NCBI C++ ToolKit
CSearch< LEGACY, NHITS > Member List

This is the complete list of members for CSearch< LEGACY, NHITS >, including all inherited members.

AddIonsToHit(CMSHits *Hit, CMSHit *MSHit)CSearch< LEGACY, NHITS >protected
AddModsToHit(CMSHits *Hit, CMSHit *MSHit)CSearch< LEGACY, NHITS >protected
CSearch_Base::AddReference(void) constCObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::AddReference(void) constCObjectinline
CThread::AddReference(void) constCObjectinline
Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)CSerialObjectvirtual
CalcModIndex(int *ModIndex, int &iMod, int &NumMod, int NumFixed, int NumModSites, CMod CModList[])CSearch< LEGACY, NHITS >inlineprotected
CalcNSort(TScoreList &ScoreList, double Threshold, CMSPeak *Peaks)CSearch< LEGACY, NHITS >protected
CSearch_Base::CanBeDeleted(void) const THROWS_NONECObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanBeDeleted(void) const THROWS_NONECObjectinline
CThread::CanBeDeleted(void) const THROWS_NONECObjectinline
CSearch_Base::CanGetHits(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetHits(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetMessage(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetMessage(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetQuery_id(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetQuery_id(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetQuery_len(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetQuery_len(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetQuery_title(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetQuery_title(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CanGetStat(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CanGetStat(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::CDebugDumpable(void)CDebugDumpableinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CDebugDumpable(void)CDebugDumpableinline
CThread::CDebugDumpable(void)CDebugDumpableinline
CheckFixed(int i, int NumFixed, CMod ModList[], int *ModIndex)CSearch< LEGACY, NHITS >protected
CSearch_Base::CheckReferenceOverflow(TCount count) constCObjectprivate
ClearLadderCalc(int Max)CSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::CObject(void)CObject
CSearch_Base::CObject(const CObject &src)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CObject(void)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CObject(const CObject &src)CObject
CThread::CObject(void)CObject
CThread::CObject(const CObject &src)CObject
CSearch_Base::code_bits_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::code_bits_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CompareLadders(int iMod, CMSPeak *Peaks, bool OrLadders, const TMassPeak *MassPeak)CSearch< LEGACY, NHITS >protected
CompareLaddersTop(int iMod, CMSPeak *Peaks, const TMassPeak *MassPeak)CSearch< LEGACY, NHITS >protected
CSearch_Base::ComputeSeeds()CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ComputeSeeds()CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CopySettings(CRef< CSearch > fromObj)CSearch< LEGACY, NHITS >
CountModSites(int &NumModSites, int NumMod, CMod ModList[])CSearch< LEGACY, NHITS >protected
CreateLadders(const char *Sequence, int iSearch, int position, int endposition, int *Masses, int iMissed, CAA &AA, int iMod, CMod ModList[], int NumMod)CSearch< LEGACY, NHITS >protected
CreateModCombinations(int Missed, const char *PepStart[], int Masses[], int EndMasses[], int NumMod[], int NumMassAndMask[], int NumModSites[], CMod ModList[][32])CSearch< LEGACY, NHITS >protected
CreateSequence(int Start, int Stop, string &seqstring, CSeqDBSequence &Sequence)CSearch< LEGACY, NHITS >protected
CSearch(void)CSearch< LEGACY, NHITS >inline
CSearch(const CSearch &value)CSearch< LEGACY, NHITS >private
CSearch(const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)CSearch< LEGACY, NHITS >inline
CSearch(int tNum)CSearch< LEGACY, NHITS >
CSearch_Base::CSearch_Base(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base::CSearch_Base(const CSearch_Base &)CSearch_Base< LEGACY, NHITS, derived_t >private
CSearch_Base::CSearch_Base(const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CSearch_Base(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CSearch_Base(const TIndex_Impl &index_impl, const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const TSearchOptions &options)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::CSerialObject(void)CSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CSerialObject(void)CSerialObject
CThread(void)CThread
CThread(const CThread &)CThreadprivate
DebugDump(CDebugDumpContext ddc, unsigned int depth) constCSerialObjectvirtual
CSearch_Base::DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) constCDebugDumpable
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) constCDebugDumpable
CThread::DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) constCDebugDumpable
CSearch_Base::DebugDumpText(ostream &out, const string &bundle, unsigned int depth) constCDebugDumpable
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::DebugDumpText(ostream &out, const string &bundle, unsigned int depth) constCDebugDumpable
CThread::DebugDumpText(ostream &out, const string &bundle, unsigned int depth) constCDebugDumpable
CSearch_Base::DECLARE_INTERNAL_TYPE_INFO()CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::DECLARE_INTERNAL_TYPE_INFO()CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
DecodeOffset(TWord offset)CSearch< LEGACY, NHITS >inline
DeleteThis(void)CObjectprotectedvirtual
DeleteVariableOverlap(int &NumMod, CMod ModList[])CSearch< LEGACY, NHITS >protected
Detach(void)CThread
Discard(void)CThread
DoDeleteThisObject(void)CObjectvirtual
DoNotDeleteThisObject(void)CObjectvirtual
DoubleCompare(list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward, list< CMSMatchedPeakSet * > &Double, bool DoubleForward)CSearch< LEGACY, NHITS >protected
CSearch_Base::DumpToConsole(void) constCDebugDumpable
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::DumpToConsole(void) constCDebugDumpable
CThread::DumpToConsole(void) constCDebugDumpable
CSearch_Base::E_memberIndex enum nameCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::E_memberIndex enum nameCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::EAllocFillMode enum nameCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::EAllocFillMode enum nameCObject
CThread::EAllocFillMode enum nameCObject
CSearch_Base::eAllocFillNone enum valueCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eAllocFillNone enum valueCObject
CThread::eAllocFillNone enum valueCObject
CSearch_Base::eAllocFillPattern enum valueCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eAllocFillPattern enum valueCObject
CThread::eAllocFillPattern enum valueCObject
CSearch_Base::eAllocFillZero enum valueCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eAllocFillZero enum valueCObject
CThread::eAllocFillZero enum valueCObject
CSearch_Base::eCounterBitsCanBeDeletedCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterBitsCanBeDeletedCObjectstatic
CThread::eCounterBitsCanBeDeletedCObjectstatic
CSearch_Base::eCounterBitsInPlainHeapCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterBitsInPlainHeapCObjectstatic
CThread::eCounterBitsInPlainHeapCObjectstatic
CSearch_Base::eCounterBitsPlaceMaskCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterBitsPlaceMaskCObjectstatic
CThread::eCounterBitsPlaceMaskCObjectstatic
CSearch_Base::eCounterStateMaskCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterStateMaskCObjectstatic
CThread::eCounterStateMaskCObjectstatic
CSearch_Base::eCounterStepCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterStepCObjectstatic
CThread::eCounterStepCObjectstatic
CSearch_Base::eCounterValidCObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::eCounterValidCObjectstatic
CThread::eCounterValidCObjectstatic
CSearch_Base::EnableDebugDump(bool on)CDebugDumpablestatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::EnableDebugDump(bool on)CDebugDumpablestatic
CThread::EnableDebugDump(bool on)CDebugDumpablestatic
EnzymeCSearch< LEGACY, NHITS >private
Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) constCSerialObjectvirtual
ERunMode enum nameCThread
Exit(void *exit_data)CThreadstatic
CSearch_Base::ExtendLeft(TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) constCSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ExtendLeft(TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::ExtendRight(TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) constCSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ExtendRight(TTrackedSeed &seed, TSeqPos nmax=~(TSeqPos) 0) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
FixedModsCSearch< LEGACY, NHITS >private
fRunAllowST enum valueCThread
fRunBound enum valueCThread
fRunCloneRequestContext enum valueCThread
fRunDefault enum valueCThread
fRunDetached enum valueCThread
fRunNice enum valueCThread
fRunUnbound enum valueCThread
CSearch_Base::GetAllocFillMode(void)CObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetAllocFillMode(void)CObjectstatic
CThread::GetAllocFillMode(void)CObjectstatic
GetCurrentThread(void)CThreadstatic
GetEnzyme(void) constCSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::GetHits(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetHits(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
GetIterative(void) constCSearch< LEGACY, NHITS >inline
GetLadderCalc(int i) constCSearch< LEGACY, NHITS >inlineprotected
GetLadderContainer(void) constCSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::GetMessage(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetMessage(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::GetNamespaceName(void) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetNamespaceName(void) constCSerialObject
CSearch_Base::GetNamespacePrefix(void) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetNamespacePrefix(void) constCSerialObject
Getnumseq(void) constCSearch< LEGACY, NHITS >inlineprotected
GetOidSet(void) constCSearch< LEGACY, NHITS >inlineprotected
GetPoissonOnly(void) constCSearch< LEGACY, NHITS >inline
CSearch_Base::GetQuery_id(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetQuery_id(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::GetQuery_len(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetQuery_len(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::GetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::GetQuery_title(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetQuery_title(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
GetRequest(void) constCSearch< LEGACY, NHITS >inlineprotected
GetResponse(void) constCSearch< LEGACY, NHITS >inlineprotected
GetRestrictedSearch(void) constCSearch< LEGACY, NHITS >inlineprotected
GetSelf(void)CThreadstatic
GetSettings(void) constCSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::GetStat(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::GetStat(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
GetSystemID(TThreadSystemID *id)CThreadstatic
GetThisTypeInfo(void) const =0CSerialObjectpure virtual
GetThreadHandle()CThreadinlineprotected
GetThreadsCount()CThreadinlinestatic
CSearch_Base::HasNamespaceName(void) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::HasNamespaceName(void) constCSerialObject
CSearch_Base::HasNamespacePrefix(void) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::HasNamespacePrefix(void) constCSerialObject
CSearch_Base::index_impl_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::index_impl_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
InitBlast(const char *blastdb, bool use_mmap=false)CSearch< LEGACY, NHITS >
initCallbackCSearch< LEGACY, NHITS >private
initCallbackDataCSearch< LEGACY, NHITS >private
CSearch_Base::InitCounter(void)CObjectinlineprivate
InitializeMainThreadId(void)CThreadstatic
InitLadders(std::list< EMSIonSeries > &Ions)CSearch< LEGACY, NHITS >protected
InitModIndex(int *ModIndex, int &iMod, int NumMod, int NumModSites, CMod ModList[])CSearch< LEGACY, NHITS >inlineprotected
initModsetCSearch< LEGACY, NHITS >private
initRequestInCSearch< LEGACY, NHITS >private
initResponseInCSearch< LEGACY, NHITS >private
initSettingsInCSearch< LEGACY, NHITS >private
CSearch_Base::InvalidObject(void) constCObjectprivate
CSearch_Base::IsAllocatedInPool(void) const THROWS_NONECObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsAllocatedInPool(void) const THROWS_NONECObjectinline
CThread::IsAllocatedInPool(void) const THROWS_NONECObjectinline
IsAppExiting(void)CThreadinlinestatic
iSearchGlobalCSearch< LEGACY, NHITS >privatestatic
IsMain(void)CThreadstatic
CSearch_Base::IsSetHits(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetHits(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetMessage(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetMessage(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetQuery_id(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetQuery_id(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetQuery_len(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetQuery_len(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetQuery_masking(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetQuery_title(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetQuery_title(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::IsSetStat(void) constCSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::IsSetStat(void) constCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
IsTerminated(void) constCThreadinline
IterativeCSearch< LEGACY, NHITS >private
Join(void **exit_data=0)CThread
LadderCalcCSearch< LEGACY, NHITS >private
LadderContainerCSearch< LEGACY, NHITS >private
CSearch_Base::locs_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::locs_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::m_CounterCObjectmutableprivate
m_ExitDataCThreadprivate
m_HandleCThreadprivate
CSearch_Base::m_HitsCSearch_Base< LEGACY, NHITS, derived_t >private
m_IsDetachedCThreadprivate
m_IsJoinedCThreadprivate
m_IsRunCThreadprivate
m_IsTerminatedCThreadprivate
CSearch_Base::m_MessageCSearch_Base< LEGACY, NHITS, derived_t >private
m_ParentRequestContextCThreadprivate
CSearch_Base::m_Query_idCSearch_Base< LEGACY, NHITS, derived_t >private
CSearch_Base::m_Query_lenCSearch_Base< LEGACY, NHITS, derived_t >private
CSearch_Base::m_Query_maskingCSearch_Base< LEGACY, NHITS, derived_t >private
CSearch_Base::m_Query_titleCSearch_Base< LEGACY, NHITS, derived_t >private
m_SelfRefCThreadprivate
CSearch_Base::m_set_StateCSearch_Base< LEGACY, NHITS, derived_t >private
CSearch_Base::m_StatCSearch_Base< LEGACY, NHITS, derived_t >private
Main(void)CSearch< LEGACY, NHITS >virtual
MakeBoolMap(bool *ModMask, int *ModIndex, int &iMod, int &NumMod)CSearch< LEGACY, NHITS >inlineprotected
MakeBoolMask(int *ModIndex, int iMod)CSearch< LEGACY, NHITS >inlineprotected
MakeIntFromBoolMap(bool *ModMask, int &NumMod)CSearch< LEGACY, NHITS >inlineprotected
MakeModString(string &seqstring, string &modseqstring, CMSHit *MSHit)CSearch< LEGACY, NHITS >protectedstatic
MakeOidSet(void)CSearch< LEGACY, NHITS >protected
MassAndMaskCSearch< LEGACY, NHITS >private
MassArrayCSearch< LEGACY, NHITS >private
MatchAndSort(CMSPeak *Peaks, CMSHit &Hit, EMSPeakListTypes Which, int minintensity, const TSeriesChargePairList::const_iterator &iPairList, list< CMSMatchedPeakSet * > &SingleForward, list< CMSMatchedPeakSet * > &SingleBackward)CSearch< LEGACY, NHITS >protected
MaxModPerPepCSearch< LEGACY, NHITS >private
MaxMZCSearch< LEGACY, NHITS >privatestatic
CSearch_Base::min_offset_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::min_offset_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::ms_UnassignedByteCSerialObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ms_UnassignedByteCSerialObjectstatic
CSearch_Base::ms_UnassignedStrCSerialObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ms_UnassignedStrCSerialObjectstatic
MyRequestCSearch< LEGACY, NHITS >private
MyResponseCSearch< LEGACY, NHITS >private
MySettingsCSearch< LEGACY, NHITS >private
numseqCSearch< LEGACY, NHITS >private
CSearch_Base::ObjectStateCanBeDeleted(TCount count)CObjectinlineprivatestatic
CSearch_Base::ObjectStateIsAllocatedInPool(TCount count)CObjectinlineprivatestatic
CSearch_Base::ObjectStateReferenced(TCount count)CObjectinlineprivatestatic
CSearch_Base::ObjectStateReferencedOnlyOnce(TCount count)CObjectinlineprivatestatic
CSearch_Base::ObjectStateUnreferenced(TCount count)CObjectinlineprivatestatic
CSearch_Base::ObjectStateValid(TCount count)CObjectinlineprivatestatic
OidSetCSearch< LEGACY, NHITS >private
OnExit(void)CSearch< LEGACY, NHITS >virtual
CSearch_Base::operator delete(void *ptr)CObject
CSearch_Base::operator delete(void *ptr, void *place)CObject
CSearch_Base::operator delete(void *ptr, CObjectMemoryPool *place)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator delete(void *ptr)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator delete(void *ptr, void *place)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator delete(void *ptr, CObjectMemoryPool *place)CObject
CThread::operator delete(void *ptr)CObject
CThread::operator delete(void *ptr, void *place)CObject
CThread::operator delete(void *ptr, CObjectMemoryPool *place)CObject
CSearch_Base::operator delete[](void *ptr)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator delete[](void *ptr)CObject
CThread::operator delete[](void *ptr)CObject
CSearch_Base::operator new(size_t size)CObject
CSearch_Base::operator new(size_t size, void *place)CObject
CSearch_Base::operator new(size_t size, CObjectMemoryPool *place)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator new(size_t size)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator new(size_t size, void *place)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator new(size_t size, CObjectMemoryPool *place)CObject
CThread::operator new(size_t size)CObject
CThread::operator new(size_t size, void *place)CObject
CThread::operator new(size_t size, CObjectMemoryPool *place)CObject
CSearch_Base::operator new[](size_t size)CObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator new[](size_t size)CObject
CThread::operator new[](size_t size)CObject
CSearch_Base::operator()()CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::operator()()CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
operator=(const CSearch &value)CSearch< LEGACY, NHITS >private
CSearch_Base::CSerialObject::operator=(const CObject &src) THROWS_NONECObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::CSerialObject::operator=(const CObject &src) THROWS_NONECObjectinline
CObject::operator=(const CObject &src) THROWS_NONECObjectinline
CSearch_Base::options_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::options_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
PepCharge(CMSHit &Hit, int SeriesCharge, int Ion, int MinIntensity, int Which, CMSPeak *Peaks, int Maxproductions)CSearch< LEGACY, NHITS >
PoissonOnlyCSearch< LEGACY, NHITS >private
PrecursorMassArrayCSearch< LEGACY, NHITS >private
CSearch_Base::ProcessBoundaryOffset(TWord offset, TWord bounds)CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ProcessBoundaryOffset(TWord offset, TWord bounds)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::ProcessOffset(TWord offset)CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ProcessOffset(TWord offset)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::ProcessRoot(TTrackedSeeds &seeds, const SSeedRoot *root)CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ProcessRoot(TTrackedSeeds &seeds, const SSeedRoot *root)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::qoff_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::qoff_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::qstart_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::qstart_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::qstop_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::qstop_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::query_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::query_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
rdfpCSearch< LEGACY, NHITS >private
CSearch_Base::Referenced(void) const THROWS_NONECObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::Referenced(void) const THROWS_NONECObjectinline
CThread::Referenced(void) const THROWS_NONECObjectinline
CSearch_Base::ReferencedOnlyOnce(void) const THROWS_NONECObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ReferencedOnlyOnce(void) const THROWS_NONECObjectinline
CThread::ReferencedOnlyOnce(void) const THROWS_NONECObjectinline
CSearch_Base::ReleaseReference(void) constCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ReleaseReference(void) constCObject
CThread::ReleaseReference(void) constCObject
CSearch_Base::RemoveLastReference(TCount count) constCObjectprivate
CSearch_Base::RemoveReference(void) constCObjectinline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::RemoveReference(void) constCObjectinline
CThread::RemoveReference(void) constCObjectinline
ReSearch(const int Number) constCSearch< LEGACY, NHITS >protected
CSearch_Base::Reset(void)CSearch_Base< LEGACY, NHITS, derived_t >virtual
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::Reset(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >virtual
ResetGlobals(void)CSearch< LEGACY, NHITS >static
CSearch_Base::ResetHits(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetHits(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::ResetMessage(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetMessage(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::ResetQuery_id(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetQuery_id(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::ResetQuery_len(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetQuery_len(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::ResetQuery_masking(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetQuery_masking(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::ResetQuery_title(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetQuery_title(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::ResetStat(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ResetStat(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
RestrictedSearchCSearch< LEGACY, NHITS >private
CSearch_Base::roots_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::roots_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
Run(TRunMode flags=fRunDefault)CThread
Search(CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)CSearch< LEGACY, NHITS >
CSearch_Base::SearchInt()CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SearchInt()CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::seeds_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::seeds_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::SetAllocFillMode(EAllocFillMode mode)CObjectstatic
CSearch_Base::SetAllocFillMode(const string &value)CObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetAllocFillMode(EAllocFillMode mode)CObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetAllocFillMode(const string &value)CObjectstatic
CThread::SetAllocFillMode(EAllocFillMode mode)CObjectstatic
CThread::SetAllocFillMode(const string &value)CObjectstatic
SetCurrentThreadName(const CTempString &)CThreadstatic
SetEnzyme(void)CSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::SetHits(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetHits(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
SetIons(list< EMSIonSeries > &Ions)CSearch< LEGACY, NHITS >protected
SetIterative(void)CSearch< LEGACY, NHITS >inline
SetLadderCalc(int i)CSearch< LEGACY, NHITS >inlineprotected
SetLadderContainer(void)CSearch< LEGACY, NHITS >inlineprotected
SetMassAndMask(int i, int j)CSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::SetMessage(const TMessage &value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetMessage(TMessage &&value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetMessage(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetMessage(const TMessage &value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetMessage(TMessage &&value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetMessage(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
SetOidSet(void)CSearch< LEGACY, NHITS >inlineprotected
SetPoissonOnly(void)CSearch< LEGACY, NHITS >inline
CSearch_Base::SetQuery_id(const TQuery_id &value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetQuery_id(TQuery_id &&value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetQuery_id(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_id(const TQuery_id &value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_id(TQuery_id &&value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_id(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::SetQuery_len(TQuery_len value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetQuery_len(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_len(TQuery_len value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_len(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::SetQuery_masking(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_masking(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base::SetQuery_title(const TQuery_title &value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetQuery_title(TQuery_title &&value)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base::SetQuery_title(void)CSearch_Base< LEGACY, NHITS, derived_t >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_title(const TQuery_title &value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_title(TQuery_title &&value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetQuery_title(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >inline
SetRankScore(void)CSearch< LEGACY, NHITS >inline
SetRequest(void)CSearch< LEGACY, NHITS >inlineprotected
SetResponse(void)CSearch< LEGACY, NHITS >inlineprotected
SetRestrictedSearch(void)CSearch< LEGACY, NHITS >inlineprotected
SetResult(CRef< CMSPeakSet > PeakSet)CSearch< LEGACY, NHITS >
SetSettings(void)CSearch< LEGACY, NHITS >inlineprotected
CSearch_Base::SetStat(TStat &value)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base::SetStat(void)CSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetStat(TStat &value)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetStat(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
SetSubjInfo()CSearch< LEGACY, NHITS >inline
SetupSearch(CRef< CMSRequest > MyRequestIn, CRef< CMSResponse > MyResponseIn, CRef< CMSModSpecSet > Modset, CRef< CMSSearchSettings > SettingsIn, TOMSSACallback Callback=0, void *CallbackData=0)CSearch< LEGACY, NHITS >
CSearch_Base::SetVerifyDataGlobal(ESerialVerifyData verify)CSerialObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetVerifyDataGlobal(ESerialVerifyData verify)CSerialObjectstatic
CSearch_Base::SetVerifyDataThread(ESerialVerifyData verify)CSerialObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::SetVerifyDataThread(ESerialVerifyData verify)CSerialObjectstatic
SetWaitForAllThreadsTimeout(const CTimeout &timeout)CThreadstatic
SharedPeakSetCSearch< LEGACY, NHITS >static
CSearch_Base::sm_DumpEnabledCDebugDumpableprivatestatic
sm_IsExitingCThreadprivatestatic
sm_ThreadsCountCThreadprivatestatic
sm_WaitForThreadsTimeoutCThreadprivatestatic
CSearch_Base::soff_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::soff_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
Spectrum2Peak(CRef< CMSPeakSet > PeakSet)CSearch< LEGACY, NHITS >protected
CSearch_Base::subj_end_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::subj_end_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::subj_end_off_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::subj_end_off_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::subj_start_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::subj_start_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::subj_start_off_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::subj_start_off_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::subject_CSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::subject_CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
TBase typedefCSearch< LEGACY, NHITS >private
CSearch_Base::TCount typedefCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TCount typedefCObject
CThread::TCount typedefCObject
CSearch_Base::TCounter typedefCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TCounter typedefCObject
CThread::TCounter typedefCObject
CSearch_Base::TDerived typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TDerived typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
TestPersist(void)CSearch< LEGACY, NHITS >inline
CSearch_Base::THits typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::THits typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
ThreadNumCSearch< LEGACY, NHITS >private
CSearch_Base::ThrowNullPointerException(void)CObjectstatic
CSearch_Base::ThrowNullPointerException(const type_info &type)CObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ThrowNullPointerException(void)CObjectstatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ThrowNullPointerException(const type_info &type)CObjectstatic
CThread::ThrowNullPointerException(void)CObjectstatic
CThread::ThrowNullPointerException(const type_info &type)CObjectstatic
CSearch_Base::ThrowUnassigned(TMemberIndex index) constCSerialObject
CSearch_Base::ThrowUnassigned(TMemberIndex index, const char *file_name, int file_line) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ThrowUnassigned(TMemberIndex index) constCSerialObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::ThrowUnassigned(TMemberIndex index, const char *file_name, int file_line) constCSerialObject
TID typedefCThread
TIndex_Impl typedefCSearch< LEGACY, NHITS >private
CSearch_Base::TLockerType typedefCObject
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TLockerType typedefCObject
CThread::TLockerType typedefCObject
CSearch_Base::TmemberIndex typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TmemberIndex typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TMessage typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TMessage typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
Tparent typedefCSearch< LEGACY, NHITS >private
CSearch_Base::TQuery_id typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TQuery_id typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TQuery_len typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TQuery_len typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TQuery_masking typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TQuery_masking typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TQuery_title typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TQuery_title typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
TRunMode typedefCThread
TSearchOptions typedefCSearch< LEGACY, NHITS >private
CSearch_Base::TStat typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TStat typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TSubjectMap typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TSubjectMap typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TTrackedSeed typedefCSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TTrackedSeed typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::TTrackedSeeds typedefCSearch_Base< LEGACY, NHITS, derived_t >
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TTrackedSeeds typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >
CSearch_Base::TTrackedSeedsSet typedefCSearch_Base< LEGACY, NHITS, derived_t >protected
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::TTrackedSeedsSet typedefCSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >protected
CSearch_Base::UnassignedByte(void)CSerialObjectinlinestatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::UnassignedByte(void)CSerialObjectinlinestatic
CSearch_Base::UnassignedString(void)CSerialObjectinlinestatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::UnassignedString(void)CSerialObjectinlinestatic
CSearch_Base::UnassignedStringUTF8(void)CSerialObjectinlinestatic
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::UnassignedStringUTF8(void)CSerialObjectinlinestatic
UpdateWithNewPep(int Missed, const char *PepStart[], const char *PepEnd[], int NumMod[], CMod ModList[][32], int Masses[], int EndMasses[], int NumModSites[], CRef< CMSModSpecSet > &Modset)CSearch< LEGACY, NHITS >protected
UseRankScoreCSearch< LEGACY, NHITS >private
VariableModsCSearch< LEGACY, NHITS >private
WaitForAllThreads(void)CThreadprivatestatic
Wrapper(TWrapperArg arg)CThreadprivatestatic
WriteBioseqs(void)CSearch< LEGACY, NHITS >protected
CSearch_Base::x_GetVerifyData(void)CSerialObjectprivatestatic
x_InitializeThreadId(void)CThreadprivate
~CDebugDumpable(void)CDebugDumpablevirtual
~CObject(void)CObjectvirtual
~CSearch(void)CSearch< LEGACY, NHITS >
~CSearch(void)CSearch< LEGACY, NHITS >
CSearch_Base::~CSearch_Base(void)CSearch_Base< LEGACY, NHITS, derived_t >virtual
CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >::~CSearch_Base(void)CSearch_Base< LEGACY, NHITS, CSearch< LEGACY, NHITS > >virtual
~CSerialObject(void)CSerialObjectvirtual
~CThread(void)CThreadprotectedvirtual
Modified on Sat Apr 13 11:45:31 2024 by modify_doxy.py rev. 669887