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NCBI C++ ToolKit: src/algo/blast/unit_tests/blast_format/blastfmtutil_unit_test.cpp Source File

;

: m_Obj(obj), m_Name(name)

is_prot =

;

BOOST_REQUIRE(defline.

());

kDbName(

);

scope =

(*obj);

list< CRef< CBlast_def_line > >& bdl = bdls->

();

BOOST_WARN_MESSAGE((*iter)->IsSetLinks(),

);

((*iter)->IsSetLinks()){

(list< int >, iter2, (*iter)->GetLinks()){

((*iter2) &

){

((*iter2) &

){

BOOST_REQUIRE (linkout &

);

list<TGi> use_this_gi;

CBlastFormatUtil::GetAlnScores(*(align.front()), score, bits, evalue,

sum_n, num_ident, use_this_gi);

BOOST_REQUIRE(score == 1296);

BOOST_REQUIRE(sum_n == -1);

BOOST_REQUIRE(use_this_gi.front() ==

(18426812));

BOOST_REQUIRE_CLOSE(bits, 503.263, 0.0001);

BOOST_REQUIRE(num_ident == 331);

evalue_str, bit_score_str, raw_score_str, total_bit_score_str;

CBlastFormatUtil::GetScoreString(evalue, bits, 0, 0,

evalue_str, bit_score_str,

BOOST_REQUIRE(evalue_str ==

(

));

BOOST_REQUIRE(bit_score_str ==

(

));

list<CRef<CSeq_align> > & align = align_set.

();

kDbName(

);

scope =

(*obj);

list_size = 31;

ref_score[list_size]={100, 47, -1, -1, -1, -1, -1, -1, -1, -1,

-1, -1, -1, -1, -1, -1, 45, -1, -1, -1,

-1, -1, -1, -1, -1, -1, -1, -1, -1, 40, 40 };

BOOST_REQUIRE(align.size() == list_size);

(*iter)->GetNamedScore(

, score);

BOOST_REQUIRE(score == ref_score[

]);

BLAST formatter utilities.

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

BOOST_AUTO_TEST_CASE(GetBlastDeflineFromGenbank)

double const kMaxDoubleDiff

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &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)

EDbType

Describes the type of blast database to use.

@ eNucleotide

nucleotide database

static string GetLoaderNameFromArgs(CConstRef< CSeqDB > db_handle)

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

static string GetLoaderNameFromArgs(CReader *reader=0)

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static void InsertSubjectScores(objects::CSeq_align_set &org_align_set, const objects::CBioseq_Handle &query_handle, TSeqRange query_range=TSeqRange(), ESubjectScores score_type=eQueryCovPerSubj)

@ eSerial_AsnText

ASN.1 text.

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

static bool AvoidGi(void)

Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI).

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

TGi GetGiForAccession(const string &acc, CScope &scope, EGetIdType flags=0)

Given an accession string retrieve the GI id.

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.

bool Empty(void) const THROWS_NONE

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

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

const Tdata & Get(void) const

Get the member data.

const Tdata & Get(void) const

Get the member data.

TGi & SetGi(void)

Select the variant.

list< CRef< CSeq_align > > TAlign

list< CRef< CSeq_id > > TId

const TData & GetData(void) const

Get the Data member data.

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

Defines NCBI C++ exception handling.

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

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

Defines BLAST database access classes.

CRef< CObjectManager > m_Obj

DataLoaderRevoker(CRef< CObjectManager > obj, string name)

DataLoaderRevoker(const string &name)

Configuration structure for the CBlastScopeSource.

@ eUseGenbankDataLoader

Use the Genbank data loader.

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

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