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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__object__loader_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/loaders/fasta_object_loader.cpp Source File

: m_Params(params), m_FileNames(

)

;

wxString& fn = *it;

(

exception& e) {

rdr.SetCanceler(canceled);

vector<CConstRef<CSeq_id>> wellknown_ids;

vector<CRef<CSeq_entry> >

;

(entry->

()) {

(

= 0;

<

.size(); ++

) {

vector< CRef<CSeq_loc> > expanded_locs;

expanded_locs.push_back(loc_int);

(

loc_iter(loc); loc_iter; ++loc_iter) {

loc_int->

().SetFrom(loc_iter.GetRange().GetFrom());

loc_int->

().SetTo(loc_iter.GetRange().GetTo());

loc_int->

(

);

expanded_locs.push_back(loc_int);

feat->

().SetRegion(

);

feat->

().SetImp().SetKey(

);

feat->

().SetImp().SetDescr(

);

annot->

().SetFtable().push_back(feat);

annot->

().SetLocs().push_back(*iter);

(

&

: wellknown_ids) {

rdr.SetCanceler(canceled);

void LoadFromStream(CNcbiIstream &istr, TObjects &objects, CErrorContainer *errCont=0, ICanceled *canceled=0)

virtual bool Execute(ICanceled &canceled)

CFastaLoadParams m_Params

vector< wxString > m_FileNames

virtual string GetDescription() const

virtual bool PreExecute()

virtual bool PostExecute()

virtual TObjects & GetObjects()

void LoadAlignsFromStream(CNcbiIstream &istr, TObjects &objects, CErrorContainer *errCont=0, ICanceled *canceled=0)

CFastaObjectLoader(const CFastaLoadParams &params)

CRef< objects::CScope > m_Scope

void x_ShowErrorsDlg(const wxString &title)

void x_UpdateHTMLResults(const wxString &object, objects::ILineErrorListener *errCont, const string &exception="", const string &error_msg="", const wxString &objectName=wxT("File:"))

FASTA sequences reader class that does post-processing: * Overrides the local ids; * Removes the well...

CRef< objects::CSeq_entry > ReadSequences(vector< CConstRef< objects::CSeq_id >> *wellknown_ids=nullptr, int max_seqs=kMax_Int, objects::ILineErrorListener *pMessageListener=0)

Read multiple sequences and remove the well-known sequences from the entry.

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Template class for iteration on objects of class C.

Interface for testing cancellation request in a long lasting operation.

vector< SObject > TObjects

Operators to edit gaps in sequences.

static CFastaReader::TFlags s_GetFlags(const CFastaLoadParams &params)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

bool GetReadFirst() const

bool GetForceLocalIDs() const

bool GetMakeDelta() const

int GetLowercaseOption() const

bool GetSkipInvalid() const

bool GetIgnoreGaps() const

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

long TFlags

binary OR of EFlags

@ fDLOptional

Don't require a leading defline.

@ fHyphensIgnoreAndWarn

When a hyphen is encountered in seq data, ignore it but warn.

@ fRequireID

Reject deflines that lack IDs.

@ fAddMods

Parse defline mods and add to SeqEntry.

@ fForceType

Force specified type regardless of accession.

@ fParseRawID

Try to identify raw accessions.

@ fNoSplit

Don't split out ambiguous sequence regions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fParseGaps

Make a delta sequence if gaps found.

@ fOneSeq

Just read the first sequence found.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

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

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

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

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,...

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

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual bool IsCanceled(void) const =0

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static const char label[]

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsNull(void) const

Check if variant Null is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

const TInst & GetInst(void) const

Get the Inst member data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TLength GetLength(void) const

Get the Length member data.

static wxAcceleratorEntry entries[3]

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