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NCBI C++ ToolKit: src/algo/blast/proteinkmer/kblastapi.cpp Source File

numSearches=

(resultSet->GetNumQueries());

(

index=0; index<numSearches; index++)

(TBlastKmerScoreVector::const_iterator iter=scores.begin(); iter != scores.end(); ++iter)

(oid_v.size() == 0)

(oid_v.begin(), oid_v.end());

(vector<int>::iterator iter=oid_v.begin(); iter!=oid_v.end(); ++iter)

vector< CConstRef<objects::CSeq_id> > seqid_vec;

vector< CRef<CBlastAncillaryData> > ancill_vec;

num_subjects = 0;

(subject_infosrc !=

) {

num_subjects =

(subject_infosrc->

());

(index=0; index<local_query_data->

(); index++)

seqid_vec.push_back(query_id);

sa_vec.push_back(tmp_align);

pair<double, double> tmp_pair(-1.0, -1.0);

ancill_vec.push_back(tmp_ancillary_data);

(

=1;

< num_subjects;

++)

msg_vec.push_back(

);

seqid_vec.push_back(query_id);

sa_vec.push_back(tmp_align);

ancill_vec.push_back(tmp_ancillary_data);

msg_vec.resize(seqid_vec.size());

blastkmer->SetGiListLimit(

);

vector< CRef<CScope> > scope_v = objmgr_qf->

();

numSearches=

(resultSet->GetNumQueries());

(

index=0; index<numSearches; index++)

queryId =

.GetQueryId();

(TQueryMessages::const_iterator iter=

.begin(); iter !=

.end(); ++iter)

cerr << queryId <<

<< (*iter)->GetMessage() <<

;

(scores.size() > 0)

.GetTSL(subjectTSL, scope_v[0]);

query_vector_temp.push_back(tsl_v[index]);

query_vector_temp.push_back(tsl_v[index]);

.push_back(qmsg);

search_results;

Declares the CBlastAdvancedProteinOptionsHandle class.

Declares the CBlastProteinOptionsHandle class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined construct...

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EResultType

Specifies the style of Seq-aligns that should be built from the internal BLAST data structures.

@ eDatabaseSearch

Seq-aligns in the style of a database search.

@ eSequenceComparison

Seq-aligns in the BLAST 2 Sequence style (one alignment per query-subject pair)

vector< pair< CRef< CSeq_id >, double > > TBlastKmerScoreVector

Vector of pairs of seq-ids and scores.

Class used to return ancillary data from a blast search, i.e.

Class of optiosn for the KMEr search.

void SetNumTargetSeqs(int matches)

Sets the number of matches (subject sequences) to return.

void SetThresh(double thresh)

Set the threshold.

void SetMinHits(int minhits)

Set the minimum number of LSH hits to initiate a calculation of the Jaccard distance.

This class represents the results for one KMER search (one query).

CRef< IQueryFactory > m_QueryFactory

Holds the query seqloc and scope.

CRef< CSeqDBNegativeList > m_NegGIList

Negative GIList to limit search by.

CRef< CSeqDBGiList > m_GIList

GIList to limit search by.

CRef< CBlastpKmerOptionsHandle > m_OptsHandle

Options for KMER search.

CRef< CLocalDbAdapter > m_Database

Database to search.

CRef< CSearchResultSet > Run(void)

Run a KMER and then BLAST search.

Class to perform a KMER-BLASTP search.

Encapsulates ALL the BLAST algorithm's options.

Handle to the KMER BLASTP options.

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.

Search Results for All Queries.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

void SetNumberOfThreads(int num_threads, bool force_mt=false)

Setting the number of threads.

bool GiToOid(TGi gi, int &oid) const

Translate a GI to an OID.

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and...

Abstract base class to encapsulate retrieval of sequence identifiers.

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

virtual CConstRef< objects::CSeq_loc > GetSeq_loc(size_t index)=0

Get the Seq_loc for the sequence indicated by index.

string GetDatabaseName() const

Returns the database name if appropriate, else kEmptyStr for subject sequences.

const_iterator begin() const

Returns const_iterator to beginning of container, provided to facilitate STL-style iteration.

void SetDbLength(Int8 len)

Sets DbLength.

int GetCandidateSeqs() const

Gets the max number of candidate matches to process with BLAST.

Int8 GetDbLength() const

Returns DbLength.

TSeqLocVector GetTSeqLocVector()

Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector pr...

int GetMinHits() const

Returns the number of hits to initiate calculation of Jaccard distance.

CRef< CSearchResultSet > Run()

Executes the search.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

BlastSeqSrc * MultiSeqBlastSeqSrcInit(TSeqLocVector &seq_vector, EBlastProgramType program, bool dbscan_mode=false)

Initialize the sequence source structure.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

IBlastSeqInfoSrc * MakeSeqInfoSrc()

Retrieves or constructs the IBlastSeqInfoSrc.

vector< value_type >::iterator iterator

iterator type definition

virtual size_t GetNumQueries()=0

Get the number of queries.

virtual size_t Size() const =0

Returns the size of the underlying container of sequences.

void push_back(value_type &element)

Add a value to the back of this container.

vector< CRef< objects::CScope > > ExtractScopes()

Retrieve the CScope objects associated with the query sequences associated with this object.

const_iterator end() const

Returns const_iterator to end of container, provided to facilitate STL-style iteration.

double GetThresh() const

Returns threshold for Jaccard distance (range: 0-1)

bool IsDbScanMode() const

Returns true if this is not a database but is database scanning mode.

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

Add bioseq, return bioseq handle.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

CRef< CSearchResultSet > s_MakeEmptyResults(CRef< IQueryFactory > qf, const CBlastOptions &opts, CRef< CLocalDbAdapter > dbAdapter, TSearchMessages &msg_vec)

static void s_GetSequencesIntoScope(CRef< CBlastKmerResultsSet > resultSet, CRef< CScope > scope, CRef< CSeqDB > seqdb)

Places all the needed subject sequences into a scope.

void s_AddNewResultSet(CRef< CSearchResultSet > resultSet, CRef< CSearchResultSet > myResultSet)

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

constexpr auto sort(_Init &&init)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

Defines BLAST database access classes.

Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval fro...

Implementation of the BlastSeqSrc interface for a vector of sequence locations.

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.

Complete type definition of Blast Sequence Source ADT.

Uniform BLAST Search Interface.

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