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NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbgilistset.hpp Source File

EGiListType

Gilist types.

TNodeListMap m_PIGNodeListMap

TNodeListMap m_GINodeListMap

Map of filenames to alias node specified GI lists.

void x_ResolveNegativeList(CSeqDBAtlas &atlas, const CSeqDBVolSet &volset, CRef< CSeqDBNegativeList > neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

void x_ResolvePositiveList(CSeqDBAtlas &atlas, const CSeqDBVolSet &volset, CRef< CSeqDBGiList > user_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

CSeqDBGiListSet(CSeqDBAtlas &atlas, const CSeqDBVolSet &vol_set, TListRef user_list, TNegativeRef neg_list, CSeqDBLockHold &locked, const CSeqDBLMDBSet &lmdb_set)

Constructor.

TListRef m_UserList

User-specified GI list.

TNodeListMap m_SINodeListMap

Map of filenames to alias node specified SI lists.

TNegativeRef m_NegativeList

User-specified Negative GI list.

void x_TranslateFromUserList(CSeqDBGiList &gilist)

Translate a volume gilist from the user gilist.

void x_TranslatePigsFromUserList(CSeqDBGiList &gilist)

CSeqDBAtlas & m_Atlas

Memory management layer object.

TNodeListMap m_TINodeListMap

Map of filenames to alias node specified TI lists.

void x_TranslateTisFromUserList(CSeqDBGiList &gilist)

Translate a volume gilists's TIs from the user gilist's TIs.

map< string, TListRef > TNodeListMap

Type used for maps of filenames to ID lists.

void x_TranslateGisFromUserList(CSeqDBGiList &gilist)

Translate a volume gilists's GIs from the user gilist's GIs.

TListRef GetNodeIdList(const CSeqDB_Path &filename, const CSeqDBVol *volp, EGiListType list_type, CSeqDBLockHold &locked)

Get a reference to a named GI list.

CRef< CSeqDBNegativeList > TNegativeRef

Type used for a reference to a GI list.

CRef< CSeqDBGiList > TListRef

Type used for a reference to a GI list.

Uint8 GetMaskOpts() const

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

Defines exception class and several constants for SeqDB.

Manages a set of database volumes.

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