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NCBI C++ ToolKit: src/algo/align/util/tabular_fmt.cpp Source File

}

(

== 1) {

);

ostr <<

;

CScope::TIds::const_iterator

= it;

(

!= ids.end()) {

, m_GetIdType(id_type)

, m_TagOnly(tag_only)

ostr <<

;

ostr <<

;

ostr <<

;

}

(

== 0) {

}

(

== 1) {

);

: m_Row(

), m_NoMinus(nominus)

ostr <<

;

}

(

== 1) {

);

}

(

== 1) {

);

ostr <<

(

.GetFrom(),

.GetTo()) + 1;

: m_Row(

), m_NoMinus(nominus)

ostr <<

;

}

(

== 1) {

);

}

(

== 1) {

);

ostr <<

(

.GetFrom(),

.GetTo()) + 1;

ostr <<

;

}

(

== 1) {

);

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

== 0 ?

:

);

(score == numeric_limits<double>::quiet_NaN()) {

ostr << (

) score;

ostr <<

;

ostr << (

)

->GetScore(align,

);

ostr <<

;

ostr <<

;

ostr << (

)

->GetScore(align,

);

ostr <<

;

ostr <<

;

ostr <<

;

pct_id =

->GetScore(align,

:

);

pct_id =

(pct_id, 99.99);

ostr << (

== 0 ?

:

);

?

:

);

(pct_cov != 100) {

pct_cov =

(pct_cov, 99.99);

ostr <<

;

ostr <<

;

ostr <<

;

ostr << (

)

->GetScore(align,

);

ostr <<

;

ostr << (

)

->GetScore(align,

);

is_gapped =

;

ranges.push_back(range);

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

vector<TSeqPos> mm_pos;

);

(!exon->IsSetParts()) {

exon_qstrand = exon->IsSetProduct_strand()

? exon->GetProduct_strand() : QStrand;

exon_sstrand = exon->IsSetGenomic_strand()

? exon->GetGenomic_strand() : SStrand;

: exon->GetProduct_end().GetNucpos();

: exon->GetGenomic_end();

(part->Which()) {

pos += direction * part->GetMatch();

(

= 0;

< part->GetMismatch(); ++

) {

mm_pos.push_back(pos);

pos += direction * part->GetProduct_ins();

pos += direction * part->GetGenomic_ins();

);

QueryStr, SubjtStr;

QueryVec.

()-QAlignRange.

(), QueryStr);

SubjtVec.

()-SAlignRange.

(), SubjtStr);

QS = QueryStr.substr(0,50);

SS = SubjtStr.substr(0,50);

list<TSeqRange> QSegRanges, SSegRanges;

list<TSeqRange>::const_iterator SSegIter = SSegRanges.begin();

(list<TSeqRange>, QSegIter, QSegRanges) {

QOffset, SOffset;

QMOffset = QAlignRange.

()-QuerySeg.

();

SMOffset = SAlignRange.

()-SubjtSeg.

();

(

Loop = 0; Loop < QuerySeg.

(); Loop++) {

QLoop = QOffset+Loop;

SLoop = SOffset+Loop;

(QueryStr[QLoop] == SubjtStr[SLoop]) {

(

== 1)

(mm_pos.begin(), mm_pos.end());

(vector<TSeqPos>, it, mm_pos) {

(it != mm_pos.begin()) {

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

GappedRC -= AlignedRC;

(it != GappedRC.

()) {

ostr << it->GetFrom()+1 <<

<< it->GetTo()+1;

ostr <<

;

ostr <<

;

score =

->GetScore(align,

);

score == numeric_limits<double>::quiet_NaN()) {

ios_base::fmtflags cur_flags=ostr.flags();

ostr << scientific << score;

ostr.unsetf(ios_base::scientific);

ostr << setiosflags(cur_flags);

ostr <<

;

ostr <<

;

score =

->GetScore(align,

);

score == numeric_limits<double>::quiet_NaN()) {

mantissa = score;

(mantissa >= 10.0) {

(mantissa < 1.0) {

}

(score < 0.0) {

(mantissa <= -10.0) {

(mantissa > -1.0) {

ostr <<

;

ostr <<

;

score =

->GetScore(align,

);

score == numeric_limits<double>::quiet_NaN()) {

mantissa = score;

(mantissa >= 10.0) {

(mantissa < 1.0) {

}

(score < 0.0) {

(mantissa <= -10.0) {

(mantissa > -1.0) {

ostr <<

;

ostr <<

;

score =

->GetScore(align,

);

ostr <<

;

score =

->GetScore(align,

);

& col_name)

: m_ScoreName(score_name)

, m_ColName(col_name)

ostr <<

<< (

== 0 ?

:

)

<< (

== 0 ?

:

)

objects::CSeq_align& align)

(

== 0 ?

:

) +

(

);

ostr <<

<< (

== 0 ?

:

)

<< (

== 0 ?

:

)

objects::CSeq_align& align)

(

== 0 ?

:

) +

(

);

ostr <<

;

}

(

== 1) {

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

);

ostr <<

.GenerateDefline(bsh);

ostr <<

;

ostr <<

;

((*it)->IsId()) {

ostr << (*it)->GetId();

((*it)->IsStr()) {

ostr << (*it)->GetStr();

ostr <<

;

ostr <<

;

ostr <<

->GetData().GetStr();

ostr <<

;

}

(

== 1) {

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

);

(feat_iter.

() == 1) {

ostr <<

;

ostr << (

== 0 ?

:

);

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr << (

== 0 ?

:

);

ostr << (

== 0 ?

:

);

+

);

pair<const CProt_pos*, const CProt_pos*> TProteinExon;

vector<TProteinExon> protein_exons;

vector<TSeqRange> nuc_exons;

align_range.

(align_range.

()+1);

intron_ranges += align_range;

protein_exons.push_back(

nuc_exons.push_back(exon_range);

intron_ranges -= exon_range;

list<TSeqRange> range_list;

(!nuc_exons.empty()) {

range_list.insert(range_list.end(), nuc_exons.begin(),

}

(!intron_ranges.

()) {

range_list.insert(range_list.end(), intron_ranges.

(),

intron_ranges.

());

range_list.reverse();

(vector<TProteinExon>, it, protein_exons) {

(it != protein_exons.begin()) {

ostr <<

<< it->first->GetAmin()+1

<<

<< it->first->GetFrame()

<<

<< it->second->GetAmin()+1

<<

<< it->second->GetFrame() <<

;

(list<TSeqRange>, it, range_list) {

(it != range_list.begin()) {

ostr << it->GetLength();

ostr <<

;

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

);

:

);

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

ostr <<

;

);

);

desc_iter; ++desc_iter)

ostr << desc_iter->GetComment().substr(

.size() + 2);

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

0: ostr <<

;

;

1: ostr <<

;

;

);

ostr <<

;

0: ostr <<

;

;

1: ostr <<

;

;

);

: ostr <<

;

;

: ostr <<

;

;

: ostr <<

;

;

);

== 0 ?

:

));

taxid =

->GetSpecies(taxid);

taxid =

->GetGenus(taxid);

taxid =

->GetSuperkingdom(taxid);

is_species =

;

is_uncultured =

;

->GetOrgRef(taxid, is_species, is_uncultured, blast_name);

org->GetLabel(&

);

ostr <<

;

ostr <<

;

}

(

== 0) {

ostr <<

;

}

(

== 1) {

ostr <<

;

);

(

Index = 0; Index < Denseg.

(); Index++) {

QGap = (Denseg.

()[2*Index] == -1);

}

(

== 0 && QGap) {

);

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

( (*SubIter)->CanGetSubtype() &&

(*SubIter)->CanGetName() ) {

Chrom = (*SubIter)->GetName();

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

( (*SubIter)->CanGetSubtype() &&

(*SubIter)->CanGetName() ) {

Clone = (*SubIter)->GetName();

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

TechStr =

;

ostr <<

;

}

(

== 1) {

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

Plus=

, Minus=

;

(Minus && !Plus)

(Plus && Minus)

& Plus,

& Minus)

&

)

: m_ColName(col_name)

ostr <<

<<

<<

;

ostr <<

;

ostr <<

;

ostr << double(align_length) / double(align_range);

ostr <<

;

);

(

Loop = 0; Loop < NumSeg; Loop++) {

Length = Lens[Loop];

( Starts[ (Loop*2) ] == -1)

( Starts[ (Loop*2)+1 ] == -1)

ostr << Length <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr << (

==

?

:

) <<

;

}

(

== 1) {

);

ostr <<

;

}

(

== 1) {

);

ostr << (

==

?

:

);

ostr <<

;

?

:

)

(obj.

(

)) {

?

:

)

(obj.

(

)) {

(obj.

(

)) {

Assm = Seq->GetFullAssembly();

Assm.

(unit_assm);

chain_start = accession.find_first_of(

);

chain_end = accession.find(

);

ostr << accession.substr(chain_start, chain_end-chain_start);

ostr << Seq->GetChrName();

: m_Row(

), m_Gencoll(gencoll)

ostr <<

;

}

(

== 1) {

ostr <<

;

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

(Seq->CanGetPatch_type()) {

: m_Row(

), m_Gencoll(gencoll)

ostr <<

;

}

(

== 1) {

);

ostr <<

;

ostr <<

;

}

(

== 1) {

ostr <<

;

);

list<TSeqRange>& Gaps)

(!Seq->CanGetStructure())

( (*DeltaIter)->IsLiteral()) {

(!(*DeltaIter)->GetLiteral().CanGetSeq_data() ||

(*DeltaIter)->GetLiteral().GetSeq_data().IsGap()) {

GapRange.

(CurrStart);

GapRange.

((*DeltaIter)->GetLiteral().GetLength());

Gaps.push_back(GapRange);

CurrStart += (*DeltaIter)->GetLiteral().

();

}

( (*DeltaIter)->IsLoc()) {

(Assembly, *(*DeltaIter)->GetLoc().GetId(), CurrStart, Gaps);

CurrStart += (*DeltaIter)->GetLoc().GetTotalRange().GetLength();

list<TSeqRange> Gaps;

(SeqLength == 0) {

(list<TSeqRange>, GapIter, Gaps) {

ostr <<

;

);

: m_IndelType(indel_type)

, m_CoordinateRow(coordinate_row)

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

+

vector<CSeq_align::SIndel> indels;

ostr <<

<< (

== 0 ?

:

);

ostr << (

== 0 ?

:

) <<

;

snp_count = 0, snp_pos = 0;

(

deletion_pos = 0; deletion_pos <

.size();

subject_with_del =

;

subject_with_del.insert(deletion_pos, 1,

[deletion_pos]);

(

== subject_with_del) {

.insert(deletion_pos, 1,

);

(

index = 0; index <

.size(); ++index) {

(snp_count == 1) {

: m_CoordinateRow(

)

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

+

: m_CoordinateRow(

)

ostr <<

;

ostr <<

;

ostr <<

;

ostr <<

;

-> GetSeq().GetAnnot().front()

-> GetData().GetFtable().front();

cds->

().SetCdregion().ResetCode_break();

missing_stop =

;

trans.resize(trans.size() - 1);

missing_stop =

;

(

changed_codons_count = 0, internal_stop_pos = trans.find(

);

internal_stop_pos != string::npos || missing_stop;

internal_stop_pos = trans.find(

, internal_stop_pos+1))

(internal_stop_pos == string::npos) {

internal_stop_pos = trans.size() - 1;

missing_stop =

;

(changed_codons_count++) {

&unavailable_string)

: m_Scores(&scores), m_Ostr(ostr), m_UnavailableString(unavailable_string)

formatter_it->second->SetGencoll(gencoll);

&separators,

vector<string> &toks)

paren_level = 0;

(!paren_level && separators.find(*char_it) != string::npos) {

(!next_tok.empty()) {

toks.push_back(next_tok);

(*char_it ==

) {

}

(*char_it ==

) {

+

);

next_tok += *char_it;

(!next_tok.empty()) {

toks.push_back(next_tok);

+

);

re1(

);

re2(

);

text_re1(

);

text_re2(

);

vector<string> toks;

(vector<string>, it, toks) {

}

(re1.

(s)) {

score_name = re1.

(*it, 1);

col_name = re1.

(*it, 2);

}

(re2.

(s)) {

score_name = re2.

(*it, 1);

}

(text_re1.

(s)) {

score_name = text_re1.

(*it, 1);

col_name = text_re1.

(*it, 2);

}

(text_re2.

(s)) {

score_name = text_re2.

(*it, 1);

(*it)->PrintHeader(

);

list< CIRef<IFormatter> >::const_iterator

= it;

(*it)->Print(

, align);

list< CIRef<IFormatter> >::const_iterator

= it;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

size_t GetSize(void) const

CRef< objects::CSeq_feat > ConvertAlignToAnnot(const objects::CSeq_align &align, objects::CSeq_annot &annot, objects::CBioseq_set &seqs, Int8 gene_id=0, const objects::CSeq_feat *cdregion_on_mrna=NULL)

Convert an alignment to an annotation.

void SetFlags(TFeatureGeneratorFlags)

void SetAllowedUnaligned(TSeqPos)

CConstRef< objects::CSeq_align > CleanAlignment(const objects::CSeq_align &align)

Clean an alignment according to our best guess of its biological representation.

string GetAccession() const

Retrieve the accession for this assembly.

string GetName() const

Retrieve the name of this assembly.

void Find(const CSeq_id_Handle &id, TSequenceList &sequences) const

Find all references to a given sequence within an assembly.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

ostream & AsString(ostream &s) const

void GetLabel(string *label) const

const_iterator end() const

const_iterator begin() const

TSeqPos GetTotalGapCount(TDim row=-1) const

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

CRangeCollection< TSeqPos > GetAlignedBases(TDim row) const

Retrieves the locations of aligned bases in the given row, excluding gaps and incontinuities.

vector< SIndel > GetNonFrameshiftsWithinRange(const TSeqRange &range, TDim row=-1) const

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TSeqPos GetSeqStop(TDim row) const

TDim CheckNumRows(void) const

Validatiors.

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.

vector< SIndel > GetFrameshiftsWithinRange(const TSeqRange &range, TDim row=-1) const

vector< SIndel > GetIndelsWithinRange(const TSeqRange &range, TDim row=-1) const

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.

TSeqPos GetNumGapOpenings(TDim row=-1) const

Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in th...

objects::CScoreLookup * m_Scores

CTabularFormatter_AlignEnd(int row, bool nominus=false)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping alignment identifiers

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_AlignStart(int row, bool nominus=false)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_AlignStrand(int row)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_AllSeqIds(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping any score in an alignment

CTabularFormatter_AnyScore(const string &score_name, const string &col_name)

formatter for dumping any score in an alignment

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_AssemblyInfo(int row, EAssemblyType type, EInfo info)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CConstRef< objects::CGC_Assembly > m_Gencoll

virtual void SetGencoll(CConstRef< objects::CGC_Assembly > gencoll)

formatter for dumping alignment identifiers

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

TSeqPos x_CalcBiggestGap(const objects::CSeq_align &align)

CTabularFormatter_BiggestGapBases(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping cigar of alignments

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Cigar()

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

formatter for dumping sequence deflines

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_Defline(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

objects::sequence::CDeflineGenerator generator

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void x_RecurseStrands(const objects::CSeq_align &align, bool &Plus, bool &Minus)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_DiscStrand(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

formatter for Shannon's entropy

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping exons

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_FixedText(const string &col_name, const string &text)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_GapRanges(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_GeneSymbol(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_Indels(EIndelType indel_type, int coordinate_row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_MismatchPositions(int row)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CConstRef< objects::CGC_Assembly > m_Gencoll

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_NearestGap(int row, CConstRef< objects::CGC_Assembly > gencoll)

formatter for dumping organism names

std::unique_ptr< objects::CTaxon1 > m_Taxon1

~CTabularFormatter_OrgName()

CTabularFormatter_OrgName(int row, EField field=eFullTaxName)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CConstRef< objects::CGC_Assembly > m_Gencoll

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_PatchType(int row, CConstRef< objects::CGC_Assembly > gencoll)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_PercentId(bool gapped=false)

void PrintHeader(CNcbiOstream &ostr) const

formatter for dumping sequence Prot-refs (protein only)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_ProtRef(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

formatter for BLAST seg %

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

CTabularFormatter_SeqChrom(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_SeqClone(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_SeqId(int row, objects::sequence::EGetIdType id_type, bool tag_only=false, bool protein=false)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

objects::sequence::EGetIdType m_GetIdType

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_SeqLength(int row)

CTabularFormatter_StartCodonChanges(int row)

void PrintHelpText(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHeader(CNcbiOstream &ostr) const

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_StopCodonChanges(int row)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

formatter for dumping tax-ids

void PrintHelpText(CNcbiOstream &ostr) const

CTabularFormatter_TaxId(int row)

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Tech(int row)

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

void Print(CNcbiOstream &ostr, const objects::CSeq_align &align)

CTabularFormatter_Traceback()

void PrintHelpText(CNcbiOstream &ostr) const

void PrintHeader(CNcbiOstream &ostr) const

Simple tabular alignment formatter This is a replacement for the BLAST tabular formatter that support...

void SetGencoll(CConstRef< objects::CGC_Assembly > gencoll)

void RegisterField(const string &field_name, IFormatter *field_formatter)

objects::CScoreLookup * m_Scores

void Format(const objects::CSeq_align &align)

static void s_RegisterStandardFields(CTabularFormatter &formatter)

void SetFormat(const string &format)

string m_UnavailableString

CTabularFormatter(CNcbiOstream &ostr, objects::CScoreLookup &scores, const string &unavailable_string="")

list< CIRef< IFormatter > > m_Formatters

TFormatterMap m_FormatterMap

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#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 & FindName(TEnumValueType value, bool allowBadValue) const

Find name of the enum by its numeric value.

const string AsFastaString(void) const

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

@ eContent

Untagged human-readable accession or the like.

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool IsPartialStop(ESeqLocExtremes ext) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_ForceGi

return only a gi-based seq-id

@ eGetId_HandleDefault

returns the ID associated with a bioseq-handle

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

vector< CSeq_id_Handle > TIds

const CSeqFeatData & GetData(void) const

TMol GetBioseqMolType(void) const

Get some values from core:

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

TRange GetRange(void) const

Get range for mapped seq-feat's location.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & SetLength(position_type length)

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetSub(CTempString str, size_t idx=0) const

Get pattern/subpattern from previous GetMatch().

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eNocase

Case insensitive compare.

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool CanGetSubtype(void) const

Check if it is safe to call GetSubtype method.

list< CRef< CSubSource > > TSubtype

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

TInt GetInt(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

TUnit & SetUnit(void)

Select the variant.

const TProtpos & GetProtpos(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetId(void) const

alignment id Check if a value has been assigned to Id data member.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

list< CRef< CObject_id > > TId

list< CRef< CUser_object > > TExt

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

bool CanGetSegs(void) const

Check if it is safe to call GetSegs method.

TDim GetDim(void) const

Get the Dim member data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsDisc(void) const

Check if variant Disc is selected.

const TExt & GetExt(void) const

Get the Ext member data.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

TNucpos GetNucpos(void) const

Get the variant 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.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

const TLocation & GetLocation(void) const

Get the Location member data.

void SetData(TData &value)

Assign a value to Data data member.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

ENa_strand

strand of nucleic acid

bool IsGeneral(void) const

Check if variant General is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ eNa_strand_both

in forward orientation

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

const TSource & GetSource(void) const

Get the variant data.

TTech GetTech(void) const

Get the Tech member data.

bool IsSetTech(void) const

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

bool CanGetTech(void) const

Check if it is safe to call GetTech method.

list< CRef< CDelta_seq > > Tdata

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

unsigned int

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

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

static void text(MDB_val *v)

constexpr auto sort(_Init &&init)

Magic spell ;-) needed for some weird compilers... very empiric.

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

#define row(bind, expected)

static void s_Split(const string &format, const string &separators, vector< string > &toks)

Split a string, but ignore separators within parentheses.

TSeqPos s_FindGaps(const CGC_Assembly &Assembly, const CSeq_id &Id, const TSeqPos Offset, list< TSeqRange > &Gaps)

void s_AlignToSeqRanges(const CSeq_align &align, int row, list< TSeqRange > &ranges)

static string s_CodonVariation(const CSeq_align &align, TSeqPos pos, CScope &scope, int row)

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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