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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/splign__formatter_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/splign/splign_formatter.cpp Source File

78

m_splign_results(splign.GetResult())

86 const char

kSeqId_not_set [] =

"lcl|ID_not_set"

;

114 const string

querystr (use_fasta_style_ids?

117 const string

subjstr (use_fasta_style_ids?

123 for

(

size_t i

(0), seg_dim (ii->m_Segments.size());

< seg_dim; ++

) {

127

oss << (ii->m_QueryStrand?

'+'

'-'

)

132

oss << seg.

m_idty

'\t'

;

138

oss << seg.

m_len

'\t' 139

<< seg.

m_box

[0] + 1 <<

'\t'

<< seg.

m_box

[1] + 1 <<

'\t'

;

142

oss << seg.

m_box

[2] + 1 <<

'\t' 143

<< seg.

m_box

[3] + 1 <<

'\t'

;

153 if

(print_exon_scores) {

162 else if

(

== seg_dim - 1) {

169 if

(print_exon_scores) {

177 const bool

polya_present (ii->m_PolyA > 0 && ii->m_PolyA < ii->m_QueryLen);

184 if

(ii->m_QueryStrand) {

185

polya_len = ii->m_QueryLen - ii->m_PolyA;

188

start = 1 + ii->m_PolyA;

189

stop = ii->m_QueryLen;

192

polya_len = 1 + ii->m_PolyA;

199

oss << c1 << ii->m_Id <<

'\t'

<< querystr <<

'\t'

<< subjstr

200

"\t-\t"

<< polya_len <<

'\t'

;

201

oss << start <<

'\t'

<< stop

202

"\t-\t-\t<poly-"

<< c2 <<

">\t-"

;

203 if

(print_exon_scores) {

218 copy

(strx.begin(), strx.end(), s.begin() + 9 - strx.size());

233 const size_t

extra_chars = 5;

235 const string

kNotSet (

"id_not_set"

);

244 string

query_sequence_sense;

253 const string

kTenner (10,

' '

);

261 const bool

qstrand = ii->m_QueryStrand;

262 const bool

sstrand = ii->m_SubjStrand;

263 const char

qc = qstrand?

'+'

'-'

;

264 const char

sc = sstrand?

'+'

'-'

;

266

oss << endl << '>

' << qc << ii->m_Id << '\t' 267 << querystr << '

(

' << qc << ")\t" 268 << subjstr << '

(

' << sc << '

)

' << endl; 270 size_t exons_total = 0; 271 ITERATE(CSplign::TSegments, jj, ii->m_Segments) { 277 string query_sequence; 279 query_sequence = query_sequence_sense; 282 query_sequence.resize(query_sequence_sense.size()); 283 transform(query_sequence_sense.rbegin(), query_sequence_sense.rend(), 284 query_sequence.begin(),SCompliment()); 287 string cds_sequence, query_protein; 288 if(ii->m_Cds_start < ii->m_Cds_stop) { 290 cds_sequence.resize(ii->m_Cds_stop - ii->m_Cds_start + 1); 291 copy(query_sequence.begin() + ii->m_Cds_start, 292 query_sequence.begin() + ii->m_Cds_stop + 1, 293 cds_sequence.begin()); 294 CSeqTranslator::Translate(cds_sequence, query_protein); 297 size_t exon_count = 0, seg_count = 0; 298 int query_aa_idx (0); 299 int qframe(ii->m_Cds_start < ii->m_Cds_stop? -2: -3); 300 ITERATE(CSplign::TSegments, jj, ii->m_Segments) { 302 const CSplign::TSegment & s (*jj); 305 size_t qbeg = s.m_box[0]; 306 size_t qfin = s.m_box[1]; 307 size_t sbeg = s.m_box[2]; 308 size_t sfin = s.m_box[3]; 319 if(exon_count + 1 < exons_total) { 350 sv_subj.GetSeqData(sv_subj.begin() + TSeqPos(s0), 351 sv_subj.begin() + TSeqPos(s1 + 1), str); 352 vector<char> subj (str.size()); 354 copy(str.begin(), str.end(), subj.begin()); 357 reverse(str.begin(), str.end()); 358 transform(str.begin(), str.end(), 359 subj.begin(), SCompliment()); 363 const size_t Q0 (q0); 364 q0 = query_sequence.size() - q1 - 1; 365 q1 = query_sequence.size() - Q0 - 1; 368 vector<char> query (q1 - q0 + 1); 369 copy(query_sequence.begin() + q0, query_sequence.begin() + q1 + 1, 372 const bool do_print (segnum == -1 || int(seg_count) == segnum); 375 oss << endl << " Exon " << (exon_count + 1) << " (" 376 << (1 + s.m_box[0]) << '

' << (1 + s.m_box[1]) << '

' 377 << (1 + s.m_box[2]) << '

' << (1 + s.m_box[3]) << ") " 378 << "Len = " << s.m_len << ' ' 379 << "Identity = " << s.m_idty << endl; 387 MakeLeftHeader(qbeg + 1, &l1); 388 MakeLeftHeader(sbeg + 1, &l3); 392 trans.assign(extra_chars, '

'); 394 trans.append(s.m_details); 395 if(exon_count + 1 < exons_total) { 396 trans.append(extra_chars, '

'); 399 for(size_t t = 0, td = trans.size(), iq = 0, is = 0; t < td; ++t) { 401 char c = trans[t], c1, c2, c3, c0, c4; 403 if(qframe == -2 && q0 + iq == ii->m_Cds_start) { 407 if(qframe >= 0 && q0 + iq >= ii->m_Cds_stop) { 444 NCBI_THROW(CAlgoAlignException, 446 g_msg_UnknownTranscriptSymbol + c); 450 if(qframe >= -1 && (c == 'M' || c == 'R' || c == 'D')) { 451 qframe = (qframe + 1) % 3; 453 if(c != '

' && c != '

' && qframe == 1) { 454 c0 = query_protein[query_aa_idx++]; 462 if(l1.size() == 10 + line_width) { 465 oss << l0 << endl << l1 << endl 466 << l2 << endl << l3 << endl << endl; 469 l0 = l1 = l2 = l3 = kTenner; 485 MakeLeftHeader(q0 + 1, &l1); 486 MakeLeftHeader(s0 + 1, &l3); 493 oss << l0 << endl << l1 << endl << l2 << endl << l3 << endl; 496 l0 = l1 = l2 = l3 = kTenner; 502 if(qframe >= 0) qframe = -3; // disable further translation 509 return CNcbiOstrstreamToString(oss); 514 double CalcIdentity(const string& transcript) 517 ITERATE(string, ii, transcript) { 519 ++matches; // std::count() not supported by some compilers 522 return double(matches) / transcript.size(); 526 CRef<CSeq_align> CSplignFormatter::x_Compartment2SeqAlign ( 527 const vector<size_t>& boxes, 528 const vector<string>& transcripts, 529 const vector<float>& scores ) const 531 const size_t num_exons (boxes.size() / 4); 533 CRef<CSeq_align> sa (new CSeq_align); 537 // this is a discontinuous alignment 538 sa->SetType(CSeq_align::eType_disc); 541 // create seq-align-set 542 CSeq_align_set& sas = sa->SetSegs().SetDisc(); 543 list<CRef<CSeq_align> >& sas_data = sas.Set(); 545 for(size_t i = 0; i < num_exons; ++i) { 547 CRef<CSeq_align> sa (new CSeq_align); 550 sa->SetType(CSeq_align::eType_global); 553 CRef<CScore> score (new CScore); 554 score->SetId().SetStr("splign"); 555 score->SetValue().SetReal(scores[i]); 556 CSeq_align::TScore& scorelist = sa->SetScore(); 557 scorelist.push_back(score); 559 // add percent identity 560 CRef<CScore> idty (new CScore); 561 idty->SetId().SetStr("idty"); 562 idty->SetValue().SetReal(CalcIdentity(transcripts[i])); 563 scorelist.push_back(idty); 565 CDense_seg& ds = sa->SetSegs().SetDenseg(); 567 const size_t* box = &(*(boxes.begin() + i*4)); 568 const TSeqPos query_start = Convert(box[0]); 569 ENa_strand query_strand = box[0] <= box[1]? eNa_strand_plus: 571 const TSeqPos subj_start = Convert(box[2]); 572 ENa_strand subj_strand = box[2] <= box[3]? eNa_strand_plus: 574 ds.FromTranscript(query_start, query_strand, subj_start, subj_strand, 576 // don't

include strands when both are

positive 581

vector< CRef< CSeq_id > > &ids = ds.SetIds();

585

ids.push_back(id_query);

589

ids.push_back(id_subj);

591

sas_data.push_back(sa);

626 const bool

spliced_seg (flag & 0x0001);

627 const bool

with_parts (flag & 0x0002);

669 if

(polya > 0 && polya < query_len) {

674 for

(

size_t i

(0), seg_dim ((*ii).m_Segments.size());

< seg_dim; ++

) {

681 TSeqPos

qmin, qmax, smin, smax;

700

exon->SetProduct_start().SetNucpos(qmin);

701

exon->SetProduct_end().SetNucpos(qmax);

703

exon->SetGenomic_start(smin);

704

exon->SetGenomic_end(smax);

711

score->SetId().SetStr(

"splign"

);

712

score->SetValue().SetReal(seg.

m_score

);

713

scores.push_back(score);

719

score->SetId().SetStr(

"idty"

);

720

score->SetValue().SetReal(seg.

m_idty

);

721

scores.push_back(score);

724 if

(

>0 && !(*ii).m_Segments[

-1].m_exon) {

725

exon->SetPartial(

true

);

728 const size_t

adim (seg.

m_annot

.size());

729 if

(

>0 && (*ii).m_Segments[

-1].m_exon) {

731 if

(adim > 2 && seg.

m_annot

[2] ==

'<'

) {

733

acc.push_back(seg.

m_annot

[0]);

734

acc.push_back(seg.

m_annot

[1]);

735

exon->SetAcceptor_before_exon().SetBases(acc);

739 if

(

+1<seg_dim && !(*ii).m_Segments[

+1].m_exon) {

740

exon->SetPartial(

true

);

743 if

(

+1<seg_dim && (*ii).m_Segments[

+1].m_exon) {

745 if

(adim > 2 && seg.

m_annot

[adim - 3] ==

'>'

) {

747

dnr.push_back(seg.

m_annot

[adim - 2]);

748

dnr.push_back(seg.

m_annot

[adim - 1]);

749

exon->SetDonor_after_exon().SetBases(dnr);

760 "Alignment details not available"

);

780

exons.push_back(exon);

790

uo->

SetType

().SetStr(

"origin"

);

809

vector<size_t> boxes;

810

vector<string> transcripts;

811

vector<float> scores;

813 for

(

size_t i

(0), seg_dim (ii->m_Segments.size());

< seg_dim; ++

) {

818

scores.push_back(seg.

m_score

);

User-defined methods of the data storage class.

void remove_if(Container &c, Predicate *__pred)

static string s_RunLengthEncode(const string &in)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CRef< objects::CSeq_align_set > AsSeqAlignSet(const CSplign::TResults *results=0, int flags=eAF_SplicedSegWithParts) const

Format alignment as a seq-align-set.

CConstRef< objects::CSeq_id > m_QueryId

void SetSeqIds(CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)

CRef< objects::CSeq_align > x_Compartment2SeqAlign(const vector< size_t > &boxes, const vector< string > &transcripts, const vector< float > &scores) const

CSplignFormatter(const CSplign::TResults &results)

string AsExonTable(const CSplign::TResults *results=0, int flags=eTF_None) const

CConstRef< objects::CSeq_id > m_SubjId

const CSplign::TResults m_splign_results

string AsAlignmentText(CRef< objects::CScope > scope, const CSplign::TResults *results=0, size_t line_width=80, int segnum=-1) const

Format alignment as plain text.

CSplign is the central library object for computing spliced cDNA-to-genomic alignments.

static CVersionAPI & s_GetVersion(void)

Retrieve the library's version object.

vector< SAlignedCompartment > TResults

void Print(const CCompactSAMApplication::AlignInfo &ai)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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

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

const_iterator begin(void) const

const_iterator end(void) const

bool IsNull(void) const THROWS_NONE

Check if pointer is null â same effect as Empty().

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static CStringUTF8 AsUTF8(const CTempString &src, EEncoding encoding, EValidate validate=eNoValidate)

Convert into UTF8 from a C/C++ string.

@ fVersionInfo

Print version info.

TData & SetData(void)

Assign a value to Data data member.

void SetLabel(TLabel &value)

Assign a value to Label data member.

TStr & SetStr(void)

Select the variant.

void SetType(TType &value)

Assign a value to Type data member.

void SetData(TData &value)

Assign a value to Data data member.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CScore > > Tdata

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TExons & SetExons(void)

Assign a value to Exons data member.

void SetProduct_strand(TProduct_strand value)

Assign a value to Product_strand data member.

void SetProduct_length(TProduct_length value)

Assign a value to Product_length data member.

void SetDim(TDim value)

Assign a value to Dim data member.

list< CRef< CUser_object > > TExt

void SetType(TType value)

Assign a value to Type data member.

TExt & SetExt(void)

Assign a value to Ext data member.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

list< CRef< CSpliced_exon > > TExons

void SetPoly_a(TPoly_a value)

Assign a value to Poly_a data member.

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

list< CRef< CSpliced_exon_chunk > > TParts

void SetGenomic_strand(TGenomic_strand value)

Assign a value to Genomic_strand data member.

list< CRef< CSeq_align > > Tdata

@ eProduct_type_transcript

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

CRef< CSpliced_exon_chunk > CreateSplicedExonChunk(char cur, size_t count)

void MakeLeftHeader(size_t x, string *ps)

const char g_msg_UnknownTranscriptSymbol[]

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

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