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

;

num_hsps_total = 12;

num_hsps_plus = 4;

scores[num_hsps_total] =

{62, 51, 49, 44, 44, 44, 43, 43, 43, 48, 45, 46};

q_offsets[num_hsps_total] =

{3244, 1045, 3133, 9204, 3163, 8179, 1090, 1328, 2300, 832, 6776, 3633};

s_offsets[num_hsps_total] =

{700, 662, 812, 1385, 146, 538, 930, 1340, 1373, 1917, 1467, 966};

q_ends[num_hsps_total] =

{3430, 1159, 3283, 9300, 3328, 8287, 1174, 1388, 2408, 937, 6968, 3759};

s_ends[num_hsps_total] =

{761, 699, 861, 1418, 205, 564, 958, 1360, 1403, 1952, 1531, 1007};

evalues[num_hsps_total] =

{0.0546847, 1.0657, 2.00126, 7.04787, 7.83533, 8.12416, 9.05612, 9.84108, 9.90728, 2.53047, 5.47761, 3.70474};

num_hsps =

.Size();

BOOST_REQUIRE_EQUAL(num_hsps_plus, num_hsps);

BOOST_REQUIRE_EQUAL(num_hsps_total - num_hsps_plus, num_hsps);

BOOST_REQUIRE_EQUAL(num_hsps_total, num_hsps);

align_num = 0;

list<CRef<CStd_seg> >& stdseg = hitlist.

().

();

stdseg.front()->GetLoc().front()->GetInt().GetStrand();

(align_num < num_hsps_total &&

strands[align_num] != curr_strand)

BOOST_REQUIRE(align_num < num_hsps_total);

& curr_score = **sitr;

(curr_score.

().

() ==

) {

BOOST_REQUIRE_CLOSE(evalues[align_num],

(curr_score.

().

() ==

) {

BOOST_REQUIRE_EQUAL(scores[align_num],

off1 = locs[0]->GetInt().GetFrom();

off2 = locs[1]->GetInt().GetFrom();

BOOST_REQUIRE_EQUAL(q_offsets[align_num], off1);

BOOST_REQUIRE_EQUAL(s_offsets[align_num], off2);

(seqloc[0]->IsEmpty()) {

off2 += seqloc[1]->GetInt().GetTo() -

seqloc[1]->GetInt().GetFrom() + 1;

(seqloc[1]->IsEmpty()) {

off1 += seqloc[0]->GetInt().GetTo() -

seqloc[0]->GetInt().GetFrom() + 1;

off1 += seqloc[0]->GetInt().GetTo() -

seqloc[0]->GetInt().GetFrom() + 1;

off2 += seqloc[1]->GetInt().GetTo() -

seqloc[1]->GetInt().GetFrom() + 1;

BOOST_REQUIRE_EQUAL(q_ends[align_num], off1);

BOOST_REQUIRE_EQUAL(s_ends[align_num], off2);

m_DbName =

;

m_DbName =

;

unique_ptr<SSeqLoc>

(

query_v.push_back(*

);

unique_ptr<SSeqLoc>

(

query_v.push_back(*

);

BOOST_REQUIRE_EQUAL(0, off1);

BOOST_REQUIRE_EQUAL(0, off2);

BOOST_REQUIRE_EQUAL(1016, (

)denseg.

()[0]);

kNumHits = 2;

kOids[kNumHits] = { 3, 1 };

kNumHsps[kNumHits] = { 2, 3 };

kTotalHsps = 5;

kScores[kTotalHsps] = { 7458, 6898, 7055, 6997, 6542};

kLengths[kTotalHsps] = { 36, 21, 15, 15, 10};

query_loc->

().SetGi(kQueryGi);

query_v.push_back(

(query_loc, query_scope));

BOOST_REQUIRE_EQUAL(1,

->num_queries);

BOOST_REQUIRE(

->hitlist_array[0]);

BOOST_REQUIRE_EQUAL(kNumHits,

->hitlist_array[0]->hsplist_count);

(

index = 0; index < kNumHits; ++index) {

->hitlist_array[0]->hsplist_array[index];

BOOST_REQUIRE_EQUAL(kOids[index], hsp_list->

);

BOOST_REQUIRE_EQUAL(kNumHsps[index], hsp_list->

);

(

index1 = 0; index1 < kNumHsps[index];

++index1, ++hsp_index) {

BOOST_REQUIRE_EQUAL(kScores[hsp_index], hsp->

);

BOOST_REQUIRE_EQUAL(kLengths[hsp_index],

BOOST_REQUIRE_EQUAL(kTotalHsps, hsp_index);

=

;

BOOST_REQUIRE(!freq_file.

());

query_v.push_back(*

);

BOOST_REQUIRE_THROW(

(query_factory, opts, dbinfo),

User-defined methods of the data storage class.

Common definitions for protein and nucleotide lookup tables.

Declares the CBlastRPSOptionsHandle class.

Utility function to convert internal BLAST result structures into objects::CSeq_align_set objects.

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

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

Defines BLAST error codes (user errors included)

Wrapper class for BlastHSPResults .

Search class to perform the preliminary stage of the BLAST search.

Handle to the rpsblast options to the BLAST algorithm.

Wrapper class for BlastSeqSrc .

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Handle to the options for translated nucleotide-RPS blast.

Search Results for All Queries.

static CTestObjMgr & Instance()

void SetCompositionBasedStats(bool mode)

Set composition based statistics mode.

CRef< SInternalData > Run()

Borrow the internal data and results results.

BlastSeqSrc * SeqDbBlastSeqSrcInit(const string &dbname, bool is_prot, Uint4 first_seq=0, Uint4 last_seq=0, Int4 mask_algo_id=-1, ESubjectMaskingType mask_type=eNoSubjMasking)

Initialize the sequence source structure.

CRef< CSearchResultSet > Run()

Executes the search.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

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

Sets FilterString.

CRef< TBlastHSPStream > m_HspStream

HSP output of the preliminary stage goes here.

BlastHSPResults * ComputeBlastHSPResults(BlastHSPStream *stream, Uint4 max_num_hsps=0, bool *rm_hsps=NULL, vector< bool > *rm_hsps_info=NULL) const

Return HSPs in a structure other than the HSPStream? Provide conversion? How to combine this with CBl...

@ eBlastDbIsProtein

protein

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual bool Exists(void) const

Check existence of file.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

const TStr & GetStr(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

vector< CRef< CSeq_loc > > TLoc

vector< CRef< CScore > > TScore

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

const TStd & GetStd(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TValue & GetValue(void) const

Get the Value member data.

bool IsStd(void) const

Check if variant Std is selected.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

TReal GetReal(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Main class to perform a BLAST search on the local machine.

Wrapper for all lookup tables used in BLAST.

void CheckForBlastSeqSrcErrors(const BlastSeqSrc *seqsrc)

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

#define TRUE

bool replacment for C indicating true.

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

void testNuclHitList(const CSeq_align_set &results, ENa_strand strand)

BOOST_AUTO_TEST_CASE(WholeSequenceMatch)

Declares the CRPSTBlastnOptionsHandle class.

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

The structure to hold all HSPs for a given sequence after the gapped alignment.

Int4 oid

The ordinal id of the subject sequence this HSP list is for.

Int4 hspcnt

Number of HSPs saved.

BlastHSP ** hsp_array

Array of pointers to individual HSPs.

Structure holding all information about an HSP.

BlastSeg query

Query sequence info.

Int4 score

This HSP's raw score.

Int4 offset

Start of hsp.

void NuclSearch(ENa_strand strand)

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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