Dip Class Reference

#include <Coverdepth.h>

Inheritance diagram for Dip:

List of all members.

Public Member Functions
	Dip ()
	Dip (int tl, int bl, int br, int tr, int lh, int blh, int brh, int rh)
void	incrementPosition (int B)
bool	isGood () const
bool	betterThan (const Dip &dip) const
int	bottomLeft () const
int	bottomRight () const
int	bottomWidth () const
int	height () const
int	leftHeight () const
int	rightHeight () const
int	bottomHeight () const
pair< int, int >	breakPoint (char dir='+') const
int	ratio () const
float	fineratio () const
float	fineRatio () const
bool	isNull () const
Public Attributes
int	posTL
int	posBL
int	posBR
int	posTR
int	LH
int	RH
int	BLH
int	BRH
Static Public Attributes
static int	intronAvoid = 30
Friends
ostream &	operator<< (ostream &ous, const Dip &v)

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Detailed Description

This is a utiity class used by Coverdepth class It is mainly used by findDip and searchDip.

This class includes two special derived class LeftDropoff and RightDropoff I need to make sure the operations on this base class should make sense to derived class because derived class has not special member. I simply make the extra member identical to redundant informaiotn. Always in + direction, from small to large.

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Constructor & Destructor Documentation

Dip::Dip

(

)

[inline]

Dip::Dip	(	int	tl,
		int	bl,
		int	br,
		int	tr,
		int	lh,
		int	blh,
		int	brh,
		int	rh
	)			[inline]

four postion, then four heights from left to right

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Member Function Documentation

void Dip::incrementPosition

(

int

B

)

References posBL, posBR, posTL, and posTR.

bool Dip::isGood

(

)

const

if the bottom width < 5 it is considered bad. ratio > 4 is considered good height > 60 && ratio > 3 is considered good. All others are thought bad.

Reimplemented in RightDropoff, and LeftDropoff.

References BLH, bottomWidth(), BRH, height(), min, and ratio().

Referenced by Coverdepth::digDip(), Coverdepth::findVDip(), and testDip().

bool Dip::betterThan

(

const Dip &

dip

)

const

this is comparing the height and the width of the dips.

References bottomHeight(), bottomWidth(), fineratio(), and height().

int Dip::bottomLeft

(

)

const [inline]

int Dip::bottomRight

(

)

const [inline]

int Dip::bottomWidth

(

)

const [inline]

Referenced by betterThan(), breakPoint(), isGood(), and operator<<().

int Dip::height

(

)

const [inline]

tallest ends - shorted bottom

Reimplemented in RightDropoff, and LeftDropoff.

References max, and min.

Referenced by betterThan(), and isGood().

int Dip::leftHeight

(

)

const [inline]

Referenced by breakPoint().

int Dip::rightHeight

(

)

const [inline]

Referenced by breakPoint().

int Dip::bottomHeight

(

)

const [inline]

References min.

Referenced by betterThan().

pair< int, int > Dip::breakPoint

(

char

dir = '+'

)

const

If LH and RH > 10*BH, then can get rid of the joining part, otherwise, pick the middle point.

Parameters:

dir

tell the orientation of the two values first before second in 5' to 3' direction. if '+' the first<second, else first>second

References bottomWidth(), leftHeight(), posBL, posBR, ratio(), and rightHeight().

Referenced by ESTAssembly::breakPrefixModel(), ESTAssembly::breakSuffixModel(), ESTAssemblyid::breakup(), ESTAssembly::prune3PrimeUTR(), and ESTAssembly::prune5PrimeUTR().

int Dip::ratio

(

)

const [inline]

Reimplemented in RightDropoff, and LeftDropoff.

References max, and min.

Referenced by breakPoint(), and isGood().

float Dip::fineratio

(

)

const [inline]

the higer of the top / shorter of the bottom

References max, and min.

Referenced by betterThan().

float Dip::fineRatio

(

)

const [inline]

Reimplemented in RightDropoff, and LeftDropoff.

References max, and min.

Referenced by Coverdepth::findDropoff().

bool Dip::isNull

(

)

const [inline]

empty object

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Dip &	v
	)			[friend]

set this objecet into a right Dropoff

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Member Data Documentation

int Dip::posTL

TL TR \ / \ / BL/BR

pos TL, BL, BR, TR

Referenced by incrementPosition(), Coverdepth::makeDip(), operator<<(), and Coverdepth::produceDip().

int Dip::posBL

Referenced by breakPoint(), incrementPosition(), Coverdepth::makeDip(), operator<<(), and Coverdepth::produceDip().

int Dip::posBR

Referenced by breakPoint(), incrementPosition(), Coverdepth::makeDip(), operator<<(), and Coverdepth::produceDip().

int Dip::posTR

Referenced by incrementPosition(), Coverdepth::makeDip(), operator<<(), and Coverdepth::produceDip().

int Dip::LH

hights I am allowing the bottom to tilt a little bit, in this case, BH is the lower of the height of the two bottom ends.

Referenced by RightDropoff::fineRatio(), RightDropoff::height(), Coverdepth::makeDip(), operator<<(), Coverdepth::produceDip(), and RightDropoff::ratio().

int Dip::RH

Referenced by LeftDropoff::fineRatio(), LeftDropoff::height(), Coverdepth::makeDip(), operator<<(), Coverdepth::produceDip(), and LeftDropoff::ratio().

int Dip::BLH

bottom Left Height, bottom Right Height

Referenced by RightDropoff::better(), Coverdepth::digDip(), LeftDropoff::fineRatio(), LeftDropoff::height(), LeftDropoff::isGood(), isGood(), Coverdepth::makeDip(), operator<<(), Coverdepth::produceDip(), and LeftDropoff::ratio().

int Dip::BRH

Referenced by LeftDropoff::better(), RightDropoff::fineRatio(), RightDropoff::height(), RightDropoff::isGood(), isGood(), Coverdepth::makeDip(), operator<<(), Coverdepth::produceDip(), and RightDropoff::ratio().

int Dip::intronAvoid = 30 [static]

how far Dip away from introns

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

• range/Coverdepth.h
• range/Coverdepth.cpp