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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCSparseGraph.html below:

NCBI C++ ToolKit: CSparseGraph Class Reference

#include <gui/widgets/seq_graphic/sparse_graph.hpp>

CSparseGraph () CSparseGraph (const CSparseGraph &data) virtual ~CSparseGraph () void InitFromCompoundID (CCompoundID id) virtual void Init (TGraphCachePool &icache_pool) virtual void Save (TGraphCachePool &icache_pool) bool IsCacheGood () const inline methods More...
void Update (const TSeqRange &range, const TUpdateMap &update) void GetMissingRegions (const TSeqRange &range, vector< TSeqRange > &missing_ranges) 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 void x_WriteMap (ICache &icache, bm::word_t *tb=0) void x_WriteData (ICache &icache, const string &data_key, TSparseVector &sv) void x_ReadMap (ICache &icache, string &tag, string &remote_path, string &last_modified, time_t &last_checked, string &md5, bm::bvector<> &bv, bm::word_t *tb=0) bool x_ReadData (ICache &icache, const string &data_key, const string &tag, TSparseVector &sv, bm::word_t *tb=0) void x_CheckRemoteData () void x_Sync (TGraphCachePool &icache_pool) virtual void DeleteThis (void) Virtual method "deleting" this object. More...

CSparseGraph.

Definition at line 54 of file sparse_graph.hpp.

◆ TSparseVector ◆ TUpdateMap ◆ TValType ◆ CSparseGraph() [1/2] CSparseGraph::CSparseGraph ( ) ◆ CSparseGraph() [2/2]

Definition at line 107 of file sparse_graph.cpp.

References _ASSERT, CTime::AddHour(), data, CTime::eCurrent, m_Data, m_DataMap, m_DataSize, m_IsCacheGood, m_LastChecked, m_LastModified, m_LastSynced, m_NetCacheKey, m_RemotePath, m_SeqId, and m_SessionTag.

◆ ~CSparseGraph() ◆ CreateCompoundID() ◆ GetMissingRegions()

Definition at line 128 of file sparse_graph.cpp.

References bm::bvector< Alloc >::count_range(), first(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, last(), m_DataMap, m_DataMutex, m_DataSize, and mask.

Referenced by CWigGraph::GetDataCoverage(), and CWigGraph::Prefetch().

◆ Init() ◆ InitFromCompoundID() void CSparseGraph::InitFromCompoundID ( CCompoundID id ) ◆ IsCacheGood() bool CSparseGraph::IsCacheGood ( ) const inline ◆ Save()

Reimplemented in CWigGraph.

Definition at line 349 of file sparse_graph.cpp.

References BM_DECLARE_TEMP_BLOCK, data, CStopWatch::Elapsed(), CStopWatch::eStart, CDiagContext::Extra(), GetDiagContext(), m_Data, m_NetCacheKey, CDiagContext_Extra::Print(), sw, x_Sync(), x_WriteData(), and x_WriteMap().

Referenced by CWigGraph::Save().

◆ Update()

Definition at line 335 of file sparse_graph.cpp.

References _ASSERT, data, CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), m_Data, m_DataMap, m_DataMutex, NCBI_THROW, bm::bvector< Alloc >::set_range(), and map_checker< Container >::size().

Referenced by CGraphStatCollector_Graph::UpdateGroup(), and CWigGraph::x_FetchData().

◆ x_CheckRemoteData() void CSparseGraph::x_CheckRemoteData ( ) protected

Definition at line 371 of file sparse_graph.cpp.

References bm::bvector< Alloc >::clear(), data, CTime::eCurrent, NStr::eNocase, CDiagContext::Extra(), GetDiagContext(), CUrlUtils::GetLastModified(), CUrlUtils::IfModifiedSince(), m_Data, m_DataMap, m_DataMutex, m_IsCacheGood, m_LastChecked, m_LastModified, m_RemotePath, CDiagContext_Extra::Print(), NStr::StartsWith(), and t.

◆ x_ReadData()

Definition at line 508 of file sparse_graph.cpp.

References buffer, ERR_POST, Error(), eUnknown, CRWStreambuf::fOwnReader, ICache::GetReadStream(), ICache::GetSize(), int, NCBI_THROW, NcbiEmptyString, ncbi::grid::netcache::search::fields::size, bm::sparse_vector_deserialize(), tag, and val.

◆ x_ReadMap()

Definition at line 447 of file sparse_graph.cpp.

References CChecksum::AddChars(), buffer, bm::bvector< Alloc >::clear(), bm::deserialize(), CChecksum::eMD5, eUnknown, CRWStreambuf::fOwnReader, CChecksum::GetMD5Digest(), ICache::GetReadStream(), ICache::GetSize(), int, m_NetCacheKey, md5(), NCBI_THROW, NcbiEmptyString, ncbi::grid::netcache::search::fields::size, tag, and val.

◆ x_Sync()

Definition at line 204 of file sparse_graph.cpp.

References BM_DECLARE_TEMP_BLOCK, data, ERR_POST, Error(), CDiagContext::Extra(), f, GetDiagContext(), max(), md5(), NcbiEmptyString, CDiagContext_Extra::Print(), s_GetMD5Tag(), and tag.

Referenced by Init(), and Save().

◆ x_WriteData()

Definition at line 431 of file sparse_graph.cpp.

References bm::sparse_vector_serial_layout< SV >::buf(), eUnknown, CRWStreambuf::fOwnWriter, ICache::GetWriteStream(), int, m_SessionTag, NCBI_THROW, NcbiEmptyString, bm::sparse_vector_serial_layout< SV >::size(), bm::sparse_vector_serialize(), and val.

Referenced by Save().

◆ x_WriteMap() ◆ m_Data

map of sprasvectors, the key is used as a part of suffix of NetCache key (m_NetCacheKey + "_" + this map key

Definition at line 88 of file sparse_graph.hpp.

Referenced by CPileUpGraph::CPileUpGraph(), CSparseGraph(), CWigGraph::CWigGraph(), CWigGraph::GetData(), CPileUpGraph::GetNumberOfReads(), CWigGraph::Init(), Save(), CWigGraph::Save(), Update(), CPileUpGraph::UpdateAlignStats(), x_CheckRemoteData(), CWigGraph::x_DecodeDelta(), and CWigGraph::x_FetchSummary().

◆ m_DataMap ◆ m_DataMutex mutex CSparseGraph::m_DataMutex protected ◆ m_DataSize size_t CSparseGraph::m_DataSize = 0 protected ◆ m_IsCacheGood ◆ m_LastChecked time_t CSparseGraph::m_LastChecked = 0 protected ◆ m_LastModified string CSparseGraph::m_LastModified protected ◆ m_LastSynced CTime CSparseGraph::m_LastSynced protected ◆ m_NetCacheKey string CSparseGraph::m_NetCacheKey protected ◆ m_RemotePath string CSparseGraph::m_RemotePath protected ◆ m_SeqId ◆ m_SessionTag string CSparseGraph::m_SessionTag protected

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

include/gui/widgets/seq_graphic/sparse_graph.hpp
src/gui/widgets/seq_graphic/sparse_graph.cpp

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