NCBI C++ ToolKit
Public Member Functions | Static Public Member Functions | List of all members
CPileUpGraph Class Reference

Search Toolkit Book for CPileUpGraph

CPileUpGraph. More...

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

+ Inheritance diagram for CPileUpGraph:
+ Collaboration diagram for CPileUpGraph:

Public Member Functions

 CPileUpGraph (const string &data_key)
 
void UpdateAlignStats (const TSeqRange &range, float window, CAlnStatGlyph::TStatVec &stats)
 
int GetNumberOfReads (const TSeqRange &range)
 
- Public Member Functions inherited from CSparseGraph
 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)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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...
 
- Public Member Functions inherited from CDebugDumpable
 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
 

Static Public Member Functions

static string GetStorageName ()
 
static string CreateCacheKey (objects::CScope &scope, const objects::CSeq_id &seq_id, const string &remote_path)
 CPileUpGraph. More...
 
- Static Public Member Functions inherited from CSparseGraph
static CCompoundID CreateCompoundID (objects::CScope &scope, const objects::CSeq_id &seq_id, const string &remote_path)
 CSparseGraph. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Additional Inherited Members

- Public Types inherited from CSparseGraph
using TValType = uint64_t
 
typedef map< string, vector< TValType > * > TUpdateMap
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Types inherited from CSparseGraph
typedef bm::sparse_vector< TValType, bm::bvector<> > TSparseVector
 
- Protected Member Functions inherited from CSparseGraph
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)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CSparseGraph
string m_SessionTag
 A current session tag, used to separate session netcache blobs from the blobs saved by other sessions. More...
 
string m_NetCacheKey
 data access key More...
 
bm::bvector m_DataMap
 bvector shows the regions m_Data exist More...
 
string m_SeqId
 NCBI seq_id, e.g. NC_000001. More...
 
size_t m_DataSize = 0
 size of each vector of m_Data More...
 
map< string, unique_ptr< TSparseVector > > m_Data
 map of sprasvectors, the key is used as a part of suffix of NetCache key (m_NetCacheKey + "_" + this map key More...
 
mutex m_DataMutex
 data access mutex More...
 
string m_RemotePath
 path to remote data or srz accession More...
 
string m_LastModified
 timestamp of the remote data last modified date as reported by www server More...
 
time_t m_LastChecked = 0
 timestamp: last time when m_LastModified was checked More...
 
bool m_IsCacheGood = true
 false value indicates that remote data were updated and the cache was reset More...
 
CTime m_LastSynced
 

Detailed Description

CPileUpGraph.

Definition at line 100 of file sparse_graph.hpp.

Constructor & Destructor Documentation

◆ CPileUpGraph()

CPileUpGraph::CPileUpGraph ( const string data_key)

Member Function Documentation

◆ CreateCacheKey()

string CPileUpGraph::CreateCacheKey ( objects::CScope &  scope,
const objects::CSeq_id &  seq_id,
const string remote_path 
)
static

◆ GetNumberOfReads()

int CPileUpGraph::GetNumberOfReads ( const TSeqRange range)

◆ GetStorageName()

static string CPileUpGraph::GetStorageName ( )
inlinestatic

Definition at line 103 of file sparse_graph.hpp.

◆ UpdateAlignStats()

void CPileUpGraph::UpdateAlignStats ( const TSeqRange range,
float  window,
CAlnStatGlyph::TStatVec stats 
)

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:31 2024 by modify_doxy.py rev. 669887