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NCBI C++ ToolKit: src/algo/blast/format/blastxml2_format.cpp Source File

frame = (start - 1) % 3 + 1;

frame = -((seq_length - end) % 3 + 1);

ncbi::TMaskedQueryRegions & mask_info,

master_gentic_code,

slave_genetic_code)

query_is_na, subject_is_na;

query_length, subject_length;

score, num_ident;

list<TGi> use_this_gi;

CBlastFormatUtil::GetAlnScores(kAlign, score, bit_score, evalue, sum_n,

num_ident, use_this_gi);

sprintf(

,

, 6, bit_score );

bit_score = atof(

);

sprintf(

,

, 6, evalue );

evalue = atof(

);

xhsp->SetBit_score(bit_score);

xhsp->SetScore(score);

xhsp->SetEvalue(evalue);

query_is_na = kQueryBioseqHandle.

();

subject_is_na = kSubjBioseqHandle.

();

xhsp->SetQuery_from(0);

xhsp->SetQuery_to(0);

xhsp->SetHit_from(0);

xhsp->SetIdentity(num_ident);

xhsp_list.push_back(xhsp);

(query_is_na && subject_is_na)

final_aln = densegAln;

masked_query_seq;

kIsBlastn =

(query_is_na && subject_is_na && !kTranslated);

reversed_ds->

(kDenseg);

ds_pt = &(*reversed_ds);

q_start, q_end, s_start, s_end, q_frame=0, s_frame=0;

num_gaps = 0;

align_length = 0;

(!kTranslated && query_is_na && subject_is_na) {

xhsp->SetQuery_strand(

);

xhsp->SetHit_strand(

);

xhsp->SetHit_strand(

);

}

(kTranslated) {

q_start, q_end, query_length);

xhsp->SetQuery_frame(q_frame);

s_start, s_end, subject_length);

xhsp->SetHit_frame(s_frame);

xhsp->SetQuery_from(q_start);

xhsp->SetQuery_to(q_end);

xhsp->SetHit_from(s_start);

xhsp->SetHit_to(s_end);

(mask_info.empty())

num_positives = 0;

middle_seq = query_seq;

kMaxOffset =

(query_seq.size(),

(

= 0;

< kMaxOffset; ++

) {

(query_seq[

] == subject_seq[

]) {

middle_seq[

] =

;

(*matrix)(query_seq[

], subject_seq[

]) > 0 &&

middle_seq[

] = kIsBlastn ?

:

;

middle_seq[

] =

;

xhsp->SetIdentity(num_ident);

xhsp->SetGaps(num_gaps);

xhsp->SetAlign_len(align_length);

(mask_info.empty())

xhsp->SetQseq(query_seq);

xhsp->SetQseq(masked_query_seq);

xhsp->SetHseq(subject_seq);

xhsp->SetMidline(middle_seq);

(!(query_is_na && subject_is_na && !kTranslated) )

xhsp->SetPositive(num_positives);

xhsp_list.push_back(xhsp);

ncbi::TMaskedQueryRegions & mask_info,

ungapped,

master_gentice_code,

slave_genetic_code,

hasTaxDB)

& kSeqId = kAlignSet.

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

list <CRef<blastxml2::CHitDescr> > & descr_list = hit->SetDescription();

(bdlRef.

() && bdlRef->

() && (!bdlRef->

().empty())) {

hit_exp->SetAccession(accession);

hit_exp->SetTitle(defline.

());

hit_exp->SetTaxid(tax_id);

descr_list.push_back(hit_exp);

list<CRef<objects::CSeq_id> > ids;

hit_exp->SetAccession(accession);

hit_exp->SetTitle(sequence::CDeflineGenerator().GenerateDefline(subj_handle));

descr_list.push_back(hit_exp);

hit->SetDescription().push_back(hit_exp);

matrix, mask_info, master_gentice_code, slave_genetic_code);

mask_info, master_gentice_code, slave_genetic_code);

CSeq_align_set::Tdata::const_iterator iter = alnset->Get().begin();

ncbi::TMaskedQueryRegions & mask_info =

->GetMaskLocations();

ungapped = !(

->IsGappedSearch());

master_gentice_code =

->GetQueryGeneticCode();

slave_genetic_code =

->GetDbGeneticCode();

hasTaxDB =

->CanGetTaxInfo();

(iter != alnset->Get().end()) {

new_hit->SetNum(index);

((*iter)->GetSegs().IsDisc()) {

ungapped, master_gentice_code, slave_genetic_code, hasTaxDB);

( ; iter != alnset->Get().end(); ++iter) {

(!current_id->

(*next_id)) {

one_subject_alnset.

().push_back(*iter);

disc_align_wrap.

().SetDisc(one_subject_alnset);

mask_info, ungapped, master_gentice_code, slave_genetic_code, hasTaxDB);

hits.push_back(new_hit);

matrix_name =

->GetMatrixName();

params.SetMatrix(matrix_name);

params.SetExpect(

->GetEvalueThreshold());

((

=

->GetMatchReward()) != 0)

params.SetSc_match(

);

((

=

->GetMismatchPenalty()) != 0)

params.SetSc_mismatch(

);

(

->IsGappedSearch()) {

params.SetGap_open(

->GetGapOpeningCost());

params.SetGap_extend(

->GetGapExtensionCost());

params.SetPattern(

);

params.SetFilter(

);

params.SetBl2seq_mode(

);

((

=

->GetCompositionBasedStats()) != 0)

params.SetCbs(

);

params.SetEntrez_query(

);

((

=

->GetQueryGeneticCode()) != 0)

params.SetQuery_gencode(

);

((

=

->GetDbGeneticCode()) != 0)

params.SetDb_gencode(

);

(!

->IsBl2seq()) {

.SetDb_num(

->GetDbNumSeqs());

.SetHsp_len(

->GetLengthAdjustment(num));

.SetEff_space(

->GetEffectiveSearchSpace(num));

.SetLambda(

->GetLambda(num));

.SetEntropy(

->GetEntropy(num));

* q_id = q_loc->GetId();

q_title = sequence::CDeflineGenerator().GenerateDefline(bh);

search.SetQuery_title(q_title);

(!

->GetMaskLocations().empty()) {

list<CRef< blastxml2::CRange> > & masks = search.SetQuery_masking();

masks.push_back(rng);

blastxml2::CStatistics &

= search.SetStat();

=

->GetMessages(num);

(

->GetAlignmentSet(num).Empty()) {

+= CBlastFormatUtil::kNoHitsFound;

search.SetMessage(

);

search.SetMessage(

);

list<CRef<blastxml2::CHit> > & hit_list = search.SetHits();

blastxml2::CReport & report = bxmlout.SetReport();

program_name =

->GetBlastProgramName();

report.SetProgram(program_name);

(!

->GetSubjectIds().empty()) {

report.SetSearch_target().SetSubjects() =

->GetSubjectIds();

report.SetSearch_target().SetDb(

->GetDatabaseName());

blastxml2::CParameters & params = report.SetParams();

blastxml2::CResults &

= report.SetResults();

(

->IsBl2seq()) {

list<CRef<blastxml2::CSearch> > & bl2seq =

.SetBl2seq();

(

=0;

<

->GetNumOfSearchResults();

++ ) {

bl2seq.push_back(search);

(

->IsIterativeSearch()) {

list<CRef<blastxml2::CIteration> > & iterations =

.SetIterations();

(

=0;

<

->GetNumOfSearchResults();

++ ) {

itr->SetIter_num(

+1);

blastxml2::CSearch & search = itr->SetSearch();

iterations.push_back(itr);

blastxml2::CSearch & search =

.SetSearch();

typeInfo = bxmlout.GetThisTypeInfo();

xml_out->SetEnforcedStdXml();

xml_out->Write(&bxmlout, typeInfo );

typeInfo = bxmlout.GetThisTypeInfo();

xml_out->SetReferenceSchema();

xml_out->SetUseSchemaLocation(

);

xml_out->SetEnforcedStdXml();

xml_out->SetDTDFilePrefix(

);

xml_out->SetDefaultSchemaNamespace(

);

xml_out->Write(&bxmlout, typeInfo );

blastxml2::CBlastOutput2 bxmlout;

blastxml2::CBlastOutput2 bxmlout;

(!out_stream.is_open())

xml_out->SetReferenceSchema();

xml_out->SetUseSchemaLocation(

);

xml_out->SetEnforcedStdXml();

xml_out->SetDTDFilePrefix(

);

xml_out->SetDefaultSchemaNamespace(

);

blastxml2::CBlastXML2 xml2;

typeInfo = xml2.GetThisTypeInfo();

xml_out->Write(&xml2, typeInfo);

string::size_type end_pos = out_str.find(

);

out_str.erase(end_pos);

*out_stream << out_str;

blastxml2::CBlastOutput2 bxmlout;

bxmlout.SetError().SetCode(exit_code);

bxmlout.SetError().SetMessage(err_msg);

*out_stream <<

;

typeInfo = bxmlout.GetThisTypeInfo();

json_out->Write(&bxmlout, typeInfo );

typeInfo = bxmlout.GetThisTypeInfo();

json_out->Write(&bxmlout, typeInfo );

blastxml2::CBlastOutput2 bxmlout;

(!out_stream.is_open())

blastxml2::CBlastOutput2 bxmlout;

User-defined methods of the data storage class.

Declares singleton objects to store the version and reference for the BLAST engine.

BLAST formatter utilities.

Declares class to display one-line descriptions at the top of the BLAST report.

EProgram

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

@ ePHIBlastn

Nucleotide PHI BLAST.

@ ePHIBlastp

Protein PHI BLAST.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDeltaBlast

Delta Blast.

static void s_WriteXML2ObjectNoHeader(blastxml2::CBlastOutput2 &bxmlout, CNcbiOstream *out_stream)

static void s_SetBlastXMLSearch(blastxml2::CSearch &search, const IBlastXML2ReportData *data, int num)

static void s_SetBlastXMlHitList(list< CRef< blastxml2::CHit > > &hits, const IBlastXML2ReportData *data, int num)

Fills the list of blastxml2::CHit objects, given a list of Seq-aligns.

static void s_SeqAlignToXMLHit(CRef< blastxml2::CHit > &hit, const CSeq_align &align_in, CRef< CScope > scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions &mask_info, bool ungapped, int master_gentice_code, int slave_genetic_code, bool hasTaxDB)

Fill the blastxml2::CHit object in BLAST XML output, given an alignment and other information.

static void s_FillBlastOutput(blastxml2::CBlastOutput2 &bxmlout, const IBlastXML2ReportData *data)

static void s_WriteJSONObjectNoHeader(blastxml2::CBlastOutput2 &bxmlout, CNcbiOstream *out_stream)

static int s_GetTranslationFrame(bool plus_strand, int start, int end, int seq_length)

Returns translation frame given the strand, alignment endpoints and total sequence length.

static CReference::EPublication s_GetBlastPublication(EProgram program)

Given BLAST task, returns enumerated value for the publication to be referenced.

static void s_WriteJSONObject(blastxml2::CBlastOutput2 &bxmlout, CNcbiOstream *out_stream)

static void s_SetBlastXMLStatistics(blastxml2::CStatistics &stats, const IBlastXML2ReportData *data, int num)

Fills the search statistics part of the BLAST XML output for all queries.

static void s_SetBlastXMLParameters(blastxml2::CParameters &params, const IBlastXML2ReportData *data)

Fills the parameters part of the BLAST XML output.

static const CSeq_id * s_GetSubjectId(const CSeq_align &align)

Retrieves subject Seq-id from a Seq-align.

static void s_WriteXML2Object(blastxml2::CBlastOutput2 &bxmlout, CNcbiOstream *out_stream)

static void s_SeqAlignSetToXMLHsps(list< CRef< blastxml2::CHsp > > &xhsp_list, const CSeq_align_set &alnset, CRef< CScope > scope, const CBlastFormattingMatrix *matrix, const ncbi::TMaskedQueryRegions &mask_info, int master_gentic_code, int slave_genetic_code)

Creates a list of blastxml2::CHsp structures for the XML output, given a list of Seq-aligns.

static string GetLabel(CConstRef< objects::CSeq_id > id, bool with_version=false)

Return a label for an ID Tries to recreate behavior of GetLabel before a change that prepends "ti|" t...

256x256 matrix used for calculating positives etc.

virtual void WriteFileHeader(TTypeInfo type)

virtual ~CBlastOStreamJson(void)

virtual void EndOfWrite(void)

CBlastOStreamJson(CNcbiOstream &stream, EOwnership deleteOut)

CBlastOStreamXml(CNcbiOstream &stream, EOwnership deleteOut)

virtual ~CBlastOStreamXml(void)

virtual void WriteFileHeader(TTypeInfo type)

void Reverse(void)

Reverse the segments' orientation.

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

overloaded Assign()

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalign(const objects::CSeq_align_set &alnset)

static functions Need to call this if the seqalign is stdseg or dendiag for ungapped blast alignment ...

SeqLocCharOption

character used to display seqloc, such as masked sequence

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static void GetTaxInfo(TTaxId taxid, SSeqDBTaxInfo &info)

Get taxonomy information.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

objects::ENa_strand GetStrand() const

Convert the frame to a strand.

const objects::CSeq_interval & GetInterval() const

CRef< CSeq_align > CreateTranslatedDensegFromNADenseg(void) const

Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl...

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

TSeqPos GetTotalGapCount(TDim row=-1) const

Retrieves the total number of gaps in the given row an alignment; all gaps by default.

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

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

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.

static void GetSeqIdList(const objects::CBioseq_Handle &bh, list< CRef< objects::CSeq_id > > &ids)

Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references,...

static string GetSeqIdListString(const list< CRef< objects::CSeq_id > > &id, bool show_gi)

Creates a '|' delimited string, corresponding to a list of Seq-ids.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

Interface for filling the top layer of the XML report.

Collection of masked regions for a single query sequence.

string GetSeqIdString(const CSeq_id &id)

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

main entry point for tests

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

static string GetString(EPublication pub)

Reference for requested publication.

EPublication

Enumerates the various BLAST publications.

@ eMaxPublications

Used as sentinel value.

@ ePhiBlast

1998 NAR paper

@ eCompBasedStats

2001 NAR paper

@ eGappedBlast

1997 NAR paper

@ eMegaBlast

2000 J Compt Biol paper

@ eDeltaBlast

2012 Biology Direct on DeltaBLAST

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

@ eNoOwnership

No ownership is assumed.

void BlastXML2_FormatError(int exit_code, string err_msg, CNcbiOstream *out_stream)

static void GetWholeAlnSeqStrings(string &query, string &subject, const objects::CDense_seg &ds, objects::CScope &scope, int master_gen_code, int slave_gen_code)

static string BlastGetVersion(const string program)

Returns the version and release date, e.g.

void BlastXML2_FormatReport(const IBlastXML2ReportData *data, CNcbiOstream *out_stream)

Fills all fields in the data structure for a BLAST XML report.

void BlastJSON_FormatReport(const IBlastXML2ReportData *data, string file_name)

void BlastXML2_PrintHeader(CNcbiOstream *out_stream)

void BlastJSON_PrintHeader(CNcbiOstream *out_stream)

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

@ eSerialVerifyData_No

do not verify

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

virtual void EndOfWrite(void)

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

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

TSeqPos GetBioseqLength(void) const

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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void IncIndentLevel(size_t step=2)

void PutEol(bool indent=true)

void DecIndentLevel(size_t step=2)

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

enum ENcbiOwnership EOwnership

Ownership relations between objects.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

const TSeqid & GetSeqid(void) const

Get the Seqid member data.

bool IsSetTitle(void) const

simple title Check if a value has been assigned to Title data member.

TTaxid GetTaxid(void) const

Get the Taxid member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetTaxid(void) const

Check if a value has been assigned to Taxid data member.

const Tdata & Get(void) const

Get the member data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

const TStd & GetStd(void) const

Get the variant data.

const TDendiag & GetDendiag(void) const

Get the variant data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsDisc(void) const

Check if variant Disc is selected.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

bool IsLocal(void) const

Check if variant Local is selected.

static CRef< CSeq_align > CreateDensegFromDendiag(CSeq_align const &aln)

Defines BLAST database access classes.

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

string scientific_name

Scientific name, such as "Aotus vociferans".

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