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NCBI C++ ToolKit: include/algo/blast/igblast/igblast.hpp Source File

(

=0;

<10; ++

) {

va_or_vd_as_heavy_chain);

reliable_J_match =

(

}

(sx != sy) {

}

(lx !=

) {

(x_id < y_id);

Keeps track of the version of IgBLAST in the NCBI C++ toolkit.

Search Results for One Query.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence...

Class for the messages for an individual query sequence.

const_iterator end() const

const_iterator find(const key_type &key) const

void x_AnnotateDomain(CRef< CSearchResultSet > &gl_results, CRef< CSearchResultSet > &dm_results, vector< CRef< CIgAnnotation > > &annot)

Annotate the query chaintype and domains based on blast results.

CRef< IQueryFactory > m_Subject

CRef< CSearchResultSet > Run()

Run the Ig-BLAST engine.

CRef< CSeq_align_set > & SetSeqAlign()

CIgAnnotationInfo(CConstRef< CIgBlastOptions > &ig_options)

double reliable_J_match_factor

list< string > m_AirrField

int GetJDomain(const string &sid)

void x_AnnotateC(CRef< CSearchResultSet > &results_c, CRef< CSearchResultSet > &results_j, vector< CRef< CIgAnnotation > > &annot)

CRef< CLocalDbAdapter > m_LocalDb

bool GetDomainInfo(const string sid, int *domain_info)

ScorePositionSort(CRef< CScope > scope)

vector< string > m_ChainType

static void s_SortResultsByEvalue(CRef< CSearchResultSet > &results)

Sort blast results according to evalue.

void x_AnnotateDJ(CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)

Annotate the D and J genes based on blast results.

CRef< CLocalDbAdapter > m_Db[5]

void x_FindDJAln(CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq, bool va_or_vd_as_heavy_chain)

CIgBlast & operator=(const CIgBlast &rhs)

Prohibit assignment operator.

CRef< objects::CSeq_align_set > m_Alignment

alignments for this query

void x_ProcessCResult(CRef< CSearchResultSet > &results_C, vector< CRef< CIgAnnotation > > &annots)

void x_SetAnnotation(vector< CRef< CIgAnnotation > > &annot, CRef< CSearchResultSet > &final_results)

Append annotation info to the final results.

void x_SetupNoOverlapDSearch(const vector< CRef< CIgAnnotation > > &annots, CRef< CSearchResultSet > &results, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)

map< string, int > m_Fwr4EndOffset

map< string, int > m_DomainIndex

CRef< CIgAnnotation > & SetIgAnnotation()

void x_ScreenByAlignLength(CRef< CSearchResultSet > &results, int length)

int GetFrameOffset(const string sid)

void x_SetupDJSearch(const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)

Prepare blast option handle and query for D, J germline database search.

vector< string > m_TopGeneIds

bool operator()(CRef< CSeq_align > &x, CRef< CSeq_align > &y)

void SetNumberOfThreads(size_t nthreads)

Set MT mode.

CConstRef< CIgBlastOptions > m_IgOptions

void x_SetupCRegionSearch(const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)

CRef< CBlastOptionsHandle > m_Options

vector< int > m_DomainData

static void s_AppendResults(CRef< CSearchResultSet > &results, int num_aligns, int gene, CRef< CSearchResultSet > &final_results)

Append blast results to the final results.

const string GetDomainChainType(const string sid)

void x_SetupDbSearch(vector< CRef< CIgAnnotation > > &annot, CRef< IQueryFactory > &qf)

Prepare blast option handle and query for specified database search.

map< string, int > m_FrameOffset

map< string, string > m_DJChainType

void x_AnnotateD(CRef< CSearchResultSet > &results_D, vector< CRef< CIgAnnotation > > &annot)

bool s_CompareSeqAlignByScoreAndPosition(const CRef< CSeq_align > &x, const CRef< CSeq_align > &y, CRef< CScope > scope)

void x_FillJDomain(CRef< CSeq_align > &align, CRef< CIgAnnotation > &annot)

void x_ProcessDJResult(CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)

const string GetDJChainType(const string sid)

CIgBlast(CRef< CBlastQueryVector > query_factory, CRef< CSearchDatabase > blastdb, CRef< IQueryFactory > subjects, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, string entrez_query, CRef< CScope > scope)

Remote Igblast search API.

void x_ExtendAlign3end(CRef< CSearchResultSet > &results)

CIgAnnotationInfo m_AnnotationInfo

int GetFwr4EndOffset(const string &sid)

CIgBlast(const CIgBlast &rhs)

Prohibit copy constructor.

map< string, int > m_JDomainInfo

void x_FindDJ(CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, CRef< CIgAnnotation > &annot, CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq)

void x_AnnotateJ(CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)

CRef< CBlastQueryVector > m_Query

CIgAnnotation()

Constructor.

CIgBlastResults(CConstRef< objects::CSeq_id > query, CRef< objects::CSeq_align_set > align, const TQueryMessages &errs, CRef< CBlastAncillaryData > ancillary_data)

Constructor.

void x_ExtendAlign5end(CRef< CSearchResultSet > &results)

void x_AnnotateV(CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)

Annotate the V gene based on blast results.

void x_ProcessDGeneResult(CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)

void x_SetChainType(CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)

Set the subject chain type and frame info.

const CRef< CIgAnnotation > & GetIgAnnotation() const

string m_CustomInternalData

map< string, string > m_DomainChainType

CRef< CSearchDatabase > m_RemoteDb

CRef< CIgAnnotation > m_Annotation

void x_SetupVSearch(CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)

Prepare blast option handle and query for V germline database search.

void x_ConvertResultType(CRef< CSearchResultSet > &results)

Convert bl2seq result to database search mode.

CIgBlast(CRef< CBlastQueryVector > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, CRef< CScope > scope)

Local Igblast search API.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

@ eContent

Untagged human-readable accession or the like.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

ENa_strand

strand of nucleic acid

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

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

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

Uniform BLAST Search Interface.

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