NCBI C++ ToolKit
|
Search Toolkit Book for CSeq_loc_CI_Impl
Classes | |
struct | PByLevel |
struct | SEquivSet |
Public Types | |
typedef SSeq_loc_CI_RangeInfo::TRange | TRange |
typedef vector< SSeq_loc_CI_RangeInfo > | TRanges |
typedef vector< SEquivSet > | TEquivSets |
typedef set< const SEquivSet * > | TUsedEquivs |
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< Uint8 > | TCounter |
Counter type is CAtomiCounter. More... | |
typedef Uint8 | TCount |
Alias for value type of counter. More... | |
Public Member Functions | |
CSeq_loc_CI_Impl (void) | |
CSeq_loc_CI_Impl (const CSeq_loc &loc, CSeq_loc_CI::EEmptyFlag empty_flag, CSeq_loc_CI::ESeqLocOrder order) | |
virtual | ~CSeq_loc_CI_Impl (void) |
TRanges & | GetRanges (void) |
const TRanges & | GetRanges (void) const |
bool | IsEnd (size_t idx) const |
void | DeleteRange (size_t idx) |
SSeq_loc_CI_RangeInfo & | InsertRange (size_t idx, CSeq_loc::E_Choice type) |
bool | WasPoint (const SSeq_loc_CI_RangeInfo &info) const |
bool | ShouldBePoint (const SSeq_loc_CI_RangeInfo &info) const |
void | UpdatePoint (CSeq_point &pnt, const SSeq_loc_CI_RangeInfo &info) const |
void | UpdatePoint (SSeq_loc_CI_RangeInfo &info) |
void | SetPoint (SSeq_loc_CI_RangeInfo &info) |
void | UpdateLoc (SSeq_loc_CI_RangeInfo &info) |
bool | CanBePoint (const SSeq_loc_CI_RangeInfo &info) const |
bool | CanBeInterval (const SSeq_loc_CI_RangeInfo &info) const |
bool | CanBePoint (size_t idx) const |
bool | CanBeInterval (size_t idx) const |
bool | CanBePacked_pnt (size_t idx_begin, size_t idx_end) const |
bool | CanBePacked_int (size_t idx_begin, size_t idx_end) const |
CRef< CInt_fuzz > | MakeFuzz (const CInt_fuzz &fuzz) const |
CRef< CSeq_point > | MakePoint (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_loc > | MakeLocPoint (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_interval > | MakeInterval (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_loc > | MakeLocInterval (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_loc > | MakeLocPacked_pnt (size_t idx_begin, size_t idx_end) const |
CRef< CSeq_loc > | MakeLocPacked_int (size_t idx_begin, size_t idx_end) const |
bool | CanBeBond (size_t idx_begin, size_t idx_end) const |
size_t | GetBondBegin (size_t idx) const |
size_t | GetBondEnd (size_t idx) const |
pair< size_t, size_t > | GetBondRange (size_t idx) const |
bool | IsInBond (const SSeq_loc_CI_RangeInfo &info) const |
bool | IsInBond (size_t idx) const |
bool | IsBondPartA (size_t idx) const |
bool | IsBondPartB (size_t idx) const |
void | x_BreakBond (size_t idx) |
void | x_CreateBond (size_t idx) |
void | x_AddBondPartB (size_t idx) |
void | RemoveBond (size_t idx) |
void | MakeBondA (size_t idx) |
void | MakeBondAB (size_t idx) |
void | MakeBondB (size_t idx) |
CRef< CSeq_loc > | MakeLocBond (size_t idx_begin, size_t idx_end) const |
bool | HasEquivSets (void) const |
bool | IsInEquivSet (size_t idx) const |
size_t | GetEquivSetsCount (size_t idx) const |
const SEquivSet & | GetEquivSet (size_t idx, size_t level) const |
pair< size_t, size_t > | GetEquivSetRange (size_t idx, size_t level) const |
pair< size_t, size_t > | GetEquivPartRange (size_t idx, size_t level) const |
size_t | HasEquivBreak (size_t begin, size_t end) const |
const SEquivSet * | FindInnerEquivSet (size_t begin, size_t end, const TUsedEquivs &used_equivs) const |
CRef< CSeq_loc > | MakeLocOther (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_loc > | MakeRangeLoc (const SSeq_loc_CI_RangeInfo &info) const |
CRef< CSeq_loc > | MakeLoc (CSeq_loc_I::EMakeType make_type) const |
CRef< CSeq_loc > | MakeLoc (size_t idx_begin, size_t idx_end, CSeq_loc_I::EMakeType make_type, TUsedEquivs &used_equivs) const |
bool | HasChanges (void) const |
void | SetHasChanges (void) |
CSeq_loc_I::EEquivMode | GetEquivMode (void) const |
void | SetEquivMode (CSeq_loc_I::EEquivMode mode) |
Public Member Functions inherited from CObject | |
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... | |
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 Member Functions | |
CSeq_loc_CI_Impl (const CSeq_loc_CI_Impl &) | |
CSeq_loc_CI_Impl & | operator= (const CSeq_loc_CI_Impl &) |
void | x_ProcessLocation (const CSeq_loc &loc) |
void | x_ProcessInterval (const CSeq_interval &seq_int, const CSeq_loc &loc) |
void | x_ProcessPoint (const CSeq_point &seq_pnt, const CSeq_loc &loc) |
Static Private Member Functions | |
static void | x_SetId (SSeq_loc_CI_RangeInfo &info, const CSeq_id &id) |
Private Attributes | |
CConstRef< CSeq_loc > | m_Location |
TRanges | m_Ranges |
TEquivSets | m_EquivSets |
CSeq_loc_CI::EEmptyFlag | m_EmptyFlag |
bool | m_HasChanges |
CSeq_loc_I::EEquivMode | m_EquivMode |
Additional Inherited Members | |
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 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 CObject | |
virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Definition at line 1054 of file Seq_loc.cpp.
typedef vector<SEquivSet> CSeq_loc_CI_Impl::TEquivSets |
Definition at line 1173 of file Seq_loc.cpp.
Definition at line 1063 of file Seq_loc.cpp.
typedef vector<SSeq_loc_CI_RangeInfo> CSeq_loc_CI_Impl::TRanges |
Definition at line 1064 of file Seq_loc.cpp.
typedef set<const SEquivSet*> CSeq_loc_CI_Impl::TUsedEquivs |
Definition at line 1340 of file Seq_loc.cpp.
CSeq_loc_CI_Impl::CSeq_loc_CI_Impl | ( | void | ) |
Definition at line 1400 of file Seq_loc.cpp.
CSeq_loc_CI_Impl::CSeq_loc_CI_Impl | ( | const CSeq_loc & | loc, |
CSeq_loc_CI::EEmptyFlag | empty_flag, | ||
CSeq_loc_CI::ESeqLocOrder | order | ||
) |
Definition at line 1407 of file Seq_loc.cpp.
References CSeq_loc_CI::eOrder_Positional, CSeq_loc::IsReverseStrand(), m_Ranges, and x_ProcessLocation().
|
inlinevirtual |
Definition at line 1061 of file Seq_loc.cpp.
|
private |
bool CSeq_loc_CI_Impl::CanBeBond | ( | size_t | idx_begin, |
size_t | idx_end | ||
) | const |
Definition at line 1855 of file Seq_loc.cpp.
References _ASSERT, CanBePoint(), count, GetBondRange(), HasEquivBreak(), info, IsInBond(), and m_Ranges.
Referenced by MakeLoc().
bool CSeq_loc_CI_Impl::CanBeInterval | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 1843 of file Seq_loc.cpp.
References info.
Referenced by CanBeInterval(), CanBePacked_int(), and MakeLoc().
|
inline |
Definition at line 1223 of file Seq_loc.cpp.
References CanBeInterval(), and m_Ranges.
bool CSeq_loc_CI_Impl::CanBePacked_int | ( | size_t | idx_begin, |
size_t | idx_end | ||
) | const |
Definition at line 2243 of file Seq_loc.cpp.
References _ASSERT, CanBeInterval(), HasEquivBreak(), and IsInBond().
Referenced by MakeLoc().
bool CSeq_loc_CI_Impl::CanBePacked_pnt | ( | size_t | idx_begin, |
size_t | idx_end | ||
) | const |
Definition at line 2205 of file Seq_loc.cpp.
References _ASSERT, CanBePoint(), HasEquivBreak(), info, IsInBond(), SSeq_loc_CI_RangeInfo::m_Fuzz, SSeq_loc_CI_RangeInfo::m_IdHandle, SSeq_loc_CI_RangeInfo::m_IsSetStrand, m_Ranges, and SSeq_loc_CI_RangeInfo::m_Strand.
Referenced by MakeLoc().
bool CSeq_loc_CI_Impl::CanBePoint | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 1828 of file Seq_loc.cpp.
References info.
Referenced by CanBeBond(), CanBePacked_pnt(), CanBePoint(), MakeLoc(), and MakeRangeLoc().
|
inline |
Definition at line 1219 of file Seq_loc.cpp.
References CanBePoint(), and m_Ranges.
void CSeq_loc_CI_Impl::DeleteRange | ( | size_t | idx | ) |
Definition at line 1654 of file Seq_loc.cpp.
References ERASE_ITERATE, CSeq_loc_CI_Impl::SEquivSet::GetElementsCount(), CSeq_loc_CI_Impl::SEquivSet::GetStartIndex(), m_EquivSets, CSeq_loc_CI_Impl::SEquivSet::m_Parts, m_Ranges, CSeq_loc_CI_Impl::SEquivSet::m_StartIndex, offset, SetHasChanges(), and VECTOR_ERASE.
Referenced by CSeq_loc_I::Delete().
const CSeq_loc_CI_Impl::SEquivSet * CSeq_loc_CI_Impl::FindInnerEquivSet | ( | size_t | begin, |
size_t | end, | ||
const TUsedEquivs & | used_equivs | ||
) | const |
Definition at line 1630 of file Seq_loc.cpp.
References set< Key, Compare >::end(), set< Key, Compare >::find(), CSeq_loc_CI_Impl::SEquivSet::GetEndIndex(), CSeq_loc_CI_Impl::SEquivSet::GetStartIndex(), ITERATE, and m_EquivSets.
Referenced by MakeLoc().
size_t CSeq_loc_CI_Impl::GetBondBegin | ( | size_t | idx | ) | const |
Definition at line 1881 of file Seq_loc.cpp.
References _ASSERT, CSeq_loc_Base::IsBond(), and m_Ranges.
Referenced by GetBondRange(), IsBondPartA(), and IsBondPartB().
size_t CSeq_loc_CI_Impl::GetBondEnd | ( | size_t | idx | ) | const |
Definition at line 1892 of file Seq_loc.cpp.
References _ASSERT, CSeq_loc_Base::IsBond(), and m_Ranges.
Referenced by GetBondRange().
|
inline |
Definition at line 1244 of file Seq_loc.cpp.
References GetBondBegin(), and GetBondEnd().
Referenced by CanBeBond(), CSeq_loc_CI::GetBondRange(), MakeBondA(), MakeBondAB(), MakeBondB(), MakeLoc(), and RemoveBond().
|
inline |
Definition at line 1362 of file Seq_loc.cpp.
References m_EquivMode.
Referenced by CSeq_loc_I::GetEquivMode(), and InsertRange().
|
inline |
Definition at line 1329 of file Seq_loc.cpp.
References CSeq_loc_CI_Impl::SEquivSet::FindPartByElementIndex(), GetEquivSet(), CSeq_loc_CI_Impl::SEquivSet::GetPartEndIndex(), and CSeq_loc_CI_Impl::SEquivSet::GetPartStartIndex().
Referenced by CSeq_loc_CI::GetEquivPartRange(), and CSeq_loc_I::GetEquivPartRange().
Definition at line 1309 of file Seq_loc.cpp.
References ITERATE, m_EquivSets, NCBI_THROW_FMT, and ct::sort().
Referenced by GetEquivPartRange(), and GetEquivSetRange().
|
inline |
Definition at line 1324 of file Seq_loc.cpp.
References CSeq_loc_CI_Impl::SEquivSet::GetEndIndex(), GetEquivSet(), and CSeq_loc_CI_Impl::SEquivSet::GetStartIndex().
Referenced by CSeq_loc_CI::GetEquivSetRange(), and CSeq_loc_I::GetEquivSetRange().
|
inline |
Definition at line 1299 of file Seq_loc.cpp.
References count, ITERATE, and m_EquivSets.
Referenced by CSeq_loc_CI::GetEquivSetsCount().
|
inline |
Definition at line 1175 of file Seq_loc.cpp.
References m_Ranges.
Referenced by CSeq_loc_CI::GetSize(), CSeq_loc_I::x_GetRangeInfo(), CSeq_loc_CI::x_GetRangeInfo(), CSeq_loc_CI::x_IsValid(), and CSeq_loc_I::x_IsValidForInsert().
Definition at line 1176 of file Seq_loc.cpp.
References m_Ranges.
|
inline |
Definition at line 1352 of file Seq_loc.cpp.
References m_HasChanges.
Referenced by CSeq_loc_I::HasChanges().
size_t CSeq_loc_CI_Impl::HasEquivBreak | ( | size_t | begin, |
size_t | end | ||
) | const |
Definition at line 1600 of file Seq_loc.cpp.
References CSeq_loc_CI_Impl::SEquivSet::FindPartByElementIndex(), CSeq_loc_CI_Impl::SEquivSet::GetEndIndex(), CSeq_loc_CI_Impl::SEquivSet::GetPartEndIndex(), CSeq_loc_CI_Impl::SEquivSet::GetStartIndex(), ITERATE, m_EquivSets, and min().
Referenced by CanBeBond(), CanBePacked_int(), CanBePacked_pnt(), and MakeLoc().
|
inline |
Definition at line 1286 of file Seq_loc.cpp.
References m_EquivSets.
Referenced by CSeq_loc_CI::HasEquivSets().
SSeq_loc_CI_RangeInfo & CSeq_loc_CI_Impl::InsertRange | ( | size_t | idx, |
CSeq_loc::E_Choice | type | ||
) |
Definition at line 1693 of file Seq_loc.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_I::eEquiv_append, CSeq_loc_I::eEquiv_new_equiv, CSeq_loc_I::eEquiv_new_part, CSeq_loc_I::eEquiv_prepend, CSeq_loc_CI_Impl::SEquivSet::FindPartByElementIndex(), CSeq_loc_CI_Impl::SEquivSet::GetEndIndex(), GetEquivMode(), CSeq_loc_CI_Impl::SEquivSet::GetStartIndex(), info, ITERATE, m_EquivSets, CSeq_loc_CI_Impl::SEquivSet::m_Parts, m_Ranges, CSeq_loc_CI_Impl::SEquivSet::m_StartIndex, NON_CONST_ITERATE, SetEquivMode(), SetHasChanges(), ct::sort(), and CSeq_loc_Base::Which().
Referenced by CSeq_loc_I::InsertEmpty(), CSeq_loc_I::InsertInterval(), CSeq_loc_I::InsertNull(), CSeq_loc_I::InsertPoint(), and CSeq_loc_I::InsertWhole().
|
inline |
Definition at line 1256 of file Seq_loc.cpp.
References GetBondBegin(), and IsInBond().
Referenced by CSeq_loc_CI::IsBondA().
|
inline |
Definition at line 1260 of file Seq_loc.cpp.
References GetBondBegin(), and IsInBond().
Referenced by CSeq_loc_CI::IsBondB().
|
inline |
Definition at line 1178 of file Seq_loc.cpp.
References m_Ranges.
Referenced by CSeq_loc_CI::operator==().
|
inline |
Definition at line 1248 of file Seq_loc.cpp.
References info.
Referenced by CanBeBond(), CanBePacked_int(), CanBePacked_pnt(), IsBondPartA(), IsBondPartB(), IsInBond(), CSeq_loc_CI::IsInBond(), MakeBondA(), MakeBondAB(), MakeBondB(), MakeLoc(), and RemoveBond().
|
inline |
Definition at line 1252 of file Seq_loc.cpp.
References IsInBond(), and m_Ranges.
|
inline |
Definition at line 1290 of file Seq_loc.cpp.
References ITERATE, and m_EquivSets.
Referenced by CSeq_loc_CI::IsInEquivSet().
void CSeq_loc_CI_Impl::MakeBondA | ( | size_t | idx | ) |
Definition at line 1919 of file Seq_loc.cpp.
References GetBondRange(), IsInBond(), NCBI_THROW_FMT, compile_time_bits::range(), SetHasChanges(), x_BreakBond(), and x_CreateBond().
Referenced by CSeq_loc_I::MakeBondA().
void CSeq_loc_CI_Impl::MakeBondAB | ( | size_t | idx | ) |
Definition at line 1950 of file Seq_loc.cpp.
References GetBondRange(), IsInBond(), m_Ranges, NCBI_THROW_FMT, compile_time_bits::range(), SetHasChanges(), x_AddBondPartB(), x_BreakBond(), and x_CreateBond().
Referenced by CSeq_loc_I::MakeBondAB().
void CSeq_loc_CI_Impl::MakeBondB | ( | size_t | idx | ) |
Definition at line 1991 of file Seq_loc.cpp.
References _ASSERT, GetBondRange(), IsInBond(), NCBI_THROW_FMT, compile_time_bits::range(), SetHasChanges(), x_AddBondPartB(), x_BreakBond(), and x_CreateBond().
Referenced by CSeq_loc_I::MakeBondB().
Definition at line 2059 of file Seq_loc.cpp.
References Ref().
Referenced by MakeInterval(), MakeLocPacked_pnt(), and UpdatePoint().
CRef< CSeq_interval > CSeq_loc_CI_Impl::MakeInterval | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2138 of file Seq_loc.cpp.
References info, MakeFuzz(), MakeId(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
Referenced by MakeLocInterval(), and MakeLocPacked_int().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeLoc | ( | CSeq_loc_I::EMakeType | make_type | ) | const |
Definition at line 2426 of file Seq_loc.cpp.
References m_Ranges.
Referenced by MakeLoc(), and CSeq_loc_I::MakeSeq_loc().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeLoc | ( | size_t | idx_begin, |
size_t | idx_end, | ||
CSeq_loc_I::EMakeType | make_type, | ||
TUsedEquivs & | used_equivs | ||
) | const |
Definition at line 2312 of file Seq_loc.cpp.
References AddLoc(), CanBeBond(), CanBeInterval(), CanBePacked_int(), CanBePacked_pnt(), CanBePoint(), CSeq_loc_I::eMake_CompactType, CSeq_loc_I::eMake_PreserveType, FindInnerEquivSet(), CSeq_loc_mix_Base::Get(), GetBondRange(), CSeq_loc_Base::GetMix(), HasEquivBreak(), info, set< Key, Compare >::insert(), IsInBond(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), CSeq_loc_Base::IsPacked_pnt(), ITERATE, SSeq_loc_CI_RangeInfo::m_Loc, m_Ranges, MakeLoc(), MakeLocBond(), MakeLocInterval(), MakeLocOther(), MakeLocPacked_int(), MakeLocPacked_pnt(), MakeLocPoint(), NCBI_THROW, compile_time_bits::range(), CSeq_loc_equiv_Base::Set(), CSeq_loc::SetEquiv(), CSeq_loc::SetMix(), and WasPoint().
Definition at line 2036 of file Seq_loc.cpp.
References m_Ranges, MakePoint(), and CSeq_loc::SetBond().
Referenced by MakeLoc().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeLocInterval | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2158 of file Seq_loc.cpp.
References info, MakeInterval(), and CSeq_loc::SetInt().
Referenced by CSeq_loc_I::InsertInterval(), MakeLoc(), and MakeRangeLoc().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeLocOther | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2167 of file Seq_loc.cpp.
References info, MakeId(), NCBI_THROW, CSeq_loc::SetEmpty(), CSeq_loc::SetNull(), and CSeq_loc::SetWhole().
Referenced by MakeLoc(), and MakeRangeLoc().
Definition at line 2284 of file Seq_loc.cpp.
References m_Ranges, MakeInterval(), and CSeq_loc::SetPacked_int().
Referenced by MakeLoc().
Definition at line 2262 of file Seq_loc.cpp.
References info, SSeq_loc_CI_RangeInfo::m_Fuzz, SSeq_loc_CI_RangeInfo::m_IsSetStrand, m_Ranges, SSeq_loc_CI_RangeInfo::m_Strand, MakeFuzz(), MakeId(), CPacked_seqpnt_Base::SetFuzz(), CPacked_seqpnt_Base::SetId(), CSeq_loc::SetPacked_pnt(), CPacked_seqpnt_Base::SetPoints(), and CPacked_seqpnt_Base::SetStrand().
Referenced by MakeLoc().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeLocPoint | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2101 of file Seq_loc.cpp.
References info, MakePoint(), and CSeq_loc::SetPnt().
Referenced by MakeLoc(), MakeRangeLoc(), and SetPoint().
CRef< CSeq_point > CSeq_loc_CI_Impl::MakePoint | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2092 of file Seq_loc.cpp.
References info, and UpdatePoint().
Referenced by MakeLocBond(), and MakeLocPoint().
CRef< CSeq_loc > CSeq_loc_CI_Impl::MakeRangeLoc | ( | const SSeq_loc_CI_RangeInfo & | info | ) | const |
Definition at line 2191 of file Seq_loc.cpp.
References CanBePoint(), info, MakeLocInterval(), MakeLocOther(), MakeLocPoint(), and ShouldBePoint().
Referenced by CSeq_loc_CI::GetRangeAsSeq_loc().
|
private |
void CSeq_loc_CI_Impl::RemoveBond | ( | size_t | idx | ) |
Definition at line 1903 of file Seq_loc.cpp.
References GetBondRange(), IsInBond(), NCBI_THROW_FMT, compile_time_bits::range(), SetHasChanges(), and x_BreakBond().
Referenced by CSeq_loc_I::RemoveBond().
|
inline |
Definition at line 1366 of file Seq_loc.cpp.
References m_EquivMode.
Referenced by InsertRange(), and CSeq_loc_I::SetEquivMode().
|
inline |
Definition at line 1357 of file Seq_loc.cpp.
References m_HasChanges.
Referenced by DeleteRange(), InsertRange(), MakeBondA(), MakeBondAB(), MakeBondB(), RemoveBond(), UpdateLoc(), and UpdatePoint().
void CSeq_loc_CI_Impl::SetPoint | ( | SSeq_loc_CI_RangeInfo & | info | ) |
Definition at line 2085 of file Seq_loc.cpp.
References info, and MakeLocPoint().
Referenced by CSeq_loc_I::InsertPoint(), CSeq_loc_I::SetPoint(), and x_BreakBond().
|
inline |
Definition at line 1192 of file Seq_loc.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, and info.
Referenced by MakeRangeLoc().
void CSeq_loc_CI_Impl::UpdateLoc | ( | SSeq_loc_CI_RangeInfo & | info | ) |
Definition at line 2118 of file Seq_loc.cpp.
References CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, info, and SetHasChanges().
Referenced by CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc_I::SetRange(), and CSeq_loc_I::SetTo().
void CSeq_loc_CI_Impl::UpdatePoint | ( | CSeq_point & | pnt, |
const SSeq_loc_CI_RangeInfo & | info | ||
) | const |
Definition at line 2065 of file Seq_loc.cpp.
References info, MakeFuzz(), MakeId(), CSeq_point_Base::ResetFuzz(), CSeq_point_Base::ResetStrand(), CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_point_Base::SetPoint(), and CSeq_point_Base::SetStrand().
Referenced by MakePoint(), CSeq_loc_I::ResetFuzz(), CSeq_loc_I::ResetStrand(), CSeq_loc_I::SetFuzz(), CSeq_loc_I::SetPoint(), CSeq_loc_I::SetSeq_id_Handle(), CSeq_loc_I::SetStrand(), and UpdatePoint().
void CSeq_loc_CI_Impl::UpdatePoint | ( | SSeq_loc_CI_RangeInfo & | info | ) |
Definition at line 2109 of file Seq_loc.cpp.
References info, SetHasChanges(), UpdatePoint(), and WasPoint().
|
inline |
Definition at line 1188 of file Seq_loc.cpp.
References info.
Referenced by MakeLoc(), CSeq_loc_I::SetPoint(), and UpdatePoint().
|
inline |
Definition at line 1274 of file Seq_loc.cpp.
References m_Ranges.
Referenced by MakeBondAB(), and MakeBondB().
|
inline |
Definition at line 1264 of file Seq_loc.cpp.
References m_Ranges, and SetPoint().
Referenced by MakeBondA(), MakeBondAB(), MakeBondB(), and RemoveBond().
|
inline |
Definition at line 1268 of file Seq_loc.cpp.
References m_Ranges, and CSeq_loc::SetBond().
Referenced by MakeBondA(), MakeBondAB(), and MakeBondB().
|
private |
Definition at line 1559 of file Seq_loc.cpp.
References _ASSERT, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Packed_int, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), info, CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), m_Ranges, CSeq_loc_Base::Which(), and x_SetId().
Referenced by x_ProcessLocation().
Definition at line 1439 of file Seq_loc.cpp.
References data, CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_CI::eEmpty_Allow, CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), COpenRange< TSeqPos >::GetEmpty(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CPacked_seqpnt_Base::GetFuzz(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Base::GetWhole(), info, CSeq_bond_Base::IsSetB(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::IsSetStrand(), ITERATE, m_EmptyFlag, m_EquivSets, CSeq_loc_CI_Impl::SEquivSet::m_Parts, m_Ranges, CSeq_loc_CI_Impl::SEquivSet::m_StartIndex, NCBI_THROW_FMT, pi, s_ReserveMore(), CSeq_loc_Base::SelectionName(), CSeq_loc_Base::Which(), x_ProcessInterval(), x_ProcessPoint(), and x_SetId().
Referenced by CSeq_loc_CI_Impl().
|
private |
Definition at line 1581 of file Seq_loc.cpp.
References _ASSERT, CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Pnt, CSeq_point_Base::GetFuzz(), CSeq_point_Base::GetId(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), info, CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::IsSetStrand(), m_Ranges, CSeq_loc_Base::Which(), and x_SetId().
Referenced by x_ProcessLocation().
|
staticprivate |
Definition at line 1422 of file Seq_loc.cpp.
References CSeq_id_Handle::GetHandle(), and info.
Referenced by x_ProcessInterval(), x_ProcessLocation(), and x_ProcessPoint().
|
private |
Definition at line 1392 of file Seq_loc.cpp.
Referenced by x_ProcessLocation().
|
private |
Definition at line 1396 of file Seq_loc.cpp.
Referenced by GetEquivMode(), and SetEquivMode().
|
private |
Definition at line 1390 of file Seq_loc.cpp.
Referenced by DeleteRange(), FindInnerEquivSet(), GetEquivSet(), GetEquivSetsCount(), HasEquivBreak(), HasEquivSets(), InsertRange(), IsInEquivSet(), and x_ProcessLocation().
|
private |
Definition at line 1394 of file Seq_loc.cpp.
Referenced by HasChanges(), and SetHasChanges().
Definition at line 1386 of file Seq_loc.cpp.
|
private |
Definition at line 1388 of file Seq_loc.cpp.
Referenced by CanBeBond(), CanBeInterval(), CanBePacked_pnt(), CanBePoint(), CSeq_loc_CI_Impl(), DeleteRange(), GetBondBegin(), GetBondEnd(), GetRanges(), InsertRange(), IsEnd(), IsInBond(), MakeBondAB(), MakeLoc(), MakeLocBond(), MakeLocPacked_int(), MakeLocPacked_pnt(), x_AddBondPartB(), x_BreakBond(), x_CreateBond(), x_ProcessInterval(), x_ProcessLocation(), and x_ProcessPoint().