CSeqMapSwitchPoint Class Reference
[Sequence Representations]

Search Toolkit Book for CSeqMapSwitchPoint

#include <seq_map_switch.hpp>

Inheritance diagram for CSeqMapSwitchPoint:

[legend]Collaboration diagram for CSeqMapSwitchPoint:

[legend]List of all members.

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Detailed Description

Definition at line 57 of file seq_map_switch.hpp.

Public Types
typedef pair< TSeqPos, TSeqPos >	TInsertDelete
typedef map< TSeqPos, TInsertDelete >	TDifferences
Public Member Functions
TInsertDelete	GetDifferences (TSeqPos new_pos, TSeqPos add=0) const
int	GetLengthDifference (TSeqPos new_pos, TSeqPos add=0) const
int	GetSequenceDifference (TSeqPos new_pos, TSeqPos add=0) const
TSeqPos	GetInsert (TSeqPos pos) const
TSeqPos	GetLeftInPlaceInsert (void) const
TSeqPos	GetRightInPlaceInsert (void) const
void	ChangeSwitchPoint (TSeqPos pos, TSeqPos add)
void	InsertInPlace (TSeqPos add_left, TSeqPos add_right)
bool	operator< (const CSeqMapSwitchPoint &p) const
Public Attributes
CBioseq_Handle	m_Master
TSeqPos	m_MasterPos
CConstRef< CSeq_align >	m_FirstAlign
CSeq_id_Handle	m_LeftId
TSeqPos	m_LeftPos
bool	m_LeftMinusStrand
CSeq_id_Handle	m_RightId
TSeqPos	m_RightPos
bool	m_RightMinusStrand
CRange< TSeqPos >	m_MasterRange
CRange< TSeqPos >	m_ExactMasterRange
TDifferences	m_LeftDifferences
TDifferences	m_RightDifferences

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Member Typedef Documentation

typedef map<TSeqPos, TInsertDelete> CSeqMapSwitchPoint::TDifferences

Definition at line 89 of file seq_map_switch.hpp.

typedef pair<TSeqPos, TSeqPos> CSeqMapSwitchPoint::TInsertDelete

Definition at line 87 of file seq_map_switch.hpp.

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Member Function Documentation

void CSeqMapSwitchPoint::ChangeSwitchPoint (  TSeqPos  pos, TSeqPos  add )

Definition at line 510 of file seq_map_switch.cpp. References COpenRange< Position >::GetFrom(), COpenRange< Position >::GetTo(), m_Master, m_MasterRange, and NCBI_THROW.

CSeqMapSwitchPoint::TInsertDelete CSeqMapSwitchPoint::GetDifferences (  TSeqPos  new_pos, TSeqPos  add = 0 )  const

Definition at line 449 of file seq_map_switch.cpp. References m_LeftDifferences, m_MasterPos, m_RightDifferences, and x_GetDifferences().

TSeqPos CSeqMapSwitchPoint::GetInsert (  TSeqPos  pos  )  const

Definition at line 462 of file seq_map_switch.cpp. References COpenRange< Position >::GetFrom(), COpenRange< Position >::GetTo(), m_Master, m_MasterRange, and NCBI_THROW.

TSeqPos CSeqMapSwitchPoint::GetLeftInPlaceInsert (  void   )  const

Definition at line 490 of file seq_map_switch.cpp. References map_checker< Container >::begin(), map_checker< Container >::empty(), and m_LeftDifferences. Referenced by InsertInPlace().

int CSeqMapSwitchPoint::GetLengthDifference (  TSeqPos  new_pos, TSeqPos  add = 0 )  const [inline]

Definition at line 95 of file seq_map_switch.hpp.

TSeqPos CSeqMapSwitchPoint::GetRightInPlaceInsert (  void   )  const

Definition at line 500 of file seq_map_switch.cpp. References map_checker< Container >::begin(), map_checker< Container >::empty(), and m_RightDifferences. Referenced by InsertInPlace().

int CSeqMapSwitchPoint::GetSequenceDifference (  TSeqPos  new_pos, TSeqPos  add = 0 )  const [inline]

Definition at line 101 of file seq_map_switch.hpp.

void CSeqMapSwitchPoint::InsertInPlace (  TSeqPos  add_left, TSeqPos  add_right )

Definition at line 582 of file seq_map_switch.cpp. References GetLeftInPlaceInsert(), GetRightInPlaceInsert(), m_Master, and NCBI_THROW.

bool CSeqMapSwitchPoint::operator< (  const CSeqMapSwitchPoint &  p  )  const [inline]

Definition at line 114 of file seq_map_switch.hpp. References _ASSERT, m_Master, m_Master, and m_MasterPos.

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Member Data Documentation

CRange<TSeqPos> CSeqMapSwitchPoint::m_ExactMasterRange

Definition at line 82 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

CConstRef<CSeq_align> CSeqMapSwitchPoint::m_FirstAlign

Definition at line 67 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

TDifferences CSeqMapSwitchPoint::m_LeftDifferences

Definition at line 90 of file seq_map_switch.hpp. Referenced by GetDifferences(), GetLeftInPlaceInsert(), and x_GetSwitchPoint().

CSeq_id_Handle CSeqMapSwitchPoint::m_LeftId

Definition at line 70 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

bool CSeqMapSwitchPoint::m_LeftMinusStrand

Definition at line 72 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

TSeqPos CSeqMapSwitchPoint::m_LeftPos

Definition at line 71 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

CBioseq_Handle CSeqMapSwitchPoint::m_Master

Definition at line 62 of file seq_map_switch.hpp. Referenced by ChangeSwitchPoint(), GetInsert(), InsertInPlace(), operator<(), and x_GetSwitchPoint().

TSeqPos CSeqMapSwitchPoint::m_MasterPos

Definition at line 64 of file seq_map_switch.hpp. Referenced by GetDifferences(), operator<(), and x_GetSwitchPoint().

CRange<TSeqPos> CSeqMapSwitchPoint::m_MasterRange

Definition at line 80 of file seq_map_switch.hpp. Referenced by ChangeSwitchPoint(), GetInsert(), and x_GetSwitchPoint().

TDifferences CSeqMapSwitchPoint::m_RightDifferences

Definition at line 90 of file seq_map_switch.hpp. Referenced by GetDifferences(), GetRightInPlaceInsert(), and x_GetSwitchPoint().

CSeq_id_Handle CSeqMapSwitchPoint::m_RightId

Definition at line 75 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

bool CSeqMapSwitchPoint::m_RightMinusStrand

Definition at line 77 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

TSeqPos CSeqMapSwitchPoint::m_RightPos

Definition at line 76 of file seq_map_switch.hpp. Referenced by x_GetSwitchPoint().

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The documentation for this class was generated from the following files:

• include/objmgr/seq_map_switch.hpp
• src/objmgr/seq_map_switch.cpp

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