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

;

vector<TGi>& gis);

operator()(

);

x_TestSingleSequence_Local(

index);

x_TestSingleSequence_Remote(

index);

x_TestSingleProtein_Local(

index,

x_TestSingleNucleotide_Local(

index,

x_TestSingleTranslatedNucl_Local(

index,

x_TestSingleProtein_Remote(

&

,

x_TestSingleNucleotide_Remote(

&

,

x_TestLocalStrand(

&

,

& strand =

);

: m_QueryFactory(query_factory), m_Gis(1, gi)

vector<TGi>& gis)

: m_QueryFactory(query_factory), m_Gis(gis)

BOOST_REQUIRE(!gis.empty());

: m_QueryFactory(query_factory)

BOOST_REQUIRE(!seqlocs.empty());

is_protein_sequence =

;

is_protein_sequence = bioseq->

().

();

.reserve(seqlocs->size());

BOOST_REQUIRE(index == seqlocs->size());

(

= 0;

<

.size();

++) {

ctx_index = index * 2;

runtime_error(

+

(

);

+=

;

runtime_error(

);

* sequence,

& strand)

(

);

+=

;

+=

+ strand +

;

BOOST_REQUIRE_MESSAGE(

(sequence[

]) ==

(kBase),

BOOST_REQUIRE(index <= qinfo->last_context);

BOOST_REQUIRE(queries.

());

BOOST_REQUIRE(qinfo !=

);

BOOST_REQUIRE(seq_blk !=

);

( !msgs.empty() ) {

message += (*m)->GetMessage();

BOOST_REQUIRE_EQUAL(

.size(),

BOOST_REQUIRE(queries.

());

IRemoteQueryData::TSeqLocs::const_iterator itr = seqlocs.begin();

BOOST_REQUIRE_EQUAL(

.size(), seqlocs.size());

BOOST_REQUIRE(index >= 0);

BOOST_REQUIRE(index <

(seqlocs.size()));

(

= 0; itr != seqlocs.end(); ++itr, ++

) {

(

== index)

;

BOOST_REQUIRE(itr != seqlocs.end());

* seqid = (*itr)->GetId();

BOOST_REQUIRE(seqid !=

);

cout << seqid_string << endl;

BOOST_REQUIRE_MESSAGE(seqid_string.find(gi_string) !=

,

(; bioseq; ++bioseq) {

(seq_index !=

(index)) {

BOOST_REQUIRE(seq_index <

.size());

BOOST_REQUIRE_EQUAL(sv.

(), nconv);

kResidue = sv[

];

BOOST_REQUIRE_EQUAL(sv.

(), nconv);

kBase = sv[

];

BaseTest = (kCompressedBase & 0xF0) >> 4;

BaseTest = kCompressedBase & 0x0F;

BOOST_REQUIRE_MESSAGE(

(kBase) ==

(BaseTest),

(vector<TGi>, itr, gis) {

(vector<TGi>, itr, gis) {

queries.push_back(*sl);

(vector<TGi>, itr, gis) {

(vector<TGi>, itr, gis) {

kExpectedSize = 416+624+310;

BOOST_REQUIRE_EQUAL(kExpectedSize,

kExpectedSize = 247249719;

BOOST_REQUIRE_EQUAL(kExpectedSize,

gis.push_back(

(38092615));

s_ObjMgr_QueryFactory_LocalDataFromTSeqLocVector(gis);

s_ObjMgr_QueryFactory_LocalDataFromTSeqLocVector(gis);

gis.push_back(

(38092615));

s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(gis);

s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(gis);

queries.push_back(*sl);

s_ObjMgrFree_QueryFactory_LocalDataFromBioseq(kGi);

s_ObjMgrFree_QueryFactory_LocalDataFromBioseq(kGi);

s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(gis);

s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(gis);

Declares the BLAST exception class.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

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

Defines BLAST error codes (user errors included)

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

NCBI C++ Object Manager free implementation of IQueryFactory.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

static bool IsAa(EMol mol)

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

void x_TestSingleNucleotide_Remote(const CSeq_id &id, const CSeq_inst &seq_inst)

void x_CompareSequenceData(CSeqVector &sv, const Uint1 *sequence, const string &strand="")

void x_TestSingleTranslatedNucl_Local(int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)

void x_TestSingleSequence_Local(int index)

void x_TestLocalStrand(const CSeq_id &id, int ctx_index, ENa_strand strand, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)

void x_Init(const IRemoteQueryData::TSeqLocs *seqlocs=0)

vector< ENa_strand > m_Strands

void x_TestSingleProtein_Local(int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)

CConstRef< CBlastOptions > m_Options

CRef< IQueryFactory > m_QueryFactory

void x_TestSingleSequence_Remote(int index)

CSequenceDataTester(CRef< IQueryFactory > query_factory, TGi gi)

void x_TestSingleProtein_Remote(const CSeq_id &id, const CSeq_inst &seq_inst)

void x_TestSingleNucleotide_Local(int index, const BlastQueryInfo *qinfo, const BLAST_SequenceBlk *seqblk)

ENa_strand x_GetStrand(int index)

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 CSeqVector GetSeqVector(const CSeq_id &id, ENa_strand strand=eNa_strand_plus)

Return a sequence vector for some kind of id or location.

static CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Return a biosequence handle for some kind of id.

static CTestObjMgr & Instance()

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

Class for the messages for an individual query sequence.

objects::ENa_strand GetStrandOption() const

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

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

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

list< CRef< objects::CSeq_loc > > TSeqLocs

Type definition for CSeq_loc set used as queries in the BLAST remote search class.

const Uint1 NCBI4NA_TO_BLASTNA[]

Translates between ncbi4na and blastna.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

virtual CRef< objects::CBioseq_set > GetBioseqSet()=0

Accessor for the CBioseq_set.

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

void GetQueryMessages(size_t index, TQueryMessages &qmsgs)

Retrieve error/warning messages for a specific query.

virtual TSeqLocs GetSeqLocs()=0

Accessor for the TSeqLocs.

size_t GetSumOfSequenceLengths()

Compute the sum of all the sequence's lengths.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_CURRENT_FUNCTION

Get current function name.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const TPrim & Get(void) const

const string AsFastaString(void) const

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

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

Given an accession string retrieve the GI id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool IsProtein(void) const

void SetCoding(TCoding coding)

bool IsNucleotide(void) const

TObjectType * GetNonNullPointer(void)

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

@ e_Gi

GenInfo Integrated Database.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TRepr GetRepr(void) const

Get the Repr member data.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsNcbistdaa(void) const

Check if variant Ncbistdaa is selected.

bool IsNcbi4na(void) const

Check if variant Ncbi4na is selected.

TLength GetLength(void) const

Get the Length member data.

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ eRepr_raw

continuous sequence

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Ncbi4na

4 bit nucleic acid code

unsigned int

A callback function used to compare two keys in a database.

Implementation of the uniform BLAST search interface for searching locally installed BLAST databases.

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

Defines NCBI C++ diagnostic APIs, classes, and macros.

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

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

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

BOOST_AUTO_TEST_CASE(ObjMgr_QueryFactory_LocalData_GetSumOfSequenceLengths)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to hold a sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Int4 query_length

Length of this query, strand or frame.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

int num_queries

Number of query sequences.

static void create_EmptyBlastQueryVector()

static void s_ObjMgrFree_QueryFactory_LocalDataFromBioseq_set(const vector< TGi > &gis)

static void create_EmptyTSeqLocVector()

static void s_ObjMgr_QueryFactory_LocalDataFromTSeqLocVector(const vector< TGi > &gis)

static void s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(const vector< TGi > &gis)

static void s_ObjMgrFree_QueryFactory_LocalDataFromBioseq(TGi kGi)

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

Uniform BLAST Search Interface.

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