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CValidator::CCacheImpl Class Reference

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Cache various information for one validation run. More...

#include <objtools/validator/cache_impl.hpp>

+ Collaboration diagram for CValidator::CCacheImpl:

Classes

class  CPubdescInfo
 
struct  SFeatKey
 
struct  SFeatStrKey
 

Public Types

enum  EFeatKeyStr { eFeatKeyStr_Label , eFeatKeyStr_LocusTag }
 
typedef std::vector< CMappedFeatTFeatValue
 
typedef CMappedFeat TFeatToBioseqKey
 
typedef set< CBioseq_HandleTFeatToBioseqValue
 
typedef CConstRef< CSeq_idTIdToBioseqKey
 
typedef CBioseq_Handle TIdToBioseqValue
 

Public Member Functions

const CPubdescInfoGetPubdescToInfo (CConstRef< CPubdesc > pub)
 
const TFeatValueGetFeatFromCache (const SFeatKey &featKey)
 
AutoPtr< TFeatValueGetFeatFromCacheMulti (const vector< SFeatKey > &featKeys)
 
const TFeatValueGetFeatStrKeyToFeats (const SFeatStrKey &feat_str_key, const CTSE_Handle &tse)
 
const TFeatToBioseqValueGetBioseqsOfFeatCache (const TFeatToBioseqKey &feat_to_bioseq_key, const CTSE_Handle &tse)
 
const TIdToBioseqValueGetIdToBioseq (const TIdToBioseqKey &key, const CTSE_Handle &tse)
 
CBioseq_Handle GetBioseqHandleFromLocation (CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)
 
void Clear ()
 

Static Public Attributes

static const CSeqFeatData::E_Choice kAnyFeatType
 
static const CSeqFeatData::ESubtype kAnyFeatSubtype
 
static const CBioseq_Handle kAnyBioseq
 
static const CTSE_Handle kEmptyTSEHandle
 

Private Types

typedef map< CConstRef< CPubdesc >, CConstRef< CPubdescInfo > > TPubdescCache
 
typedef map< SFeatKey, TFeatValueTFeatCache
 
typedef map< SFeatStrKey, TFeatValueTFeatStrKeyToFeatsCache
 
typedef map< TFeatToBioseqKey, TFeatToBioseqValueTFeatToBioseqCache
 
typedef map< TIdToBioseqKey, TIdToBioseqValueTIdToBioseqCache
 

Private Attributes

TPubdescCache m_pubdescCache
 
TFeatCache m_featCache
 
TFeatStrKeyToFeatsCache m_featStrKeyToFeatsCache
 
TFeatToBioseqCache m_featToBioseqCache
 
TIdToBioseqCache m_IdToBioseqCache
 

Static Private Attributes

static const CBioseq_Handle kEmptyBioseqHandle
 
static const TFeatValue kEmptyFeatValue
 

Detailed Description

Cache various information for one validation run.

This is easy because the validator won't change the contents of what it's validating.

Not thread-safe within one CCacheImpl, but it's fine for each thread to have its own CCacheImpl.

Definition at line 125 of file cache_impl.hpp.

Member Typedef Documentation

◆ TFeatCache

Definition at line 251 of file cache_impl.hpp.

◆ TFeatStrKeyToFeatsCache

Definition at line 254 of file cache_impl.hpp.

◆ TFeatToBioseqCache

Definition at line 257 of file cache_impl.hpp.

◆ TFeatToBioseqKey

Definition at line 210 of file cache_impl.hpp.

◆ TFeatToBioseqValue

Definition at line 211 of file cache_impl.hpp.

◆ TFeatValue

Definition at line 164 of file cache_impl.hpp.

◆ TIdToBioseqCache

Definition at line 260 of file cache_impl.hpp.

◆ TIdToBioseqKey

Definition at line 221 of file cache_impl.hpp.

◆ TIdToBioseqValue

Definition at line 222 of file cache_impl.hpp.

◆ TPubdescCache

Definition at line 248 of file cache_impl.hpp.

Member Enumeration Documentation

◆ EFeatKeyStr

Enumerator
eFeatKeyStr_Label 
eFeatKeyStr_LocusTag 

Definition at line 179 of file cache_impl.hpp.

Member Function Documentation

◆ Clear()

void CCacheImpl::Clear ( void  )

◆ GetBioseqHandleFromLocation()

CBioseq_Handle CCacheImpl::GetBioseqHandleFromLocation ( CScope scope,
const CSeq_loc loc,
const CTSE_Handle tse 
)

◆ GetBioseqsOfFeatCache()

const CCacheImpl::TFeatToBioseqValue & CCacheImpl::GetBioseqsOfFeatCache ( const TFeatToBioseqKey feat_to_bioseq_key,
const CTSE_Handle tse 
)

◆ GetFeatFromCache()

const CCacheImpl::TFeatValue & CCacheImpl::GetFeatFromCache ( const SFeatKey featKey)

◆ GetFeatFromCacheMulti()

AutoPtr< CCacheImpl::TFeatValue > CCacheImpl::GetFeatFromCacheMulti ( const vector< SFeatKey > &  featKeys)

◆ GetFeatStrKeyToFeats()

const CCacheImpl::TFeatValue & CCacheImpl::GetFeatStrKeyToFeats ( const SFeatStrKey feat_str_key,
const CTSE_Handle tse 
)

◆ GetIdToBioseq()

const CCacheImpl::TIdToBioseqValue & CCacheImpl::GetIdToBioseq ( const TIdToBioseqKey key,
const CTSE_Handle tse 
)

◆ GetPubdescToInfo()

const CCacheImpl::CPubdescInfo & CCacheImpl::GetPubdescToInfo ( CConstRef< CPubdesc pub)

Member Data Documentation

◆ kAnyBioseq

const CBioseq_Handle CCacheImpl::kAnyBioseq
static

Definition at line 203 of file cache_impl.hpp.

Referenced by GetFeatStrKeyToFeats().

◆ kAnyFeatSubtype

const CSeqFeatData::ESubtype CCacheImpl::kAnyFeatSubtype
static

◆ kAnyFeatType

const CSeqFeatData::E_Choice CCacheImpl::kAnyFeatType
static

◆ kEmptyBioseqHandle

const CBioseq_Handle CCacheImpl::kEmptyBioseqHandle
staticprivate

Definition at line 244 of file cache_impl.hpp.

Referenced by GetBioseqHandleFromLocation().

◆ kEmptyFeatValue

const CCacheImpl::TFeatValue CCacheImpl::kEmptyFeatValue
staticprivate

Definition at line 245 of file cache_impl.hpp.

Referenced by GetFeatFromCache(), and GetFeatStrKeyToFeats().

◆ kEmptyTSEHandle

const CTSE_Handle CCacheImpl::kEmptyTSEHandle
static

Definition at line 237 of file cache_impl.hpp.

Referenced by CValidError_imp::GetTSE_Handle().

◆ m_featCache

TFeatCache CValidator::CCacheImpl::m_featCache
private

Definition at line 252 of file cache_impl.hpp.

Referenced by Clear(), and GetFeatFromCache().

◆ m_featStrKeyToFeatsCache

TFeatStrKeyToFeatsCache CValidator::CCacheImpl::m_featStrKeyToFeatsCache
private

Definition at line 255 of file cache_impl.hpp.

Referenced by Clear(), and GetFeatStrKeyToFeats().

◆ m_featToBioseqCache

TFeatToBioseqCache CValidator::CCacheImpl::m_featToBioseqCache
private

Definition at line 258 of file cache_impl.hpp.

Referenced by Clear(), and GetBioseqsOfFeatCache().

◆ m_IdToBioseqCache

TIdToBioseqCache CValidator::CCacheImpl::m_IdToBioseqCache
private

Definition at line 261 of file cache_impl.hpp.

Referenced by Clear(), and GetIdToBioseq().

◆ m_pubdescCache

TPubdescCache CValidator::CCacheImpl::m_pubdescCache
private

Definition at line 249 of file cache_impl.hpp.

Referenced by Clear(), and GetPubdescToInfo().


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:25:02 2024 by modify_doxy.py rev. 669887