * GetLoader(void) const

Get pointer to the loader.

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

Add data loader by name.

vector< TTaxId > TTaxIds

Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that d...

vector< TSeqPos > TSequenceLengths

Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found.

TTaxId GetTaxId(const CSeq_id &id, TGetFlags flags=0)

Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxono...

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.

TSequenceTypes GetSequenceTypes(const TSeq_id_Handles &idhs, TGetFlags flags=0)

CSeq_inst::TMol GetSequenceType(const CSeq_id &id, TGetFlags flags=0)

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not fo...

vector< CSeq_inst::TMol > TSequenceTypes

Get molecular types of sequences (protein/dna/rna) Return CSeq_inst::eMol_not_set for sequences that ...

TSequenceLengths GetSequenceLengths(const TSeq_id_Handles &idhs, TGetFlags flags=0)

TTaxIds GetTaxIds(const TSeq_id_Handles &idhs, TGetFlags flags=0)

vector< CSeq_id_Handle > TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

@ kPriority_NotSet

Deprecated: use kPriority_Default instead.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool State_NoData(void) const

CConstRef< CSeq_id > GetSeqId(void) const

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

const TInst & GetInst(void) const

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gi

GenInfo Integrated Database.

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

const Tdata & Get(void) const

Get the member data.

TLength GetLength(void) const

Get the Length member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ eMol_na

just a nucleic acid

char * dbname(DBPROCESS *dbproc)

Get name of current database.

BOOST_AUTO_TEST_CASE(LocalFetchNucleotideBioseq)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

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