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

: m_Params(params), m_FileNames(

)

;

= 0;

(annot_name.empty()) {

wxString& fn = *it;

fmt =

.GuessFormat();

fileName =

(wxFileName(fn).GetFullName());

reader->SetCanceler(&canceled);

reader->ReadSeqAnnots(annots,

.GetIstream(), errCont.

());

(annot_name.empty())

(*annot_iter)->SetNameDesc(

);

.emplace_back(**annot_iter,

,

+ fileName);

(gff2 && gff2->AtSequenceData()) {

(

exception& e) {

EFormat

The formats are checked in the same order as declared here.

@ eGff2

GFF2, CGff2Reader, any GFF-like that doesn't fit the others.

@ eGtf

New GTF, CGtfReader.

@ eGff3

GFF3, CGff3Reader.

string GetAssemblyAcc() const

bool GetUseMapping() const

void x_CreateMapper(const string &assembly)

void x_UpdateMap(objects::CSeq_annot &annot)

bool x_ShowMappingDlg(IObjectLoader::TObjects &objects)

@ fNumericIdsAsLocal

numeric identifiers are local IDs

@ fAllIdsAsLocal

all identifiers are local IDs

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.

Interface for testing cancellation request in a long lasting operation.

vector< SObject > TObjects

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#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 & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

virtual TObjects & GetObjects()

wxString GetNameFeatSet() const

vector< wxString > m_FileNames

CGffObjectLoader(const CGffLoadParams &params, const vector< wxString > &filenames)

virtual string GetDescription() const

virtual bool Execute(ICanceled &canceled)

virtual bool PostExecute()

CMapAssemblyParams GetMapAssembly() const

int GetParseSeqIds() const

int GetFileFormat() const

virtual bool PreExecute()

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

@ fQuickIDCheck

Just check local IDs' first characters.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

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

static const char label[]

string ToStdString(const wxString &s)

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