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

(

(fn).Exists() && ! fs.fail()) {

fs.getline(line, 256);

(line[0] ==

)

;

suffix = (ig_opt->

) ?

:

;

);

(vector<string>,

, lines) {

vector<string> tokens;

(!tokens.empty()) {

(

=1;

<11; ++

) {

(lines.size() == 0) {

(vector<string>,

, lines) {

vector<string> tokens;

(!tokens.empty()) {

(tokens.size() == 3) {

}

(tokens.size() == 4) {

}

(tokens.size() == 5) {

(lines.size() == 0) {

(

<<

);

(vector<string>,

, lines) {

vector<string> tokens;

(!tokens.empty()) {

((*result)->HasAlignments()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(it != align_list.end()) {

((

)((*it)->GetAlignLength()) - (

)((*it)->GetTotalGapCount(0)) < length){

it = align_list.erase(it);

((*result)->HasAlignments()) {

top_hit_actual_len = 0;

highest_score = 0;

(score >= highest_score) {

highest_score = score;

extend_strand = (*align)->GetSeqStrand(0);

(*align)->GetSegs().GetDenseg().GetStarts()[1]);

allowed_len =

((*align)->GetSegs().GetDenseg().GetStarts()[1],

query_len - ((*align)->GetSegs().GetDenseg().GetStarts()[0] +

(

)(*align)->GetSegs().GetDenseg().GetLens()[0]));

top_hit_actual_len =

(desired_len, allowed_len);

top_hit_actual_len =

(desired_len,

((*align)->GetSegs().GetDenseg().GetStarts()[0],

(*align)->GetSegs().GetDenseg().GetStarts()[1]));

allowed_len =

((*align)->GetSegs().GetDenseg().GetStarts()[1],

query_len - ((*align)->GetSegs().GetDenseg().GetStarts()[0] +

(

)(*align)->GetSegs().GetDenseg().GetLens()[0]));

actual_len =

(top_hit_actual_len,

(desired_len, allowed_len));

actual_len =

(top_hit_actual_len,

(desired_len,

((*align)->GetSegs().GetDenseg().GetStarts()[0],

(*align)->GetSegs().GetDenseg().GetStarts()[1])));

(actual_len > 0 && (*align)->GetSeqStrand(0) == extend_strand) {

(*align)->SetSegs().SetDenseg().SetStarts()[1] -= actual_len;

(*align)->SetSegs().SetDenseg().SetLens()[0] += actual_len;

(*align)->SetSegs().SetDenseg().SetStarts()[0] -= actual_len;

(*align)->SetSegs().SetDenseg().SetStarts()[1] -= actual_len;

(*align)->SetSegs().SetDenseg().SetLens()[0] += actual_len;

((*result)->HasAlignments()) {

top_hit_actual_len = 0;

highest_score = 0;

(score >= highest_score) {

highest_score = score;

extend_strand = (*align)->GetSeqStrand(0);

j_align_stop = (*align)->GetSegs().GetDenseg().GetSeqStop(1);

j_stop - j_align_stop);

query_align_start = (*align)->GetSegs().GetDenseg().GetSeqStart(0);

allowed_query_length = query_align_start;

top_hit_actual_len =

(desired_len, allowed_query_length);

allowed_query_length = query_stop - (*align)->GetSegs().GetDenseg().GetSeqStop(0);

top_hit_actual_len =

(desired_len, allowed_query_length);

query_align_start = (*align)->GetSegs().GetDenseg().GetSeqStart(0);

allowed_query_length = query_align_start;

actual_len =

(allowed_query_length, top_hit_actual_len);

allowed_query_length = query_stop - (*align)->GetSegs().GetDenseg().GetSeqStop(0);

actual_len =

(top_hit_actual_len, allowed_query_length);

(actual_len > 0 && (*align)->GetSeqStrand(0) == extend_strand) {

num_seg = (*align)->GetSegs().GetDenseg().GetNumseg();

num_dim = (*align)->GetSegs().GetDenseg().GetDim();

(*align)->SetSegs().SetDenseg().SetStarts()[num_seg*num_dim - 2] -= actual_len;

(*align)->SetSegs().SetDenseg().SetLens()[num_seg-1] += actual_len;

num_seg = (*align)->GetSegs().GetDenseg().GetNumseg();

(*align)->SetSegs().SetDenseg().SetLens()[num_seg-1] += actual_len;

vector<CRef <CIgAnnotation> > annots;

(

gene = 1; gene < num_genes; ++gene) {

cerr <<

<< endl;

(

gene = 0; gene < num_genes; ++gene) {

cerr <<

<< endl;

skipped =

;

final_results;

(sx != sy)

(sx > sy);

(x_id < y_id);

((*annot)->m_GeneInfo[0] == -1 || (*annot)->m_GeneInfo[4] == -1 || (*annot)->m_GeneInfo[5] == -1) {

mask_list.push_back(

);

= (*annot)->m_MinusStrand;

mask_list.push_back(

);

mask_list.push_back(

);

((*annot)->m_GeneInfo[0] == -1) {

mask_list.push_back(

);

= (*annot)->m_MinusStrand;

(begin > 0 && begin <=

-1) {

(end < len -1 && end >= 0) {

((*previous_d_results)[iq].HasAlignments()){

align_d = (*previous_d_results)[iq].SetSeqAlign();

((*annot)->m_GeneInfo[0] == -1 || !align_d || align_d.

() || align_d->

()) {

mask_list.push_back(

);

= (*annot)->m_MinusStrand;

v_end_or_j_begin = (

)?

j_begin_or_v_end = (

)?

(v_end_or_j_begin > 0) {

(j_begin_or_v_end < len-1 && j_begin_or_v_end > 0) {

((*annot)->m_GeneInfo[0] ==-1) {

mask_list.push_back(

);

begin = (*annot)->m_GeneInfo[0];

end = (*annot)->m_GeneInfo[1];

mask_list.push_back(

);

mask_list.push_back(

);

(sx < 0.999999 * sy || sy < 0.999999 * sx)

;

(ix > iy)

;

(sid.substr(0, 4) ==

)

(sid.substr(4, sid.length()));

(ids.find(this_id) == string::npos) {

((*result)->HasAlignments()) {

((*it)->GetSeq_id(1).Match(align->

(1)) &&

(*it)->GetSeqStart(1) == align->

(1) &&

(*it)->GetSeqStop(1) == align->

(1))

;

(sx < 0.999999 * sy)

;

(sy < 0.999999 * sx)

;

(ix != iy)

(ix > iy);

(x_id < y_id);

(sx != sy)

(sx > sy);

(ds < js || de < je + margin)

;

(ds > js - margin || de > je)

;

va_or_vd_as_heavy_chain) {

(align_D && !align_D->

().empty()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(q_ct!=

&& q_ct!=

&& q_ct!=

&& q_ct!=

) {

(it != align_list.end()) {

it = align_list.erase(it);

}

(q_ct ==

|| q_ct ==

) {

(va_or_vd_as_heavy_chain) {

(it != align_list.end()) {

it = align_list.erase(it);

it = align_list.begin();

(it != align_list.end()) {

(q_ct!=

) {

s_ct = q_ct[1];

(d_chain_type !=

){

(d_chain_type[1] != q_ct[1]) keep =

;

sid = (*it)->GetSeq_id(1).AsFastaString();

(sid.substr(0, 4) ==

) sid = sid.substr(4, sid.length());

((sid.substr(0, 2) ==

|| sid.substr(0, 2) ==

)

&& sid[3] ==

) {

(s_ct!=

&& s_ct!=

) s_ct = q_ct[1];

(s_ct != q_ct[1]) keep =

;

(!keep) it = align_list.erase(it);

strand_found =

;

((*it)->GetSeqStrand(0) == q_st) {

strand_found =

;

it = align_list.begin();

(it != align_list.end()) {

((*it)->GetSeqStrand(0) != q_st) {

it = align_list.erase(it);

it = align_list.begin();

(it != align_list.end()) {

q_ds = (*it)->GetSeqStart(0);

q_de = (*it)->GetSeqStop(0);

(!keep) it = align_list.erase(it);

(align_J && !align_J->

().empty()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(it != align_list.end()) {

(q_ct!=

) {

s_ct = q_ct[1];

(j_chain_type !=

){

(j_chain_type[1] != q_ct[1]) keep =

;

sid = (*it)->GetSeq_id(1).AsFastaString();

(sid.substr(0, 4) ==

) sid = sid.substr(4, sid.length());

((sid.substr(0, 2) ==

|| sid.substr(0, 2) ==

)

&& sid[3] ==

) {

}

(sid[0] ==

) {

(s_ct!=

&& s_ct!=

&& s_ct!=

&&

s_ct!=

&& s_ct!=

&& s_ct!=

&& s_ct!=

) s_ct = q_ct[1];

(s_ct != q_ct[1]) keep =

;

((*it)->GetSeqStrand(0) != q_st) keep =

;

q_js = (*it)->GetSeqStart(0);

q_je = (*it)->GetSeqStop(0);

(q_je < q_ve - allowed_VJ_distance || q_js > q_ve -

) keep =

;

(q_js > q_ve + allowed_VJ_distance || q_je < q_ve +

) keep =

;

(!keep) it = align_list.erase(it);

CSeq_align_set::Tdata::iterator it;

(it != al_D.end()) {

it = al_D.erase(it);

(it != al_J.end()) {

it = al_J.erase(it);

(it != al_J.end()) {

it = al_J.erase(it);

(it != al_D.end()) {

it = al_D.erase(it);

original_align_D->

(*align_D);

original_align_J->

(*align_J);

(align_D, align_J, q_ct, q_ms, q_st, q_ve, iq,

);

((original_align_D.

() && !original_align_D->

().empty()) && (q_ct ==

|| q_ct ==

)) {

(original_align_D, original_align_J, q_ct, q_ms, q_st, q_ve, iq,

);

as_heavy_chain_score = 0;

as_light_chain_score = 0;

(original_align_J.

() && !original_align_J->

().empty()){

(original_align_D.

() && !original_align_D->

().empty()){

(align_J.

() && !align_J->

().empty()){

(as_heavy_chain_score + d_score> as_light_chain_score){

align_D->

(*original_align_D);

align_J->

(*original_align_J);

(j_cdr3end > 0 && subject_start - j_cdr3end <= 1) {

(subject_start,

(j_cdr3end + 1,

(subject_end > j_cdr3end) {

}

(j_cdr3end > 0 && subject_start - j_cdr3end <= 2) {

(subject_end > j_cdr3end) {

}

(j_cdr3end > 0 && subject_start - j_cdr3end <= 4) {

(subject_end > j_cdr3end) {

annot->

[4] = j_fwr4end_offset;

(j_fwr4end_offset >= 0) {

q_ct = (*annot)->m_ChainType[0];

q_ms = (*annot)->m_MinusStrand;

q_ve = (q_ms) ? (*annot)->m_GeneInfo[0] : (*annot)->m_GeneInfo[1] - 1;

(align_D && !align_D.Empty() && !align_D->IsEmpty()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

it = align_list.begin();

(it != align_list.end()) {

(q_ct!=

) {

s_ct = q_ct[1];

(d_chain_type !=

){

(d_chain_type[1] != q_ct[1]) keep =

;

sid = (*it)->GetSeq_id(1).AsFastaString();

(sid.substr(0, 4) ==

) sid = sid.substr(4, sid.length());

((sid.substr(0, 2) ==

|| sid.substr(0, 2) ==

)

&& sid[3] ==

) {

(s_ct!=

&& s_ct!=

) s_ct = q_ct[1];

(s_ct != q_ct[1]) keep =

;

(!keep) it = align_list.erase(it);

strand_found =

;

((*it)->GetSeqStrand(0) == q_st) {

strand_found =

;

it = align_list.begin();

(it != align_list.end()) {

((*it)->GetSeqStrand(0) != q_st) {

it = align_list.erase(it);

it = align_list.begin();

(it != align_list.end()) {

q_ds = (*it)->GetSeqStart(0);

q_de = (*it)->GetSeqStop(0);

(!keep) it = align_list.erase(it);

(align_J && align_J.

() && !align_J->

() && !align_list.empty()) {

CSeq_align_set::Tdata::iterator it = al_J.begin();

(it != al_J.end()) {

it = al_J.erase(it);

q_ms = (*annot)->m_MinusStrand;

(align_C && !align_C->

().empty()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(it != align_list.end()) {

((*it)->GetSeqStrand(0) != q_st) keep =

;

(!keep) it = align_list.erase(it);

q_ct = (*annot)->m_ChainType[0];

q_ms = (*annot)->m_MinusStrand;

q_ve = (q_ms) ? (*annot)->m_GeneInfo[0] : (*annot)->m_GeneInfo[1] - 1;

( results_D, results_J, *annot, align_D, align_J, q_ct, q_ms, q_st, q_ve, iq);

q_ct = (*annot)->m_ChainType[0];

(align_D && !align_D.

() && !align_D->

()) {

(*annot)->m_GeneInfo[2] = align->

(0);

(*annot)->m_GeneInfo[3] = align->

(0)+1;

(*annot)->m_GeneInfo[6] = align->

(0);

(*annot)->m_GeneInfo[7] = align->

(0)+1;

((*annot)->m_JDomain[3] > 0 && (*annot)->m_JDomain[1] > 0) {

(*annot)->m_CDomain[1] - 1;

(*annot)->m_CDomain[0] = query_start;

diff =

(0, (*annot)->m_CDomain[0] - (*annot)->m_JDomain[3] - 1);

((*annot)->m_JDomain[4] > 0) {

j_end -= (*annot)->m_JDomain[4];

j_stop = align_j->

().front()->GetSeqStop(1);

j_extend_max =

(0, j_end - j_stop);

extend_len =

(diff, j_extend_max);

(extend_len > 0) {

(*annot)->m_JDomain[3] += extend_len;

q_ms = (*annot)->m_MinusStrand;

(*annot)->m_GeneInfo[4] = align->

(0);

(*annot)->m_GeneInfo[5] = align->

(0)+1;

(frame_offset >= 0) {

frame_adj = (align->

(1) + 3 - frame_offset) % 3;

(*annot)->m_FrameInfo[2] = (q_ms) ?

q_ct = (*annot)->m_ChainType[0];

q_ms = (*annot)->m_MinusStrand;

(*annot)->m_GeneInfo[2] = align->

(0);

(*annot)->m_GeneInfo[3] = align->

(0)+1;

(*annot)->m_GeneInfo[4] = align->

(0);

(*annot)->m_GeneInfo[5] = align->

(0)+1;

(frame_offset >= 0) {

frame_adj = (align->

(1) + 3 - frame_offset) % 3;

(*annot)->m_FrameInfo[2] = (q_ms) ?

scope_q(*mgr), scope_s(*mgr);

annotate_subject =

;

(db_name_V == db_name_domain) {

db_domain.

(&(*db_V));

db_domain.

(

(db_name_domain, db_type));

annotate_subject =

;

((*result)->HasAlignments() && (*gl_results)[iq].HasAlignments()) {

(*gl_results)[iq].GetSeqAlign()->Get().front();

q_ends[2], q_dir;

domain_info[10];

s_map((*it)->GetSegs().GetDenseg());

s_start = (*it)->GetSeqStart(1);

s_stop = (*it)->GetSeqStop(1);

.SetId((*it)->GetSeq_id(1));

(

.HasAlignments()) {

scope_q.RemoveBioseq(hdl_q);

(

=0;

<10;

+=2) {

start = domain_info[

] - 1;

stop = domain_info[

+1] - 1;

(start <= d_stop && stop >= d_start) {

start_copy = start;

stop_copy = stop;

(start_copy < d_start) start_copy = d_start;

(stop_copy > d_stop) stop_copy = d_stop;

(start_copy <= stop_copy) {

(start > s_stop || stop < s_start)

;

(start < s_start) start = s_start;

(stop > s_stop) stop = s_stop;

(start > stop)

;

((start - q_ends[1])*q_dir > 0 || (stop - q_ends[0])*q_dir < 0)

;

((start - q_ends[0])*q_dir < 0) start = q_ends[0];

((stop - q_ends[1])*q_dir > 0) stop = q_ends[1];

((start - stop)*q_dir > 0)

;

pos = q_map.

(1, seg);

seg = q_map.

(aln_stop);

((start - stop)*q_dir > 0)

;

(i<10 && annot->m_DomainInfo[

] < 0)

+=2;

(

< 10 && domain_info[

] > 0) {

extension = (domain_info[

] - 1 -

(i<10 && annot->m_DomainInfo[

] >=0) {

(start >= 0 && (start - q_ends[1])*q_dir < 0) {

((start - q_ends[1])*q_dir <= 0) {

(frame_offset >= 0) {

q_start = (*it)->GetSeqStart(0);

q_stop = (*it)->GetSeqStop(0);

q_mid = q_start + q_stop;

q_dif = q_stop - q_start;

frame_adj = (3 - ((*it)->GetSeqStart(1) + 3 - frame_offset) % 3) %3;

annot->

[0] = (q_mid - q_dir *q_dif)/2 + q_dir * frame_adj;

q_start =

(q_start, fwr3_stop);

q_mid = q_start + q_stop;

q_dif = q_stop - q_start;

q_stop =

(q_stop, fwr3_stop);

q_mid = q_start + q_stop;

q_dif = q_stop - q_start;

frame_adj = ((*it)->GetSeqStop(1) + 3 - frame_offset) % 3;

annot->

[1] = (q_mid + q_dir *q_dif)/2 - q_dir * frame_adj;

((*result)->HasAlignments()) {

num_aligns = (*result)->GetSeqAlign()->Size();

(

=0;

<num_aligns; ++

) {

((*result)->HasAlignments()) {

(&*((*result)->GetSeqAlign())));

num_results =

->GetNumResults();

(

iq = 0; iq< num_queries && ir< num_results; ++iq) {

(!qid->

(*rid)) {

(ir < num_results && (*

)[ir].

()->Match(*qid)) {

align_list.insert(align_list.end(), add_list.begin(), add_list.end());

new_result = (final_results.

());

actual_align = 0;

((*result)->HasAlignments()) {

(&*((*result)->GetSeqAlign())));

(num_aligns >= 0) {

(align_list.size() > (CSeq_align_set::Tdata::size_type)num_aligns) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(

=0;

<num_aligns; ++

) ++it;

align_list.erase(it, align_list.end());

actual_align = num_aligns;

actual_align = align_list.size();

( !(*final_results)[iq].

()->Match(*

)) ++iq;

(!align.

()) {

CSeq_align_set::Tdata::iterator it = align_list.begin();

(it != align_list.end()) {

(!align_list.empty()) {

ig_list.insert(ig_list.end(), align_list.begin(), align_list.end());

0: ig_result->

= actual_align;

;

1: ig_result->

= actual_align;

;

2: ig_result->

= actual_align;

;

3: ig_result->

= actual_align;

;

((*result)->HasAlignments()){

(*result)->SetSeqAlign()->Set().clear();

Declares the CBl2Seq (BLAST 2 Sequences) class.

@ eSequenceComparison

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

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

ncbi::TMaskedQueryRegions mask

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TNumseg GetSeg(TSeqPos aln_pos) const

CDense_seg::TNumseg TNumseg

TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Runs the BLAST algorithm between 2 sequences.

Defines BLAST error codes (user errors included)

Creates BlastOptionsHandle objects with default values for the programs/tasks requested.

Encapsulates ALL the BLAST algorithm's options.

size_type Size() const

Returns the number of queries found in this query vector.

void SetMaskedRegions(size_type i, TMaskedQueryRegions mqr)

Assign a list of masked regions to one query.

void AddMask(size_type i, CRef< CSeqLocInfo > sli)

Add a masked region to the set for a query.

CRef< CBlastSearchQuery > GetBlastSearchQuery(size_type i) const

Get the CBlastSearchQuery object at index i.

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.

API for Remote Blast Requests.

Search Results for All Queries.

Search Results for One Query.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

CRef< CBioseq > SeqidToBioseq(const CSeq_id &seqid) const

Get a CBioseq for a given Seq-id.

structure for seqloc info

TSeqPos GetSeqStop(TDim row) const

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.

@ eRight

Towards higher aln coord (always to the right)

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

Collection of masked regions for a single query sequence.

Class for the messages for an individual query sequence.

Constants used in compositional score matrix adjustment.

@ eNoCompositionBasedStats

Don't use composition based statistics.

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.

static bool s_DJNotCompatible(const CSeq_align &d, const CSeq_align &j, bool ms, int margin)

string GetDatabaseName() const

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

void SetCompositionBasedStats(ECompoAdjustModes mode)

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

CRef< IQueryFactory > m_Subject

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

double GetEvalueThreshold() const

CRef< CSearchResultSet > Run()

Run the Ig-BLAST engine.

static bool s_CompareSeqAlignByScore(const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)

CRef< CSeq_align_set > & SetSeqAlign()

CIgAnnotationInfo(CConstRef< CIgBlastOptions > &ig_options)

int GetJDomain(const string &sid)

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

static int max_allowed_VD_distance

CRef< CLocalDbAdapter > m_LocalDb

bool GetDomainInfo(const string sid, int *domain_info)

void SetGapOpeningCost(int g)

static void s_ReadLinesFromFile(const string &fn, vector< string > &lines)

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

vector< string > m_ChainType

static void s_SortResultsByEvalue(CRef< CSearchResultSet > &results)

Sort blast results according to evalue.

const string & GetRID(void)

Gets the request id (RID) associated with the search.

static int extend_length3end

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.

static bool s_SeqAlignInSet(CSeq_align_set::Tdata &align_list, CRef< CSeq_align > &align)

CRef< CLocalDbAdapter > m_Db[5]

static int max_allowed_VJ_distance_with_D

CRef< CSearchResultSet > Run()

Executes the search.

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)

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)

CBlastOptions & SetOptions()

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

map< string, int > m_Fwr4EndOffset

void SetGapExtensionCost(int e)

map< string, int > m_DomainIndex

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

static int max_allowed_V_end_to_J_end

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.

void SetMismatchPenalty(int p)

vector< string > m_TopGeneIds

CRef< CBlastAncillaryData > GetAncillaryData() const

Accessor for the query's search ancillary.

static string s_RemoveLocalPrefix(const string &sid)

void SetHitlistSize(int s)

Sets HitlistSize.

CRef< objects::CSeq_align_set > SetSeqAlign()

Only intended to be used if you need to edit the seqlign.

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)

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

bool Submit(void)

This submits the search (if necessary) and returns immediately.

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

Prepare blast option handle and query for specified database search.

CRef< CSearchResultSet > RunEx()

Performs the same functionality as Run(), but it returns a different data type.

map< string, int > m_FrameOffset

map< string, string > m_DJChainType

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

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

static bool s_CompareSeqAlignByScoreAndName(const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)

static int max_v_j_overlap

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)

void x_ExtendAlign3end(CRef< CSearchResultSet > &results)

CIgAnnotationInfo m_AnnotationInfo

static int extend_length5end

int GetFwr4EndOffset(const string &sid)

static int max_allowed_j_deletion

void push_back(value_type &element)

Add a value to the back of this container.

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

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

Sets FilterString.

map< string, int > m_JDomainInfo

TQueryMessages GetErrors(int min_severity=eBlastSevError) const

Accessor for the error/warning messsages for this query.

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)

CConstRef< objects::CSeq_id > GetSeqId() const

Accessor for the query's sequence identifier.

void Combine(const TQueryMessages &other)

Combine other messages with these.

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

CRef< CBlastQueryVector > m_Query

static int max_allowed_VJ_distance_without_D

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)

static bool s_CompareSeqAlignByEvalue(const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)

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

Set the subject chain type and frame info.

static string s_MakeTopHitsId(const CSeq_align_set::Tdata &align_list, int num_align)

string m_CustomInternalData

map< string, string > m_DomainChainType

CRef< CSearchDatabase > m_RemoteDb

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

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

static bool s_IsSeqAlignAsGood(const CRef< CSeq_align > &x, const CRef< CSeq_align > &y)

void x_ConvertResultType(CRef< CSearchResultSet > &results)

Convert bl2seq result to database search mode.

void SetEntrezQuery(const char *x)

Restrict search to sequences matching this Entrez query.

void SetMatchReward(int r)

bool HasAlignments() const

Return true if there are any alignments for this query.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

const string AsFastaString(void) const

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

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

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

@ eContent

Untagged human-readable accession or the like.

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

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

bool Empty(void) const THROWS_NONE

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

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.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef 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.

#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::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

ENa_strand

strand of nucleic acid

Declares CIgBlast, the C++ API for the IG-BLAST engine.

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

constexpr bool empty(list< Ts... >) noexcept

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

Declares the CRemoteBlast class.

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

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

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

Structure to represent a single sequence to be fed to BLAST.

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