AMOS::Range_t Struct Reference

A gapped coordinate range. More...

#include <datatypes_AMOS.hh>

List of all members.

Public Member Functions
	Range_t ()
	Constructs an empty Range_t object.
	Range_t (const Range_t &source)
	Copy constructor.
	Range_t (Pos_t b, Pos_t e)
	Constructs a Range_t object.
	~Range_t ()
	Destroys a Range_t object.
void	clear ()
	Clears the range to an empty range [0,0).
Pos_t	getBegin () const
	Get the beginning of the range.
Pos_t	getLo () const
	Get the lo range position, (begin < end ? begin : end).
Pos_t	getHi () const
	Get the hi range position, (begin > end ? begin : end).
Pos_t	getEnd () const
	Get the end of the range.
Size_t	getLength () const
	Get the length of the range.
bool	isReverse () const
	Returns true if begin > end, otherwise false.
void	setBegin (Pos_t b)
	Set the beginning of the range.
void	setEnd (Pos_t e)
	Set the end of the range.
void	setRange (Pos_t b, Pos_t e)
	Set the whole range.
void	swap ()
	Exchange the beginning and end of the range.
Public Attributes
Pos_t	begin
	The begin of the range.
Pos_t	end
	The end of the range.

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Detailed Description

A gapped coordinate range.

A range of values defined by the start and end gap numbers that bracket the requested values with gap counting starting at 0 (the gap before the first value). The minimum value points to the leftmost value in the list, while the maximum value points to one after the rightmost value in the list. For example, the range [2,5) for the list 0,1,2,3,4,5,6 would define the sublist 2,3,4. Reversed ranges are also allowed, for example (5,2] would define the subset 4,3,2.

Definition at line 120 of file datatypes_AMOS.hh.

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Constructor & Destructor Documentation

AMOS::Range_t::Range_t

(

)

[inline]

Constructs an empty Range_t object.

Sets begin and end to zero, thus creating a zero length range

Definition at line 132 of file datatypes_AMOS.hh.

References clear().

AMOS::Range_t::Range_t

(

const Range_t &

source

)

[inline]

Copy constructor.

Parameters:

source

The range to be copied

Definition at line 143 of file datatypes_AMOS.hh.

AMOS::Range_t::Range_t	(	Pos_t	b,
		Pos_t	e
	)			[inline]

Constructs a Range_t object.

Sets begin and end to the parameter values

Parameters:

	b	Construct value of begin
	e	Construct value of end

Definition at line 157 of file datatypes_AMOS.hh.

References begin, and end.

AMOS::Range_t::~Range_t

(

)

[inline]

Destroys a Range_t object.

Definition at line 167 of file datatypes_AMOS.hh.

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Member Function Documentation

void AMOS::Range_t::clear

(

)

[inline]

Clears the range to an empty range [0,0).

Definition at line 176 of file datatypes_AMOS.hh.

References begin, and end.

Referenced by Range_t().

Pos_t AMOS::Range_t::getBegin

(

)

const [inline]

Get the beginning of the range.

Definition at line 185 of file datatypes_AMOS.hh.

References begin.

Pos_t AMOS::Range_t::getEnd

(

)

const [inline]

Get the end of the range.

Definition at line 212 of file datatypes_AMOS.hh.

References end.

Pos_t AMOS::Range_t::getHi

(

)

const [inline]

Get the hi range position, (begin > end ? begin : end).

Definition at line 203 of file datatypes_AMOS.hh.

References begin, and end.

Referenced by AMOS::Sequence_t::getGCContent(), and AMOS::Contig_t::getGCContent().

Size_t AMOS::Range_t::getLength

(

)

const [inline]

Get the length of the range.

Returns:

abs (end - begin)

Definition at line 223 of file datatypes_AMOS.hh.

References begin, and end.

Referenced by AMOS::Tile_t::getRightOffset().

Pos_t AMOS::Range_t::getLo

(

)

const [inline]

Get the lo range position, (begin < end ? begin : end).

Definition at line 194 of file datatypes_AMOS.hh.

References begin, and end.

Referenced by AMOS::Sequence_t::getGCContent(), and AMOS::Contig_t::getGCContent().

bool AMOS::Range_t::isReverse

(

)

const [inline]

Returns true if begin > end, otherwise false.

Returns:

true if begin > end, otherwise false

Definition at line 234 of file datatypes_AMOS.hh.

References begin, and end.

Referenced by AMOS::TiledRead_t::TiledRead_t().

void AMOS::Range_t::setBegin

(

Pos_t

b

)

[inline]

Set the beginning of the range.

Definition at line 243 of file datatypes_AMOS.hh.

References begin.

void AMOS::Range_t::setEnd

(

Pos_t

e

)

[inline]

Set the end of the range.

Definition at line 252 of file datatypes_AMOS.hh.

References end.

void AMOS::Range_t::setRange	(	Pos_t	b,
		Pos_t	e
	)			[inline]

Set the whole range.

Definition at line 261 of file datatypes_AMOS.hh.

References begin, and end.

void AMOS::Range_t::swap

(

)

[inline]

Exchange the beginning and end of the range.

Definition at line 271 of file datatypes_AMOS.hh.

References begin, and end.

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Member Data Documentation

Pos_t AMOS::Range_t::begin

The begin of the range.

Definition at line 123 of file datatypes_AMOS.hh.

Referenced by clear(), getBegin(), getHi(), getLength(), getLo(), isReverse(), AMOS::operator<<(), Range_t(), setBegin(), setRange(), and swap().

Pos_t AMOS::Range_t::end

The end of the range.

Definition at line 124 of file datatypes_AMOS.hh.

Referenced by clear(), getEnd(), getHi(), getLength(), getLo(), isReverse(), AMOS::operator<<(), Range_t(), setEnd(), setRange(), and swap().

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The documentation for this struct was generated from the following file:

• datatypes_AMOS.hh

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