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NCBI C++ ToolKit: include/gui/objutils/na_utils.hpp Source File

GetAlignType(

objects::CSeq_align& align,

objects::CScope& scope);

GetFeatSubtypes(

objects::CSeq_annot& annot,

IsGeneModelFeature(

,

subtype);

FeatSubtypes2TrackSubtypes(

& subtypes,

objects::CSeq_annot& annot);

GetSeqTableSubtype(

& headers);

(

objects::CSeq_annot& annot, objects::CScope& scope);

DataType2TrackType(

& annot_type,

& subtype,

EMetaDataSource_EmptyAfterFilteringRequest

EUidsSource_EmptyRequest

(

objects::CSeq_id&

, objects::CScope& scope);

GetAllNAAs(

& naas,

&

=

)

;

filtering =

,

isGetLinks =

)

;

filtering =

,

isGetLinks =

)

;

* canceledCallback = 0)

;

GetNATrackInfo(

& track_info,

& naa)

;

& naas)

;

SetMaxNAs(

);

x_GetNAId(

&uid,

& naa,

x_GetAllNAIdsWithContext(

&uids,

&

)

;

isIncremental =

);

x_SearchNAIds(

&uids,

& naas,

filtering,

Utilities for data/track type discovery.

Interface for testing cancellation request in a long lasting operation.

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

map< string, TGis > TEntrezIdtoGiCache

x_GetAllGIs(): NA uid+dbfrom to GIs which are associated with this NA

TGi m_Gi

GI of m_TargetSeq; it may be ZERO_GI for one of two reasons: either a target seq is not given at all ...

CTrackInfo::TTrackInfoList TTrackInfoList

objects::CBioseq_Handle m_BioseqHandle

Derived values which make sense only if m_TargetSeq is set.

static TNAAtoUidCache sm_NAAtoUidCache

static CTrackInfo::TTrackInfoList GetTrackInfo(const objects::CSeq_annot &annot, objects::CScope &scope)

EMetaDataSource

source of obtained NA metadata were internal caches hit, partially hit or totally missed during some ...

vector< TEntrezId > TEntrezIds

CNAUtils(const objects::CSeq_id &id)

Ctor with target sequence id.

string TNAA

typedefs for NAA meta-data

static TEntrezIdtoGiCache sm_UidtoGiCache

CRef< objects::CScope > m_Scope

Scope helping resolve sequences and retrieve annotations.

map< string, CRef< CAnnotMetaData > > TNAMetaDataSet

map< TEntrezId, CRef< CAnnotMetaData > > TEntrezIdtoMetaDataCache

x_GetNAMetaData() NAA numeric uid to CAnnotMetaData

CNAUtils(const objects::CSeq_id &id, objects::CScope &scope)

Ctor with target sequence id and a scope.

DECLARE_CLASS_STATIC_FAST_MUTEX(sm_UidtoGiCacheMutex)

map< TNAA, TEntrezId > TNAAtoUidCache

caching of eutils-related data: x_GetNAId(): NAA string to its numeric uid

objects::CSeq_id_Handle m_SeqIdHandle

sequence handles

static CTrackInfo::TTrackInfoList GetTrackInfo(objects::CSeq_annot_Handle annot_handle)

Get data track information from a seq-annot.

DECLARE_CLASS_STATIC_FAST_MUTEX(sm_UidtoMetaDataCacheMutex)

DECLARE_CLASS_STATIC_FAST_MUTEX(sm_NAAtoUidCacheMutex)

CSeqUtils::TEntrezIds TEntrezIds

int m_MaxNAMeta

maximal number of NAAs for retrieving meta-data.

static TEntrezIdtoMetaDataCache sm_UidtoMetaDataCache

EEntrezDB

eutils databases that can be used

list< CRef< CTrackInfo > > TTrackInfoList

CConstRef< objects::CSeq_id > m_TargetSeq

The target sequence associating with the NAAs.

set< TGi > TGis

get all GIs for a given NA accession

@ EMetaDataSource_EmptyRequest

#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.

#define NCBI_GUIOBJUTILS_EXPORT

const struct ncbi::grid::netcache::search::fields::SIZE size

const struct ncbi::grid::netcache::search::fields::SUBKEY subkey

static CS_CONTEXT * context

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