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NCBI_DEFINE_ERR_SUBCODE_X (1) BEGIN_NAMESPACE (objects) unsigned x_SetBitCount (Uint8 v) void x_SetOS8 (vector< char > &os, Uint8 data) void x_AdjustRange (CRange< TSeqPos > &range, const CSNPDbSeqIterator &it) TSeqPos x_RoundPos (TSeqPos pos, TSeqPos step) TSeqPos x_RoundPosUp (TSeqPos pos, TSeqPos step) void x_RoundRange (CRange< TSeqPos > &range, TSeqPos step) void x_AdjustGraphRange (CRange< TSeqPos > &range, const CSNPDbSeqIterator &it, const TSeqPos comp) CRef< CSeq_annot > x_NewAnnot (const string &annot_name=kDefaultAnnotName) void x_CollectOverviewGraph (SGraphMaker &g, const CSNPDbSeqIterator &seq_it, CRange< TSeqPos > range, SGraphMaker::EGraphSet graph_set, SGraphMaker::EGapsType gaps_type) void x_CollectCoverageGraph (SGraphMaker &g, const CSNPDbSeqIterator &seq_it, CRange< TSeqPos > range, SGraphMaker::EGraphSet graph_set) CRef< CSeqTable_column > x_MakeColumn (CSeqTable_column_info::EField_id id, const char *name=0) CRef< CSeqTable_column > x_MakeColumn (const char *name) template<size_t ValueSize> static bool x_IsStringConstant (const string &str, const char(&value)[ValueSize]) template<class T > static T & x_GetPrivate (CRef< T > &ref) static CObject_id & x_GetObject_id (CRef< CObject_id > &cache, const char *name) template<class Values > bool sx_HasNonZero (const Values &values, TSeqPos index, TSeqPos count) template<class TValues > void sx_AddBits2 (vector< char > &bits, TSeqPos bit_values, TSeqPos pos_index, const TValues &values) static void sx_AddBits (vector< char > &bits, TSeqPos kChunkSize, const CSeq_graph &graph) TSeqPos sx_CalcFeatChunkPages (const CSNPDbSeqIterator &it) string sx_CombineWithZoomLevel (const string &acc, int zoom_level) template<class Cont > Cont::value_type::TObjectType & sx_AddNew (Cont &cont) void sx_SetZoomLevel (CSeq_annot &annot, int zoom_level) void sx_SetOverviewName (CSeq_annot &annot, CSNPDbSeqIterator::TFlags flags, const string &annot_name, int overview_zoom) END_NAMESPACE (objects) ◆ ALLELE_CACHE ◆ NCBI_USE_ERRCODE_X #define NCBI_USE_ERRCODE_X SNPReaderDefinition at line 74 of file snpread.cpp.
◆ RC_NO_MORE_ALIGNMENTS #define RC_NO_MORE_ALIGNMENTS RC(rcApp, rcQuery, rcSearching, rcRow, rcNotFound)Definition at line 80 of file snpread.cpp.
◆ x_SetStringConstant #define x_SetStringConstant ( obj, Field, value ) Value:}
#define NCBI_NAME2(Name1, Name2)
Name concatenation macro with two names.
const TYPE & Get(const CNamedParameterList *param)
const GenericPointer< typename T::ValueType > T2 value
static bool x_IsStringConstant(const string &str, const char(&value)[ValueSize])
Definition at line 2515 of file snpread.cpp.
◆ BEGIN_NAMESPACE() BEGIN_NAMESPACE ( objects ) ◆ END_NAMESPACE() END_NAMESPACE ( objects ) ◆ NCBI_DEFINE_ERR_SUBCODE_X() NCBI_DEFINE_ERR_SUBCODE_X ( 1 ) ◆ sx_AddBits()Definition at line 2783 of file snpread.cpp.
References _ASSERT, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CSeq_interval_Base::GetFrom(), CSeq_graph_Base::GetGraph(), CSeq_loc_Base::GetInt(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_interval::GetLength(), CSeq_graph_Base::GetLoc(), CSeq_graph_Base::GetNumval(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), CSeq_graph_Base::C_Graph::IsByte(), kChunkSize, and sx_AddBits2().
Referenced by CSNPDbSeqIterator::GetEntry(), and CSNPDbSeqIterator::GetSplitInfoAndVersion().
◆ sx_AddBits2() ◆ sx_AddNew()template<class Cont >
Cont::value_type::TObjectType& sx_AddNew ( Cont & cont ) ◆ sx_CalcFeatChunkPages() ◆ sx_CombineWithZoomLevel() ◆ sx_HasNonZero() ◆ sx_SetOverviewName() void sx_SetOverviewName ( CSeq_annot & annot, CSNPDbSeqIterator::TFlags flags, const string & annot_name, int overview_zoom ) ◆ sx_SetZoomLevel() ◆ x_AdjustGraphRange() ◆ x_AdjustRange() ◆ x_CollectCoverageGraph() ◆ x_CollectOverviewGraph() ◆ x_GetObject_id() ◆ x_GetPrivate() ◆ x_IsStringConstant()template<size_t ValueSize>
◆ x_MakeColumn() [1/2] ◆ x_MakeColumn() [2/2] ◆ x_NewAnnot() ◆ x_RoundPos() ◆ x_RoundPosUp() ◆ x_RoundRange() ◆ x_SetBitCount() unsigned x_SetBitCount ( Uint8 v ) inline ◆ x_SetOS8() void x_SetOS8 ( vector< char > & os, Uint8 data ) inline ◆ BEGIN_LOCAL_NAMESPACE ◆ BEGIN_NCBI_NAMESPACE ◆ BEGIN_STD_NAMESPACE ◆ END_LOCAL_NAMESPACE ◆ END_NCBI_NAMESPACE ◆ END_STD_NAMESPACE ◆ kChunkIdFeat ◆ kChunkIdGraph ◆ kChunkIdMul ◆ kCoverageZoom ◆ kDefaultAnnotName const char kDefaultAnnotName[] = "SNP" static ◆ kDefaultFeatChunkPages ◆ kFeatChunksPerGraphChunk ◆ kFeatSubtypesToChars const char kFeatSubtypesToChars[] = "U-VSMLDIR" static ◆ kMaxSNPLength ◆ kMaxTableAlleles ◆ kOverviewZoom ◆ kPage2FeatErrorWorkaround ◆ kPageSizeDefinition at line 82 of file snpread.cpp.
Referenced by CSNPDb_Impl::CSNPDb_Impl(), CSNPDb_Impl::GetPageSize(), CSNPDbSeqIterator::GetSNPRange(), CSNPDbGraphIterator::Select(), CSNPDbPageIterator::Select(), CScoringJob::x_CalculateAlignmentScores(), x_CollectCoverageGraph(), CSNPDbFeatIterator::x_GetGraphVDBRowId(), CSNPDb_Impl::x_GetGraphVDBRowId(), CSNPDbPageIterator::x_Next(), and CSNPDb_Impl::x_Update().
◆ kPreloadSeqList ◆ kTargetFeatsPerChunk ◆ kTSEIdRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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