Range Support

Collaboration diagram for Range Support:

Classes
class	CAlignRange< Position >
	CAlignRange Represents an element of pairwise alignment of two sequences. More...
struct	PAlignRangeToLess< TAlignRange >
struct	PAlignRangeFromLess< TAlignRange >
struct	SPositionTraitsBySignedness< Signed, Position >
struct	SPositionTraitsBySignedness< true, Position >
struct	SPositionTraitsBySignedness< false, Position >
struct	SPositionTraits< Position >
struct	SPositionTraits< float >
struct	SPositionTraits< double >
struct	SPositionTraits< long double >
class	COpenRange< Position >
class	CRange< Position >
	CRange –. More...
class	CRangeMapBase< Traits >
class	CRangeMapIterator< Traits >
class	CRangeMap< Mapped, Position >
class	CRangeMultimap< Mapped, Position >
class	CRangeMapTraitsBase< Position, Mapped >
class	CRangeMapTraits< Position, Mapped >
class	CRangeMultimapTraits< Position, Mapped >
class	CRangeMapIteratorTraits< MapTraits >
class	CRangeMapConstIteratorTraits< MapTraits >

Typedefs
typedef Position	CAlignRange< Position >::position_type
typedef CAlignRange< Position >	CAlignRange< Position >::TThisType
typedef CRange< Position >	CAlignRange< Position >::TRange
typedef TAlignRange::position_type	PAlignRangeToLess< TAlignRange >::position_type
typedef TAlignRange::position_type	PAlignRangeFromLess< TAlignRange >::position_type
typedef Position	COpenRange< Position >::position_type
typedef COpenRange< Position >	COpenRange< Position >::TThisType
typedef COpenRange< Position >	CRange< Position >::TParent
typedef TParent::position_type	CRange< Position >::position_type
typedef CRange< Position >	CRange< Position >::TThisType
typedef CRange< TSeqPos >	TSeqRange
	typedefs for sequence ranges More...
typedef CRange< TSignedSeqPos >	TSignedSeqRange
typedef Position	CRangeMapTraitsBase< Position, Mapped >::position_type
typedef CRange< position_type >	CRangeMapTraitsBase< Position, Mapped >::range_type
typedef Mapped	CRangeMapTraitsBase< Position, Mapped >::mapped_type
typedef pair< const range_type, mapped_type >	CRangeMapTraitsBase< Position, Mapped >::value_type
typedef CRangeMapTraitsBase< Position, Mapped >	CRangeMapTraits< Position, Mapped >::TParent
typedef CRangeMap< Mapped, Position >	CRangeMapTraits< Position, Mapped >::TRangeMap
typedef map< typename TParent::range_type, Mapped >	CRangeMapTraits< Position, Mapped >::TLevelMap
typedef map< Position, TLevelMap >	CRangeMapTraits< Position, Mapped >::TSelectMap
typedef CRangeMapTraitsBase< Position, Mapped >	CRangeMultimapTraits< Position, Mapped >::TParent
typedef CRangeMultimap< Mapped, Position >	CRangeMultimapTraits< Position, Mapped >::TRangeMap
typedef multimap< typename TParent::range_type, Mapped >	CRangeMultimapTraits< Position, Mapped >::TLevelMap
typedef map< Position, TLevelMap >	CRangeMultimapTraits< Position, Mapped >::TSelectMap
typedef MapTraits	CRangeMapIteratorTraits< MapTraits >::TMapTraits
typedef CRangeMapIteratorTraits< TMapTraits >	CRangeMapIteratorTraits< MapTraits >::TIteratorTraits
typedef CRangeMapIteratorTraits< TMapTraits >	CRangeMapIteratorTraits< MapTraits >::TNCIteratorTraits
typedef TMapTraits::TRangeMap &	CRangeMapIteratorTraits< MapTraits >::TRangeMapRef
typedef TMapTraits::TSelectMap &	CRangeMapIteratorTraits< MapTraits >::TSelectMapRef
typedef TMapTraits::TLevelMap &	CRangeMapIteratorTraits< MapTraits >::TLevelMapRef
typedef TMapTraits::TSelectMap::iterator	CRangeMapIteratorTraits< MapTraits >::TSelectIter
typedef TMapTraits::TLevelMap::iterator	CRangeMapIteratorTraits< MapTraits >::TLevelIter
typedef TMapTraits::value_type &	CRangeMapIteratorTraits< MapTraits >::reference
typedef TMapTraits::value_type *	CRangeMapIteratorTraits< MapTraits >::pointer
typedef CRangeMapIterator< TIteratorTraits >	CRangeMapIteratorTraits< MapTraits >::iterator
typedef CRangeMapIterator< TNCIteratorTraits >	CRangeMapIteratorTraits< MapTraits >::non_const_iterator
typedef MapTraits	CRangeMapConstIteratorTraits< MapTraits >::TMapTraits
typedef CRangeMapConstIteratorTraits< TMapTraits >	CRangeMapConstIteratorTraits< MapTraits >::TIteratorTraits
typedef CRangeMapIteratorTraits< TMapTraits >	CRangeMapConstIteratorTraits< MapTraits >::TNCIteratorTraits
typedef const TMapTraits::TRangeMap &	CRangeMapConstIteratorTraits< MapTraits >::TRangeMapRef
typedef const TMapTraits::TSelectMap &	CRangeMapConstIteratorTraits< MapTraits >::TSelectMapRef
typedef const TMapTraits::TLevelMap &	CRangeMapConstIteratorTraits< MapTraits >::TLevelMapRef
typedef TMapTraits::TSelectMap::const_iterator	CRangeMapConstIteratorTraits< MapTraits >::TSelectIter
typedef TMapTraits::TLevelMap::const_iterator	CRangeMapConstIteratorTraits< MapTraits >::TLevelIter
typedef const TMapTraits::value_type &	CRangeMapConstIteratorTraits< MapTraits >::reference
typedef const TMapTraits::value_type *	CRangeMapConstIteratorTraits< MapTraits >::pointer
typedef CRangeMapIterator< TIteratorTraits >	CRangeMapConstIteratorTraits< MapTraits >::iterator
typedef CRangeMapIterator< TNCIteratorTraits >	CRangeMapConstIteratorTraits< MapTraits >::non_const_iterator
typedef Traits	CRangeMapIterator< Traits >::TTraits
typedef TTraits::position_type	CRangeMapIterator< Traits >::position_type
typedef TTraits::range_type	CRangeMapIterator< Traits >::range_type
typedef TTraits::mapped_type	CRangeMapIterator< Traits >::mapped_type
typedef TTraits::value_type	CRangeMapIterator< Traits >::value_type
typedef TTraits::reference	CRangeMapIterator< Traits >::reference
typedef TTraits::pointer	CRangeMapIterator< Traits >::pointer
typedef TTraits::TRangeMap	CRangeMapIterator< Traits >::TRangeMap
typedef TTraits::TSelectMapRef	CRangeMapIterator< Traits >::TSelectMapRef
typedef TTraits::TSelectIter	CRangeMapIterator< Traits >::TSelectIter
typedef TTraits::TLevelIter	CRangeMapIterator< Traits >::TLevelIter
typedef TTraits::iterator	CRangeMapIterator< Traits >::TThisType
typedef Traits	CRangeMapBase< Traits >::TRangeMapTraits
typedef CRangeMapIteratorTraits< TRangeMapTraits >	CRangeMapBase< Traits >::TIteratorTraits
typedef CRangeMapConstIteratorTraits< TRangeMapTraits >	CRangeMapBase< Traits >::TConstIteratorTraits
typedef size_t	CRangeMapBase< Traits >::size_type
typedef TRangeMapTraits::position_type	CRangeMapBase< Traits >::position_type
typedef TRangeMapTraits::range_type	CRangeMapBase< Traits >::range_type
typedef TRangeMapTraits::mapped_type	CRangeMapBase< Traits >::mapped_type
typedef TRangeMapTraits::value_type	CRangeMapBase< Traits >::value_type
typedef range_type	CRangeMapBase< Traits >::key_type
typedef TRangeMapTraits::TRangeMap	CRangeMapBase< Traits >::TThisType
typedef TIteratorTraits::iterator	CRangeMapBase< Traits >::iterator
typedef TConstIteratorTraits::iterator	CRangeMapBase< Traits >::const_iterator
typedef TRangeMapTraits::TSelectMap	CRangeMapBase< Traits >::TSelectMap
typedef TSelectMap::value_type	CRangeMapBase< Traits >::select_value
typedef TSelectMap::iterator	CRangeMapBase< Traits >::TSelectMapI
typedef TRangeMapTraits::TLevelMap	CRangeMapBase< Traits >::TLevelMap
typedef TLevelMap::iterator	CRangeMapBase< Traits >::TLevelMapI
typedef CRangeMapBase< CRangeMapTraits< Position, Mapped > >	CRangeMap< Mapped, Position >::TParent
typedef TParent::size_type	CRangeMap< Mapped, Position >::size_type
typedef TParent::position_type	CRangeMap< Mapped, Position >::position_type
typedef TParent::range_type	CRangeMap< Mapped, Position >::range_type
typedef TParent::mapped_type	CRangeMap< Mapped, Position >::mapped_type
typedef TParent::value_type	CRangeMap< Mapped, Position >::value_type
typedef TParent::key_type	CRangeMap< Mapped, Position >::key_type
typedef TParent::iterator	CRangeMap< Mapped, Position >::iterator
typedef TParent::const_iterator	CRangeMap< Mapped, Position >::const_iterator
typedef TParent::TRangeMapTraits	CRangeMap< Mapped, Position >::TRangeMapTraits
typedef TParent::TSelectMap	CRangeMap< Mapped, Position >::TSelectMap
typedef TParent::select_value	CRangeMap< Mapped, Position >::select_value
typedef TParent::TSelectMapI	CRangeMap< Mapped, Position >::TSelectMapI
typedef TParent::TLevelMap	CRangeMap< Mapped, Position >::TLevelMap
typedef TParent::TLevelMapI	CRangeMap< Mapped, Position >::TLevelMapI
typedef CRangeMapBase< CRangeMultimapTraits< Position, Mapped > >	CRangeMultimap< Mapped, Position >::TParent
typedef TParent::size_type	CRangeMultimap< Mapped, Position >::size_type
typedef TParent::position_type	CRangeMultimap< Mapped, Position >::position_type
typedef TParent::range_type	CRangeMultimap< Mapped, Position >::range_type
typedef TParent::mapped_type	CRangeMultimap< Mapped, Position >::mapped_type
typedef TParent::value_type	CRangeMultimap< Mapped, Position >::value_type
typedef TParent::key_type	CRangeMultimap< Mapped, Position >::key_type
typedef TParent::iterator	CRangeMultimap< Mapped, Position >::iterator
typedef TParent::const_iterator	CRangeMultimap< Mapped, Position >::const_iterator
typedef TParent::TRangeMapTraits	CRangeMultimap< Mapped, Position >::TRangeMapTraits
typedef TParent::TSelectMap	CRangeMultimap< Mapped, Position >::TSelectMap
typedef TParent::select_value	CRangeMultimap< Mapped, Position >::select_value
typedef TParent::TSelectMapI	CRangeMultimap< Mapped, Position >::TSelectMapI
typedef TParent::TLevelMap	CRangeMultimap< Mapped, Position >::TLevelMap
typedef TParent::TLevelMapI	CRangeMultimap< Mapped, Position >::TLevelMapI

Enumerations
enum	CAlignRange< Position >::EFlags { CAlignRange< Position >::fReversed = 0x01 , CAlignRange< Position >::fFirstRev = 0x02 }

Functions
	CAlignRange< Position >::CAlignRange (void)
	CAlignRange< Position >::CAlignRange (position_type first_from, position_type second_from, position_type len, bool direct=true, bool first_direct=true)
bool	CAlignRange< Position >::IsDirect () const
bool	CAlignRange< Position >::IsReversed () const
bool	CAlignRange< Position >::IsFirstDirect () const
bool	CAlignRange< Position >::IsFirstReversed () const
position_type	CAlignRange< Position >::GetFirstFrom (void) const
position_type	CAlignRange< Position >::GetFirstToOpen (void) const
position_type	CAlignRange< Position >::GetFirstTo (void) const
position_type	CAlignRange< Position >::GetSecondFrom (void) const
position_type	CAlignRange< Position >::GetSecondToOpen (void) const
position_type	CAlignRange< Position >::GetSecondTo (void) const
TRange	CAlignRange< Position >::GetFirstRange () const
TRange	CAlignRange< Position >::GetSecondRange () const
bool	CAlignRange< Position >::Empty (void) const
bool	CAlignRange< Position >::NotEmpty (void) const
position_type	CAlignRange< Position >::GetLength (void) const
TThisType &	CAlignRange< Position >::SetFirstFrom (position_type from)
TThisType &	CAlignRange< Position >::SetSecondFrom (position_type second_from)
TThisType &	CAlignRange< Position >::SetLength (position_type len)
TThisType &	CAlignRange< Position >::Set (position_type first_from, position_type second_from, position_type len)
void	CAlignRange< Position >::SetDirect (bool direct=true)
void	CAlignRange< Position >::SetReversed (bool reversed=true)
void	CAlignRange< Position >::SetFirstDirect (bool direct=true)
void	CAlignRange< Position >::SetFirstReversed (bool reversed=true)
bool	CAlignRange< Position >::operator== (const TThisType &r) const
bool	CAlignRange< Position >::operator!= (const TThisType &r) const
position_type	CAlignRange< Position >::GetSecondPosByFirstPos (position_type pos) const
position_type	CAlignRange< Position >::GetFirstPosBySecondPos (position_type pos) const
bool	CAlignRange< Position >::FirstContains (position_type pos) const
bool	CAlignRange< Position >::SecondContains (position_type pos) const
TThisType	CAlignRange< Position >::IntersectionWith (const CRange< position_type > &r) const
	Intersection. More...
TThisType &	CAlignRange< Position >::IntersectWith (const CRange< position_type > &r)
TThisType &	CAlignRange< Position >::IntersectSecondWith (const CRange< position_type > &r)
bool	CAlignRange< Position >::IntersectingWith (const CRange< position_type > &r) const
bool	CAlignRange< Position >::IsAbutting (const TThisType &r) const
TThisType &	CAlignRange< Position >::CombineWithAbutting (const TThisType &r)
TThisType	CAlignRange< Position >::CombinationWithAbutting (const TThisType &r) const
static position_type	CAlignRange< Position >::GetEmptyFrom (void)
static position_type	CAlignRange< Position >::GetEmptyToOpen (void)
static position_type	CAlignRange< Position >::GetEmptyTo (void)
static position_type	CAlignRange< Position >::GetEmptyLength (void)
static TThisType	CAlignRange< Position >::GetEmpty (void)
static position_type	CAlignRange< Position >::GetPositionMin (void)
static position_type	CAlignRange< Position >::GetPositionMax (void)
bool	PAlignRangeToLess< TAlignRange >::operator() (const TAlignRange &r, position_type pos)
bool	PAlignRangeToLess< TAlignRange >::operator() (position_type pos, const TAlignRange &r)
bool	PAlignRangeToLess< TAlignRange >::operator() (const TAlignRange &r1, const TAlignRange &r2)
bool	PAlignRangeToLess< TAlignRange >::operator() (const TAlignRange *r, position_type pos)
bool	PAlignRangeToLess< TAlignRange >::operator() (position_type pos, const TAlignRange *r)
bool	PAlignRangeToLess< TAlignRange >::operator() (const TAlignRange *r1, const TAlignRange *r2)
bool	PAlignRangeFromLess< TAlignRange >::operator() (const TAlignRange &r, position_type pos)
bool	PAlignRangeFromLess< TAlignRange >::operator() (position_type pos, const TAlignRange &r)
bool	PAlignRangeFromLess< TAlignRange >::operator() (const TAlignRange &r_1, const TAlignRange &r_2)
static bool	SPositionTraitsBySignedness< true, Position >::IsNegative (Position pos)
static bool	SPositionTraitsBySignedness< false, Position >::IsNegative (Position)
	COpenRange< Position >::COpenRange (void)
	COpenRange< Position >::COpenRange (position_type from, position_type toOpen)
position_type	COpenRange< Position >::GetFrom (void) const
position_type	COpenRange< Position >::GetToOpen (void) const
position_type	COpenRange< Position >::GetTo (void) const
bool	COpenRange< Position >::Empty (void) const
bool	COpenRange< Position >::NotEmpty (void) const
position_type	COpenRange< Position >::GetLength (void) const
TThisType &	COpenRange< Position >::SetFrom (position_type from)
TThisType &	COpenRange< Position >::SetToOpen (position_type toOpen)
TThisType &	COpenRange< Position >::SetTo (position_type to)
TThisType &	COpenRange< Position >::SetOpen (position_type from, position_type toOpen)
TThisType &	COpenRange< Position >::Set (position_type from, position_type to)
TThisType &	COpenRange< Position >::SetLength (position_type length)
TThisType &	COpenRange< Position >::SetLengthDown (position_type length)
bool	COpenRange< Position >::operator== (const TThisType &r) const
bool	COpenRange< Position >::operator!= (const TThisType &r) const
bool	COpenRange< Position >::operator< (const TThisType &r) const
bool	COpenRange< Position >::operator<= (const TThisType &r) const
bool	COpenRange< Position >::operator> (const TThisType &r) const
bool	COpenRange< Position >::operator>= (const TThisType &r) const
static position_type	COpenRange< Position >::GetPositionMin (void)
static position_type	COpenRange< Position >::GetPositionMax (void)
static position_type	COpenRange< Position >::GetWholeFrom (void)
static position_type	COpenRange< Position >::GetWholeToOpen (void)
static position_type	COpenRange< Position >::GetWholeTo (void)
static position_type	COpenRange< Position >::GetWholeLength (void)
static TThisType	COpenRange< Position >::GetWhole (void)
bool	COpenRange< Position >::IsWholeFrom (void) const
bool	COpenRange< Position >::IsWholeTo (void) const
bool	COpenRange< Position >::IsWhole (void) const
static position_type	COpenRange< Position >::GetEmptyFrom (void)
static position_type	COpenRange< Position >::GetEmptyToOpen (void)
static position_type	COpenRange< Position >::GetEmptyTo (void)
static position_type	COpenRange< Position >::GetEmptyLength (void)
static TThisType	COpenRange< Position >::GetEmpty (void)
TThisType	COpenRange< Position >::IntersectionWith (const TThisType &r) const
TThisType &	COpenRange< Position >::IntersectWith (const TThisType &r)
TThisType	COpenRange< Position >::operator& (const TThisType &r) const
TThisType &	COpenRange< Position >::operator&= (const TThisType &r)
bool	COpenRange< Position >::IntersectingWith (const TThisType &r) const
bool	COpenRange< Position >::AbuttingWith (const TThisType &r) const
TThisType &	COpenRange< Position >::CombineWith (const TThisType &r)
TThisType	COpenRange< Position >::CombinationWith (const TThisType &r) const
TThisType &	COpenRange< Position >::operator+= (const TThisType &r)
TThisType	COpenRange< Position >::operator+ (const TThisType &r) const
	CRange< Position >::CRange (void)
	CRange< Position >::CRange (position_type from, position_type to)
	CRange< Position >::CRange (const TParent &range)
TThisType &	CRange< Position >::operator= (const TParent &range)
template<class Position >
CNcbiOstream &	operator<< (CNcbiOstream &out, const COpenRange< Position > &range)
static position_type	CRangeMapTraitsBase< Position, Mapped >::get_max_length (const range_type &key)
	CRangeMapIterator< Traits >::CRangeMapIterator (void)
	CRangeMapIterator< Traits >::CRangeMapIterator (const typename TTraits::non_const_iterator &iter)
const range_type &	CRangeMapIterator< Traits >::GetRange (void) const
TSelectIter	CRangeMapIterator< Traits >::GetSelectIter (void) const
TSelectIter	CRangeMapIterator< Traits >::GetSelectIterEnd (void) const
TLevelIter	CRangeMapIterator< Traits >::GetLevelIter (void) const
TLevelIter	CRangeMapIterator< Traits >::GetLevelIterEnd (void) const
bool	CRangeMapIterator< Traits >::Valid (void) const
	CRangeMapIterator< Traits >::DECLARE_OPERATOR_BOOL (Valid())
bool	CRangeMapIterator< Traits >::operator== (const TThisType &iter) const
bool	CRangeMapIterator< Traits >::operator!= (const TThisType &iter) const
range_type	CRangeMapIterator< Traits >::GetInterval (void) const
reference	CRangeMapIterator< Traits >::operator* (void) const
pointer	CRangeMapIterator< Traits >::operator-> (void) const
bool	CRangeMapIterator< Traits >::SetLevelIter (TLevelIter levelIter)
TLevelIter	CRangeMapIterator< Traits >::FirstLevelIter (void)
void	CRangeMapIterator< Traits >::SetEnd (TSelectMapRef selectMap)
void	CRangeMapIterator< Traits >::SetBegin (TSelectMapRef selectMap)
void	CRangeMapIterator< Traits >::SetBegin (const range_type &range, TSelectMapRef selectMap)
void	CRangeMapIterator< Traits >::Find (const range_type &key, TSelectMapRef selectMap)
TThisType &	CRangeMapIterator< Traits >::operator++ (void)
	CRangeMapBase< Traits >::CRangeMapBase (void)
TSelectMapI	CRangeMapBase< Traits >::insertLevel (position_type key)
bool	CRangeMapBase< Traits >::empty (void) const
size_type	CRangeMapBase< Traits >::size (void) const
const_iterator	CRangeMapBase< Traits >::end (void) const
const_iterator	CRangeMapBase< Traits >::begin (void) const
const_iterator	CRangeMapBase< Traits >::begin (const range_type &range) const
iterator	CRangeMapBase< Traits >::end (void)
iterator	CRangeMapBase< Traits >::begin (void)
iterator	CRangeMapBase< Traits >::begin (const range_type &range)
const_iterator	CRangeMapBase< Traits >::find (const key_type &key) const
iterator	CRangeMapBase< Traits >::find (const key_type &key)
void	CRangeMapBase< Traits >::erase (iterator iter)
size_type	CRangeMapBase< Traits >::erase (const key_type &key)
void	CRangeMapBase< Traits >::clear (void)
void	CRangeMapBase< Traits >::swap (TThisType &rangeMap)
	CRangeMap< Mapped, Position >::CRangeMap (void)
pair< iterator, bool >	CRangeMap< Mapped, Position >::insert (const value_type &value)
mapped_type &	CRangeMap< Mapped, Position >::operator[] (const key_type &key)
	CRangeMultimap< Mapped, Position >::CRangeMultimap (void)
iterator	CRangeMultimap< Mapped, Position >::insert (const value_type &value)

Variables
position_type	CAlignRange< Position >::m_FirstFrom
position_type	CAlignRange< Position >::m_SecondFrom
	start More...
position_type	CAlignRange< Position >::m_Length
	start on the aligned sequence More...
int	CAlignRange< Position >::m_Flags
	length of the segment More...
position_type	COpenRange< Position >::m_From
position_type	COpenRange< Position >::m_ToOpen
range_type	CRangeMapIterator< Traits >::m_Range
TSelectIter	CRangeMapIterator< Traits >::m_SelectIter
TSelectIter	CRangeMapIterator< Traits >::m_SelectIterEnd
TLevelIter	CRangeMapIterator< Traits >::m_LevelIter
TSelectMap	CRangeMapBase< Traits >::m_SelectMap

Friends
class	CRangeMapIterator< Traits >::CRangeMapBase< typename TTraits::TMapTraits >
class	CRangeMapIterator< Traits >::CRangeMap< mapped_type, position_type >
class	CRangeMapIterator< Traits >::CRangeMultimap< mapped_type, position_type >

Detailed Description

Typedef Documentation

const_iterator [1/3]

template<class Traits >

typedef TConstIteratorTraits::iterator CRangeMapBase< Traits >::const_iterator

Definition at line 399 of file rangemap.hpp.

const_iterator [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::const_iterator CRangeMap< Mapped, Position >::const_iterator

Definition at line 553 of file rangemap.hpp.

const_iterator [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::const_iterator CRangeMultimap< Mapped, Position >::const_iterator

Definition at line 615 of file rangemap.hpp.

iterator [1/5]

template<typename MapTraits >

typedef CRangeMapIterator<TIteratorTraits> CRangeMapIteratorTraits< MapTraits >::iterator

Definition at line 144 of file rangemap.hpp.

iterator [2/5]

template<typename MapTraits >

typedef CRangeMapIterator<TIteratorTraits> CRangeMapConstIteratorTraits< MapTraits >::iterator

Definition at line 164 of file rangemap.hpp.

iterator [3/5]

template<class Traits >

typedef TIteratorTraits::iterator CRangeMapBase< Traits >::iterator

Definition at line 398 of file rangemap.hpp.

iterator [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::iterator CRangeMap< Mapped, Position >::iterator

Definition at line 552 of file rangemap.hpp.

iterator [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::iterator CRangeMultimap< Mapped, Position >::iterator

Definition at line 614 of file rangemap.hpp.

key_type [1/3]

template<class Traits >

typedef range_type CRangeMapBase< Traits >::key_type

Definition at line 395 of file rangemap.hpp.

key_type [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::key_type CRangeMap< Mapped, Position >::key_type

Definition at line 550 of file rangemap.hpp.

key_type [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::key_type CRangeMultimap< Mapped, Position >::key_type

Definition at line 612 of file rangemap.hpp.

mapped_type [1/5]

template<typename Position , typename Mapped >

typedef Mapped CRangeMapTraitsBase< Position, Mapped >::mapped_type

Definition at line 65 of file rangemap.hpp.

mapped_type [2/5]

template<class Traits >

typedef TTraits::mapped_type CRangeMapIterator< Traits >::mapped_type

Definition at line 177 of file rangemap.hpp.

mapped_type [3/5]

template<class Traits >

typedef TRangeMapTraits::mapped_type CRangeMapBase< Traits >::mapped_type

Definition at line 393 of file rangemap.hpp.

mapped_type [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::mapped_type CRangeMap< Mapped, Position >::mapped_type

Definition at line 548 of file rangemap.hpp.

mapped_type [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::mapped_type CRangeMultimap< Mapped, Position >::mapped_type

Definition at line 610 of file rangemap.hpp.

non_const_iterator [1/2]

template<typename MapTraits >

typedef CRangeMapIterator<TNCIteratorTraits> CRangeMapIteratorTraits< MapTraits >::non_const_iterator

Definition at line 145 of file rangemap.hpp.

non_const_iterator [2/2]

template<typename MapTraits >

typedef CRangeMapIterator<TNCIteratorTraits> CRangeMapConstIteratorTraits< MapTraits >::non_const_iterator

Definition at line 165 of file rangemap.hpp.

pointer [1/3]

template<typename MapTraits >

typedef TMapTraits::value_type* CRangeMapIteratorTraits< MapTraits >::pointer

Definition at line 142 of file rangemap.hpp.

pointer [2/3]

template<typename MapTraits >

typedef const TMapTraits::value_type* CRangeMapConstIteratorTraits< MapTraits >::pointer

Definition at line 162 of file rangemap.hpp.

pointer [3/3]

template<class Traits >

typedef TTraits::pointer CRangeMapIterator< Traits >::pointer

Definition at line 181 of file rangemap.hpp.

position_type [1/10]

template<class Position >

typedef Position CAlignRange< Position >::position_type

Definition at line 65 of file align_range.hpp.

position_type [2/10]

template<class TAlignRange >

typedef TAlignRange::position_type PAlignRangeToLess< TAlignRange >::position_type

Definition at line 51 of file align_range_oper.hpp.

position_type [3/10]

template<class TAlignRange >

typedef TAlignRange::position_type PAlignRangeFromLess< TAlignRange >::position_type

Definition at line 82 of file align_range_oper.hpp.

position_type [4/10]

template<class Position >

typedef Position COpenRange< Position >::position_type

Definition at line 120 of file range.hpp.

position_type [5/10]

template<class Position >

typedef TParent::position_type CRange< Position >::position_type

Definition at line 391 of file range.hpp.

position_type [6/10]

template<typename Position , typename Mapped >

typedef Position CRangeMapTraitsBase< Position, Mapped >::position_type

Definition at line 63 of file rangemap.hpp.

position_type [7/10]

template<class Traits >

typedef TTraits::position_type CRangeMapIterator< Traits >::position_type

Definition at line 175 of file rangemap.hpp.

position_type [8/10]

template<class Traits >

typedef TRangeMapTraits::position_type CRangeMapBase< Traits >::position_type

Definition at line 391 of file rangemap.hpp.

position_type [9/10]

template<typename Mapped , typename Position = int>

typedef TParent::position_type CRangeMap< Mapped, Position >::position_type

Definition at line 546 of file rangemap.hpp.

position_type [10/10]

template<typename Mapped , typename Position = int>

typedef TParent::position_type CRangeMultimap< Mapped, Position >::position_type

Definition at line 608 of file rangemap.hpp.

range_type [1/5]

template<typename Position , typename Mapped >

typedef CRange<position_type> CRangeMapTraitsBase< Position, Mapped >::range_type

Definition at line 64 of file rangemap.hpp.

range_type [2/5]

template<class Traits >

typedef TTraits::range_type CRangeMapIterator< Traits >::range_type

Definition at line 176 of file rangemap.hpp.

range_type [3/5]

template<class Traits >

typedef TRangeMapTraits::range_type CRangeMapBase< Traits >::range_type

Definition at line 392 of file rangemap.hpp.

range_type [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::range_type CRangeMap< Mapped, Position >::range_type

Definition at line 547 of file rangemap.hpp.

range_type [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::range_type CRangeMultimap< Mapped, Position >::range_type

Definition at line 609 of file rangemap.hpp.

reference [1/3]

template<typename MapTraits >

typedef TMapTraits::value_type& CRangeMapIteratorTraits< MapTraits >::reference

Definition at line 141 of file rangemap.hpp.

reference [2/3]

template<typename MapTraits >

typedef const TMapTraits::value_type& CRangeMapConstIteratorTraits< MapTraits >::reference

Definition at line 161 of file rangemap.hpp.

reference [3/3]

template<class Traits >

typedef TTraits::reference CRangeMapIterator< Traits >::reference

Definition at line 180 of file rangemap.hpp.

select_value [1/3]

template<class Traits >

typedef TSelectMap::value_type CRangeMapBase< Traits >::select_value

protected

Definition at line 404 of file rangemap.hpp.

select_value [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::select_value CRangeMap< Mapped, Position >::select_value

Definition at line 557 of file rangemap.hpp.

select_value [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::select_value CRangeMultimap< Mapped, Position >::select_value

Definition at line 619 of file rangemap.hpp.

size_type [1/3]

template<class Traits >

typedef size_t CRangeMapBase< Traits >::size_type

Definition at line 390 of file rangemap.hpp.

size_type [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::size_type CRangeMap< Mapped, Position >::size_type

Definition at line 545 of file rangemap.hpp.

size_type [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::size_type CRangeMultimap< Mapped, Position >::size_type

Definition at line 607 of file rangemap.hpp.

TConstIteratorTraits

template<class Traits >

typedef CRangeMapConstIteratorTraits<TRangeMapTraits> CRangeMapBase< Traits >::TConstIteratorTraits

Definition at line 388 of file rangemap.hpp.

TIteratorTraits [1/3]

template<typename MapTraits >

typedef CRangeMapIteratorTraits<TMapTraits> CRangeMapIteratorTraits< MapTraits >::TIteratorTraits

Definition at line 133 of file rangemap.hpp.

TIteratorTraits [2/3]

template<typename MapTraits >

typedef CRangeMapConstIteratorTraits<TMapTraits> CRangeMapConstIteratorTraits< MapTraits >::TIteratorTraits

Definition at line 153 of file rangemap.hpp.

TIteratorTraits [3/3]

template<class Traits >

typedef CRangeMapIteratorTraits<TRangeMapTraits> CRangeMapBase< Traits >::TIteratorTraits

Definition at line 387 of file rangemap.hpp.

TLevelIter [1/3]

template<typename MapTraits >

typedef TMapTraits::TLevelMap::iterator CRangeMapIteratorTraits< MapTraits >::TLevelIter

Definition at line 140 of file rangemap.hpp.

TLevelIter [2/3]

template<typename MapTraits >

typedef TMapTraits::TLevelMap::const_iterator CRangeMapConstIteratorTraits< MapTraits >::TLevelIter

Definition at line 160 of file rangemap.hpp.

TLevelIter [3/3]

template<class Traits >

typedef TTraits::TLevelIter CRangeMapIterator< Traits >::TLevelIter

Definition at line 186 of file rangemap.hpp.

TLevelMap [1/5]

template<typename Position , typename Mapped >

typedef map<typename TParent::range_type, Mapped> CRangeMapTraits< Position, Mapped >::TLevelMap

Definition at line 113 of file rangemap.hpp.

TLevelMap [2/5]

template<typename Position , typename Mapped >

typedef multimap<typename TParent::range_type, Mapped> CRangeMultimapTraits< Position, Mapped >::TLevelMap

Definition at line 123 of file rangemap.hpp.

TLevelMap [3/5]

template<class Traits >

typedef TRangeMapTraits::TLevelMap CRangeMapBase< Traits >::TLevelMap

protected

Definition at line 406 of file rangemap.hpp.

TLevelMap [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::TLevelMap CRangeMap< Mapped, Position >::TLevelMap

Definition at line 559 of file rangemap.hpp.

TLevelMap [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::TLevelMap CRangeMultimap< Mapped, Position >::TLevelMap

Definition at line 621 of file rangemap.hpp.

TLevelMapI [1/3]

template<class Traits >

typedef TLevelMap::iterator CRangeMapBase< Traits >::TLevelMapI

protected

Definition at line 407 of file rangemap.hpp.

TLevelMapI [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::TLevelMapI CRangeMap< Mapped, Position >::TLevelMapI

Definition at line 560 of file rangemap.hpp.

TLevelMapI [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::TLevelMapI CRangeMultimap< Mapped, Position >::TLevelMapI

Definition at line 622 of file rangemap.hpp.

TLevelMapRef [1/2]

template<typename MapTraits >

typedef TMapTraits::TLevelMap& CRangeMapIteratorTraits< MapTraits >::TLevelMapRef

Definition at line 138 of file rangemap.hpp.

TLevelMapRef [2/2]

template<typename MapTraits >

typedef const TMapTraits::TLevelMap& CRangeMapConstIteratorTraits< MapTraits >::TLevelMapRef

Definition at line 158 of file rangemap.hpp.

TMapTraits [1/2]

template<typename MapTraits >

typedef MapTraits CRangeMapIteratorTraits< MapTraits >::TMapTraits

Definition at line 132 of file rangemap.hpp.

TMapTraits [2/2]

template<typename MapTraits >

typedef MapTraits CRangeMapConstIteratorTraits< MapTraits >::TMapTraits

Definition at line 152 of file rangemap.hpp.

TNCIteratorTraits [1/2]

template<typename MapTraits >

typedef CRangeMapIteratorTraits<TMapTraits> CRangeMapIteratorTraits< MapTraits >::TNCIteratorTraits

Definition at line 134 of file rangemap.hpp.

TNCIteratorTraits [2/2]

template<typename MapTraits >

typedef CRangeMapIteratorTraits<TMapTraits> CRangeMapConstIteratorTraits< MapTraits >::TNCIteratorTraits

Definition at line 154 of file rangemap.hpp.

TParent [1/5]

template<class Position >

typedef COpenRange<Position> CRange< Position >::TParent

Definition at line 390 of file range.hpp.

TParent [2/5]

template<typename Position , typename Mapped >

typedef CRangeMapTraitsBase<Position, Mapped> CRangeMapTraits< Position, Mapped >::TParent

private

Definition at line 110 of file rangemap.hpp.

TParent [3/5]

template<typename Position , typename Mapped >

typedef CRangeMapTraitsBase<Position, Mapped> CRangeMultimapTraits< Position, Mapped >::TParent

private

Definition at line 120 of file rangemap.hpp.

TParent [4/5]

template<typename Mapped , typename Position = int>

typedef CRangeMapBase< CRangeMapTraits<Position, Mapped> > CRangeMap< Mapped, Position >::TParent

private

Definition at line 542 of file rangemap.hpp.

TParent [5/5]

template<typename Mapped , typename Position = int>

typedef CRangeMapBase< CRangeMultimapTraits<Position, Mapped> > CRangeMultimap< Mapped, Position >::TParent

private

Definition at line 604 of file rangemap.hpp.

TRange

template<class Position >

typedef CRange<Position> CAlignRange< Position >::TRange

Definition at line 67 of file align_range.hpp.

TRangeMap [1/3]

template<typename Position , typename Mapped >

typedef CRangeMap<Mapped, Position> CRangeMapTraits< Position, Mapped >::TRangeMap

Definition at line 112 of file rangemap.hpp.

TRangeMap [2/3]

template<typename Position , typename Mapped >

typedef CRangeMultimap<Mapped, Position> CRangeMultimapTraits< Position, Mapped >::TRangeMap

Definition at line 122 of file rangemap.hpp.

TRangeMap [3/3]

template<class Traits >

typedef TTraits::TRangeMap CRangeMapIterator< Traits >::TRangeMap

Definition at line 183 of file rangemap.hpp.

TRangeMapRef [1/2]

template<typename MapTraits >

typedef TMapTraits::TRangeMap& CRangeMapIteratorTraits< MapTraits >::TRangeMapRef

Definition at line 136 of file rangemap.hpp.

TRangeMapRef [2/2]

template<typename MapTraits >

typedef const TMapTraits::TRangeMap& CRangeMapConstIteratorTraits< MapTraits >::TRangeMapRef

Definition at line 156 of file rangemap.hpp.

TRangeMapTraits [1/3]

template<class Traits >

typedef Traits CRangeMapBase< Traits >::TRangeMapTraits

Definition at line 386 of file rangemap.hpp.

TRangeMapTraits [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::TRangeMapTraits CRangeMap< Mapped, Position >::TRangeMapTraits

Definition at line 555 of file rangemap.hpp.

TRangeMapTraits [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::TRangeMapTraits CRangeMultimap< Mapped, Position >::TRangeMapTraits

Definition at line 617 of file rangemap.hpp.

TSelectIter [1/3]

template<typename MapTraits >

typedef TMapTraits::TSelectMap::iterator CRangeMapIteratorTraits< MapTraits >::TSelectIter

Definition at line 139 of file rangemap.hpp.

TSelectIter [2/3]

template<typename MapTraits >

typedef TMapTraits::TSelectMap::const_iterator CRangeMapConstIteratorTraits< MapTraits >::TSelectIter

Definition at line 159 of file rangemap.hpp.

TSelectIter [3/3]

template<class Traits >

typedef TTraits::TSelectIter CRangeMapIterator< Traits >::TSelectIter

Definition at line 185 of file rangemap.hpp.

TSelectMap [1/5]

template<typename Position , typename Mapped >

typedef map<Position, TLevelMap> CRangeMapTraits< Position, Mapped >::TSelectMap

Definition at line 114 of file rangemap.hpp.

TSelectMap [2/5]

template<typename Position , typename Mapped >

typedef map<Position, TLevelMap> CRangeMultimapTraits< Position, Mapped >::TSelectMap

Definition at line 124 of file rangemap.hpp.

TSelectMap [3/5]

template<class Traits >

typedef TRangeMapTraits::TSelectMap CRangeMapBase< Traits >::TSelectMap

protected

Definition at line 403 of file rangemap.hpp.

TSelectMap [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::TSelectMap CRangeMap< Mapped, Position >::TSelectMap

Definition at line 556 of file rangemap.hpp.

TSelectMap [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::TSelectMap CRangeMultimap< Mapped, Position >::TSelectMap

Definition at line 618 of file rangemap.hpp.

TSelectMapI [1/3]

template<class Traits >

typedef TSelectMap::iterator CRangeMapBase< Traits >::TSelectMapI

protected

Definition at line 405 of file rangemap.hpp.

TSelectMapI [2/3]

template<typename Mapped , typename Position = int>

typedef TParent::TSelectMapI CRangeMap< Mapped, Position >::TSelectMapI

Definition at line 558 of file rangemap.hpp.

TSelectMapI [3/3]

template<typename Mapped , typename Position = int>

typedef TParent::TSelectMapI CRangeMultimap< Mapped, Position >::TSelectMapI

Definition at line 620 of file rangemap.hpp.

TSelectMapRef [1/3]

template<typename MapTraits >

typedef TMapTraits::TSelectMap& CRangeMapIteratorTraits< MapTraits >::TSelectMapRef

Definition at line 137 of file rangemap.hpp.

TSelectMapRef [2/3]

template<typename MapTraits >

typedef const TMapTraits::TSelectMap& CRangeMapConstIteratorTraits< MapTraits >::TSelectMapRef

Definition at line 157 of file rangemap.hpp.

TSelectMapRef [3/3]

template<class Traits >

typedef TTraits::TSelectMapRef CRangeMapIterator< Traits >::TSelectMapRef

Definition at line 184 of file rangemap.hpp.

TSeqRange

typedef CRange<TSeqPos> TSeqRange

typedefs for sequence ranges

Definition at line 419 of file range.hpp.

TSignedSeqRange

typedef CRange<TSignedSeqPos> TSignedSeqRange

Definition at line 420 of file range.hpp.

TThisType [1/5]

template<class Position >

typedef CAlignRange<Position> CAlignRange< Position >::TThisType

Definition at line 66 of file align_range.hpp.

TThisType [2/5]

template<class Position >

typedef COpenRange<Position> COpenRange< Position >::TThisType

Definition at line 121 of file range.hpp.

TThisType [3/5]

template<class Position >

typedef CRange<Position> CRange< Position >::TThisType

Definition at line 392 of file range.hpp.

TThisType [4/5]

template<class Traits >

typedef TTraits::iterator CRangeMapIterator< Traits >::TThisType

Definition at line 189 of file rangemap.hpp.

TThisType [5/5]

template<class Traits >

typedef TRangeMapTraits::TRangeMap CRangeMapBase< Traits >::TThisType

Definition at line 397 of file rangemap.hpp.

TTraits

template<class Traits >

typedef Traits CRangeMapIterator< Traits >::TTraits

Definition at line 174 of file rangemap.hpp.

value_type [1/5]

template<typename Position , typename Mapped >

typedef pair<const range_type, mapped_type> CRangeMapTraitsBase< Position, Mapped >::value_type

Definition at line 66 of file rangemap.hpp.

value_type [2/5]

template<class Traits >

typedef TTraits::value_type CRangeMapIterator< Traits >::value_type

Definition at line 178 of file rangemap.hpp.

value_type [3/5]

template<class Traits >

typedef TRangeMapTraits::value_type CRangeMapBase< Traits >::value_type

Definition at line 394 of file rangemap.hpp.

value_type [4/5]

template<typename Mapped , typename Position = int>

typedef TParent::value_type CRangeMap< Mapped, Position >::value_type

Definition at line 549 of file rangemap.hpp.

value_type [5/5]

template<typename Mapped , typename Position = int>

typedef TParent::value_type CRangeMultimap< Mapped, Position >::value_type

Definition at line 611 of file rangemap.hpp.

Enumeration Type Documentation

EFlags

template<class Position >

enum CAlignRange::EFlags

Enumerator
fReversed
fFirstRev

Definition at line 69 of file align_range.hpp.

Function Documentation

AbuttingWith()

template<class Position >

bool COpenRange< Position >::AbuttingWith ( const TThisType &  r ) const

inline

Definition at line 336 of file range.hpp.

Referenced by CEquivRange::AbuttingWith(), CVecscreen::x_BuildNonOverlappingRange(), CFeatGlyph::x_DrawFeatureBar(), CMergeTree::x_EvalGap(), and CDepthCollection::ZeroFill().

begin() [1/4]

template<class Traits >

iterator CRangeMapBase< Traits >::begin ( const range_type &  range )

inline

Definition at line 476 of file rangemap.hpp.

begin() [2/4]

template<class Traits >

const_iterator CRangeMapBase< Traits >::begin ( const range_type &  range ) const

inline

Definition at line 457 of file rangemap.hpp.

begin() [3/4]

template<class Traits >

iterator CRangeMapBase< Traits >::begin ( void  )

inline

Definition at line 470 of file rangemap.hpp.

begin() [4/4]

template<class Traits >

const_iterator CRangeMapBase< Traits >::begin ( void  ) const

inline

Definition at line 451 of file rangemap.hpp.

Referenced by variation::CVariationUtil::CCdregionIndex::Get(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), variation::SFastLocSubtract::operator()(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CPhrap_Contig::x_CreateSeq_align(), CTSE_Info::x_FindSeq_feat(), and CAnnot_Collector::x_SearchRange().

CAlignRange() [1/2]

template<class Position >

CAlignRange< Position >::CAlignRange ( position_type  first_from, position_type  second_from, position_type  len, bool  direct = true, bool  first_direct = true  )

inline

Definition at line 82 of file align_range.hpp.

References CAlignRange< Position >::SetDirect(), and CAlignRange< Position >::SetFirstDirect().

CAlignRange() [2/2]

template<class Position >

CAlignRange< Position >::CAlignRange ( void  )

inline

Definition at line 74 of file align_range.hpp.

clear()

template<class Traits >

void CRangeMapBase< Traits >::clear ( void  )

inline

Definition at line 524 of file rangemap.hpp.

CombinationWith()

template<class Position >

TThisType COpenRange< Position >::CombinationWith ( const TThisType &  r ) const

inline

Definition at line 358 of file range.hpp.

Referenced by s_MergeRangeList(), CVecscreen::x_BuildNonOverlappingRange(), CVecscreen::x_MergeInclusiveSeqalign(), and CVecscreen::x_MergeLowerRankSeqalign().

CombinationWithAbutting()

template<class Position >

TThisType CAlignRange< Position >::CombinationWithAbutting ( const TThisType &  r ) const

inline

Definition at line 319 of file align_range.hpp.

References CAlignRange< Position >::CombineWithAbutting(), and r().

CombineWith()

template<class Position >

TThisType& COpenRange< Position >::CombineWith ( const TThisType &  r )

inline

Definition at line 345 of file range.hpp.

Referenced by CGraphRanges::AddRange(), CHit::AddUpSubHits(), CFeatHistogramDS::CFeatHistogramDS(), CIdRangeMap::CIdRangeMap(), CModelExon::Extend(), CFeatGlyph::GetRange(), CSeq_align::GetSeqRange(), CSparseAlignment::Init(), CModelCluster< Model >::Insert(), readGFF3(), s_SeqLocToTotalRangesInfoMapByStrand(), CModelCluster< Model >::Splice(), CSparseAln::x_Build(), CFeatGlyph::x_DrawFeatureBar(), CAllOtherFeaturesTrack::x_OnAllJobsFinished(), CTrackContainer::x_OnJobCompleted(), CAlignedFeatureGraph::x_PlaceCluster(), and CUnorderedSplitter::x_SplitDeltaExt().

CombineWithAbutting()

template<class Position >

TThisType& CAlignRange< Position >::CombineWithAbutting ( const TThisType &  r )

inline

Definition at line 302 of file align_range.hpp.

References _ASSERT, CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::IsAbutting(), CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_Length, r(), CAlignRange< Position >::SetFirstFrom(), and CAlignRange< Position >::SetSecondFrom().

Referenced by CAlignRange< Position >::CombinationWithAbutting(), and CAlignRangeCollection< CAlignRange< TSeqPos > >::insert().

COpenRange() [1/2]

template<class Position >

COpenRange< Position >::COpenRange ( position_type  from, position_type  toOpen  )

inline

Definition at line 128 of file range.hpp.

COpenRange() [2/2]

template<class Position >

COpenRange< Position >::COpenRange ( void  )

inline

Definition at line 124 of file range.hpp.

CRange() [1/3]

template<class Position >

CRange< Position >::CRange ( const TParent &  range )

inline

Definition at line 402 of file range.hpp.

CRange() [2/3]

template<class Position >

CRange< Position >::CRange ( position_type  from, position_type  to  )

inline

Definition at line 398 of file range.hpp.

CRange() [3/3]

template<class Position >

CRange< Position >::CRange ( void  )

inline

Definition at line 395 of file range.hpp.

CRangeMap()

template<typename Mapped , typename Position = int>

CRangeMap< Mapped, Position >::CRangeMap ( void  )

inlineexplicit

Definition at line 563 of file rangemap.hpp.

CRangeMapBase()

template<class Traits >

CRangeMapBase< Traits >::CRangeMapBase ( void  )

inlineprotected

Definition at line 410 of file rangemap.hpp.

CRangeMapIterator() [1/2]

template<class Traits >

CRangeMapIterator< Traits >::CRangeMapIterator ( const typename TTraits::non_const_iterator &  iter )

inline

Definition at line 203 of file rangemap.hpp.

CRangeMapIterator() [2/2]

template<class Traits >

CRangeMapIterator< Traits >::CRangeMapIterator ( void  )

inline

Definition at line 198 of file rangemap.hpp.

CRangeMultimap()

template<typename Mapped , typename Position = int>

CRangeMultimap< Mapped, Position >::CRangeMultimap ( void  )

inlineexplicit

Definition at line 625 of file rangemap.hpp.

DECLARE_OPERATOR_BOOL()

template<class Traits >

CRangeMapIterator< Traits >::DECLARE_OPERATOR_BOOL

(

Valid()

)

Empty() [1/2]

template<class Position >

bool CAlignRange< Position >::Empty ( void  ) const

inline

Definition at line 141 of file align_range.hpp.

References CAlignRange< Position >::m_Length.

Empty() [2/2]

template<class Position >

bool COpenRange< Position >::Empty ( void  ) const

inline

Definition at line 148 of file range.hpp.

Referenced by CAlignCollapser::AddAlignment(), CGeneModel::AddExon(), CGraphRanges::AddRange(), CHandleRange::AddRange(), CDepthCollection::AddRange(), CDensityMap< CntType >::AddRange(), CBamFileRangeSet::AddRanges(), AddSupport(), CChain::CalculateDropLimits(), CFeatHistogramDS::CFeatHistogramDS(), CChainer::CChainerImpl::CheckCompatibility(), CheckSparseAln(), CCDSInfo::Clip(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), CModelExon::CModelExon(), IAlnMultiDataSource::CollectAlignStats(), CGeneModel::CombineCdsInfo(), CCDSInfo::CombineWith(), CSeq_loc_Conversion::CombineWith(), SPhyloCSFSlice::CompactRange(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CGeneModel::CutExons(), CDataLoader::DetailsToChoice(), CEquivRange::Distance(), CAlignGlyph::DrawPWAlignElem(), DumpSparseAln(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CEquivRange::Empty(), CAlignCollapser::FilterAlignments(), CGeneSelector::FilterGenes(), CChainer::CChainerImpl::FilterOutTandemOverlap(), CChainer::CChainerImpl::FindAltsForGeneSeeds(), FindPolyA(), FindStartsStops(), CGeneModel::FShiftedLen(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CGnomonEngine::GetAnnot(), CVDBGraphSeqIterator::GetAnnot(), CParse::GetGenes(), CGuiObjectInfoSeq_align::GetInsertionRanges(), SBamIndexRefIndex::GetLimitRange(), CHandleRange::GetRight(), CGnomonEngine::GetScore(), CEditScript::GetScore(), CSeq_align::GetSeqRange(), CHandleRange::GetStrandsFlag(), CChain::HarborsNested(), CGene::HarborsNested(), CSeqScores::Init(), CCddInputData::CHit::IntersectWith(), CSeq_loc_CI::IsEmpty(), IAlnSegment::IsGap(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), CEditScript::MakeEditScript(), Map(), CGnomonAnnotator_Base::MapModelsToOrigContig(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CAlignMap::MapRangeEditedToOrig(), CAlignMap::MapRangeOrigToEdited(), CTestNameToInfoMapLoader::operator()(), SOutsideRange::operator()(), ParseAttributes(), CGnomonAnnotator::Predict(), readGFF3(), CAlignModel::RecalculateAlignMap(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CAlignMarkHandler::Render(), CRuler::Render(), CChainer::CChainerImpl::ReplicatePStops(), CChain::RestoreReasonableConfirmedStart(), s_AlignDist(), s_MapSlaveFeatureToMaster(), s_SeqLocToTotalRangesInfoMapByStrand(), CClippedScorer::ScoreAlignments(), CSNPDbGraphIterator::Select(), CSNPDbPageIterator::Select(), CFeatureSearchJob::SeqLocToString(), CChain::SetConfirmedEnds(), CChain::SetConsistentCoverage(), CChainer::CChainerImpl::SetFlagsForChains(), CCDSInfo::SetReadingFrame(), CAlignCompare::SAlignment::Slice(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), SModelData::SModelData(), CEquivRangeBuilder::SplitIntersections(), CSeq_align::SplitOnLongDiscontinuity(), CBlobSplitterImpl::SplitPieces(), ProjectCDS::transform_align(), DoNotBelieveFrameShiftsWithoutCdsEvidence::transform_align(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CFeatureGenerator::SImplementation::TrimHolesToCodons(), TrimAlignment::TrimTranscript(), CMultAlign::Variations(), CHit::VerifyHit(), CAnnot_Collector::x_AddPostMappings(), CAnnot_Collector::x_AddPostMappingsCvt(), CPhrap_Read::x_AddQualityFeat(), CMultiAligner::x_AlignProfileProfileUsingHit(), CAlignMarkHandler::x_AlnRangeFromSeqRange(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CAlignGlyph::x_CalcIntervals(), CScoringJob::x_CalculateAlignmentScores(), CHitMatrixDataSource::x_CalculateHitsRange(), CDenseg_CI::x_CheckSegment(), CSparse_CI::x_CheckSegment(), CSGAlignStatJob::x_CreatePileUpGraphs(), CMatePairGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawGaps(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CAlignGlyph::x_DrawMultiAlign(), CCdsGlyph::x_DrawProjectedProtSeq(), CFeatGlyph::x_DrawProjectedRuler(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawUnalignedBar(), CAlignGlyph::x_DrawUnalignedRowSequence(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CDisplaySeqalign::x_GetFeatureInfo(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeqGlyph::x_IntersectVisible(), CGencollIdMapper::x_IsLoc_Int_InAGap(), CMappingRange::x_Map_Fuzz(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSparse_CI::x_NextSegment(), CTextSelHandler::x_OnChangeSelRange(), CLinearSelHandler::x_OnEndSelRange(), CTextSelHandler::x_OnEndSelRange(), CMultiAligner::x_RealignBlocks(), CAlnVecRow::x_RenderAlignSegments(), CAlignGlyph::x_RenderAveragableScores(), CGraphOverlay::x_RenderContent(), CGraphTrack::x_RenderContent(), CTraceGraphTrack::x_RenderContent(), CRuler::x_RenderRange(), CRuler::x_RenderScale(), CSeqGraphicPane::x_RenderTooltipConnector(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CGraphOverlay::x_UpdateBoundingBox(), CGraphTrack::x_UpdateBoundingBox(), CGeneModelTrack::x_UpdateData(), CSeqGlyph::x_Visible_V(), and CHitMatrixWidget::x_ZoomToHits().

empty()

template<class Traits >

bool CRangeMapBase< Traits >::empty ( void  ) const

inline

Definition at line 428 of file rangemap.hpp.

Referenced by SIdAnnotObjs::x_CleanRangeMaps(), CSeq_align_Mapper_Base::x_ConvertSegment(), CSeq_align_Mapper::x_ConvertSegmentCvt(), SIdAnnotObjs::x_RangeMapIsEmpty(), and CTSE_Info::x_UnmapAnnotObject().

end() [1/2]

template<class Traits >

iterator CRangeMapBase< Traits >::end ( void  )

inline

Definition at line 464 of file rangemap.hpp.

end() [2/2]

template<class Traits >

const_iterator CRangeMapBase< Traits >::end ( void  ) const

inline

Definition at line 445 of file rangemap.hpp.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase().

erase() [1/2]

template<class Traits >

size_type CRangeMapBase< Traits >::erase ( const key_type &  key )

inline

Definition at line 511 of file rangemap.hpp.

erase() [2/2]

template<class Traits >

void CRangeMapBase< Traits >::erase ( iterator  iter )

inline

Definition at line 498 of file rangemap.hpp.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), and CTSE_Info::x_UnmapAnnotObject().

find() [1/2]

template<class Traits >

iterator CRangeMapBase< Traits >::find ( const key_type &  key )

inline

Definition at line 490 of file rangemap.hpp.

find() [2/2]

template<class Traits >

const_iterator CRangeMapBase< Traits >::find ( const key_type &  key ) const

inline

Definition at line 484 of file rangemap.hpp.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), CSeq_annot_Finder::x_Find(), and CTSE_Info::x_UnmapAnnotObject().

Find()

template<class Traits >

void CRangeMapIterator< Traits >::Find ( const range_type &  key, TSelectMapRef  selectMap  )

private

Definition at line 357 of file rangemap.hpp.

References ncbi::grid::netcache::search::fields::key.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::find().

FirstContains()

template<class Position >

bool CAlignRange< Position >::FirstContains ( position_type  pos ) const

inline

Definition at line 233 of file align_range.hpp.

References CAlignRange< Position >::GetFirstToOpen(), and CAlignRange< Position >::m_FirstFrom.

Referenced by CAlignRange< Position >::GetSecondPosByFirstPos().

FirstLevelIter()

template<class Traits >

TLevelIter CRangeMapIterator< Traits >::FirstLevelIter ( void  )

inlineprivate

Definition at line 288 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_Range, and CRangeMapIterator< Traits >::m_SelectIter.

Referenced by CRangeMapIterator< Traits >::operator++(), and CRangeMapIterator< Traits >::SetBegin().

get_max_length()

template<typename Position , typename Mapped >

static position_type CRangeMapTraitsBase< Position, Mapped >::get_max_length ( const range_type &  key )

inlinestatic

Definition at line 86 of file rangemap.hpp.

References CHAR_BIT, ncbi::grid::netcache::search::fields::key, and len.

GetEmpty() [1/2]

template<class Position >

static TThisType CAlignRange< Position >::GetEmpty ( void  )

inlinestatic

Definition at line 341 of file align_range.hpp.

GetEmpty() [2/2]

template<class Position >

static TThisType COpenRange< Position >::GetEmpty ( void  )

inlinestatic

Definition at line 306 of file range.hpp.

Referenced by CRangeCollection< TSeqPos >::GetLimits(), CRangeSet< CPairwiseAln::TPos >::GetLimits(), s_GetSeqRange(), s_LocToRange(), COligoSpecificityCheck::x_GetSlaveRangeGivenMasterRange(), and CBamRawAlignIterator::x_Select().

GetEmptyFrom() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetEmptyFrom ( void  )

inlinestatic

Definition at line 325 of file align_range.hpp.

References CAlignRange< Position >::GetPositionMax().

GetEmptyFrom() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetEmptyFrom ( void  )

inlinestatic

Definition at line 290 of file range.hpp.

Referenced by CRangeCollection< TSeqPos >::GetFrom(), CRangeSet< CPairwiseAln::TPos >::GetFrom(), CHistogramGlyph::SetAxisRange(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), and CGraphOverlay::x_OnLayoutChanged().

GetEmptyLength() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetEmptyLength ( void  )

inlinestatic

Definition at line 337 of file align_range.hpp.

GetEmptyLength() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetEmptyLength ( void  )

inlinestatic

Definition at line 302 of file range.hpp.

GetEmptyTo() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetEmptyTo ( void  )

inlinestatic

Definition at line 333 of file align_range.hpp.

References CAlignRange< Position >::GetEmptyToOpen().

GetEmptyTo() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetEmptyTo ( void  )

inlinestatic

Definition at line 298 of file range.hpp.

Referenced by CRangeCollection< TSeqPos >::GetTo(), CRangeSet< CPairwiseAln::TPos >::GetTo(), CHistogramGlyph::SetAxisRange(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), and CGraphOverlay::x_OnLayoutChanged().

GetEmptyToOpen() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetEmptyToOpen ( void  )

inlinestatic

Definition at line 329 of file align_range.hpp.

References CAlignRange< Position >::GetPositionMax().

Referenced by CAlignRange< Position >::GetEmptyTo().

GetEmptyToOpen() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetEmptyToOpen ( void  )

inlinestatic

Definition at line 294 of file range.hpp.

Referenced by CRangeCollection< TSeqPos >::GetToOpen(), and CRangeSet< CPairwiseAln::TPos >::GetToOpen().

GetFirstFrom()

template<class Position >

position_type CAlignRange< Position >::GetFirstFrom ( void  ) const

inline

Definition at line 109 of file align_range.hpp.

References CAlignRange< Position >::m_FirstFrom.

Referenced by CheckPairwiseAln(), CAlignRange< Position >::CombineWithAbutting(), DumpPairwiseAln(), CAlignRange< Position >::GetFirstRange(), CDiagHitElement::GetQueryStart(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectingWith(), CAlignRange< Position >::IntersectWith(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CSparseAln::x_Build(), CDiagRangeCollection::x_Diff(), CAlnMixMerger::x_Merge(), and CMergedPairwiseAln::x_ValidNeighboursOnFirstDim().

GetFirstPosBySecondPos()

template<class Position >

position_type CAlignRange< Position >::GetFirstPosBySecondPos ( position_type  pos ) const

inline

Definition at line 224 of file align_range.hpp.

References CAlignRange< Position >::GetSecondTo(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_FirstFrom, CAlignRange< Position >::m_SecondFrom, and CAlignRange< Position >::SecondContains().

GetFirstRange()

template<class Position >

TRange CAlignRange< Position >::GetFirstRange ( ) const

inline

Definition at line 133 of file align_range.hpp.

References CAlignRange< Position >::GetFirstFrom(), and CAlignRange< Position >::GetFirstTo().

GetFirstTo()

template<class Position >

position_type CAlignRange< Position >::GetFirstTo ( void  ) const

inline

Definition at line 117 of file align_range.hpp.

References CAlignRange< Position >::GetFirstToOpen().

Referenced by CAlignRange< Position >::GetFirstRange(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectingWith(), CAlignRange< Position >::IntersectWith(), and s_TranslatePairwiseToAlnCoords().

GetFirstToOpen()

template<class Position >

position_type CAlignRange< Position >::GetFirstToOpen ( void  ) const

inline

Definition at line 113 of file align_range.hpp.

References CAlignRange< Position >::m_FirstFrom, and CAlignRange< Position >::m_Length.

Referenced by CAlignRange< Position >::CombineWithAbutting(), ConvertStdsegToPairwiseAln(), CAlignRange< Position >::FirstContains(), CAlignRange< Position >::GetFirstTo(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IsAbutting(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), CSparseAln::x_Build(), CDiagRangeCollection::x_Diff(), and CMergedPairwiseAln::x_ValidNeighboursOnFirstDim().

GetFrom()

template<class Position >

position_type COpenRange< Position >::GetFrom ( void  ) const

inline

Definition at line 134 of file range.hpp.

Referenced by CSeq_loc_Conversion_Set::Convert(), DumpPairwiseAln(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), SBamIndexRefIndex::GetAlnOverStarts(), SBamIndexParams::GetBinRange(), CBamRawAlignIterator::GetCIGARPos(), SBamIndexRefIndex::GetLimitRange(), CPagedFile::GetPage(), CBamRawAlignIterator::GetRefSeqPos(), CSNPDbFeatIterator::GetSNPPosition(), CSeq_loc::GetStart(), s_CompareRanges(), s_SetSplitQuerySeqInterval(), CSNPDbGraphIterator::Select(), CSNPDbPageIterator::Select(), CSplitQueryBlk::SetChunkBounds(), CAnnot_Collector::x_CollectMapped(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CBamRawAlignIterator::x_NeedToSkip(), CAnnot_Collector::x_SearchMapped(), and CSplitQueryTestFixture::x_ValidateChunkBounds().

GetInterval()

template<class Traits >

range_type CRangeMapIterator< Traits >::GetInterval ( void  ) const

inline

Definition at line 253 of file rangemap.hpp.

References CRangeMapIterator< Traits >::GetLevelIter().

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), and CSeq_annot_Finder::x_Find().

GetLength() [1/2]

template<class Position >

position_type CAlignRange< Position >::GetLength ( void  ) const

inline

Definition at line 150 of file align_range.hpp.

References CAlignRange< Position >::m_Length.

Referenced by CDiagHitElement::GetQueryLength(), CDiagHitElement::GetSubjectLength(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), s_TranslateAnchorToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), CSparseAln::x_Build(), and CAlnMixMerger::x_Merge().

GetLength() [2/2]

template<class Position >

position_type COpenRange< Position >::GetLength ( void  ) const

inline

Definition at line 158 of file range.hpp.

Referenced by CMultAlign::AddAlignment(), CSAM_CIGAR_Formatter::AddRow(), AlignModelToSeqalign(), CAlnGraphic::AlnGraphicDisplay(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), BOOST_AUTO_TEST_CASE(), BuildAlignDataSource(), CEquivRangeBuilder::CalcMatches(), CChain::CalculateSupportAndWeightFromMembers(), CAlignModel::CAlignModel(), CAnnotObject_Ref::CAnnotObject_Ref(), CGeneModel::CdsInvariant(), CLocMapper_Default::CGappedRange::CGappedRange(), check_no_overlaps(), CChainer::CChainerImpl::CheckCompatibility(), CAlignCollapser::CleanSelfTranscript(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), IAlnMultiDataSource::CollectAlignStats(), CChain::CollectTrustedmRNAsProts(), CombineCorrectionsAndIndels(), CSeq_loc_Conversion_Set::ConvertInterval(), ConvertSeqLocsToPairwiseAln(), ConvertStdsegToPairwiseAln(), CSeq_loc_Conversion::CSeq_loc_Conversion(), EffectiveExonLength(), CMacroEngineParallel::Exec(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CAlignCollapser::FilterAlignments(), FindPolyTail(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSeqGraphicWidget::FindText(), CAlignMap::FShiftedLen(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CGeneModel::GetCdsDnaSequence(), CBamRawAlignIterator::GetCIGARRefSize(), CBamRawAlignIterator::GetCIGARShortSize(), CSeq_loc::GetCircularLength(), CAlignCollapser::GetCollapsedAlgnments(), CSeq_loc_Conversion::GetDstPoint(), CShowBlastDefline::GetFormattingInfo(), NSnpAnnot::GetGraph_CI(), CAlnStatGlyph::GetHTMLActiveAreas(), CHistogramGlyph::GetHTMLActiveAreas(), CLocMapper_Default::CGappedRange::GetIdentity(), CGuiObjectInfoSeq_align::GetInsertionRanges(), CSeq_featHandler::GetLabel(), NSnp::GetLength(), CCddInputData::CHitSegment::GetLength(), CPagedFile::GetPage(), GetProteinWeight(), CDenseSegHitElement::GetQueryLength(), CStdSegHitElement::GetQueryLength(), CCSraShortReadIterator::GetShortLen(), CSNPDbFeatIterator::GetSNPLength(), CDenseSegHitElement::GetSubjectLength(), CStdSegHitElement::GetSubjectLength(), GetUnalignedRegionLength(), CGeneModel::HasCompatibleOverlap(), CCrossPanelIR::HitTest(), CSparseAlignment::Init(), SChunkTranslator::Init(), CAlnGraphic::Init(), CBlastFormatUtil::InsertSubjectScores(), CSeq_align::IntronLengthRange(), CGeneModel::isCompatible(), CSeq_loc_CI::IsPoint(), CSeqGlyph::LessBySeqSize(), CmRNACDSLinker::LinkByLabelAndLocation(), CChainer::CChainerImpl::LRCanChainItoJ(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CEquivRangeBuilder::Merge(), ProteinWithBigHole::model_predicate(), CGeneModel::MutualExtension(), CSeqGraphicWidget::OnGoToMarker(), CwxExportVectorImageDlg::OnSaveClick(), CAlignSort::SAlignExtractor::operator()(), operator<<(), PatchTargetSequence(), CChain::PeaksAndLimits(), CGnomonAnnotator::Predict(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_AlignLengthRatio::Print(), readGFF3(), CDense_seg::RemapToLoc(), CLinearSelHandler::Render(), RestoreModelReadingFrame(), CChain::RestoreReasonableConfirmedStart(), RetrievePartsOfLargeChromosome(), CChainer::CChainerImpl::RightLeft(), s_CreateObjList(), s_FindGaps(), s_GetUncoveredLength(), variation::CVariationUtil::s_ResolveIntronicOffsets(), CExpansionScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CGnomonEngine::SelectBestReadingFrame(), SeqLocAllowed(), CReportEntry::SetCds(), CBlastTabularInfo::SetFields(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CBlobSplitterImpl::SplitPieces(), sx_CalcFeatChunkPages(), CLocMapper_Default::CGappedRange::ToString(), CutShortPartialExons::transform_align(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), CEditScript::VerifyScript(), CGuiObjectInfoSeq_feat::x_AddGroupLocationRows(), CGuiObjectInfoSeq_feat::x_AddLocationRows(), CMultiAligner::x_AlignProfileProfileUsingHit(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CMultiAligner::x_BuildAlignmentIterative(), CPhyTreeCalc::x_CalcAlnSegInfo(), CScoringJob::x_CalculateAlignmentScores(), CVisibleRange::x_Clamp(), CAdvancedAlignCleanup::x_CleanupProsplignCompartment(), CAlnSpanVertModel::x_ConvertRowsToSpans(), CSeq_align_Mapper::x_ConvertSegmentCvt(), CInversionMergeAligner::x_CreateDiscAlignment(), CSGAlignmentJob::x_CreateFeatGlyph(), CSGAlignStatJob::x_CreatePileUpGraphs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CDisplaySeqalign::x_DoFills(), CCpgSearchJob::x_DoSearch(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CMatePairGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CLinkedFeatsGroup::x_DrawChildrenOnParent(), CCrossPanelIR::x_DrawCrossAlignment(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawFeatureBar_sv(), CSeqGlyph::x_DrawInnerLabelColumns(), CSeqGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithXPinned(), CVcfGlyph::x_DrawLabelWithXPinned(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CAlignGlyph::x_DrawPWAlign(), CCrossPanelIR::x_DrawSequence(), CVcfGlyph::x_DrawVariationBar(), CSGAlignStatJob::x_Execute(), CSGFeatureJob::x_Execute(), CSGSegmentMapJob::x_Execute(), CSFTranslationJob::x_Execute(), CVcfFeatureJob::x_Execute(), CSnpJob::x_FetchGraphs(), COligoSpecificityCheck::x_FillGlobalAlignInfo(), CDisplaySeqalign::x_FillInserts(), CMultiAligner::x_FindConservedColumns(), CMultiAligner::x_FindConstraints(), COligoSpecificityCheck::x_FindOverlappingHSP(), CCIGAR_Formatter::x_FormatLine(), CAlnVecRow::x_GetAlignmentTooltip_Gap(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CDistances::x_GetSelfScores(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CAlignedFeatureGraph::x_GetTooltip(), CAlnVecRow::x_GetTooltipSequence(), CGuiObjectInfoSeq_align::x_GetTooltipSequence(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CShowBlastDefline::x_InitDeflineTable(), CSeq_loc_Mapper::x_InitGCSequence(), CSparse_CI::x_InitSegment(), COligoSpecificityCheck::x_IsPcrLengthInRange(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), x_MatchSubHits(), variation_ref::CHgvsParser::x_nuc_inv(), CAlignedFeatureGraph::x_PlaceCluster(), CAlnSpanVertModel::x_PopulateRows(), CGeneModelFeatJob::x_ProcessLandMarkFeatures(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CMultiAligner::x_RealignBlocks(), CSeqGraphicPane::x_RenderTooltipConnector(), CInversionMergeAligner::x_RunMerger(), CMagicBlastResults::x_SetInfo(), CUnorderedSplitter::x_SplitDeltaExt(), CAlnStatGlyph::x_UpdateBoundingBox(), CClonePlacementGlyph::x_UpdateBoundingBox(), CFeatGlyph::x_UpdateBoundingBox(), CLayoutTrack::x_UpdateBoundingBox(), CNamedGroup::x_UpdateBoundingBox(), CTraceGlyph::x_UpdateBoundingBox(), CVcfGlyph::x_UpdateBoundingBox(), CAlignmentTrack::x_UpdateData(), CGraphOverlay::x_UpdateLegend(), CHistogramGlyph::x_UpdateLegend(), CValidError_align::x_ValidateAlignPercentIdentity(), CSplitQueryTestFixture::x_ValidateChunkBounds(), and CGff3Writer::xAssignAlignmentDensegGap().

GetLevelIter()

template<class Traits >

TLevelIter CRangeMapIterator< Traits >::GetLevelIter ( void  ) const

inline

Definition at line 225 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_LevelIter.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), CRangeMapIterator< Traits >::GetInterval(), CRangeMapIterator< Traits >::operator*(), CRangeMapIterator< Traits >::operator->(), and CRangeMapIterator< Traits >::operator==().

GetLevelIterEnd()

template<class Traits >

TLevelIter CRangeMapIterator< Traits >::GetLevelIterEnd ( void  ) const

inline

Definition at line 229 of file rangemap.hpp.

References CRangeMapIterator< Traits >::GetSelectIter().

Referenced by CRangeMapIterator< Traits >::SetLevelIter().

GetPositionMax() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetPositionMax ( void  )

inlinestatic

Definition at line 349 of file align_range.hpp.

References max().

Referenced by CAlignRange< Position >::GetEmptyFrom(), and CAlignRange< Position >::GetEmptyToOpen().

GetPositionMax() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetPositionMax ( void  )

inlinestatic

Definition at line 250 of file range.hpp.

Referenced by CAlnSpanVertModel::x_PopulateRows().

GetPositionMin() [1/2]

template<class Position >

static position_type CAlignRange< Position >::GetPositionMin ( void  )

inlinestatic

Definition at line 345 of file align_range.hpp.

References min().

GetPositionMin() [2/2]

template<class Position >

static position_type COpenRange< Position >::GetPositionMin ( void  )

inlinestatic

Definition at line 246 of file range.hpp.

GetRange()

template<class Traits >

const range_type& CRangeMapIterator< Traits >::GetRange ( void  ) const

inline

Definition at line 212 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_Range.

GetSecondFrom()

template<class Position >

position_type CAlignRange< Position >::GetSecondFrom ( void  ) const

inline

Definition at line 121 of file align_range.hpp.

References CAlignRange< Position >::m_SecondFrom.

Referenced by CAlignRange< Position >::GetSecondRange(), CDiagHitElement::GetSubjectStart(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IsAbutting(), operator<<(), CAlignRange< Position >::operator==(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), CSparseAln::x_Build(), CDiagRangeCollection::x_DiffSecond(), CAlnMixMerger::x_Merge(), and CMergedPairwiseAln::x_ValidNeighboursOnSecondDim().

GetSecondPosByFirstPos()

template<class Position >

position_type CAlignRange< Position >::GetSecondPosByFirstPos ( position_type  pos ) const

inline

Definition at line 211 of file align_range.hpp.

References CAlignRange< Position >::FirstContains(), CAlignRange< Position >::GetSecondTo(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_FirstFrom, and CAlignRange< Position >::m_SecondFrom.

GetSecondRange()

template<class Position >

TRange CAlignRange< Position >::GetSecondRange ( ) const

inline

Definition at line 137 of file align_range.hpp.

References CAlignRange< Position >::GetSecondFrom(), and CAlignRange< Position >::GetSecondTo().

GetSecondTo()

template<class Position >

position_type CAlignRange< Position >::GetSecondTo ( void  ) const

inline

Definition at line 129 of file align_range.hpp.

References CAlignRange< Position >::GetSecondToOpen().

Referenced by CAlignRange< Position >::GetFirstPosBySecondPos(), CAlignRange< Position >::GetSecondPosByFirstPos(), CAlignRange< Position >::GetSecondRange(), InitSplicedsegFromPairwiseAln(), and CAlignRange< Position >::IntersectSecondWith().

GetSecondToOpen()

template<class Position >

position_type CAlignRange< Position >::GetSecondToOpen ( void  ) const

inline

Definition at line 125 of file align_range.hpp.

References CAlignRange< Position >::m_Length, and CAlignRange< Position >::m_SecondFrom.

Referenced by ConvertStdsegToPairwiseAln(), CAlignRange< Position >::GetSecondTo(), InitSplicedsegFromPairwiseAln(), CAlignRange< Position >::IsAbutting(), CAlignRange< Position >::SecondContains(), CSparseAln::x_Build(), CDiagRangeCollection::x_DiffSecond(), and CMergedPairwiseAln::x_ValidNeighboursOnSecondDim().

GetSelectIter()

template<class Traits >

TSelectIter CRangeMapIterator< Traits >::GetSelectIter ( void  ) const

inline

Definition at line 217 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_SelectIter.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), CRangeMapIterator< Traits >::GetLevelIterEnd(), and CRangeMapIterator< Traits >::operator==().

GetSelectIterEnd()

template<class Traits >

TSelectIter CRangeMapIterator< Traits >::GetSelectIterEnd ( void  ) const

inline

Definition at line 221 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_SelectIterEnd.

Referenced by CRangeMapIterator< Traits >::operator==().

GetTo()

template<class Position >

position_type COpenRange< Position >::GetTo ( void  ) const

inline

Definition at line 142 of file range.hpp.

Referenced by CSeq_loc_Conversion_Set::Convert(), SBamIndexParams::GetBinRange(), SBamIndexRefIndex::GetLimitRange(), CSeq_loc::GetStop(), CAnnot_Collector::x_CollectMapped(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CAnnot_Collector::x_SearchMapped().

GetToOpen()

template<class Position >

position_type COpenRange< Position >::GetToOpen ( void  ) const

inline

Definition at line 138 of file range.hpp.

Referenced by CDensityMap< CntType >::AddRange(), CSAM_CIGAR_Formatter::AddRow(), BOOST_AUTO_TEST_CASE(), CdsTrnaOverlapStr(), CFeatHistogramDS::CFeatHistogramDS(), CIdRangeMap::CIdRangeMap(), CAlignGlyph::DrawPWAlignElem(), DumpPairwiseAln(), SAnnotObject_Key::end(), CPrefetchSeqData::Execute(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CVDBGraphSeqIterator::GetAnnot(), CSNPDbSeqIterator::GetEntry(), CFeatHistogramDS::GetLimit(), SBamIndexRefIndex::GetLimitRange(), CMaskedRangeSet::GetRanges(), CGuiObjectInfoSeq_align::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CSparseAln::GetSeqString(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CAnnotMapping_Info::GetToOpen(), CBam2Seq_graph::MakeSeq_entry(), CPairwise_CI::operator bool(), SSortSourceByLoc::operator()(), operator<<(), PatchTargetSequence(), PrintSAM(), CAlignMarkHandler::Render(), CLinearSelHandler::Render(), s_CheckAbutting(), s_CompareRanges(), s_GetCigarString(), s_SeqLocToRangeInfoMap(), s_SeqLocToRangeInfoMapByStrand(), s_SeqLocToTotalRangeInfoMap(), s_SetSplitQuerySeqInterval(), CSplitQueryBlk::SetChunkBounds(), CFeatHistogramDS::Update(), CSGAnnotJob::x_AddGraphToMap(), CDensityMap< score_type >::x_CalcNbins(), CAdvancedAlignCleanup::x_CleanupProsplignAsGenomic(), CSGAlignStatJob::x_CollectAlignStats(), x_CollectCoverageGraph(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CAlignGlyph::x_ConvertAlnTaillRngToSeqRng(), CSGAlignStatJob::x_CreatePileUpGraphs(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CFeatGlyph::x_DrawFeatureBar(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawInternalUnalignedRegions(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_DrawUnalignedBar(), CGuiObjectInfoSeq_align::x_GetAlignmentTooltip_Insert(), CDensegGraphicDataSource::x_GetAlnStringFromCigar(), CAnnotObject_Less::x_GetExtremes(), CAlignMarkHandler::x_HitTest(), CAlignMarkHandler::x_InitDeltaMap(), CBlastHitMatrix::x_InitPort(), CDenseg_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CID2SNPProcessor_Impl::x_LoadBlob(), CBamRawAlignIterator::x_NeedToSkip(), CSNPDbGraphIterator::x_Next(), CLinearSelHandler::x_OnChangeSelRange(), CTextSelHandler::x_OnChangeSelRange(), CAlnSpanVertModel::x_PopulateRows(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CRuler::x_RenderAllPosLabels(), CAlignGlyph::x_RenderAveragableScores(), CRuler::x_RenderBackground(), CAlnVecRow::x_RenderInserts(), CAlignGlyph::x_RenderNonAveragableScores(), CRuler::x_RenderOriginAndMetric(), CHitMatrixWidget::x_SetPortLimits(), CSeqGraphicRenderer::x_SetupModelLimits(), CAlignMarkHandler::x_UpdateMarks(), CSeq_annot_SortedIter::x_Valid(), CSplitQueryTestFixture::x_ValidateChunkBounds(), CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk(), and CHitMatrixWidget::x_ZoomToHits().

GetWhole()

template<class Position >

static TThisType COpenRange< Position >::GetWhole ( void  )

inlinestatic

Definition at line 272 of file range.hpp.

Referenced by CSeqTableLocColumns::GetRange(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CBamRefSeqInfo::LoadMainSplit(), s_GetSeqRange(), x_CreateLocalCDDEntryChunk(), and CAnnot_Collector::x_SearchAll().

GetWholeFrom()

template<class Position >

static position_type COpenRange< Position >::GetWholeFrom ( void  )

inlinestatic

Definition at line 256 of file range.hpp.

Referenced by CRangeCollection< TSeqPos >::x_CombineWith(), and CAnnotWriterApp::xGetFrom().

GetWholeLength()

template<class Position >

static position_type COpenRange< Position >::GetWholeLength ( void  )

inlinestatic

Definition at line 268 of file range.hpp.

GetWholeTo()

template<class Position >

static position_type COpenRange< Position >::GetWholeTo ( void  )

inlinestatic

Definition at line 264 of file range.hpp.

Referenced by CAnnotWriterApp::xGetTo().

GetWholeToOpen()

template<class Position >

static position_type COpenRange< Position >::GetWholeToOpen ( void  )

inlinestatic

Definition at line 260 of file range.hpp.

insert() [1/2]

template<typename Mapped , typename Position = int>

pair<iterator, bool> CRangeMap< Mapped, Position >::insert ( const value_type &  value )

inline

Definition at line 567 of file rangemap.hpp.

References map_checker< Container >::end(), CRangeMapBase< CRangeMapTraits< int, Mapped > >::insertLevel(), CRangeMapIterator< Traits >::m_LevelIter, CRangeMapBase< CRangeMapTraits< int, Mapped > >::m_SelectMap, NCBI_THROW, and rapidjson::value.

Referenced by CRangeMap< Mapped, Position >::operator[]().

insert() [2/2]

template<typename Mapped , typename Position = int>

iterator CRangeMultimap< Mapped, Position >::insert ( const value_type &  value )

inline

Definition at line 629 of file rangemap.hpp.

References map_checker< Container >::end(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::insertLevel(), CRangeMapIterator< Traits >::m_LevelIter, CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, CRangeMapIterator< Traits >::m_SelectIterEnd, CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::m_SelectMap, NCBI_THROW, and rapidjson::value.

Referenced by CSeq_loc_Conversion_Set::x_Add(), CPhrap_Contig::x_AddAlignRanges(), and CTSE_Info::x_MapAnnotObject().

insertLevel()

template<class Traits >

TSelectMapI CRangeMapBase< Traits >::insertLevel ( position_type  key )

inlineprotected

Definition at line 417 of file rangemap.hpp.

IntersectingWith() [1/2]

template<class Position >

bool CAlignRange< Position >::IntersectingWith ( const CRange< position_type > &  r ) const

inline

Definition at line 282 of file align_range.hpp.

References CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstTo(), CRange_Base::GetTo(), and r().

IntersectingWith() [2/2]

template<class Position >

bool COpenRange< Position >::IntersectingWith ( const TThisType &  r ) const

inline

Definition at line 331 of file range.hpp.

Referenced by CEquivRange::CalcRelativeDuo(), CChain::CalculateSupportAndWeightFromMembers(), CChain::CChain(), CChainer::CChainerImpl::CheckCompatibility(), CChainer::CChainerImpl::CombineCompatibleChains(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CCDSInfo::Cut(), NSnpAnnot::EstimateSNPCount(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGetFeature::GetFeatInfo(), CChain::HarborsNested(), CSeqScores::Init(), CEquivRange::IntersectingWith(), CGeneModel::IntersectingWith(), CHandleRange::IntersectingWithTotalRange(), C2DLayoutEngine::Layout(), CChainer::CChainerImpl::MakeChains(), CAlignFilter::Match(), CDepthCollection::MinDepthForRange(), CSeqGraphicPane::OnSearchTip(), CGnomonAnnotator::Predict(), CTestSingleAln_All::RunTest(), s_Distance(), s_GetUncoveredLength(), s_IsOverlapping(), s_MergeRangeList(), s_SeqIntervalToSeqLocInfo(), s_SetSplitQuerySeqInterval(), CReportEntry::SetCds(), CChain::SetConfirmedStartStopForCompleteProteins(), CEquivRangeBuilder::SplitIntersections(), CMultiAligner::x_AssignRPSResFreqs(), CVecscreen::x_BuildNonOverlappingRange(), CFeatureGenerator::SImplementation::x_CheckMatch(), CQuerySplitter::x_ComputeQueryIndicesForChunks(), CQuerySet::x_ContainsAlignment(), CSGAlignmentJob::x_CreateCAlignGlyph(), CInversionMergeAligner::x_CreateDiscAlignment(), CDisplaySeqalign::x_DisplayRowDataSet(), CCrossPanelIR::x_DrawCrossAlignment(), CFeatGlyph::x_DrawFeatureBar(), CTranslationGlyph::x_Intersecting(), CLayeredLayout::x_LayerBySize(), CVecscreen::x_MergeInclusiveSeqalign(), CVecscreen::x_MergeLowerRankSeqalign(), CAllOtherFeaturesTrack::x_OnAllJobsFinished(), CTrackContainer::x_OnJobCompleted(), CDisplaySeqalign::x_PrintFeatures(), CDisplaySeqalign::x_ProcessRowDataSet(), CInversionMergeAligner::x_RunMerger(), and COligoSpecificityCheck::x_SavePrimerInfo().

IntersectionWith() [1/2]

template<class Position >

TThisType CAlignRange< Position >::IntersectionWith ( const CRange< position_type > &  r ) const

inline

Intersection.

Definition at line 242 of file align_range.hpp.

References CAlignRange< Position >::IntersectWith(), and r().

IntersectionWith() [2/2]

template<class Position >

TThisType COpenRange< Position >::IntersectionWith ( const TThisType &  r ) const

inline

Definition at line 312 of file range.hpp.

Referenced by CDepthCollection::AddRange(), CFeatTrim::Apply(), CEquivRange::Distance(), CHandleRange::GetOverlappingRange(), GetTrnaAnticodon(), CRenderingContext::IntersectVisible(), CRenderingContext::IntersectVisible_Y(), CCddInputData::CHit::IntersectWith(), CTrackContainer::NoSubtrackEver(), SOutsideRange::operator()(), CTrackContainer::RemoveEmptyTracks(), TMaskedQueryRegions::RestrictToSeqInt(), s_AlignDist(), CClippedScorer::ScoreAlignments(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), COligoSpecificityCheck::x_AnalyzeLeftAndRightPrimer(), COligoSpecificityCheck::x_AnalyzeOnePrimer(), CQuerySet::x_ContainsAlignment(), CSeqGlyph::x_DrawInnerLabelColumns(), CFeatGlyph::x_DrawInnerLabels(), CVcfGlyph::x_DrawInnerLabels(), CAlignGlyph::x_DrawMultiAlign(), CAlnVecRow::x_GetAlignmentTooltip_Helper(), CRangeCollection< TSeqPos >::x_IntersectWith(), CRangeSet< CPairwiseAln::TPos >::x_IntersectWith(), CGencollIdMapper::x_IsLoc_Int_InAGap(), x_MatchSubHits(), CTrackContainer::x_ReinitTrack(), CSeqGraphicPane::x_RenderTooltipConnector(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CUnorderedSplitter::x_TrimRows(), CSixFramesTransTrack::x_UpdateData(), CVcfWriter::x_WriteData(), CGff2Writer::xAssignFeatureAttributePartial(), CGff3Writer::xWriteNucleotideFeature(), and CGff3Writer::xWriteProteinFeature().

IntersectSecondWith()

template<class Position >

TThisType& CAlignRange< Position >::IntersectSecondWith ( const CRange< position_type > &  r )

inline

Definition at line 265 of file align_range.hpp.

References CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::GetSecondTo(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_FirstFrom, CAlignRange< Position >::m_Length, CAlignRange< Position >::m_SecondFrom, max(), min(), and r().

IntersectWith() [1/2]

template<class Position >

TThisType& CAlignRange< Position >::IntersectWith ( const CRange< position_type > &  r )

inline

Definition at line 248 of file align_range.hpp.

References CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstTo(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::m_FirstFrom, CAlignRange< Position >::m_Length, CAlignRange< Position >::m_SecondFrom, max(), min(), and r().

Referenced by CAlignRange< Position >::IntersectionWith().

IntersectWith() [2/2]

template<class Position >

TThisType& COpenRange< Position >::IntersectWith ( const TThisType &  r )

inline

Definition at line 317 of file range.hpp.

Referenced by CPairwise_CI::x_InitSegment(), CAlnVecRow::x_RenderAlignSegments(), and CTraceGraph::x_RenderContour().

IsAbutting()

template<class Position >

bool CAlignRange< Position >::IsAbutting ( const TThisType &  r ) const

inline

Definition at line 287 of file align_range.hpp.

References CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::GetLength(), CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::GetSecondToOpen(), CAlignRange< Position >::IsDirect(), r(), and swap().

Referenced by CAlignRange< Position >::CombineWithAbutting(), CAlignRangeCollection< CAlignRange< TSeqPos > >::insert(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges().

IsDirect()

template<class Position >

bool CAlignRange< Position >::IsDirect ( void  ) const

inline

Definition at line 96 of file align_range.hpp.

References CAlignRange< Position >::fReversed, and CAlignRange< Position >::m_Flags.

Referenced by CheckPairwiseAln(), CAlignRange< Position >::CombineWithAbutting(), DumpPairwiseAln(), CDiagHitElement::GetSubjectStrand(), CAlignRange< Position >::IsAbutting(), operator<<(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwiseToAlnCoords(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimSecondFrom(), CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges(), and CSparseAln::x_Build().

IsFirstDirect()

template<class Position >

bool CAlignRange< Position >::IsFirstDirect ( ) const

inline

Definition at line 102 of file align_range.hpp.

References CAlignRange< Position >::fFirstRev, and CAlignRange< Position >::m_Flags.

Referenced by DumpPairwiseAln(), and CSparseAln::x_Build().

IsFirstReversed()

template<class Position >

bool CAlignRange< Position >::IsFirstReversed ( ) const

inline

Definition at line 105 of file align_range.hpp.

References CAlignRange< Position >::fFirstRev, and CAlignRange< Position >::m_Flags.

IsNegative() [1/2]

template<class Position >

static bool SPositionTraitsBySignedness< true, Position >::IsNegative ( Position  pos )

inlinestatic

Definition at line 67 of file range.hpp.

IsNegative() [2/2]

template<class Position >

static bool SPositionTraitsBySignedness< false, Position >::IsNegative ( Position  )

inlinestatic

Definition at line 78 of file range.hpp.

IsReversed()

template<class Position >

bool CAlignRange< Position >::IsReversed ( void  ) const

inline

Definition at line 99 of file align_range.hpp.

References CAlignRange< Position >::fReversed, and CAlignRange< Position >::m_Flags.

Referenced by CAlignRange< Position >::CombineWithAbutting(), CAlignRange< Position >::GetFirstPosBySecondPos(), CAlignRange< Position >::GetSecondPosByFirstPos(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IntersectWith(), CDiagRangeCollection::TrimFirstTo(), and CDiagRangeCollection::TrimSecondTo().

IsWhole()

template<class Position >

bool COpenRange< Position >::IsWhole ( void  ) const

inline

Definition at line 284 of file range.hpp.

Referenced by CGraphRanges::AddRange(), CVisibleRange::Clamp(), CSparseAln::GetAlnSeqString(), CSparseAln::GetSeqString(), CSeq_loc_CI::IsWhole(), CResolveRequest::Process(), s_GetUncoveredLength(), CVisibleRange::x_Clamp(), CPairwise_CI::x_Init(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CDenseg_CI::x_InitIterator(), CPairwise_CI::x_InitSegment(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_MapNextRange(), CGff2Writer::xAssignFeatureAttributeCodeBreak(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xAssignSourceEndpoints(), CGff3Writer::xWriteFeatureCds(), and CGff3Writer::xWriteSequenceHeader().

IsWholeFrom()

template<class Position >

bool COpenRange< Position >::IsWholeFrom ( void  ) const

inline

Definition at line 276 of file range.hpp.

IsWholeTo()

template<class Position >

bool COpenRange< Position >::IsWholeTo ( void  ) const

inline

Definition at line 280 of file range.hpp.

NotEmpty() [1/2]

template<class Position >

bool CAlignRange< Position >::NotEmpty ( void  ) const

inline

Definition at line 145 of file align_range.hpp.

References CAlignRange< Position >::m_Length.

Referenced by CAlignRangeCollection< CAlignRange< TSeqPos > >::ValidateRanges(), and CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::ValidateRanges().

NotEmpty() [2/2]

template<class Position >

bool COpenRange< Position >::NotEmpty ( void  ) const

inline

Definition at line 152 of file range.hpp.

Referenced by CChain::AddAllMembersAndCoverage(), CDepthCollection::AddRange(), AlignModelToSeqalign(), CFeatTrim::Apply(), BOOST_AUTO_TEST_CASE(), CChain::CalculateSupportAndWeightFromMembers(), CChain::CChain(), CAlignCollapser::CleanSelfTranscript(), CGeneModel::Clip(), CChain::ClipChain(), CChain::ClipToCap(), CChain::ClipToPolyA(), CollectAttributes(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CGeneModel::Extend(), CBlastDBExtractor::ExtractFasta(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::FindGeneSeeds(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), FindStartsStops(), CDensegGraphicDataSource::GetAlnSeqString(), CParse::GetGenes(), CGeneModel::GetInDels(), CGnomonEngine::GetScore(), GetWallLimits(), CCDSInfo::HasStart(), CCDSInfo::HasStop(), CSeqScores::Init(), CAlignCollapser::InitContig(), CBlastFormatUtil::InsertSubjectScores(), CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CEquivRange::NotEmpty(), CAlnMultiWidget::OnUpdateZoomSelection(), CGeneModel::OpenLeftEnd(), CGeneModel::OpenRightEnd(), ParseAttributes(), CChain::PeaksAndLimits(), CGnomonAnnotator::Predict(), printGFF3(), readGFF3(), CCDSInfo::Remap(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), RestoreModelAttributes(), CChain::RestoreReasonableConfirmedStart(), CChain::SetBestPlacement(), CChain::SetConsistentCoverage(), CBlastTabularInfo::SetFields(), CChainer::CChainerImpl::SetFlagsForChains(), CCDSInfo::SetStop(), CAlignMap::ShrinkToRealPoints(), CAlignMap::ShrinkToRealPointsOnEdited(), spliced_exon(), CSeq_align::SplitOnLongDiscontinuity(), CutShortPartialExons::transform_align(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), CGeneModel::TrimEdgesToFrameInOtherAlignGaps(), TrimAlignment::TrimProtein(), TrimAlignment::TrimTranscript(), CMultAlign::Variations(), CMultiAligner::x_AlignProfileProfileUsingHit(), CDenseg_CI::x_CheckSegment(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CLinkedFeatsGroup::x_DrawFeatureBar(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), CAlignMarkHandler::x_HitRangeBorder(), CAlignMarkHandler::x_InitDeltaMap(), CRangeCollection< TSeqPos >::x_IntersectWith(), CRangeSet< CPairwiseAln::TPos >::x_IntersectWith(), CGBDataLoader_Native::x_MakeContentMask(), CLinearSelHandler::x_OnSelectCursor(), CTextSelHandler::x_OnSelectCursor(), CLinearSelHandler::x_OnStartSel(), CTextSelHandler::x_OnStartSel(), CTraceGraph::x_RenderContour(), CUnorderedSplitter::x_SplitDeltaExt(), CUnorderedSplitter::x_SplitSeqData(), CUnorderedSplitter::x_TrimRows(), CVcfWriter::x_WriteData(), CGff2Writer::xAssignFeatureAttributePartial(), and CAlnMultiWidget::ZoomToSelection().

operator!=() [1/3]

template<class Traits >

bool CRangeMapIterator< Traits >::operator!= ( const TThisType &  iter ) const

inline

Definition at line 247 of file rangemap.hpp.

operator!=() [2/3]

template<class Position >

bool CAlignRange< Position >::operator!= ( const TThisType &  r ) const

inline

Definition at line 207 of file align_range.hpp.

References r().

operator!=() [3/3]

template<class Position >

bool COpenRange< Position >::operator!= ( const TThisType &  r ) const

inline

Definition at line 219 of file range.hpp.

operator&()

template<class Position >

TThisType COpenRange< Position >::operator& ( const TThisType &  r ) const

inline

Definition at line 323 of file range.hpp.

operator&=()

template<class Position >

TThisType& COpenRange< Position >::operator&= ( const TThisType &  r )

inline

Definition at line 327 of file range.hpp.

operator()() [1/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( const TAlignRange &  r, position_type  pos  )

inline

Definition at line 52 of file align_range_oper.hpp.

References r().

operator()() [2/9]

template<class TAlignRange >

bool PAlignRangeFromLess< TAlignRange >::operator() ( const TAlignRange &  r, position_type  pos  )

inline

Definition at line 83 of file align_range_oper.hpp.

References r().

operator()() [3/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( const TAlignRange &  r1, const TAlignRange &  r2  )

inline

Definition at line 60 of file align_range_oper.hpp.

References r1, and r2.

operator()() [4/9]

template<class TAlignRange >

bool PAlignRangeFromLess< TAlignRange >::operator() ( const TAlignRange &  r_1, const TAlignRange &  r_2  )

inline

Definition at line 91 of file align_range_oper.hpp.

operator()() [5/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( const TAlignRange *  r, position_type  pos  )

inline

Definition at line 64 of file align_range_oper.hpp.

References r().

operator()() [6/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( const TAlignRange *  r1, const TAlignRange *  r2  )

inline

Definition at line 72 of file align_range_oper.hpp.

References r1, and r2.

operator()() [7/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( position_type  pos, const TAlignRange &  r  )

inline

Definition at line 56 of file align_range_oper.hpp.

References r().

operator()() [8/9]

template<class TAlignRange >

bool PAlignRangeFromLess< TAlignRange >::operator() ( position_type  pos, const TAlignRange &  r  )

inline

Definition at line 87 of file align_range_oper.hpp.

References r().

operator()() [9/9]

template<class TAlignRange >

bool PAlignRangeToLess< TAlignRange >::operator() ( position_type  pos, const TAlignRange *  r  )

inline

Definition at line 68 of file align_range_oper.hpp.

References r().

operator*()

template<class Traits >

reference CRangeMapIterator< Traits >::operator* ( void  ) const

inline

Definition at line 257 of file rangemap.hpp.

References CRangeMapIterator< Traits >::GetLevelIter().

operator+()

template<class Position >

TThisType COpenRange< Position >::operator+ ( const TThisType &  r ) const

inline

Definition at line 375 of file range.hpp.

operator++()

template<class Traits >

TThisType& CRangeMapIterator< Traits >::operator++ ( void  )

inline

Definition at line 336 of file rangemap.hpp.

References CRangeMapIterator< Traits >::FirstLevelIter(), CRangeMapIterator< Traits >::m_LevelIter, CRangeMapIterator< Traits >::m_SelectIter, CRangeMapIterator< Traits >::m_SelectIterEnd, and CRangeMapIterator< Traits >::SetLevelIter().

operator+=()

template<class Position >

TThisType& COpenRange< Position >::operator+= ( const TThisType &  r )

inline

Definition at line 371 of file range.hpp.

operator->()

template<class Traits >

pointer CRangeMapIterator< Traits >::operator-> ( void  ) const

inline

Definition at line 261 of file rangemap.hpp.

References CRangeMapIterator< Traits >::GetLevelIter().

operator<()

template<class Position >

bool COpenRange< Position >::operator< ( const TThisType &  r ) const

inline

Definition at line 223 of file range.hpp.

operator<<()

template<class Position >

CNcbiOstream& operator<< ( CNcbiOstream &  out, const COpenRange< Position > &  range  )

inline

Definition at line 426 of file range.hpp.

operator<=()

template<class Position >

bool COpenRange< Position >::operator<= ( const TThisType &  r ) const

inline

Definition at line 228 of file range.hpp.

operator=()

template<class Position >

TThisType& CRange< Position >::operator= ( const TParent &  range )

inline

Definition at line 408 of file range.hpp.

operator==() [1/3]

template<class Traits >

bool CRangeMapIterator< Traits >::operator== ( const TThisType &  iter ) const

inline

Definition at line 241 of file rangemap.hpp.

References _ASSERT, CRangeMapIterator< Traits >::GetLevelIter(), CRangeMapIterator< Traits >::GetSelectIter(), and CRangeMapIterator< Traits >::GetSelectIterEnd().

operator==() [2/3]

template<class Position >

bool CAlignRange< Position >::operator== ( const TThisType &  r ) const

inline

Definition at line 200 of file align_range.hpp.

References CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetLength(), CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::m_Flags, and r().

operator==() [3/3]

template<class Position >

bool COpenRange< Position >::operator== ( const TThisType &  r ) const

inline

Definition at line 215 of file range.hpp.

operator>()

template<class Position >

bool COpenRange< Position >::operator> ( const TThisType &  r ) const

inline

Definition at line 233 of file range.hpp.

operator>=()

template<class Position >

bool COpenRange< Position >::operator>= ( const TThisType &  r ) const

inline

Definition at line 238 of file range.hpp.

operator[]()

template<typename Mapped , typename Position = int>

mapped_type& CRangeMap< Mapped, Position >::operator[] ( const key_type &  key )

inline

Definition at line 594 of file rangemap.hpp.

References CRangeMap< Mapped, Position >::insert(), and ncbi::grid::netcache::search::fields::key.

SecondContains()

template<class Position >

bool CAlignRange< Position >::SecondContains ( position_type  pos ) const

inline

Definition at line 237 of file align_range.hpp.

References CAlignRange< Position >::GetSecondToOpen(), and CAlignRange< Position >::m_SecondFrom.

Referenced by CAlignRange< Position >::GetFirstPosBySecondPos().

Set() [1/2]

template<class Position >

TThisType& CAlignRange< Position >::Set ( position_type  first_from, position_type  second_from, position_type  len  )

inline

Definition at line 169 of file align_range.hpp.

References len, CAlignRange< Position >::SetFirstFrom(), CAlignRange< Position >::SetLength(), and CAlignRange< Position >::SetSecondFrom().

Set() [2/2]

template<class Position >

TThisType& COpenRange< Position >::Set ( position_type  from, position_type  to  )

inline

Definition at line 188 of file range.hpp.

Referenced by CAlnGraphic::AlnGraphicDisplay(), CSparseAlignment::Clear(), CAlnVecPrinter::ClustalStyle(), COligoSpecificityTemplate::COligoSpecificityTemplate(), FindPolyTail(), CScore_EdgeExonInfo::Get(), CRsitesGlyph::GetHTMLActiveAreas(), CLegendItemGlyph::GetHTMLActiveAreas(), CAlignFormatUtil::GetMasterCoverage(), CAlnVecRow::GetRowStatistics(), CAdvancedAlignCleanup::GetSplignCompartments(), CSparseSegment::Init(), CAlnGraphic::Init(), CSeqGraphicWidget::OnSetSeqMarkerForSelDlg(), CAlnVecPrinter::PopsetStyle(), CRenderingContext::PrepareContext(), CPhrap_Read::ReadQuality(), s_FixMinusStrandRange(), s_GetCountIdentityMismatch(), s_ProcessAlignSet(), CwxExportVectorImageDlg::SetSeqRange(), CSixFramesTransTrack::Update(), CAlnVwrApp::View8(), CVecscreen::x_BuildNonOverlappingRange(), CHitMatrixDataSource::x_CalculateHitsRange(), CSeq_loc::x_CalculateTotalRangeCheckId(), CAlignGlyph::x_DrawAlignRowSequence(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawMultiAlign(), CVecscreen::x_GetAlnInfo(), CGuiObjectInfoSeq_feat::x_GetHitSeg(), CAlnVecRow::x_GetTooltipSequence(), CGuiObjectInfoSeq_align::x_GetTooltipSequence(), CGraphOverlay::x_LoadSettings(), CGraphTrack::x_LoadSettings(), CSeq_loc_Mapper_Base::x_MapNextRange(), CVecscreen::x_MergeLowerRankSeqalign(), CSixFramesTransTrack::x_OnContentIconClicked(), CSixFramesTransTrack::x_OnGeneticIconClicked(), CSixFramesTransTrack::x_OnSettingIconClicked(), CDisplaySeqalign::x_OutputSeq(), CAlnSpanVertModel::x_PopulateRowsSpliced(), CMultiAligner::x_RealignBlocks(), CAnnot_Collector::x_SearchRange(), CSixFramesTransTrack::x_UpdateData(), and x_UpdateRanges().

SetBegin() [1/2]

template<class Traits >

void CRangeMapIterator< Traits >::SetBegin ( const range_type &  range, TSelectMapRef  selectMap  )

inlineprivate

Definition at line 319 of file rangemap.hpp.

References CRangeMapIterator< Traits >::FirstLevelIter(), CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, CRangeMapIterator< Traits >::m_SelectIterEnd, compile_time_bits::range(), and CRangeMapIterator< Traits >::SetLevelIter().

SetBegin() [2/2]

template<class Traits >

void CRangeMapIterator< Traits >::SetBegin ( TSelectMapRef  selectMap )

inlineprivate

Definition at line 309 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_LevelIter, CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, and CRangeMapIterator< Traits >::m_SelectIterEnd.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::begin().

SetDirect()

template<class Position >

void CAlignRange< Position >::SetDirect ( bool  direct = true )

inline

Definition at line 174 of file align_range.hpp.

References CAlignRange< Position >::SetReversed().

Referenced by CAlignRange< Position >::CAlignRange(), ConvertStdsegToPairwiseAln(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwiseToAlnCoords(), and CSparseAln::x_Build().

SetEnd()

template<class Traits >

void CRangeMapIterator< Traits >::SetEnd ( TSelectMapRef  selectMap )

inlineprivate

Definition at line 303 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, and CRangeMapIterator< Traits >::m_SelectIterEnd.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::end().

SetFirstDirect()

template<class Position >

void CAlignRange< Position >::SetFirstDirect ( bool  direct = true )

inline

Definition at line 187 of file align_range.hpp.

References CAlignRange< Position >::SetFirstReversed().

Referenced by CAlignRange< Position >::CAlignRange(), ConvertStdsegToPairwiseAln(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwiseToAlnCoords(), x_AdjustAnchorDirection(), and CSparseAln::x_Build().

SetFirstFrom()

template<class Position >

TThisType& CAlignRange< Position >::SetFirstFrom ( position_type  from )

inline

Definition at line 154 of file align_range.hpp.

References CAlignRange< Position >::m_FirstFrom.

Referenced by CAlignRange< Position >::CombineWithAbutting(), ConvertStdsegToPairwiseAln(), s_TranslateAnchorToAlnCoords(), s_TranslatePairwise(), s_TranslatePairwiseToAlnCoords(), CAlignRange< Position >::Set(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), and CSparseAln::x_Build().

SetFirstReversed()

template<class Position >

void CAlignRange< Position >::SetFirstReversed ( bool  reversed = true )

inline

Definition at line 191 of file align_range.hpp.

References CAlignRange< Position >::fFirstRev, and CAlignRange< Position >::m_Flags.

Referenced by CAlignRange< Position >::SetFirstDirect().

SetFrom()

template<class Position >

TThisType& COpenRange< Position >::SetFrom ( position_type  from )

inline

Definition at line 170 of file range.hpp.

Referenced by SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), SBamAlignInfo::get_cigar_alignment(), SBamIndexRefIndex::GetAlnOverStarts(), CBamAlignIterator::GetCIGARAlignment(), CWGSSeqIterator::x_AddGap(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CSNPDbFeatIterator::x_Excluded(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), and CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps().

SetLength() [1/2]

template<class Position >

TThisType& CAlignRange< Position >::SetLength ( position_type  len )

inline

Definition at line 164 of file align_range.hpp.

References len, and CAlignRange< Position >::m_Length.

Referenced by ConvertStdsegToPairwiseAln(), CAlignRange< Position >::Set(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), CDiagRangeCollection::TrimSecondTo(), and CSparseAln::x_Build().

SetLength() [2/2]

template<class Position >

TThisType& COpenRange< Position >::SetLength ( position_type  length )

inline

Definition at line 194 of file range.hpp.

Referenced by CSeq_loc_Conversion::ConvertInterval(), CEquivRangeBuilder::ExtractRangesFromSeqAlign(), SBamAlignInfo::get_cigar_alignment(), SBamIndexRefIndex::GetAlnOverStarts(), s_FindGaps(), CEquivRangeBuilder::SliceOnQuery(), CEquivRangeBuilder::SliceOnSubjt(), CWGSSeqIterator::x_AddGap(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CQuerySet::x_ContainsAlignment(), CInversionMergeAligner::x_CreateDiscAlignment(), CWGSSeqIterator::x_GetSegmentsWithExplicitGaps(), CWGSSeqIterator::x_GetSegmentsWithRecoveredGaps(), CAlignMarkHandler::x_HitTest(), CAlignMarkHandler::x_InitDeltaMap(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSplign::x_MaskSequence(), CLinearSelHandler::x_OnEndSelRange(), CTextSelHandler::x_OnEndSelRange(), and CUnorderedSplitter::x_SplitDeltaExt().

SetLengthDown()

template<class Position >

TThisType& COpenRange< Position >::SetLengthDown ( position_type  length )

inline

Definition at line 204 of file range.hpp.

Referenced by CEquivRangeBuilder::SliceOnQuery(), and CEquivRangeBuilder::SliceOnSubjt().

SetLevelIter()

template<class Traits >

bool CRangeMapIterator< Traits >::SetLevelIter ( TLevelIter  levelIter )

inlineprivate

Definition at line 269 of file rangemap.hpp.

References CRangeMapIterator< Traits >::GetLevelIterEnd(), CRangeMapIterator< Traits >::m_LevelIter, and CRangeMapIterator< Traits >::m_Range.

Referenced by CRangeMapIterator< Traits >::operator++(), and CRangeMapIterator< Traits >::SetBegin().

SetOpen()

template<class Position >

TThisType& COpenRange< Position >::SetOpen ( position_type  from, position_type  toOpen  )

inline

Definition at line 184 of file range.hpp.

Referenced by CSparseAln::GetAlnSeqString(), CLDS2_Database::GetAnnots(), CSplitQueryBlk::GetChunkBounds(), s_SeqLocToTotalRangeInfoMap(), CDenseg_CI::x_InitSegment(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CSeq_loc_Mapper_Base::x_MapNextRange(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

SetReversed()

template<class Position >

void CAlignRange< Position >::SetReversed ( bool  reversed = true )

inline

Definition at line 178 of file align_range.hpp.

References CAlignRange< Position >::fReversed, and CAlignRange< Position >::m_Flags.

Referenced by CAlignRange< Position >::SetDirect().

SetSecondFrom()

template<class Position >

TThisType& CAlignRange< Position >::SetSecondFrom ( position_type  second_from )

inline

Definition at line 159 of file align_range.hpp.

References CAlignRange< Position >::m_SecondFrom.

Referenced by CAlignRange< Position >::CombineWithAbutting(), ConvertStdsegToPairwiseAln(), CAlignRange< Position >::Set(), CDiagRangeCollection::TrimFirstFrom(), CDiagRangeCollection::TrimFirstTo(), CDiagRangeCollection::TrimSecondFrom(), and CSparseAln::x_Build().

SetTo()

template<class Position >

TThisType& COpenRange< Position >::SetTo ( position_type  to )

inline

Definition at line 180 of file range.hpp.

SetToOpen()

template<class Position >

TThisType& COpenRange< Position >::SetToOpen ( position_type  toOpen )

inline

Definition at line 175 of file range.hpp.

Referenced by CBamRawAlignIterator::CBamRawAlignIterator(), DumpPairwiseAln(), SWGSFeatChunkInfo::SFeatureSet::ExpandRange(), CVDBGraphSeqIterator::GetAnnot(), SBamIndexRefIndex::GetLimitRange(), SAnnotObject_Key::Reset(), TMaskedQueryRegions::RestrictToSeqInt(), s_ExtractSeqidsAndRanges(), s_SeqLocToTotalRangesInfoMapByStrand(), SCompartmentData::SCompartmentData(), SAnnotObject_Key::SetMultiple(), CSGFeatureJob::x_CalcIntervals(), CSplitQueryTestFixture::x_ComputeQueryChunkBounds(), CSNPDbFeatIterator::x_Excluded(), CPairwise_CI::x_InitSegment(), CSparse_CI::x_InitSegment(), CBamRefSeqInfo::x_LoadRangesCov(), CBamRefSeqInfo::x_LoadRangesStat(), CLinearSelHandler::x_OnChangeSelRange(), CTextSelHandler::x_OnChangeSelRange(), CLinearSelHandler::x_OnStartSel(), CTextSelHandler::x_OnStartSel(), and CBlastOptionsBuilder::x_ProcessOneOption().

size()

template<class Traits >

size_type CRangeMapBase< Traits >::size ( void  ) const

inline

Definition at line 432 of file rangemap.hpp.

swap()

template<class Traits >

void CRangeMapBase< Traits >::swap ( TThisType &  rangeMap )

inline

Definition at line 528 of file rangemap.hpp.

Valid()

template<class Traits >

bool CRangeMapIterator< Traits >::Valid ( void  ) const

inline

Definition at line 235 of file rangemap.hpp.

References CRangeMapIterator< Traits >::m_Range, CRangeMapIterator< Traits >::m_SelectIter, and CRangeMapIterator< Traits >::m_SelectIterEnd.

Referenced by variation::CVariationUtil::CCdregionIndex::Get(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), and variation::SFastLocSubtract::operator()().

Variable Documentation

m_FirstFrom

template<class Position >

position_type CAlignRange< Position >::m_FirstFrom

private

Definition at line 355 of file align_range.hpp.

Referenced by CAlignRange< Position >::FirstContains(), CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstPosBySecondPos(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::GetSecondPosByFirstPos(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IntersectWith(), and CAlignRange< Position >::SetFirstFrom().

m_Flags

template<class Position >

int CAlignRange< Position >::m_Flags

private

length of the segment

Definition at line 358 of file align_range.hpp.

Referenced by CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsFirstDirect(), CAlignRange< Position >::IsFirstReversed(), CAlignRange< Position >::IsReversed(), CAlignRange< Position >::operator==(), CAlignRange< Position >::SetFirstReversed(), and CAlignRange< Position >::SetReversed().

m_From

template<class Position >

position_type COpenRange< Position >::m_From

private

Definition at line 381 of file range.hpp.

m_Length

template<class Position >

position_type CAlignRange< Position >::m_Length

private

start on the aligned sequence

Definition at line 357 of file align_range.hpp.

Referenced by CAlignRange< Position >::CombineWithAbutting(), CAlignRange< Position >::Empty(), CAlignRange< Position >::GetFirstToOpen(), CAlignRange< Position >::GetLength(), CAlignRange< Position >::GetSecondToOpen(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IntersectWith(), CAlignRange< Position >::NotEmpty(), and CAlignRange< Position >::SetLength().

m_LevelIter

template<class Traits >

TLevelIter CRangeMapIterator< Traits >::m_LevelIter

private

Definition at line 353 of file rangemap.hpp.

Referenced by CRangeMapIterator< Traits >::GetLevelIter(), CRangeMap< Mapped, Position >::insert(), CRangeMultimap< Mapped, Position >::insert(), CRangeMapIterator< Traits >::operator++(), CRangeMapIterator< Traits >::SetBegin(), and CRangeMapIterator< Traits >::SetLevelIter().

m_Range

template<class Traits >

range_type CRangeMapIterator< Traits >::m_Range

private

Definition at line 350 of file rangemap.hpp.

Referenced by CRangeMapIterator< Traits >::FirstLevelIter(), CRangeMapIterator< Traits >::GetRange(), CRangeMultimap< Mapped, Position >::insert(), CRangeMapIterator< Traits >::SetBegin(), CRangeMapIterator< Traits >::SetEnd(), CRangeMapIterator< Traits >::SetLevelIter(), and CRangeMapIterator< Traits >::Valid().

m_SecondFrom

template<class Position >

position_type CAlignRange< Position >::m_SecondFrom

private

start

Definition at line 356 of file align_range.hpp.

Referenced by CAlignRange< Position >::GetFirstPosBySecondPos(), CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::GetSecondPosByFirstPos(), CAlignRange< Position >::GetSecondToOpen(), CAlignRange< Position >::IntersectSecondWith(), CAlignRange< Position >::IntersectWith(), CAlignRange< Position >::SecondContains(), and CAlignRange< Position >::SetSecondFrom().

m_SelectIter

template<class Traits >

TSelectIter CRangeMapIterator< Traits >::m_SelectIter

private

Definition at line 351 of file rangemap.hpp.

Referenced by CRangeMapIterator< Traits >::FirstLevelIter(), CRangeMapIterator< Traits >::GetSelectIter(), CRangeMultimap< Mapped, Position >::insert(), CRangeMapIterator< Traits >::operator++(), CRangeMapIterator< Traits >::SetBegin(), CRangeMapIterator< Traits >::SetEnd(), and CRangeMapIterator< Traits >::Valid().

m_SelectIterEnd

template<class Traits >

TSelectIter CRangeMapIterator< Traits >::m_SelectIterEnd

private

Definition at line 352 of file rangemap.hpp.

Referenced by CRangeMapIterator< Traits >::GetSelectIterEnd(), CRangeMultimap< Mapped, Position >::insert(), CRangeMapIterator< Traits >::operator++(), CRangeMapIterator< Traits >::SetBegin(), CRangeMapIterator< Traits >::SetEnd(), and CRangeMapIterator< Traits >::Valid().

m_SelectMap

template<class Traits >

TSelectMap CRangeMapBase< Traits >::m_SelectMap

protected

Definition at line 535 of file rangemap.hpp.

Referenced by CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::begin(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::clear(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::CRangeMapBase(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::empty(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::end(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::erase(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::find(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::insertLevel(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::size(), and CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::swap().

m_ToOpen

template<class Position >

position_type COpenRange< Position >::m_ToOpen

private

Definition at line 381 of file range.hpp.

Friends

CRangeMap< mapped_type, position_type >

template<class Traits >

friend class CRangeMap< mapped_type, position_type >

friend

Definition at line 189 of file rangemap.hpp.

CRangeMapBase< typename TTraits::TMapTraits >

template<class Traits >

friend class CRangeMapBase< typename TTraits::TMapTraits >

friend

Definition at line 189 of file rangemap.hpp.

CRangeMultimap< mapped_type, position_type >

template<class Traits >

friend class CRangeMultimap< mapped_type, position_type >

friend

Definition at line 189 of file rangemap.hpp.