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NCBI C++ ToolKit: src/gui/app/project_tools/projectfilewriter.cpp Source File

<< __LINE__ << endl

;

(!

.is_open()) {

}

(std::exception& e) {

(

<<

<< e.what());

CurrSeg !=

.EndResolved(

, RangeSelector) &&

CurrGi =

(CurrSeg.GetRefSeqid().GetSeqIdOrNull());

}

(std::exception& e) {

cout <<

<< e.what() << endl;

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

EFormat

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

@ eBinaryASN

Binary ASN.1.

@ eGtf

New GTF, CGtfReader.

@ eUnknown

unknown format

bool WriteBioseqHandle(CBioseq_Handle bsh, const string &asmblyName="", const string &asmblyAccession="") override

Write Bioseq contained in given handle Essentially, will write all features that live on the given Bi...

bool WriteSeqAnnotHandle(CSeq_annot_Handle sah, const string &asmblyName="", const string &asmblyAccession="") override

Write Seq-annot contained in given handle Essentially, write out embedded feature table.

bool WriteHeader() override

Write a file header identifying the file content as GFF version 2.

bool x_WriteObject(CNcbiOstream &Out, CConstRef< CSerialObject > Object, ESerialDataFormat Format)

TGi x_GetAnnotId(CConstRef< CSeq_annot > Annot)

bool x_WriteFile(CNcbiOstream &Out, CConstRef< CSerialObject > Object, EFormat Format)

CProjectFileWriter(CRef< CScope > tScope)

bool x_WriteGtf(CNcbiOstream &Out, CConstRef< CSerialObject > Object)

bool WriteFile(const string &Filename, CConstRef< CSerialObject > Object, EFormat Format)

TGi x_GetGi(CConstRef< CSeq_id > Id)

void AddToScope(CConstRef< CSerialObject > Object)

static CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Return a biosequence handle for some kind of id.

virtual bool WriteFooter()

Write a file trailer.

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

Operators to edit gaps in sequences.

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void GetAllTSEs(TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)

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

Add Seq-annot, return its CSeq_annot_Handle.

CSeq_annot_Handle GetSeq_annotHandle(const CSeq_annot &annot, EMissing action=eMissing_Default)

vector< CSeq_entry_Handle > TTSE_Handles

vector< CSeq_id_Handle > TId

SSeqMapSelector & SetRange(TSeqPos start, TSeqPos length)

Set range for iterator.

@ eSeqRef

reference to Bioseq

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice Which(void) const

Which variant is currently selected.

TGi GetGi(void) const

Get the variant data.

@ e_Gi

GenInfo Integrated Database.

const TFtable & GetFtable(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

Defines to provide correct exporting from DLLs in Windows.

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

Magic spell ;-) needed for some weird compilers... very empiric.

void Out(T t, int w, CNcbiOstream &to=cout)

Selector used in CSeqMap methods returning iterators.

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