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NCBI C++ ToolKit: CVCFVariantsBase Class Reference

Search Toolkit Book for CVCFVariantsBase

#include <gui/widgets/loaders/columnar_vcf_variants_base.hpp>

virtual ~CVCFVariantsBase () const CVariantDescriptors & GetDescriptors () const unsigned GetPositionForIndex (const size_t &index) const size_t GetIndexForPosition (const unsigned &pos, CPosToIndex::EType type) const virtual bool GetPositionsForVariant (const string &variant_id, vector< unsigned > &positions)=0 virtual void GetPositionsForMissingVarID (vector< unsigned > &positions)=0 TSeqPos GetStart () const TSeqPos GetStop () const unsigned Count () const unsigned Count (const TSeqRange &range) const void GetHistogram (svector &hist, const svector::size_type &bin_width) const void GetHistogram (TIndexVector &hist, const svector::size_type &bin_width) bool operator== (const CVCFVariantsBase &other) const void ListPositionVectors (CNcbiOstream &out) const TSeqPos GetLeftShiftedStartPos (const TSeqRange &range) const const vector< size_t > * GetIncludedItems () const unique_ptr< vector< size_t > > Filter (const TSeqRange &range) const CVCFVariantsBase (const CVCFVariantsBase &)=delete CVCFVariantsBase & operator= (const CVCFVariantsBase &)=delete size_t GetNumberOfIndexVecs () const const size_t & GetMaxIndex () const const unsigned & GetMaxFeatLength () const CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const CVCFVariantsBase () CVCFVariantsBase (bool load_info, const set< string > &info_fields, const map< unsigned, string > &sample_cols) void x_SerializeData () const void x_DeserializeAllData () void x_DeserializeIndexVectors (const unsigned char *&buf_ptr, size_t &nr_cols, bool skip_feat_length=false) void x_DeserializeDescr_All (const unsigned char *buf_ptr, const size_t &nr_cols) void x_DeserializeDescr_Range (const unsigned char *buf_ptr, const size_t &nr_cols, const TSeqRange *range=nullptr, const set< string > &cols_to_decode=set< string >(), bool only_start=false) bool x_DeserializeColumn (const string &col_name, const unsigned char *buf_ptr, const size_t &nr_cols) unique_ptr< vector< size_t > > x_Filter (const TSeqPos &pos) const Returns a vector of indices of the variants that cross sequence position 'pos'. More...
unique_ptr< vector< size_t > > x_NullOrFilterClinVar (const TSeqPos &pos) const virtual void DeleteThis (void) Virtual method "deleting" this object. More...

Definition at line 233 of file columnar_vcf_variants_base.hpp.

◆ svector ◆ TIndexVector ◆ TSparseOptVector ◆ TSparseStrVector ◆ ~CVCFVariantsBase() CVCFVariantsBase::~CVCFVariantsBase ( ) virtual ◆ CVCFVariantsBase() [1/3] ◆ CVCFVariantsBase() [2/3] ◆ CVCFVariantsBase() [3/3] ◆ Count() [1/2] unsigned CVCFVariantsBase::Count ( void ) const

Definition at line 833 of file columnar_vcf_variants_base.cpp.

References CPosToIndex::eMax, CPosToIndex::eMin, CPosToIndex::GetIndexForPosition(), m_Posindexmap, m_StartPos, m_StopPos, and m_VarsWithinRange.

Referenced by CVCFVariantList::CVCFVariantList(), CVcfFeatureDS::GetFeaturesCountInRange(), CTableDataVcfJob::Run(), CVcfLoadingJob::x_CreateColumnarVCFProjectItem(), CVcfFeatureJob::x_Execute(), CColumnarVCFReaderApp::x_LoadSerializedData(), CVcfLoadingJob::x_OnVCFVariantListReady(), and x_SerializeData().

◆ Count() [2/2] ◆ Filter() unique_ptr< vector< size_t > > CVCFVariantsBase::Filter ( const TSeqRange & range ) const ◆ GetDescriptors() ◆ GetHistogram() [1/2]

Definition at line 983 of file columnar_vcf_variants_base.cpp.

References BM_DECLARE_TEMP_BLOCK, bm::sparse_vector< Val, BV >::clear(), count, bm::sparse_vector< Val, BV >::get_back_inserter(), CPosToIndex::GetIndexVectors(), m_Posindexmap, n, bm::sparse_vector< Val, BV >::optimize(), and ncbi::grid::netcache::search::fields::size.

Referenced by CVcfFeatureJob::x_Execute().

◆ GetHistogram() [2/2]

Definition at line 1025 of file columnar_vcf_variants_base.cpp.

References BM_DECLARE_TEMP_BLOCK, bm::rsc_sparse_vector< Val, SV >::clear(), count, CPosToIndex::GetIndexVectors(), bm::rsc_sparse_vector< Val, SV >::load_from(), m_Posindexmap, n, bm::rsc_sparse_vector< Val, SV >::optimize(), bm::sparse_vector< Val, BV >::set(), ncbi::grid::netcache::search::fields::size, bm::rsc_sparse_vector< Val, SV >::sync(), and bm::use_null.

◆ GetIncludedItems() const vector<size_t>* CVCFVariantsBase::GetIncludedItems ( ) const inline ◆ GetIndexForPosition() ◆ GetLeftShiftedStartPos() ◆ GetMaxFeatLength() const unsigned& CVCFVariantsBase::GetMaxFeatLength ( ) const inline ◆ GetMaxIndex() const size_t& CVCFVariantsBase::GetMaxIndex ( ) const inline ◆ GetNumberOfIndexVecs() size_t CVCFVariantsBase::GetNumberOfIndexVecs ( ) const inline ◆ GetPositionForIndex() unsigned CVCFVariantsBase::GetPositionForIndex ( const size_t & index ) const ◆ GetPositionsForMissingVarID() ◆ GetPositionsForVariant() ◆ GetStart() TSeqPos CVCFVariantsBase::GetStart ( void ) const inline ◆ GetStop() TSeqPos CVCFVariantsBase::GetStop ( void ) const inline ◆ ListPositionVectors() void CVCFVariantsBase::ListPositionVectors ( CNcbiOstream & out ) const ◆ operator=() ◆ operator==() ◆ s_GetAllColNames() const vector< string > & CVCFVariantsBase::s_GetAllColNames ( ) static

contains sm_INFO, sm_SAMPLES

Definition at line 802 of file columnar_vcf_variants_base.cpp.

References sm_ALT, sm_FILTER, sm_FORMAT, sm_ID, sm_INFO, sm_QUAL, sm_REF, and sm_SAMPLES.

Referenced by CVCFVariantList::ParseLine(), CTableDataVcfJob::Run(), and CColumnarVCFReaderApp::x_LoadSerializedData().

◆ s_GetColNames() const vector< string > & CVCFVariantsBase::s_GetColNames ( ) static

does not contain sm_INFO and sm_SAMPLES

Definition at line 791 of file columnar_vcf_variants_base.cpp.

References sm_ALT, sm_FILTER, sm_FORMAT, sm_ID, sm_QUAL, and sm_REF.

Referenced by CVariantDescriptors::CVariantDescriptors(), CVCFVariantList::DeserializeAndCheck(), CVCFVariantList::GetStatistics(), CVariantDescriptors::InitInserters(), CVCFVariantList::RemoveSerializedOutput(), CVCFVariantList::SerializeVariantData(), x_DeserializeColumn(), x_DeserializeDescr_All(), x_DeserializeDescr_Range(), CVCFVariant_CI::x_Init(), and x_SerializeData().

◆ s_GetCurrentVersion() ◆ s_GetPreviousVersion() string CVCFVariantsBase::s_GetPreviousVersion ( ) static ◆ x_DeserializeAllData() void CVCFVariantsBase::x_DeserializeAllData ( ) protected ◆ x_DeserializeColumn() bool CVCFVariantsBase::x_DeserializeColumn ( const string & col_name, const unsigned char * buf_ptr, const size_t & nr_cols ) protected

Definition at line 1659 of file columnar_vcf_variants_base.cpp.

References _ASSERT, NStr::EqualNocase(), Error(), i, LOG_POST, m_Descriptors, m_Deserializer, m_OptDeserializer, NCBI_THROW, s_GetColNames(), and CVariantDescriptors::SetInfoField().

Referenced by CVCFVariantList::CVCFVariantList(), CVCFSlicedVariants::GetPositionsForMissingVarID(), and CVCFSlicedVariants::GetPositionsForVariant().

◆ x_DeserializeDescr_All() void CVCFVariantsBase::x_DeserializeDescr_All ( const unsigned char * buf_ptr, const size_t & nr_cols ) protected

Definition at line 1529 of file columnar_vcf_variants_base.cpp.

References _ASSERT, bm::bv_ref_vector< BV >::add_vectors(), bm::sparse_vector_deserializer< SV >::deserialize(), bm::sparse_vector_deserializer< SV >::deserialize_structure(), CPosToIndex::GetMaxIndex(), CPosToIndex::GetPositionForIndex(), CVariantDescriptors::GetSample(), CVariantDescriptors::GetSampleNames(), i, m_Descriptors, m_Deserializer, m_OptDeserializer, m_Posindexmap, m_StartPos, m_StopPos, NCBI_THROW, s_GetColNames(), bm::sparse_vector_deserializer< SV >::set_xor_ref(), CVariantDescriptors::SetInfoField(), CVariantDescriptors::SetNumberofInfoFields(), CVariantDescriptors::SetNumberofSampleCols(), CVariantDescriptors::SetSample(), and sm_ID.

Referenced by x_DeserializeAllData().

◆ x_DeserializeDescr_Range()

Definition at line 1725 of file columnar_vcf_variants_base.cpp.

References _ASSERT, bm::bv_ref_vector< BV >::add_vectors(), bm::sparse_vector_deserializer< SV >::deserialize(), bm::sparse_vector_deserializer< SV >::deserialize_range(), bm::sparse_vector_deserializer< SV >::deserialize_structure(), CPosToIndex::eMax, CPosToIndex::eMin, set< Key, Compare >::empty(), COpenRange< Position >::Empty(), set< Key, Compare >::end(), set< Key, Compare >::find(), CRange_Base::GetFrom(), CPosToIndex::GetIndexForPosition(), GetLeftShiftedStartPos(), CVariantDescriptors::GetSample(), CVariantDescriptors::GetSampleNames(), CRange_Base::GetTo(), i, m_Descriptors, m_Deserializer, m_MaxFeatLength, CPosToIndex::m_MaxStoredIndex, m_OptDeserializer, m_Posindexmap, m_StartPos, m_StopPos, m_VarsWithinRange, NCBI_THROW, s_GetColNames(), bm::sparse_vector_deserializer< SV >::set_xor_ref(), CVariantDescriptors::SetInfoField(), CVariantDescriptors::SetNumberofInfoFields(), CVariantDescriptors::SetNumberofSampleCols(), CVariantDescriptors::SetSample(), sm_INFO, sm_SAMPLES, and x_Filter().

Referenced by CVCFSlicedVariants::CVCFSlicedVariants().

◆ x_DeserializeIndexVectors() void CVCFVariantsBase::x_DeserializeIndexVectors ( const unsigned char *& buf_ptr, size_t & nr_cols, bool skip_feat_length = false ) protected ◆ x_Filter() unique_ptr< vector< size_t > > CVCFVariantsBase::x_Filter ( const TSeqPos & pos ) const protected

Returns a vector of indices of the variants that cross sequence position 'pos'.

Definition at line 876 of file columnar_vcf_variants_base.cpp.

References bm::str_sparse_vector< CharType, BV, STR_SIZE >::begin(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::end(), CVariantDescriptors::GetInfoField(), CVariantDescriptors::IsSetInfoField(), m_Descriptors, util::strcmp(), NStr::StringToUInt(), and x_NullOrFilterClinVar().

Referenced by Count(), Filter(), and x_DeserializeDescr_Range().

◆ x_NullOrFilterClinVar() unique_ptr< vector< size_t > > CVCFVariantsBase::x_NullOrFilterClinVar ( const TSeqPos & pos ) const protected ◆ x_SerializeData() void CVCFVariantsBase::x_SerializeData ( ) const protected

Definition at line 1090 of file columnar_vcf_variants_base.cpp.

References _ASSERT, bm::compute_sim_matrix_plan_builder< BV >::build_plan(), Count(), count, bm::sparse_vector_serializer< SV >::enable_xor_compression(), CVariantDescriptors::GetInfoField(), CVariantDescriptors::GetInfoFieldNames(), CVariantDescriptors::GetSample(), CVariantDescriptors::GetSampleNames(), Info(), bm::sparse_vector_serializer< SV >::is_xor_ref(), LOG_POST, m_Buffer, m_Descriptors, CPosToIndex::m_Indices, m_MaxFeatLength, m_Posindexmap, bm::thread_pool_executor< TPool >::run(), s_GetColNames(), bm::sparse_vector_serializer< SV >::serialize(), bm::sparse_vector_serializer< SV >::set_bookmarks(), total_size, and NStr::UIntToString().

Referenced by CVCFVariantList::GetSerializedData(), and CVCFVariantList::WriteSerializedData().

◆ m_Buffer vector<char>* CVCFVariantsBase::m_Buffer { nullptr } mutableprotected ◆ m_Descriptors

Definition at line 355 of file columnar_vcf_variants_base.hpp.

◆ m_Deserializer ◆ m_MaxFeatLength unsigned CVCFVariantsBase::m_MaxFeatLength { 0 } protected ◆ m_OptDeserializer ◆ m_Posindexmap

Definition at line 356 of file columnar_vcf_variants_base.hpp.

◆ m_StartPos TSeqPos CVCFVariantsBase::m_StartPos { 0 } protected ◆ m_StopPos TSeqPos CVCFVariantsBase::m_StopPos { 0 } protected ◆ m_VarsWithinRange unique_ptr<vector<size_t> > CVCFVariantsBase::m_VarsWithinRange protected ◆ sm_ALT ◆ sm_FILTER ◆ sm_FORMAT ◆ sm_ID

Definition at line 242 of file columnar_vcf_variants_base.hpp.

Referenced by CVCFVariantList::AreVariantIdsUnique(), CVCFVariantList::CVCFVariantList(), CVCFVariantList::FinalizeReading(), CVCFSlicedVariants::GetPositionsForMissingVarID(), CVCFSlicedVariants::GetPositionsForVariant(), CVCFVariant_CI::GetVariantID(), s_DoSearch(), s_GetAllColNames(), s_GetColNames(), x_DeserializeDescr_All(), and CVcfFeatureJob::x_Execute().

◆ sm_INFO ◆ sm_MissingValue ◆ sm_QUAL ◆ sm_REF ◆ sm_SAMPLES

The documentation for this class was generated from the following files:

include/gui/widgets/loaders/columnar_vcf_variants_base.hpp
src/gui/widgets/loaders/columnar_vcf_variants_base.cpp

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