Interval Class Reference

#include <Interval.h>

Inheritance diagram for Interval:

List of all members.

Public Member Functions
	Interval ()
	Interval (const int bb, const int ee)
	Interval (const Interval &iv)
	Interval (const string &str)
virtual	~Interval ()
int	overlap (const Interval &i) const
int	overlap (const int bb, const int ee) const
virtual int	merge (Interval *i, const int cut=5)
virtual string	toDelimitedString (const string &dl="\t") const
bool	less (const Interval &iv) const
bool	operator< (const Interval &iv) const
bool	before (const Interval &iv) const
bool	after (const Interval &iv) const
bool	isNull () const
void	setBegin (const int bb)
void	setEnd (const int ee)
void	set (const Interval &iv)
int	getBegin () const
int	begin () const
int	getEnd () const
int	end () const
virtual int	size () const
int	length () const
Private Attributes
int	b
int	e
Friends
ostream &	operator<< (ostream &ous, const Interval &iv)

---

Detailed Description

this file use the composition design pattern the Interval class is a lot simpler than the Range class that considers all 4 possibility between two ranges when comparing them. In reality, most work is done with the ranges are int the + direction such as protein alignments. This class will make things simple and fast. b<e

[b, e] closed interval

---

Constructor & Destructor Documentation

Interval::Interval

(

)

[inline]

Referenced by IntervalChain::add(), and IntervalChain::IntervalChain().

Interval::Interval	(	const int	bb,
		const int	ee
	)			[inline]

Interval::Interval

(

const Interval &

iv

)

[inline]

Interval::Interval

(

const string &

str

)

use string as input to construct a interval You can use a,b, a-b, a:b formats

References b, and e.

virtual Interval::~Interval

(

)

[inline, virtual]

---

Member Function Documentation

int Interval::overlap

(

const Interval &

i

)

const

References b, e, max, and min.

Referenced by merge().

int Interval::overlap	(	const int	bb,
		const int	ee
	)			const

References b, e, max, and min.

int Interval::merge	(	Interval *	i,
		const int	cut = 5
	)			[virtual]

Merging two Intervals. The merge only happens when the overlap > cut

Parameters:

cut

the cutoff value for merging.

Returns:

the overlapping value regardless of the merging happened or not.

It is better to use the overlap method to control the merge method.

base class merge does not invalidate input pointer.

Reimplemented in IntervalPile.

References b, e, isNull(), max, min, and overlap().

Referenced by IntervalChain::add(), IntervalPile::add(), and IntervalPile::merge().

string Interval::toDelimitedString

(

const string &

dl = "\t"

)

const [virtual]

Reimplemented in IntervalPile, and HalfAlignPile.

References b, and e.

Referenced by IntervalPile::toDelimitedString().

bool Interval::less

(

const Interval &

iv

)

const [inline]

References b, and e.

Referenced by operator<().

bool Interval::operator<

(

const Interval &

iv

)

const [inline]

References less().

bool Interval::before

(

const Interval &

iv

)

const [inline]

References b, and e.

Referenced by IntervalChain::add().

bool Interval::after

(

const Interval &

iv

)

const [inline]

References b, and e.

bool Interval::isNull

(

)

const [inline]

References b, and e.

Referenced by merge().

void Interval::setBegin

(

const int

bb

)

[inline]

References b.

Referenced by IntervalChain::add().

void Interval::setEnd

(

const int

ee

)

[inline]

References e.

Referenced by IntervalChain::add().

void Interval::set

(

const Interval &

iv

)

[inline]

References b, and e.

int Interval::getBegin

(

)

const [inline]

return the beginning of the interval. begin() will do the same

References b.

Referenced by IntervalChain::add().

int Interval::begin

(

)

const [inline]

returns the start of the interval

References b.

Referenced by longestORFPlus(), and P2Rindex().

int Interval::getEnd

(

)

const [inline]

References e.

Referenced by IntervalChain::add().

int Interval::end

(

)

const [inline]

References e.

Referenced by longestORFPlus(), and P2Rindex().

virtual int Interval::size

(

)

const [inline, virtual]

moew meaningful for composite classes derived from this base class. Such as IntervalChain and IntervalPile

Returns:

the number of elements inside this element.

Reimplemented in IntervalPile, and IntervalChain.

int Interval::length

(

)

const [inline]

return the length of the Interval For composite derived class, it is the Interval covered by all the members. it is min(b) - max(e) of all members.

References b, and e.

Referenced by HalfAlignPile::computeIntermediateResult(), and longestORFPlus().

---

Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Interval &	iv
	)			[friend]

---

Member Data Documentation

int Interval::b [private]

Referenced by after(), before(), begin(), getBegin(), Interval(), isNull(), length(), less(), merge(), overlap(), set(), setBegin(), and toDelimitedString().

int Interval::e [private]

Referenced by after(), before(), end(), getEnd(), Interval(), isNull(), length(), less(), merge(), overlap(), set(), setEnd(), and toDelimitedString().

---

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

• range/Interval.h
• range/Interval.cpp