NCBI C++ ToolKit
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
CSRSearch_Impl< index_t > Class Template Reference

Search Toolkit Book for CSRSearch_Impl

#include "sr_search_impl.hpp"
(Private to src/algo/blast/dbindex_search.)

+ Inheritance diagram for CSRSearch_Impl< index_t >:
+ Collaboration diagram for CSRSearch_Impl< index_t >:

Public Member Functions

 CSRSearch_Impl (CRef< CDbIndex > index, TSeqPos d, TSeqPos dfuzz)
 
- 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
 

Private Types

typedef index_t TIndex
 
typedef TIndex::TOffsetIterator TIter
 

Private Member Functions

virtual void search (const SSearchData &sdata, TResults &results)
 
void copyOffsets (TSRResults &resutls, TIter &offsets)
 
void mergeOffsets (TSRResults &resutls, TIter &offsets, Uint4 step)
 
void setResults4Idx (Uint4 idx, bool fw_strand, CResCache &res_cache, vector< TIter > &single_res_cache, const vector< TSeqPos > &positions)
 
bool searchExact (const CSeqVector &seq, const vector< TSeqPos > &positions, bool fw_strand, TSRResults &results, TSeqPos &max_pos, vector< TIter > &cache, vector< Uint1 > &cache_set)
 
bool searchOneMismatch (const CSeqVector &seq, const vector< TSeqPos > &positions, Uint4 max_pos, bool fw_strand, CMismatchResultsInfo &results_info, vector< TIter > &scache, const vector< Uint1 > &scache_set, CResCache &cache)
 

Private Attributes

TIndexindex_impl_
 
vector< TItersingle_res_cache [2]
 
vector< Uint1single_res_cache_set [2]
 
vector< TIterscache1 [2]
 
vector< TIterscache2 [2]
 
vector< Uint1scache_set1 [2]
 
vector< Uint1scache_set2 [2]
 

Additional Inherited Members

- Public Types inherited from CSRSearch
enum  ELevel {
  PE , PM , SE , SM ,
  EM
}
 
typedef CDbIndex::TSeqNum TSeqNum
 
typedef SResults TResults
 
typedef vector< SSRResultTSRResults
 
typedef pair< SSRResult, SSRResultTSRPairedResult
 
typedef vector< TSRPairedResultTSRPairedResults
 
typedef vector< SMismatchResultsEntryTMismatchResults
 
- 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 Member Functions inherited from CSRSearch
static CRef< CSRSearchMakeSRSearch (CRef< CDbIndex > index, TSeqPos d=0, TSeqPos dfuzz=0)
 
- 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)
 
- Static Public Attributes inherited from CSRSearch
static const Uint4 TSRRESULTS_INISIZE = 1000000UL
 
static const Uint4 TSRPAIRS_INISIZE = 10000UL
 
- 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 Member Functions inherited from CSRSearch
 CSRSearch (CRef< CDbIndex > index, TSeqPos d, TSeqPos dfuzz)
 
vector< TSeqPosGetQNmerPositions (TSeqPos sz) const
 
Uint4 getNMer (const CSeqVector &seq, TSeqPos pos, bool fw, bool &ambig) const
 
Uint4 getNMer (const CSeqVector &seq, TSeqPos pos, bool fw, bool &ambig, TSeqPos sub_pos, Uint1 sub_letter) const
 
pair< TSeqPos, TSeqPosPos2Index (TSeqPos pos, TSeqPos sz, SMismatchInfo &mismatch_info) const
 
void mergeResults (TSRResults &results, const TSRResults &src, Int4 step)
 
void combine (const TSRResults &results_1, const TSRResults &results_2, TSRPairedResults &results, Int4 adjust=0)
 
pair< TSeqNum, TSeqPosMapSOff (TSeqNum lid, TSeqPos loff, TSeqPos sz, bool &overlap) const
 
bool reportResults (TResults &r, Uint4 nr, TSeqPos qsz1, TSeqPos qsz2, const TSRPairedResults &results, bool fw1, bool fw2, bool mismatch1=false, bool mismatch2=false, TSeqPos mismatch_pos1=0, TSeqPos mismatch_pos2=0, Uint1 mismatch_letter1=(Uint1)'-', Uint1 mismatch_letter2=(Uint1)'-', Uint4 adjustment1=0, Uint4 adjustment2=0)
 
bool reportResults (TResults &r, Uint4 nr, TSeqPos qsz, const TSRResults &results, bool fw, bool mismatch=false, TSeqPos mismatch_pos=0, Uint1 mismatch_letter=(Uint1)'-', Uint4 adjustment=0, Uint4 pos_in_pair=0)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CSRSearch
unsigned long hkey_width_
 
SHKData hk_data_
 

Detailed Description

template<typename index_t>
class CSRSearch_Impl< index_t >

Definition at line 47 of file sr_search_impl.hpp.

Member Typedef Documentation

◆ TIndex

template<typename index_t >
typedef index_t CSRSearch_Impl< index_t >::TIndex
private

Definition at line 49 of file sr_search_impl.hpp.

◆ TIter

template<typename index_t >
typedef TIndex::TOffsetIterator CSRSearch_Impl< index_t >::TIter
private

Definition at line 60 of file sr_search_impl.hpp.

Constructor & Destructor Documentation

◆ CSRSearch_Impl()

template<typename index_t >
CSRSearch_Impl< index_t >::CSRSearch_Impl ( CRef< CDbIndex index,
TSeqPos  d,
TSeqPos  dfuzz 
)
inline

Definition at line 53 of file sr_search_impl.hpp.

Member Function Documentation

◆ copyOffsets()

template<typename index_t >
void CSRSearch_Impl< index_t >::copyOffsets ( TSRResults resutls,
TIter offsets 
)
private

Definition at line 148 of file sr_search_impl.hpp.

References offset, and r().

◆ mergeOffsets()

template<typename index_t >
void CSRSearch_Impl< index_t >::mergeOffsets ( TSRResults resutls,
TIter offsets,
Uint4  step 
)
private

Definition at line 163 of file sr_search_impl.hpp.

References CSRSearch::SSRResult::seqnum, and CSRSearch::SSRResult::soff.

◆ search()

template<typename index_t >
void CSRSearch_Impl< index_t >::search ( const SSearchData sdata,
TResults results 
)
privatevirtual

◆ searchExact()

template<typename index_t >
bool CSRSearch_Impl< index_t >::searchExact ( const CSeqVector seq,
const vector< TSeqPos > &  positions,
bool  fw_strand,
TSRResults results,
TSeqPos max_pos,
vector< TIter > &  cache,
vector< Uint1 > &  cache_set 
)
private

Definition at line 204 of file sr_search_impl.hpp.

References ambig(), i, and ncbi::grid::netcache::search::fields::key.

◆ searchOneMismatch()

template<typename index_t >
bool CSRSearch_Impl< index_t >::searchOneMismatch ( const CSeqVector seq,
const vector< TSeqPos > &  positions,
Uint4  max_pos,
bool  fw_strand,
CMismatchResultsInfo results_info,
vector< TIter > &  scache,
const vector< Uint1 > &  scache_set,
CResCache cache 
)
private

◆ setResults4Idx()

template<typename index_t >
void CSRSearch_Impl< index_t >::setResults4Idx ( Uint4  idx,
bool  fw_strand,
CResCache res_cache,
vector< TIter > &  single_res_cache,
const vector< TSeqPos > &  positions 
)
private

Definition at line 104 of file sr_search_impl.hpp.

References CSRSearch::CResCache::at(), i, r(), and CSRSearch::CResCache::set().

Member Data Documentation

◆ index_impl_

template<typename index_t >
TIndex& CSRSearch_Impl< index_t >::index_impl_
private

Definition at line 93 of file sr_search_impl.hpp.

◆ scache1

template<typename index_t >
vector< TIter > CSRSearch_Impl< index_t >::scache1[2]
private

Definition at line 96 of file sr_search_impl.hpp.

◆ scache2

template<typename index_t >
vector< TIter > CSRSearch_Impl< index_t >::scache2[2]
private

Definition at line 97 of file sr_search_impl.hpp.

◆ scache_set1

template<typename index_t >
vector< Uint1 > CSRSearch_Impl< index_t >::scache_set1[2]
private

Definition at line 98 of file sr_search_impl.hpp.

◆ scache_set2

template<typename index_t >
vector< Uint1 > CSRSearch_Impl< index_t >::scache_set2[2]
private

Definition at line 99 of file sr_search_impl.hpp.

◆ single_res_cache

template<typename index_t >
vector< TIter > CSRSearch_Impl< index_t >::single_res_cache[2]
private

Definition at line 94 of file sr_search_impl.hpp.

◆ single_res_cache_set

template<typename index_t >
vector< Uint1 > CSRSearch_Impl< index_t >::single_res_cache_set[2]
private

Definition at line 95 of file sr_search_impl.hpp.


The documentation for this class was generated from the following file:
Modified on Tue Feb 27 05:55:46 2024 by modify_doxy.py rev. 669887