Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/delta__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/unit_tests/api/delta_unit_test.cpp Source File

;

kPssmFile(

);

m_Pssm = TestUtil::ReadObject<CPssmWithParameters>(kPssmFile);

BOOST_REQUIRE(m_SeqEntry->

());

seqloc->

(*

);

m_Seq_locs.push_back(seqloc);

kSeqEntryFile(

);

TestUtil::ReadObject<CSeq_entry>(kSeqEntryFile);

BOOST_REQUIRE(m_SeqEntry->

());

seqloc->

(*

);

m_Seq_locs.push_back(seqloc);

x_ReadSeqEntriesFromFile();

m_OptHandle.

();

m_SearchDb.

();

m_DomainDb.

();

m_SeqEntry.

();

& seqid = (*itr)->GetSeq_id(1);

BOOST_REQUIRE(seqid.

() ||

(acc != last_acc || ver != last_ver) {

(new_gi != last_id) {

deltablast(query_factory, dbadapter, domain_dbadapter,

m_OptHandle, rps_opts);

BOOST_REQUIRE((*domain_results)[0].GetErrors().

());

kNumExpectedMatchingDomains = 3;

BOOST_REQUIRE_EQUAL(kNumExpectedMatchingDomains,

x_CountNumberUniqueIds(domain_sas));

kNumExpectedDomainHSPs = 3;

expected_domain_results[0].score = 742;

expected_domain_results[0].evalue = 5.21679e-102;

expected_domain_results[0].bit_score = 2.89507e+02;

expected_domain_results[0].num_ident = 111;

starts[] = {1, 139, 80, -1, 81, 218};

lengths[] = {79, 1, 151};

back_inserter(expected_domain_results[0].starts));

back_inserter(expected_domain_results[0].lengths));

expected_domain_results[1].score = 713;

expected_domain_results[1].evalue = 1.33296e-97;

expected_domain_results[1].bit_score = 2.78295e+02;

expected_domain_results[1].num_ident = 107;

starts[] = {1, 135, 6, -1, 8, 140, -1, 190, 58, 191, 80, -1, 81,

213, 94, -1, 95, 226, 114, -1, 116, 245, 200, -1,

lengths[] = {5, 2, 50, 1, 22, 1, 13, 1, 19, 2, 84, 2, 30};

back_inserter(expected_domain_results[1].starts));

back_inserter(expected_domain_results[1].lengths));

expected_domain_results[2].score = 673;

expected_domain_results[2].evalue = 1.63233e-91;

expected_domain_results[2].bit_score = 2.62959e+02;

expected_domain_results[2].num_ident = 106;

starts[] = {0, 137, 115, -1, 117, 252 };

lengths[] = {115, 2, 112};

back_inserter(expected_domain_results[2].starts));

back_inserter(expected_domain_results[2].lengths));

qa::CSeqAlignCmpOpts opts;

qa::CSeqAlignCmp cmp_d(expected_domain_results, actual_domain_results, opts);

identical_results = cmp_d.Run(&errors);

BOOST_REQUIRE_MESSAGE(identical_results, errors);

kNumExpectedMatchingSeqs = 8;

BOOST_REQUIRE_EQUAL(kNumExpectedMatchingSeqs, x_CountNumberUniqueIds(sas));

kNumExpectedHSPs = 9;

expected_results[0].score = 861;

expected_results[0].evalue = 2.80386e-109;

expected_results[0].bit_score = 3.35656e+02;

expected_results[0].num_ident = 101;

starts[] = {0, 941, -1, 1094, 153, 1095};

lengths[] = {153, 1, 79};

back_inserter(expected_results[0].starts));

back_inserter(expected_results[0].lengths));

expected_results[1].score = 633;

expected_results[1].evalue = 3.86624e-77;

expected_results[1].bit_score = 2.47830e+02;

expected_results[1].num_ident = 73;

starts[] = {0, 154, -1, 307, 153, 308};

lengths[] = {153, 1, 25};

back_inserter(expected_results[1].starts));

back_inserter(expected_results[1].lengths));

expected_results[2].score = 645;

expected_results[2].evalue = 6.62145e-84;

expected_results[2].bit_score = 2.52452e+02;

expected_results[2].num_ident = 80;

starts[] = {0, 190, 68, -1, 70, 258, 92, -1, 93, 280, 118, -1,

119, 305, 151, -1, 152, 337, 161, -1, 162, 346, -1,

lengths[] = {68, 2, 22, 1, 25, 1, 32, 1, 9, 1, 21, 4, 49};

back_inserter(expected_results[2].starts));

back_inserter(expected_results[2].lengths));

expected_results[3].score = 53;

expected_results[3].evalue = 3.83197e+00;

expected_results[3].bit_score = 244103049e-7;

expected_results[3].num_ident = 7;

starts[] = {127, 104, 132, -1, 134, 109};

lengths[] = {5, 2, 15};

back_inserter(expected_results[3].starts));

back_inserter(expected_results[3].lengths));

expected_results[4].score = 51;

expected_results[4].evalue = 5.55808;

expected_results[4].bit_score = 23.6440;

expected_results[4].num_ident = 5;

starts[] = {137, 20, 151, -1, 156, 34};

lengths[] = {14, 5, 17};

back_inserter(expected_results[4].starts));

back_inserter(expected_results[4].lengths));

expected_results[5].score = 51;

expected_results[5].evalue = 6.14178;

expected_results[5].bit_score = 23.6440;

expected_results[5].num_ident = 8;

starts[] = {153, 102, -1, 122, 173, 127};

lengths[] = {20, 5, 12};

back_inserter(expected_results[5].starts));

back_inserter(expected_results[5].lengths));

expected_results[6].score = 51;

expected_results[6].evalue = 6.33109;

expected_results[6].bit_score = 23.6440;

expected_results[6].num_ident = 7;

starts[] = {172, 305, 179, -1, 182, 312};

lengths[] = {7, 3, 33};

back_inserter(expected_results[6].starts));

back_inserter(expected_results[6].lengths));

expected_results[7].score = 48;

expected_results[7].evalue = 7.91913;

expected_results[7].bit_score = 22.4884;

expected_results[7].num_ident = 5;

starts[] = {155, 78};

lengths[] = {18};

back_inserter(expected_results[7].starts));

back_inserter(expected_results[7].lengths));

expected_results[8].score = 49;

expected_results[8].evalue = 8.65824;

expected_results[8].bit_score = 22.8736;

expected_results[8].num_ident = 4;

starts[] = {175, 11};

lengths[] = {14};

back_inserter(expected_results[8].starts));

back_inserter(expected_results[8].lengths));

qa::CSeqAlignCmp

(expected_results, actual_results, opts);

identical_results =

.Run(&errors);

BOOST_REQUIRE_MESSAGE(identical_results, errors);

m_OptHandle->SetEvalueThreshold(5);

deltablast(query_factory, dbadapter, domain_dbadapter,

m_OptHandle, rps_opts);

BOOST_REQUIRE((*domain_results)[0].GetErrors().

());

kNumExpectedMatchingDomains = 3;

BOOST_REQUIRE_EQUAL(kNumExpectedMatchingDomains,

x_CountNumberUniqueIds(domain_sas));

kNumExpectedDomainHSPs = 3;

expected_domain_results[0].score = 728;

expected_domain_results[0].evalue = 6.61511e-100;

expected_domain_results[0].bit_score = 2841082571e-7;

expected_domain_results[0].num_ident = 111;

starts[] = {1, 139, 80, -1, 81, 218, 162, -1, 163, 299};

lengths[] = {79, 1, 81, 1, 69};

back_inserter(expected_domain_results[0].starts));

back_inserter(expected_domain_results[0].lengths));

expected_domain_results[1].score = 698;

expected_domain_results[1].evalue = 2.17510e-95;

expected_domain_results[1].bit_score = 2725169055e-7;

expected_domain_results[1].num_ident = 107;

starts[] = {1, 135, 6, -1, 8, 140, -1, 190, 58, 191, 80, -1, 81,

213, 94, -1, 95, 226, 114, -1, 116, 245, 200, -1,

lengths[] = {5, 2, 50, 1, 22, 1, 13, 1, 19, 2, 84, 2, 30};

back_inserter(expected_domain_results[1].starts));

back_inserter(expected_domain_results[1].lengths));

expected_domain_results[2].score = 661;

expected_domain_results[2].evalue = 9.15785e-90;

expected_domain_results[2].bit_score = 2583366987e-7;

expected_domain_results[2].num_ident = 106;

starts[] = {0, 137, 115, -1, 117, 252 };

lengths[] = {115, 2, 112};

back_inserter(expected_domain_results[2].starts));

back_inserter(expected_domain_results[2].lengths));

qa::CSeqAlignCmpOpts opts;

qa::CSeqAlignCmp cmp_d(expected_domain_results, actual_domain_results, opts);

identical_results = cmp_d.Run(&errors);

BOOST_REQUIRE_MESSAGE(identical_results, errors);

kNumExpectedMatchingSeqs = 5;

BOOST_REQUIRE_EQUAL(kNumExpectedMatchingSeqs, x_CountNumberUniqueIds(sas));

kNumExpectedHSPs = 6;

expected_results[0].score = 876;

expected_results[0].evalue = 2.04885e-111;

expected_results[0].bit_score = 3414303038e-7;

expected_results[0].num_ident = 101;

starts[] = {0, 941, -1, 1094, 153, 1095};

lengths[] = {153, 1, 79};

back_inserter(expected_results[0].starts));

back_inserter(expected_results[0].lengths));

expected_results[1].score = 642;

expected_results[1].evalue = 2.54740e-78;

expected_results[1].bit_score = 2512936031e-7;

expected_results[1].num_ident = 73;

starts[] = {0, 154, -1, 307, 153, 308};

lengths[] = {153, 1, 25};

back_inserter(expected_results[1].starts));

back_inserter(expected_results[1].lengths));

expected_results[2].score = 736;

expected_results[2].evalue = 1.10324e-97;

expected_results[2].bit_score = 2875023632e-7;

expected_results[2].num_ident = 83;

starts[] = {0, 190, 68, -1, 70, 258, 92, -1, 93, 280, 118, -1,

119, 305, 151, -1, 152, 337, 161, -1, 162, 346, -1,

lengths[] = {68, 2, 22, 1, 25, 1, 32, 1, 9, 1, 28, 4, 42};

back_inserter(expected_results[2].starts));

back_inserter(expected_results[2].lengths));

expected_results[3].score = 53;

expected_results[3].evalue = 3.45771;

expected_results[3].bit_score = 2441105291e-8;

expected_results[3].num_ident = 4;

starts[] = {139, 22, 151, -1, 156, 34};

lengths[] = {12, 5, 17};

back_inserter(expected_results[3].starts));

back_inserter(expected_results[3].lengths));

expected_results[4].score = 52;

expected_results[4].evalue = 4.61874;

expected_results[4].bit_score = 2402585333e-8;

expected_results[4].num_ident = 7;

starts[] = {172, 305, 179, -1, 182, 312};

lengths[] = {7, 3, 33};

back_inserter(expected_results[4].starts));

back_inserter(expected_results[4].lengths));

expected_results[5].score = 52;

expected_results[5].evalue = 4.62283;

expected_results[5].bit_score = 2402585333e-8;

expected_results[5].num_ident = 7;

starts[] = {127, 104, 132, -1, 134, 109};

lengths[] = {5, 2, 15};

back_inserter(expected_results[5].starts));

back_inserter(expected_results[5].lengths));

qa::CSeqAlignCmp

(expected_results, actual_results, opts);

identical_results =

.Run(&errors);

BOOST_REQUIRE_MESSAGE(identical_results, errors);

deltablast(query_factory, dbadapter, domain_dbadapter,

[1].GetSeqAlign()->

().

()->GetSeq_id(0).GetPir().GetName(),

deltablast.

(0)->GetQuery().GetSeq().GetFirstId()->GetGi(),

deltablast.

(1)->GetQuery().GetSeq().GetFirstId()->GetPir().GetName(),

BOOST_REQUIRE_THROW(

deltablast(query_factory, dbadapter,

domain_dbadapter, m_OptHandle),

BOOST_REQUIRE_THROW(

deltablast(query_factory, dbadapter,

domain_dbadapter, m_OptHandle),

BOOST_REQUIRE_THROW(

deltablast(query_factory, dbadapter,

domain_dbadapter, m_OptHandle),

BOOST_REQUIRE_THROW(

deltablast(query_factory, dbadapter,

domain_dbadapter, m_OptHandle),

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the CBlastRPSOptionsHandle class.

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

const CSeq_id * GetFirstId() const

Defines BLAST error codes (user errors included)

Handle to the rpsblast options to the BLAST algorithm.

Handle to the protein-protein options to the BLAST algorithm.

A simple realization of the DELTA-BLAST algorithm: seacrch domain database, compute PSSM,...

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

bool HasQuery() const

Has this PSSM a query in it?

Search Results for All Queries.

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

@ eNoCompositionBasedStats

Don't use composition based statistics.

#define STATIC_ARRAY_SIZE(array)

Calculate the size of a static array.

BOOST_AUTO_TEST_CASE(TestSingleQuery_CBS)

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

Declares the CDeltaBlastOptionsHandle class.

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

void SetCompositionBasedStats(bool mode)

Set composition based statistics mode.

CConstRef< objects::CPssmWithParameters > GetPssm(int index=0) const

Accessor for PSSM computd from CDD hits and used in protein search.

CRef< CSearchResultSet > Run()

Run the DELTA-BLAST engine with one iteration.

ECompoAdjustModes GetCompositionBasedStats() const

Returns this mode, which mostly specifies whether composition of db sequence is taken into account wh...

CRef< CSearchResultSet > GetDomainResults()

Get results of conserved domain search (intermediate results)

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

@ eBlastDbIsProtein

protein

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static bool PreferAccessionOverGi(void)

Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SE...

void SetId(CSeq_id &id)

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

const TTag & GetTag(void) const

Get the Tag member data.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

TId GetId(void) const

Get the variant data.

void SetPssm(TPssm &value)

Assign a value to Pssm data member.

bool CanGetQuery(void) const

Check if it is safe to call GetQuery method.

const TPssm & GetPssm(void) const

Get the Pssm member data.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsGenbank(void) const

Check if variant Genbank is selected.

bool IsOther(void) const

Check if variant Other is selected.

bool IsGeneral(void) const

Check if variant General is selected.

TGi GetGi(void) const

Get the variant data.

TVersion GetVersion(void) const

Get the Version member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

const TAccession & GetAccession(void) const

Get the Accession member data.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

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

const TYPE & Get(const CNamedParameterList *param)

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

constexpr bool empty(list< Ts... >) noexcept

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

std::vector< SeqAlign > TSeqAlignSet

Vector of neutral sequence alignments.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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

API to compare CSeq-aligns produced by BLAST.

void SeqAlignSetConvert(const objects::CSeq_align_set &ss, std::vector< SeqAlign > &retval)

Converts a Seq-align-set into a neutral seqalign for use with the CSeqAlignCmp class.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

vector< CRef< CSeq_loc > > m_Seq_locs

Seq-locs for creating instances of CObjMgr_QueryFactory.

int x_CountNumberUniqueIds(CConstRef< CSeq_align_set > sas)

CRef< CPssmWithParameters > m_Pssm

CRef< CSeq_entry > m_SeqEntry

Contains a single Bioseq.

CRef< CSeq_entry > m_SeqSet

Contains a Bioseq-set with two Bioseqs, gi 7450545 and gi 129295.

CRef< CScope > m_Scope

Scope.

CRef< CSearchDatabase > m_DomainDb

CRef< CDeltaBlastOptionsHandle > m_OptHandle

void x_ReadSeqEntriesFromFile()

CRef< CSearchDatabase > m_SearchDb

~CDeltaBlastTestFixture()

Structure to represent a single sequence to be fed to BLAST.

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

Uniform BLAST Search Interface.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4