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

assigned =

;

(threeFeatType ==

) {

(threeFeatType ==

) {

(threeFeatType ==

) {

(!pXref->IsSetId() || !pXref->GetId().IsLocal() ||

!pXref->GetId().GetLocal().IsId()) {

featId = pXref->GetId().GetLocal().GetId();

(!bedRecord.SetLocation(mpChrom->GetLocation())) {

(!bedRecord.SetName(mpChrom->GetData())) {

(!bedRecord.SetScore(score)) {

(!bedRecord.SetThick(mpThick->GetLocation())) {

(!bedRecord.SetNoThick(mpChrom->GetLocation())) {

(!bedRecord.SetRgb(

)) {

(!bedRecord.SetBlocks(

mpChrom->GetLocation(), mpBlocks->GetLocation())) {

vector<int>::iterator it = std::find(

vector<int>::iterator it = std::find(

it->AddFeature(feature);

(it->IsRecordComplete());

(!it->GetBedFeature(bedRecord)) {

(!it->GetBedFeature(bedRecord)) {

vector<int>::iterator iit = std::find(

it->mFeatsAll.begin(), it->mFeatsAll.end(), featId);

(iit != it->mFeatsAll.end()) {

.push_back(threeFeatRecord);

colCount,

uFlags ) :

( ! track.

(annot) ) {

& strAssemblyName,

& strAssemblyAccession )

(

aci(seh, sel); aci; ++aci) {

(track.

(*sah.GetCompleteSeq_annot()) ) {

feature::CFeatTree featTree(pMf);

vector<CMappedFeat> vRoots = featTree.GetRootFeatures();

(

pit = vRoots.begin(); pit != vRoots.end(); ++pit) {

(isThreeFeatData) {

feature::CFeatTree& featTree,

);

(!threeFeatManager.

(feature)) {

feature::CFeatTree& featTree,

vector<CMappedFeat> vChildren;

featTree.GetChildrenTo(mf, vChildren);

(

cit = vChildren.begin(); cit != vChildren.end(); ++cit) {

feature::CFeatTree& featTree,

list<CRef<CSeq_interval> >& sublocs = pPackedInt->

().

();

list<CRef<CSeq_interval> >::const_iterator it;

(it = sublocs.begin(); it != sublocs.end(); ++it) {

feature::CFeatTree& featTree,

vector<CMappedFeat> vChildren;

featTree.GetChildrenTo(mf, vChildren);

(

cit = vChildren.begin(); cit != vChildren.end(); ++cit) {

static CRef< CScope > m_Scope

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.

Encapsulation of the BED feature record.

bool AssignName(const CMappedFeat &)

bool Write(CNcbiOstream &, unsigned int)

bool AssignLocation(CScope &, const CSeq_interval &)

bool AssignDisplayData(const CMappedFeat &, bool)

Encapsulation of a track line in the BED file format.

bool Assign(const CSeq_annot &)

bool Write(CNcbiOstream &)

CBedWriter(CScope &scope, CNcbiOstream &ostr, unsigned int colCount=12, unsigned int flags=fNormal)

Constructor.

bool xWriteChildrenThreeFeatData(CThreeFeatManager &, feature::CFeatTree &, const CMappedFeat &)

bool xWriteFeaturesThreeFeatData(CThreeFeatManager &, feature::CFeatTree &, const CMappedFeat &)

bool xWriteFeaturesTracked(const CBedTrackRecord &, feature::CFeatTree &, const CMappedFeat &)

bool WriteAnnot(const CSeq_annot &, const string &="", const string &="") override

Write a raw Seq-annot to the internal output stream.

bool xWriteTrackedAnnot(const CBedTrackRecord &, const CSeq_annot_Handle &)

bool xWriteChildrenTracked(const CBedTrackRecord &, feature::CFeatTree &, const CMappedFeat &)

bool WriteSeqEntryHandle(CSeq_entry_Handle seh, const string &asmblyName="", const string &asmblyAccession="") override

Write a Seq-entry handle to the internal output stream.

namespace ncbi::objects::

bool ProcessRecord(const CSeq_feat &, CBedFeatureRecord &)

RECORD_IT xAddRecord(const CSeq_feat &)

RECORD_IT xFindExistingRecord(const CSeq_feat &)

RECORDS::iterator RECORD_IT

bool AddFeature(const CSeq_feat &)

bool GetAnyRecord(CBedFeatureRecord &)

bool IsRecordComplete(const CSeq_feat &)

bool AddFeature(const CSeq_feat &)

bool GetBedFeature(CBedFeatureRecord &) const

bool IsRecordComplete() const

CRef< CSeq_feat > mpChrom

CRef< CSeq_feat > mpThick

CRef< CSeq_feat > mpBlocks

vector< int > mFeatsFound

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.

static void ChangeToPackedInt(CSeq_loc &loc)

static bool CompareFeatures(const CMappedFeat &lhs, const CMappedFeat &rhs)

static bool GetThreeFeatType(const CSeq_feat &, string &)

static bool GetThreeFeatRgb(const CSeq_feat &, string &)

static bool IsThreeFeatFormat(const CSeq_annot &)

static bool GetThreeFeatScore(const CSeq_feat &, int &)

Defines and provides stubs for a general interface to a variety of file formatters.

virtual SAnnotSelector & SetAnnotSelector(void)

unique_ptr< CGenbankIdResolve > mpIdResolve

#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.

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

Set object to copy of another one.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

void RemoveSeq_annot(const CSeq_annot_Handle &annot)

Revoke Seq-annot previously added using AddSeq_annot().

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

CConstRef< CSeq_annot > GetSeq_annotCore(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool IsInt(void) const

Check if variant Int is selected.

TInt GetInt(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsSetId(void) const

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

const TXref & GetXref(void) const

Get the Xref member data.

const Tdata & Get(void) const

Get the member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool CanGet(void) const

Check if it is safe to call Get method.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TUser & GetUser(void) const

Get the variant data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

bool IsUser(void) const

Check if variant User is selected.

list< CRef< CAnnotdesc > > Tdata

constexpr auto sort(_Init &&init)

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