Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order. More...

#include <objects/seqloc/Seq_loc.hpp>

Inheritance diagram for CSeq_loc_I:

Collaboration diagram for CSeq_loc_I:

Public Types
enum	EMakeType { eMake_CompactType , eMake_PreserveType }
	Options for creation modified locations Bond and equiv types are preserved if possible. More...

enum	EEquivMode { eEquiv_none , eEquiv_new_equiv , eEquiv_new_part , eEquiv_append , eEquiv_prepend }
	This enum defines a way equiv sets are expanded or created when one of Insert*() methods is called. More...

Public Types inherited from CSeq_loc_CI
enum	EEmptyFlag { eEmpty_Skip , eEmpty_Allow }
	Options for empty locations processing. More...

enum	ESeqLocOrder { eOrder_Positional , eOrder_Biological }

typedef CSeq_loc::TRange	TRange

Public Member Functions
	CSeq_loc_I (void)
	constructors More...

	CSeq_loc_I (CSeq_loc &loc)

	CSeq_loc_I (const CSeq_loc_I &iter, size_t pos)
	construct iterator at a different position in the same location More...

virtual	~CSeq_loc_I (void)
	destructor More...

bool	HasChanges (void) const
	return true of any part was changed since initialization More...

CRef< CSeq_loc >	MakeSeq_loc (EMakeType make_type=eMake_CompactType) const
	return constructed CSeq_loc with all changes More...

void	Delete (void)
	Delete current element, and make iterator to point to the next element. More...

CSeq_loc_I	InsertNull (void)
	Set of Insert*() methods. More...

CSeq_loc_I	InsertEmpty (const CSeq_id_Handle &id)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertEmpty (const CSeq_id &id)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertWhole (const CSeq_id_Handle &id)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertWhole (const CSeq_id &id)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertInterval (const CSeq_id_Handle &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertInterval (const CSeq_id &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertInterval (const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertInterval (const CSeq_id_Handle &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertPoint (const CSeq_id_Handle &id, TSeqPos pos, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

CSeq_loc_I	InsertPoint (const CSeq_id &id, TSeqPos pos, ENa_strand strand=eNa_strand_unknown)
	Insert new element before the current one (. More...

void	SetSeq_id_Handle (const CSeq_id_Handle &id)
	Set seq_id of the current location. More...

void	SetSeq_id (const CSeq_id &id)
	Set seq_id of the current location. More...

void	SetRange (const TRange &range)
	Set the range. More...

void	SetFrom (TSeqPos from)
	Set the range from position. More...

void	SetTo (TSeqPos to)
	Set the range to position. More...

void	SetPoint (TSeqPos pos)
	Set the range from and to positions. More...

void	ResetStrand (void)
	Reset the range strand. More...

void	SetStrand (ENa_strand strand)
	Set the range strand. More...

void	ResetFuzzFrom (void)
	Reset fuzz from. More...

void	SetFuzzFrom (CInt_fuzz &fuzz)
	Change fuzz from. More...

void	ResetFuzzTo (void)
	Reset fuzz to. More...

void	SetFuzzTo (CInt_fuzz &fuzz)
	Change fuzz to values. More...

void	ResetFuzz (void)
	Reset fuzz of a point. More...

void	SetFuzz (CInt_fuzz &fuzz)
	Change fuzz of a point. More...

pair< CSeq_loc_I, CSeq_loc_I >	GetEquivSetRange (size_t level=0) const
	Return iterators that cover equiv set of current position result.first is the first segment in the equiv set result.second is the first segment after the equiv set level specify equiv set if there are more than one of them level = 0 is the smallest equiv set (innermost) More...

pair< CSeq_loc_I, CSeq_loc_I >	GetEquivPartRange (size_t level=0) const
	Return iterators that cover equiv part of current position result.first is the first segment in the equiv part result.second is the first segment after the equiv part level specify equiv set if there are more than one of them level = 0 is the smallest equiv set (innermost) More...

void	SetEquivMode (EEquivMode mode)
	Change equiv modification mode. More...

void	StartNewEquiv (void)
	Change equiv modification mode to add new equiv set for the next insert operation. More...

void	StartNewEquivPart (void)
	Change equiv modification mode to add new equiv part for the next insert operation. More...

void	StopEquiv (void)
	Change equiv modification mode to normal behavior that will only update existing equiv sets. More...

EEquivMode	GetEquivMode (void) const
	Get equiv modification mode. More...

void	RemoveEquiv (size_t level=0)
	Remove equiv set, all pieces that are part of the set will be preserved as independent pieces. More...

void	MakeEquiv (const CSeq_loc_I &end_it)
	Create equiv set with one part from current position to the position pointed by end_it argument exclusive. More...

void	MakeEquivPartBreak (size_t level=0)
	Create equiv set with one part from current position to the position pointed by end_it argument exclusive. More...

void	RemoveBond (void)
	Remove bond at current position - it may be either A or B part. More...

void	MakeBondA (void)
	Make bond at current position (only A) The current part must be a point If current posision is already a bond A part, it will be updated. More...

void	MakeBondAB (void)
	Make bond at current position with the next position (A and B) The current and next parts must be points If current posision is already a bond A part, it will be updated. More...

void	MakeBondB (void)
	Make bond at previous position with the current position (A and B) The current and previous parts must be points If previous posision is already a bond A part, it will be updated. More...

Public Member Functions inherited from CSeq_loc_CI
	CSeq_loc_CI (void)
	constructors More...

	CSeq_loc_CI (const CSeq_loc &loc, EEmptyFlag empty_flag=eEmpty_Skip, ESeqLocOrder order=eOrder_Biological)

	CSeq_loc_CI (const CSeq_loc_CI &iter, size_t pos)
	construct iterator at a different position in the same location More...

virtual	~CSeq_loc_CI (void)
	destructor More...

	CSeq_loc_CI (const CSeq_loc_CI &iter)

CSeq_loc_CI &	operator= (const CSeq_loc_CI &iter)

CSeq_loc_CI &	operator++ (void)

	DECLARE_OPERATOR_BOOL (x_IsValid())

bool	operator== (const CSeq_loc_CI &iter) const

bool	operator!= (const CSeq_loc_CI &iter) const

bool	IsInBond (void) const
	Location of type equiv define set of equivalent locations. More...

bool	IsBondA (void) const
	Return true if current position is A part of a bond. More...

bool	IsBondB (void) const
	Return true if current position is B part of a bond. More...

pair< CSeq_loc_CI, CSeq_loc_CI >	GetBondRange (void) const
	Return iterators that cover bond of current position result.first is the first segment in the equiv set result.second is the first segment after the equiv set. More...

bool	HasEquivSets (void) const
	Return true if location has equiv parts. More...

bool	IsInEquivSet (void) const
	Return true if current position is in some equiv part. More...

size_t	GetEquivSetsCount (void) const
	Return number of recursuve equiv parts current position in. More...

pair< CSeq_loc_CI, CSeq_loc_CI >	GetEquivSetRange (size_t level=0) const
	Return iterators that cover equiv set of current position result.first is the first segment in the equiv set result.second is the first segment after the equiv set level specify equiv set if there are more than one of them level = 0 is the smallest equiv set (innermost) More...

pair< CSeq_loc_CI, CSeq_loc_CI >	GetEquivPartRange (size_t level=0) const
	Return iterators that cover equiv part of current position result.first is the first segment in the equiv part result.second is the first segment after the equiv part level specify equiv set if there are more than one of them level = 0 is the smallest equiv set (innermost) More...

const CSeq_id &	GetSeq_id (void) const
	Get seq_id of the current location. More...

CSeq_id_Handle	GetSeq_id_Handle (void) const

TRange	GetRange (void) const
	Get the range. More...

bool	IsSetStrand (void) const
	Get strand. More...

ENa_strand	GetStrand (void) const

CConstRef< CSeq_loc >	GetRangeAsSeq_loc (void) const
	Get seq-loc for the current iterator position. More...

const CSeq_loc &	GetEmbeddingSeq_loc (void) const
	Get the nearest seq-loc containing the current range. More...

const CSeq_loc &	GetSeq_loc (void) const

const CInt_fuzz *	GetFuzzFrom (void) const

const CInt_fuzz *	GetFuzzTo (void) const

bool	IsWhole (void) const
	True if the current location is a whole sequence. More...

bool	IsEmpty (void) const
	True if the current location is empty. More...

bool	IsPoint (void) const
	True if the current location is a single point. More...

void	Rewind (void)
	Reset the iterator to the initial state. More...

size_t	GetSize (void) const
	Get number of ranges. More...

size_t	GetPos (void) const
	Get iterator's position. More...

void	SetPos (size_t pos)
	Set iterator's position. More...

const CSeq_loc_CI &	operator* () const

Protected Member Functions
SSeq_loc_CI_RangeInfo &	x_GetRangeInfo (void)

void	x_SetSeq_id_Handle (SSeq_loc_CI_RangeInfo &info, const CSeq_id_Handle &id)

bool	x_IsValidForInsert (void) const

void	x_CheckValidForInsert (const char *where) const

virtual const char *	x_GetIteratorType (void) const

const SSeq_loc_CI_RangeInfo &	x_GetRangeInfo (void) const

Protected Member Functions inherited from CSeq_loc_CI
const SSeq_loc_CI_RangeInfo &	x_GetRangeInfo (void) const

bool	x_IsValid (void) const

void	x_CheckValid (const char *where) const

void	x_ThrowNotValid (const char *where) const

Additional Inherited Members
Protected Attributes inherited from CSeq_loc_CI
CRef< CSeq_loc_CI_Impl >	m_Impl

size_t	m_Index

Detailed Description

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Definition at line 592 of file Seq_loc.hpp.

Member Function Documentation

◆ x_GetRangeInfo()

const SSeq_loc_CI_RangeInfo & CSeq_loc_CI::x_GetRangeInfo ( void )

protected

Definition at line 575 of file Seq_loc.cpp.

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

include/objects/seqloc/Seq_loc.hpp
src/objects/seqloc/Seq_loc.cpp

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ x_GetRangeInfo()