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NCBI C++ ToolKit: src/objtools/align_format/unit_test/showdefline_unit_test.cpp Source File

;

ncbi::align_format;

line_length = 65,

translated_nuc_alignment =

,

deflines_to_show, translated_nuc_alignment,

seqalign->

() = align;

kDbName(

);

unique_ptr<CShowBlastDefline::SScoreInfo>

unique_ptr<CShowBlastDefline::SDeflineInfo>

defline[] = {

,

};

evalue_string[] = {

,

};

bit_string[] = {

,

};

sum_n[] = {1, 1};

id_url[] = {

,

};

score_url[] = {

,

};

is_new[] = {

,

};

was_checked[] = {

,

};

BOOST_REQUIRE(dl->

.find(defline[index])!=

);

BOOST_REQUIRE_EQUAL(dl->

, id_url[index]);

BOOST_REQUIRE_EQUAL(dl->

, score_url[index]);

BOOST_REQUIRE_EQUAL(dl->

, is_new[index]);

BOOST_REQUIRE_EQUAL(dl->

, was_checked[index]);

BOOST_REQUIRE_EQUAL(

->evalue_string, evalue_string[index]);

BOOST_REQUIRE_EQUAL(

->bit_string, bit_string[index]);

BOOST_REQUIRE_EQUAL(

->sum_n, sum_n[index]);

Declares class to display one-line descriptions at the top of the BLAST report.

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

EDbType

Describes the type of blast database to use.

@ eProtein

protein database

This class displays the defline for BLAST result.

SScoreInfo * x_GetScoreInfo(const objects::CSeq_align &aln, int blast_rank)

Internal function to return score info.

SDeflineInfo * x_GetDeflineInfo(CConstRef< objects::CSeq_id > id, list< string > &use_this_seqid, int blast_rank)

Internal function to return defline info.

void SetOption(int option)

options per DisplayOption

Class which registers the BLAST database and Genbank data loaders as a non-default data loaders with ...

ncbi::CRef< ncbi::objects::CScope > NewScope()

Create a new scope with the default set to the BLAST database data loader for the BLAST database spec...

static const char si[8][64]

const size_t kDfltArgNumDescriptions

Default number of one-line descriptions to display in the traditional BLAST report.

static const char location[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eSerial_AsnText

ASN.1 text.

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

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

void RevokeAllDataLoaders(void)

Revoke all registered data loaders, even if they were still used.

CObjectManager & GetObjectManager(void)

Get object manager controlling this scope.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_align > > TAlign

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)

BOOST_AUTO_TEST_CASE(LocalDeflineInfo)

static void GetDeflineInfo(CBlastOM::ELocation location)

static void TestData(CShowBlastDefline::SDeflineInfo *dl, CShowBlastDefline::SScoreInfo *si, int index)

CShowBlastDeflineTest(const CSeq_align_set &seqalign, CScope &scope, size_t line_length=65, size_t deflines_to_show=align_format::kDfltArgNumDescriptions, bool translated_nuc_alignment=false, CRange< TSeqPos > *master_range=NULL)

Data Representing each defline.

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

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