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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gff3flybase__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/gff3flybase_writer.cpp Source File

64 #define INSERTION(sf, tf) ( ((sf) & CAlnMap::fSeq) && !((tf) & CAlnMap::fSeq) ) 65 #define DELETION(sf, tf) ( !((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) ) 66 #define MATCH(sf, tf) ( ((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) ) 72 const CScore

& score)

const 76 "Gap"

"ambiguous_orientation"

"consensus_splices"

77 "pct_coverage"

"pct_identity_gap"

"pct_identity_ungap"

81 "ID"

"Target"

"Gap" 84 if

(!score.IsSetId() || !score.GetId().IsStr()) {

87 string key

= score.GetId().GetStr();

88 if

(seqId == mCurrentIdForAttributes &&

89

coreScores.find(

key

) == coreScores.end()) {

92 if

(supportedScores.find(

key

) == supportedScores.end()) {

104 const auto

& seqId = record.

StrSeqId

();

121 for

(

auto

cit = tags.begin();

122

taxonIdStr.empty() && cit != tags.end(); ++cit) {

123 const auto

tag

= **cit;

124 if

tag

.IsSetDb() ||

tag

.GetDb() !=

"taxon"

) {

127 const auto

& objid =

tag

.GetTag();

128 switch

(objid.Which()) {

132 if

(!objid.GetStr().empty()) {

133

taxonIdStr = objid.GetStr();

142 if

(!taxonIdStr.empty()) {

156 const auto

& seqId = record.

StrSeqId

();

165 auto

defline = sequence::CDeflineGenerator().GenerateDefline(bsh);

175 if

(!m_bHeaderWritten) {

176

m_Os <<

"##gff-version 3"

'\n'

;

177

m_Os <<

"#!gff-spec-version 1.20"

'\n'

;

178

m_Os <<

"##!gff-variant flybase"

'\n'

;

179

m_Os <<

"# This variant of GFF3 interprets ambiguities in the"

'\n'

;

180

m_Os <<

"# GFF3 specifications in accordance with the views of Flybase."

'\n'

;

181

m_Os <<

"# This impacts the feature tag set, and meaning of the phase."

'\n'

;

182

m_Os <<

"#!processor NCBI annotwriter"

'\n'

;

183

m_bHeaderWritten =

true

;

197

m_Os <<

"###"

'\n'

;

208 bool

isProteinProd = xSplicedSegHasProteinProd(spliced);

210 const unsigned int

tgtWidth = isProteinProd ? 3 : 1;

221

record.

SetLocation

(seqStart, seqStop, seqStrand);

263 string

seqStrand =

"+"

;

269 string

target = genomicLabel;

270

target +=

" "

+ seqStart;

271

target +=

" "

+ seqStop;

272

target +=

" "

+ seqStrand;

301 typedef

list<CRef<CScore> > SCORES;

304 for

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

306 const CScore

& score = **cit;

332 typedef

vector<CRef<CScore> > SCORES;

334 const

SCORES& scores = align.

GetScore

();

335 for

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

337 const CScore

& score = **cit;

366 catch

(std::exception&) {};

391 catch

(std::exception&) {};

403 while

(start2 < 0 && start_seg < numSegs) {

404

start2 = alnMap.

GetStart

(srcRow, start_seg++);

408 int

stop_seg = numSegs-1;

409 while

(stop2 < 0 && stop_seg >= 0) {

410

stop2 = alnMap.

GetStart

(srcRow, stop_seg--);

414 swap

(start2, stop2);

415

stop2 += alnMap.

GetLen

(start_seg-1)-1;

418

stop2 += alnMap.

GetLen

(stop_seg+1)-1;

440 unsigned int

seqStop = alnMap.

GetSeqStop

(0);

444

record.

SetLocation

(seqStart, seqStop, seqStrand);

455 typedef

vector<CRef<CScore> > SCORES;

460 const

SCORES& scores = denseSeg.

GetScores

();

461 for

(SCORES::const_iterator cit = scores.begin(); cit != scores.end();

463 const CScore

& score = **cit;

482 bool

isProteinProd = xSplicedSegHasProteinProd(spliced);

483 const unsigned int

tgtWidth = isProteinProd ? 3 : 1;

485 typedef

list<CRef<CSpliced_exon_chunk> > CHUNKS;

487 const

CHUNKS& chunks = exon.

GetParts

();

488 for

(CHUNKS::const_iterator cit = chunks.begin(); cit != chunks.end(); ++cit) {

490 switch

(chunk.

Which

()) {

504 const unsigned int

del_length = chunk.

GetGenomic_ins

()/tgtWidth;

505 if

(del_length > 0) {

509 const unsigned int

forward_shift = chunk.

GetGenomic_ins

()%tgtWidth;

510 if

(forward_shift > 0) {

518 const unsigned int

insert_length = chunk.

GetProduct_ins

()/tgtWidth;

519 if

(insert_length > 0) {

523 const unsigned int

reverse_shift = chunk.

GetProduct_ins

()%tgtWidth;

524 if

(reverse_shift > 0) {

550 if

(!align1 && align2) {

554 if

((align1 && !align2) ||

555

(!align1 && !align2) ) {

559 string

subject_accession1;

565 string

subject_accession2;

572 auto

make_key = [](

const

pair<CConstRef<CSeq_align>,

string

>& p,

CScope

& scope) {

574 const string

alignId = p.second;

576 string

subject_accession;

582 string

target_accession;

User-defined methods of the data storage class.

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

const CSeq_id & GetSeqId(TNumrow row) const

TSeqPos GetLen(TNumseg seg, int offset=0) const

const CDense_seg & GetDenseg(void) const

TSeqPos GetSeqStop(TNumrow row) const

int StrandSign(TNumrow row) const

TNumseg GetNumSegs(void) const

TSeqPos GetSeqStart(TNumrow row) const

virtual bool xAssignAlignmentDensegSeqId(CGffAlignRecord &, const CAlnMap &, unsigned int) override

virtual bool xAssignAlignmentSplicedScores(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override

bool xAssignTaxid(CBioseq_Handle, CGffAlignRecord &)

virtual bool xAssignAlignmentDensegLocation(CGffAlignRecord &, const CAlnMap &, unsigned int) override

virtual void x_SortAlignments(TAlignCache &alignCache, CScope &scope) override

virtual bool WriteHeader() override

bool xAssignDefline(CBioseq_Handle, CGffAlignRecord &)

virtual bool xAssignAlignmentSplicedTarget(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override

map< string, string > mDeflineMap

map< string, string > mTaxidMap

string mCurrentIdForAttributes

virtual bool xAssignAlignmentSplicedSeqId(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override

virtual bool xAssignAlignmentSplicedLocation(CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &) override

virtual bool xAssignAlignmentSplicedGap(CGffAlignRecord &record, const CSpliced_seg &spliced, const CSpliced_exon &exon) override

virtual bool xWriteAlignDisc(const CSeq_align &, const string &="") override

bool xIsNeededScore(const std::string &, const CScore &) const

virtual bool xAssignAlignmentScores(CGffAlignRecord &, const CSeq_align &) override

virtual bool xAssignAlignmentDensegScores(CGffAlignRecord &, const CAlnMap &, unsigned int) override

virtual bool xAssignAlignmentDensegTarget(CGffAlignRecord &, const CAlnMap &, unsigned int) override

virtual bool xWriteAlignDisc(const CSeq_align &, const string &="")

void AddInsertion(unsigned int)

void AddMatch(unsigned int)

void AddReverseShift(unsigned int)

void AddDeletion(unsigned int)

void AddForwardShift(unsigned int)

void SetPhase(unsigned int)

void SetSeqId(const string &)

void SetLocation(unsigned int, unsigned int, ENa_strand=objects::eNa_strand_unknown)

bool SetAttribute(const string &, const string &)

void SetScore(const CScore &)

virtual string StrSeqId() const

CProt_pos_Base::TFrame GetFrame() const

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).

const_iterator end() const

const_iterator find(const key_type &key) const

#define MAKE_CONST_SET(name, type,...)

API (CDeflineGenerator) for computing sequences' titles ("definitions").

unsigned int TSeqPos

Type for sequence locations and lengths.

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

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

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

EAccessionInfo

For IdentifyAccession (below)

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.

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,...

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession string for a Seq-id.

@ eGetId_Best

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

@ eGetId_ForceAcc

return only an accession based seq-id

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetId(void) const

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

const TProtpos & GetProtpos(void) const

Get the variant data.

bool IsSetFrame(void) const

position within codon (1-based) 0 = not set (meaning 1) Check if a value has been assigned to Frame d...

bool IsProtpos(void) const

Check if variant Protpos is selected.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

TMatch GetMatch(void) const

Get the variant data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

bool IsSetScores(void) const

score for each seg Check if a value has been assigned to Scores data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

TDiag GetDiag(void) const

Get the variant data.

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

const TParts & GetParts(void) const

Get the Parts member data.

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.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

bool IsSetGenomic_strand(void) const

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

const TScores & GetScores(void) const

Get the Scores member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

const Tdata & Get(void) const

Get the member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

const TScore & GetScore(void) const

Get the Score member data.

const TScores & GetScores(void) const

Get the Scores member data.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetScores(void) const

scores for this exon Check if a value has been assigned to Scores data member.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

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

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ 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

ENa_strand

strand of nucleic acid

@ e_Source

source of materials, includes Org-ref

std::false_type tagStrNocase

const struct ncbi::grid::netcache::search::fields::KEY key

SFlybaseCompareAlignments(CScope &scope)

bool operator()(const pair< CConstRef< CSeq_align >, string > &p1, const pair< CConstRef< CSeq_align >, string > &p2)

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