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

49 #if defined(NCBI_OS_UNIX) 63  bool

ignore_unsupported_options)

65

m_IgnoreUnsupportedOptions(ignore_unsupported_options)

68  if

(m_Request.Empty()) {

71  if

(m_Request->CanGetBody() && !m_Request->GetBody().IsQueue_search() ) {

105  if

(p.

NotEmpty

() && p->CanGetValue()) {

107  m_Data

->m_PsiNumOfIterations = p->GetValue().GetInteger();

111  m_Data

->m_PsiNumOfIterations =

118  m_Data

->m_OptionsHandle =

137  return m_Data

->m_OptionsHandle;

146  return m_Data

->m_PsiNumOfIterations;

161  return m_Request

->GetBody().GetQueue_search().GetProgram();

176  return m_Data

->m_QueryRange;

185  return m_Data

->m_FilteringID;

194  return m_Data

->m_FilteringKey;

205  return m_Data

->m_SubjectMaskingType;

211  return m_Request

->GetBody().GetQueue_search().GetService();

230

objects::CBlast4_parameters*

241

objects::CBlast4_parameters*

252

objects::CBlast4_parameters*

268  if

(program_opt !=

NULL

) {

271

list = b4_param->GetValue().GetInteger_list();

282  if

(list.size() > 0) {

283

rv.

insert

(list.begin(), list.end());

294  if

(list.size() > 0) {

295

rv.

insert

(list.begin(), list.end());

305

m_ClientId(client_id)

313  const string

& client_id,

314  unsigned int

psi_num_iterations)

316

m_ClientId(client_id)

321  if

(psi_num_iterations != 0)

328  const string

& client_id)

330

m_ClientId(client_id)

340  const string

& client_id,

341  unsigned int

psi_num_iterations)

343

m_ClientId(client_id)

348  if

(psi_num_iterations != 0)

373  if

(opts_handle.

Empty

())

376  "Empty reference for CBlastOptionsHandle."

);

386  "NULL argument specified: program"

);

392  "NULL argument specified: service"

);

399  if

(

NULL

== algo_opts )

402  "NULL argument specified: algo options"

);

413  "Empty reference for CSearchDatabase."

);

419  "Error: No database specified"

);

429  if

(!entrez_query_limit.empty())

435

v->

SetString

().assign(entrez_query_limit);

445  if

(!gi_list_limit.empty())

447  #ifdef NCBI_STRICT_GI 448

vector<Int8> int_gi_list;

449  ITERATE

( vector<TGi>, it, gi_list_limit ) {

450

int_gi_list.push_back(

GI_TO

(

Int8

, *it));

461 #ifdef NCBI_STRICT_TAX_ID 462

vector<int> int_taxids;

463  ITERATE

(vector<TTaxId>, it, taxids) {

464

int_taxids.push_back(

TAX_ID_TO

(

int

, *it));

473  if

(!neg_gi_list.empty())

475  #ifdef NCBI_STRICT_GI 476

vector<Int8> int_gi_list;

477  ITERATE

( vector<TGi>, it, neg_gi_list) {

478

int_gi_list.push_back(

GI_TO

(

Int8

, *it));

489 #ifdef NCBI_STRICT_TAX_ID 490

vector<int> int_taxids;

491  ITERATE

(vector<TTaxId>, it, taxids) {

492

int_taxids.push_back(

TAX_ID_TO

(

int

, *it));

530  "Empty reference for query pssm."

);

536  string

psi_program(

"blastp"

);

537  string

old_service(

"plain"

);

538  string

new_service(

"psi"

);

539  string

deltablast(

"delta_blast"

);

544  "PSI-Blast is only supported for blastp."

);

552  string

(

"PSI-Blast cannot also be "

) +

568  "Error: No queries specified"

);

575  if

(bioseq_set.

Empty

() && seqloc_list.empty())

578  "Error: No query data."

);

584  bool

has_local_ids =

false

;

586  if

(!seqloc_list.empty())

589  if

(seqloc_list.front()->IsInt())

593  const int

kRangeLength = kStop -

kStart

+ 1;

599  const int

kFullLength =

600

bioseq_set->

GetSeq_set

().front()->GetSeq().GetInst().GetLength();

602  if

(kFullLength != kRangeLength)

613

has_local_ids =

true

;

620  if

(

NULL

!= objmgrqf )

623  if

(!user_specified_masks.empty())

666  if

(bioseq_set.

Empty

())

669  "Error: No query data."

);

672

list< CRef<CBioseq> > bioseq_list;

686

p->SetName(field.GetName());

697  const

vector<int> & int_list)

700  copy

(int_list.begin(), int_list.end(), back_inserter(tmp_list));

703

p->SetName(field.GetName());

714  const

vector<Int8> & int_list)

717  copy

(int_list.begin(), int_list.end(), back_inserter(tmp_list));

720

p->SetName(field.GetName());

735

p->SetName(field.GetName());

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

ESubjectMaskingType

Define the possible subject masking types.

Declares the CBlastOptionsBuilder class.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

const string & GetName() const

Get field name (key).

static CBlast4Field & Get(EBlastOptIdx opt)

CRef< CBlast4_parameter > GetParamByName(const string name) const

Returns Blast4_parameter with specified name.

CBlast4_queue_search_request –.

CBlast4_request_body –.

Defines BLAST error codes (user errors included)

Class to build CBlastOptionsHandle from blast4 ASN objects.

virtual void GetRemoteProgramAndService_Blast3(string &p, string &s) const

Get the program and service name for remote blast.

Class to return parts of the CBlast4_request, or data associated with a CBlast4_request,...

Thrown on an attempt to access wrong choice variant.

NCBI C++ Object Manager dependant implementation of IQueryFactory.

set< TTaxId > & GetTaxIdsList()

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

std::ofstream out("events_result.xml")

main entry point for tests

static const char * str(char *buf, int n)

string GetDatabaseName() const

Accessor for the database name.

unique_ptr< CBlastOptionsBuilder > m_OptionsBuilder

void x_Process_Query(CRef< IQueryFactory > &query)

void x_Process_Pssm(CRef< CPssmWithParameters > &pssm)

void x_AddPsiNumOfIterationsToFormatOptions(unsigned int num_iters)

void x_Process_SearchDb(CRef< CSearchDatabase > &db)

string GetDBFilteringKey()

The DB filter key.

string GetService() const

Fetches service, such as psiblast, plain, megablast.

unique_ptr< CImportStrategyData > m_Data

string GetCreatedBy() const

Returns ident field from a Blast4-request.

string GetTask()

Fetches task, such as "megablast", "blastn", etc.

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

const TGiList GetNegativeGiListLimitation() const

const CRef< CSeqDBGiList > & GetNegativeGiList() const

Accessor for the negative gi list.

string GetFilteringAlgorithmKey() const

Accessor for the filtering algorithm key.

set< int > GetTaxidList()

objects::CBlast4_parameters * GetWebFormatOptions()

Options for controlling formatting (psi blast iteration number also).

static objects::CBlast4_get_search_results_reply::TMasks ConvertToRemoteMasks(const TSeqLocInfoVector &masking_locations, EBlastProgramType program, vector< string > *warnings=NULL)

Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects.

CBlastOptions & SetOptions()

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

list< CRef< objects::CSeq_loc > > TSeqLocs

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

CExportStrategy(CRef< CBlastOptionsHandle > opts_handle, const string &client_id=kEmptyStr)

Construct search strategy with :-.

void x_Process_BlastOptions(CRef< CBlastOptionsHandle > &opts_handle)

CRef< objects::CBlast4_request > GetSearchStrategy(void)

void x_GetProgramOptionIntegerList(EBlastOptIdx idx, list< int > &list)

string GetProgram() const

Fetches program, one of blastn, blastp, blastx, tblastn, tblastx.

vector< TGi > TGiList

Define a list of gis.

void FlattenBioseqSet(const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)

bool IsLocalId(const objects::CSeq_id *seqid)

Returns true if the CSeq_id is a local id.

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.

int GetDBFilteringID()

The DB filter ID.

ESubjectMaskingType GetMaskType() const

set< int > GetNegativeTaxidList()

void ExportSearchStrategy_ASN1(CNcbiOstream *out)

bool m_IgnoreUnsupportedOptions

ignore unsupported options when creating blast options builder object

void x_AddParameterToProgramOptions(objects::CBlast4Field &field, const int int_value)

EBlastProgramType NetworkProgram2BlastProgramType(const string &program, const string &service)

Function to convert from program and service name into the CORE BLAST program type This is based on t...

TSeqLocInfoVector ExtractUserSpecifiedMasks()

Retrieve any user specified masking locations.

const CRef< CSeqDBGiList > & GetGiList() const

Accessor for the gi list.

static void Pssm(const objects::CPssmWithParameters &pssm, bool require_scores=false)

Perform validation on the PSSM.

void FetchData()

Fills in CImportStrategyData and m_OptionsBuilder.

const TGiList GetGiListLimitation() const

CRef< objects::CBlast4_queries > GetQueries()

The queries either as Bioseq, seqloc, or pssm.

unsigned int GetPsiNumOfIterations()

Get number of iteration for psi blast, return 0 if num of iterations not available.

objects::CBlast4_parameters * GetAlgoOptions()

Options specific to blast searches (e.g, threshold, expect value).

CRef< objects::CBlast4_subject > GetSubject()

Returns the target sequences.

objects::CBlast4_parameters * GetProgramOptions()

Options for controlling program execution and database filtering.

TSeqRange GetQueryRange()

The start and stop on the query (if applicable)

virtual TSeqLocs GetSeqLocs()=0

Accessor for the TSeqLocs.

CRef< CBlast4_queue_search_request > m_QueueSearchRequest

TBlast4Opts * GetBlast4AlgoOpts()

ESubjectMaskingType GetSubjectMaskingType()

Get Subject Masking Type.

string GetEntrezQueryLimitation() const

Accessor for the entrez query.

CRef< objects::CBlast4_request > m_Request

void x_Process_Subject(CRef< IQueryFactory > &subject)

CRef< blast::CBlastOptionsHandle > GetOptionsHandle()

Builds and returns the OptionsHandle.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_TO(T, tax_id)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

#define MSerial_AsnText

I/O stream manipulators –.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

@ fConvErr_NoThrow

Do not throw an exception on error.

void SetIdent(const TIdent &value)

Assign a value to Ident data member.

const TService & GetService(void) const

Get the Service member data.

const TFormat_options & GetFormat_options(void) const

Get the Format_options member data.

TQuery_mask & SetQuery_mask(void)

Select the variant.

void SetAlgorithm_options(TAlgorithm_options &value)

Assign a value to Algorithm_options data member.

void SetFormat_options(TFormat_options &value)

Assign a value to Format_options data member.

TInteger_list & SetInteger_list(void)

Select the variant.

void SetBody(TBody &value)

Assign a value to Body data member.

void SetQueries(TQueries &value)

Assign a value to Queries data member.

TSequences & SetSequences(void)

Select the variant.

TSeq_loc_list & SetSeq_loc_list(void)

Select the variant.

TBioseq_set & SetBioseq_set(void)

Select the variant.

bool CanGetProgram_options(void) const

Check if it is safe to call GetProgram_options method.

void SetService(const TService &value)

Assign a value to Service data member.

void SetProgram_options(TProgram_options &value)

Assign a value to Program_options data member.

TQueue_search & SetQueue_search(void)

Select the variant.

const TProgram_options & GetProgram_options(void) const

Get the Program_options member data.

void SetProgram(const TProgram &value)

Assign a value to Program data member.

TString & SetString(void)

Select the variant.

TBig_integer_list & SetBig_integer_list(void)

Select the variant.

void SetSubject(TSubject &value)

Assign a value to Subject data member.

bool CanGetFormat_options(void) const

Check if it is safe to call GetFormat_options method.

TInteger & SetInteger(void)

Select the variant.

list< CRef< CBlast4_mask > > TMasks

TPssm & SetPssm(void)

Select the variant.

const TAlgorithm_options & GetAlgorithm_options(void) const

Get the Algorithm_options member data.

const TProgram & GetProgram(void) const

Get the Program member data.

bool CanGetAlgorithm_options(void) const

Check if it is safe to call GetAlgorithm_options method.

TDatabase & SetDatabase(void)

Select the variant.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

unsigned int

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

Names used in blast4 network communications.

EBlastOptIdx

Index of remote BLAST options.

@ eBlastOpt_Web_StepNumber

@ eBlastOpt_NegativeTaxidList

@ eBlastOpt_DbFilteringAlgorithmKey

@ eBlastOpt_NegativeGiList

@ eBlastOpt_DbFilteringAlgorithmId

@ eBlastOpt_RequiredStart

@ eBlastOpt_SubjectMaskingType

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...

Declarations of auxiliary functions/classes for PSI-BLAST.

Declares the CRemoteBlast class.

Declares the CImportStrategy and CExportStrategy.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

This is the "mutable" data for CImportStrategy.

static string kStart("Start")


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