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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/psibl2seq_unit_test.cpp Source File

;

x_ReadSeqEntriesFromFile();

x_SetupSubject(bioseq);

m_OptHandle.

();

m_SeqEntry.

();

subjects.push_back(ssl);

subjects.push_back(ssl);

kPssmFile(

);

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

kSeqEntryFile(

);

m_SeqEntry = TestUtil::ReadObject<CSeq_entry>(kSeqEntryFile);

BOOST_REQUIRE(m_Pssm &&

BOOST_REQUIRE_EQUAL(

, sa->

());

pair<TSeqRange, TSeqRange> first_hsp =

BOOST_REQUIRE_EQUAL(first_hsp.first.GetFrom(), hsp1_query.

());

BOOST_REQUIRE_EQUAL(first_hsp.first.GetTo(), hsp1_query.

());

BOOST_REQUIRE_EQUAL(first_hsp.second.GetFrom(), hsp1_subj.

());

BOOST_REQUIRE_EQUAL(first_hsp.second.GetTo(), hsp1_subj.

());

(hsp_num == 2)

pair<TSeqRange, TSeqRange> second_hsp =

BOOST_REQUIRE_EQUAL(second_hsp.first.GetFrom(), hsp2_query.

());

BOOST_REQUIRE_EQUAL(second_hsp.first.GetTo(), hsp2_query.

());

BOOST_REQUIRE_EQUAL(second_hsp.second.GetFrom(), hsp2_subj.

());

BOOST_REQUIRE_EQUAL(second_hsp.second.GetTo(), hsp2_subj.

());

BOOST_REQUIRE_EQUAL(hsp.

(), hsp1_query.

());

BOOST_REQUIRE_EQUAL(hsp.

(), hsp1_subj.

());

m_Pssm->SetPssm().SetFinalData().SetScalingFactor(2);

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

m_Pssm->SetPssm().SetFinalData().ResetScores();

m_Pssm->SetPssm().SetIntermediateData().ResetFreqRatios();

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

m_Pssm->SetPssm().ResetQuery();

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

m_Pssm->SetPssm().SetQuery(*m_SeqSet);

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

m_Pssm->SetPssm().SetIsProtein(

);

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

BOOST_REQUIRE_THROW(

blaster(empty_query, m_Subject, opts),

(

= 0;

<

(gis)/

(*gis);

++) {

CreateSSeqLoc(*seqid, range));

queries.push_back(*sl);

BOOST_REQUIRE_THROW(

blaster(qf, m_Subject, opts),

CreateSSeqLoc(*seqid, range));

queries.push_back(*sl);

CreateSSeqLoc(*seqid, range));

sequences.push_back(*sl);

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

BOOST_REQUIRE_THROW(

blaster(m_Pssm, m_Subject, m_OptHandle),

x_SetupSubject(bioseq);

blaster(m_Pssm, m_Subject, m_OptHandle);

kNumExpectedAlignments = 2;

BOOST_REQUIRE_EQUAL(kNumExpectedAlignments, sas->

());

CSeq_align_set::Tdata::const_iterator alignment_itr

= sas->

().begin();

x_ValidatePssmVsGi7450545(*alignment_itr, 1);

x_ValidatePssmVsGi7450545(*alignment_itr, 2);

kNumSubjects = 2;

x_SetupSubject(bioseq_set);

blaster(m_Pssm, m_Subject, m_OptHandle);

BOOST_REQUIRE(

[0].GetErrors().empty());

BOOST_REQUIRE_EQUAL(kNumSubjects,

(

)m_Subject->MakeLocalQueryData(&opts)->GetNumQueries());

BOOST_REQUIRE_EQUAL(kNumSubjects,

kNumExpectedAlignments = kNumSubjects;

BOOST_REQUIRE_EQUAL(kNumExpectedAlignments, sas->

().size());

CSeq_align_set::Tdata::const_iterator alignment_itr

= sas->

().begin();

x_ValidatePssmVsGi7450545(*alignment_itr, 1);

x_ValidatePssmVsGi7450545(*alignment_itr, 2);

BOOST_REQUIRE(

[1].GetErrors().empty());

x_ValidatePssmVsGi129295(*(sas2->

().begin()));

subj_gis[] = { 7450545, 40456275, 129295 };

(

= 0;

<

(subj_gis)/

(*subj_gis);

++) {

subj_loc->SetWhole().SetGi(subj_gis[

]);

subjects.push_back(

(subj_loc, scope));

blaster(m_Pssm, subj_factory, m_OptHandle);

BOOST_REQUIRE_EQUAL(subjects.size(),

.GetNumResults());

CSeq_align_set::Tdata::const_iterator alignment_itr

= sas->

().begin();

x_ValidatePssmVsGi7450545(*alignment_itr, 1);

x_ValidatePssmVsGi7450545(*alignment_itr, 2);

BOOST_REQUIRE_EQUAL(0, (

) sas2->

());

x_ValidatePssmVsGi129295(*(

[2].GetSeqAlign()->

().begin()));

query_loc->SetWhole().SetGi(7662354);

subj_gis[] = { 34535770, 46125411 };

(

= 0;

<

(subj_gis)/

(*subj_gis);

++) {

subj_loc->SetWhole().SetGi(subj_gis[

]);

subjects.push_back(

(subj_loc, scope));

psibl2seq(query_factory, subj_factory, psi_opts);

qa::CSeqAlignCmpOpts opts;

qa::CSeqAlignCmp

(results_ref, results_test, opts);

identical_results =

.Run(&errors);

BOOST_REQUIRE_MESSAGE(identical_results, errors);

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 CBl2Seq (BLAST 2 Sequences) class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

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

Runs the BLAST algorithm between 2 sequences.

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

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

CRange< TSeqPos > GetSeqRange(TDim row) const

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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

void x_SetupSubject(CConstRef< CBioseq_set > bioseq_set)

CRef< IQueryFactory > m_Subject

must be initialized with one of the two data members below

void x_ValidatePssmVsGi7450545(CConstRef< CSeq_align > sa, int hsp_num)

void x_ReadPssmFromFile()

void x_ReadSeqEntriesFromFile()

void x_ValidatePssmVsGi129295(CConstRef< CSeq_align > sa)

void x_SetupSubject(CConstRef< CBioseq > bioseq)

CRef< CSeq_entry > m_SeqSet

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

void x_ValidatePssmVsGi40456275(CConstRef< CSeq_align > sa)

CRef< CSeq_entry > m_SeqEntry

Contains a single Bioseq.

CRef< CPSIBlastOptionsHandle > m_OptHandle

CRef< CPssmWithParameters > m_Pssm

Runs a single iteration of the PSI-BLAST algorithm between 2 sequences.

Search Results for All Queries.

Tdata::size_type Size() const

static CRef< CScope > NewScope(bool with_defaults=true)

Return a new scope, possibly (by default) with default loaders, which will include the Genbank loader...

static CTestObjMgr & Instance()

Template class for iteration on objects of class C (non-medifiable version)

@ eNoCompositionBasedStats

Don't use composition based statistics.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST 2 Sequences engine.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

void PsiBlastComputePssmScores(CRef< objects::CPssmWithParameters > pssm, const CBlastOptions &opts)

Given a PSSM with frequency ratios and options, invoke the PSSM engine to compute the scores.

void SetId(CSeq_id &id)

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

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void Reset(void)

Reset reference object.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetIntermediateData(void) const

Check if it is safe to call GetIntermediateData method.

const TFinalData & GetFinalData(void) const

Get the FinalData member data.

bool CanGetFinalData(void) const

Check if it is safe to call GetFinalData method.

void SetPssm(TPssm &value)

Assign a value to Pssm data member.

bool CanGetQuery(void) const

Check if it is safe to call GetQuery method.

bool CanGetScores(void) const

Check if it is safe to call GetScores method.

bool CanGetPssm(void) const

Check if it is safe to call GetPssm method.

const TPssm & GetPssm(void) const

Get the Pssm member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetSegs(void) const

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

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

@ e_Gi

GenInfo Integrated Database.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

const TYPE & Get(const CNamedParameterList *param)

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

const struct ncbi::grid::netcache::search::fields::SIZE size

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

std::vector< SeqAlign > TSeqAlignSet

Vector of neutral sequence alignments.

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

Declares CPsiBl2Seq, the C++ API for the PSI-BLAST 2 Sequences engine.

BOOST_AUTO_TEST_CASE(TestComparePssmWithMultipleSequences)

Declarations of auxiliary functions/classes for PSI-BLAST.

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

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.

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

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

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