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NCBI C++ ToolKit: src/objmgr/split_parser.cpp Source File

(

.IsSetSkeleton() && tse.HasNoSeq_entry() ) {

( content.

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=

.GetCount();

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=

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<

Func>

: m_Chunk(chunk), m_TypeMask(type_mask)

m_Chunk.x_AddDescInfo(m_TypeMask,

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operator()(

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m_Chunk.x_AddDescInfo(m_TypeMask,

);

FAddAnnotPlace

m_Chunk.x_AddAnnotPlace(

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operator()(

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m_Chunk.x_AddAnnotPlace(

);

m_Chunk.x_AddBioseqId(

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FAddAssemblyInfo

m_Chunk.x_AddAssemblyInfo(

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&

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void SetNamed(const string &name)

CID2S_Bioseq_place_Info –.

CID2S_Bioseq_set_Ids –.

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

CID2S_Seq_annot_place_Info –.

CID2S_Seq_assembly_Info –.

CID2S_Seq_descr_Info –.

CID2S_Seq_feat_Ids_Info –.

CID2S_Seq_id_Interval –.

CID2S_Sequence_Piece –.

Data loader exceptions, used by GenBank loader.

vector< TLocation > TLocationSet

static void x_ParseLocation(TLocationSet &vec, const CID2S_Seq_loc &loc)

static void Load(CTSE_Chunk_Info &chunk, const CID2S_Chunk &data)

pair< TLocationId, TLocationRange > TLocation

static void x_AddGiInterval(TLocationSet &vec, TGi gi, TSeqPos start, TSeqPos length)

CRange< TSeqPos > TLocationRange

static CRef< CTSE_Chunk_Info > Parse(const CID2S_Chunk_Info &info)

static void x_AddInterval(TLocationSet &vec, const TLocationId &id, TSeqPos start, TSeqPos length)

static void x_AddWhole(TLocationSet &vec, const TLocationId &id)

static void x_Attach(CTSE_Chunk_Info &chunk, const CID2S_Seq_descr_Info &descr)

static void x_AddGiWhole(TLocationSet &vec, TGi gi)

void x_AddXref_ids(const SAnnotTypeSelector &type, const TFeatIdIntList &ids)

pair< TBioseqId, TBioseq_setId > TPlace

void x_LoadAnnot(const TPlace &place, const CSeq_annot &annot)

void x_LoadBioseqs(const TPlace &place, const list< CRef< CBioseq > > &bioseqs)

void x_LoadAssembly(const TBioseqId &seq_id, const TAssembly &assembly)

void x_LoadSequence(const TPlace &place, TSeqPos pos, const TSequence &seq)

void x_AddBioseqPlace(TBioseq_setId id)

void x_LoadDescr(const TPlace &place, const CSeq_descr &descr)

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

void x_AddSeq_data(const TLocationSet &location)

void AddChunk(CTSE_Chunk_Info &chunk_info)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X_ONCE(err_subcode, message)

Error posting only once during program execution with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

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

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

list< CRef< CID2S_Sequence_Piece > > TSeq_map

TCount GetCount(void) const

Get the Count member data.

const TSeq_id_ints & GetSeq_id_ints(void) const

Get the variant data.

list< CRef< CID2S_Chunk_Info > > TChunks

const TGi_range & GetGi_range(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TWhole_gi_range & GetWhole_gi_range(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSeq_annot_place & GetSeq_annot_place(void) const

Get the variant data.

const TLoc_set & GetLoc_set(void) const

Get the variant data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

TStart GetStart(void) const

Get the Start member data.

list< CRef< C_E > > Tdata

const TBioseqs & GetBioseqs(void) const

Get the Bioseqs member data.

const TFeat_ids & GetFeat_ids(void) const

Get the variant data.

TLength GetLength(void) const

Get the Length member data.

bool IsSetBioseq_sets(void) const

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

list< CRef< CID2S_Interval > > TInts

const TInts & GetInts(void) const

Get the Ints member data.

const TSeq_data & GetSeq_data(void) const

Get the variant data.

TWhole_gi GetWhole_gi(void) const

Get the variant data.

const TSeq_loc & GetSeq_loc(void) const

Get the Seq_loc member data.

list< CRef< CID2S_Seq_loc > > TLoc_set

bool IsSetBioseq_sets(void) const

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

const TGi_interval & GetGi_interval(void) const

Get the variant data.

list< CRef< CID2S_Feat_type_Info > > TFeat_types

list< CRef< CID2S_Feat_type_Info > > TXref_types

const TBioseqs & GetBioseqs(void) const

Get the Bioseqs member data.

TStart GetStart(void) const

Get the Start member data.

bool IsSetName(void) const

name is set if this is named annot name may be empty which differ from unnamed annot Check if a value...

const TInts & GetInts(void) const

Get the Ints member data.

const TXref_types & GetXref_types(void) const

Get the Xref_types member data.

TStart GetStart(void) const

Get the Start member data.

const TFeat_types & GetFeat_types(void) const

Get the Feat_types member data.

bool IsSetGraph(void) const

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

list< CRef< CID2S_Bioseq_place_Info > > TBioseq_place

const TLocal_str_ids & GetLocal_str_ids(void) const

Get the Local_str_ids member data.

list< CRef< CID2S_Feat_type_Info > > TFeat

bool IsSetAlign(void) const

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

const TBioseq_place & GetBioseq_place(void) const

Get the variant data.

list< CRef< CID2S_Chunk_Data > > TData

list< CRef< CID2S_Interval > > TInts

TStart GetStart(void) const

Get the Start member data.

TType_mask GetType_mask(void) const

Get the Type_mask member data.

const Tdata & Get(void) const

Get the member data.

bool IsSetLocal_str_ids(void) const

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

const TSeq_descr & GetSeq_descr(void) const

Get the variant data.

const TBioseq_sets & GetBioseq_sets(void) const

Get the Bioseq_sets member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetLocal_ids(void) const

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

TGi GetGi(void) const

Get the Gi member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

bool IsSetBioseqs(void) const

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

const TName & GetName(void) const

Get the Name member data.

TGi GetGi(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TFeat & GetFeat(void) const

Get the Feat member data.

const TSeq_id_interval & GetSeq_id_interval(void) const

Get the variant data.

const TSeq_assembly & GetSeq_assembly(void) const

Get the variant data.

const TLocal_ids & GetLocal_ids(void) const

Get the Local_ids member data.

E_Choice Which(void) const

Which variant is currently selected.

TBioseq_set GetBioseq_set(void) const

Get the Bioseq_set member data.

const TSeq_ids & GetSeq_ids(void) const

Get the Seq_ids member data.

const TBioseqs & GetBioseqs(void) const

Get the Bioseqs member data.

TLength GetLength(void) const

Get the Length member data.

const TSeq_id & GetSeq_id(void) const

Get the variant data.

const TWhole_seq_id & GetWhole_seq_id(void) const

Get the variant data.

const TSeq_annot & GetSeq_annot(void) const

Get the variant data.

list< CRef< CSeq_annot > > TAnnots

const TBioseq_sets & GetBioseq_sets(void) const

Get the Bioseq_sets member data.

list< CRef< CID2S_Seq_feat_Ids_Info > > TFeat_ids

TGi GetGi(void) const

Get the Gi member data.

list< CRef< CID2S_Sequence_Piece > > TSeq_data

TStart GetStart(void) const

Get the Start member data.

const TGi_ints & GetGi_ints(void) const

Get the variant data.

bool IsSetBioseqs(void) const

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

list< CRef< CID2S_Chunk_Content > > TContent

E_Choice Which(void) const

Which variant is currently selected.

TLength GetLength(void) const

Get the Length member data.

@ e_Whole_gi

whole sequence by gi

@ e_Loc_set

combination of locations

@ e_Seq_id_ints

set of intervals on the same id

@ e_Whole_seq_id

whole sequence by Seq-id

@ e_Seq_id_interval

interval on sequence by Seq-id

@ e_Gi_ints

set of intervals on the same gi

@ e_Whole_gi_range

set of whole sequences by gis

@ e_Gi_interval

interval on sequence by gi

@ e_not_set

No variant selected.

@ e_Seq_annot_place

place of Seq-annots

@ e_not_set

No variant selected.

@ e_Seq_descr

place of Seq-descrs

@ e_Seq_data

place of sequence data

@ e_Seq_assembly

place of assembly history

@ e_Bioseq_place

place of Bioseqs

@ e_Seq_annot

locations and types of annotations

@ e_Feat_ids

ids of features

@ e_Bioseq_set

Bioseq-set id.

E_Choice

Choice variants.

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void split(std::vector< std::string > *strVec, const std::string &str_, const std::string &split_)

NCBI_DEFINE_ERR_SUBCODE_X(1)

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