GenModel.cpp File Reference

#include "GenModel.h"
#include <algorithm>
#include <sstream>

Functions
void	string2Vector (vector< int > &v, const string &str)
bool	nonincreasingVector (const vector< int > &v)
bool	nondecreasingVector (const vector< int > &v)
bool	allLessVector (const vector< int > &v1, const vector< int > &v2)
Noschain	operator- (int c, const Noschain &chain)
ostream &	operator<< (ostream &ous, const Noschain &nc)
int	comparePlusChainFirstBefore (Noschain &c1, Noschain &c2)
int	comparePlusChainIdenticalLeft (Noschain &c1, Noschain &c2)
int	compareMinusChainFirstBefore (Noschain &c1, Noschain &c2)
int	compareMinusChainMinusIdenticalRight (Noschain &c1, Noschain &c2)
void	errorMessageFix1 (Noschain &c1, Noschain &c2, int status, int end)
bool	tilingPlus (const Noschain &A, const Noschain &B)
bool	tilingMinus (const Noschain &A, const Noschain &B)
Variables
int	FUZZYMARGIN = 21

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Function Documentation

bool allLessVector	(	const vector< int > &	v1,
		const vector< int > &	v2
	)

Referenced by Noschain::Noschain().

int compareMinusChainFirstBefore	(	Noschain &	c1,
		Noschain &	c2
	)

References Range::begin(), Range::end(), FUZZYMARGIN, I, Noschain::numberOfRanges(), Noschain::setBegin(), and Noschain::setEnd().

Referenced by Noschain::compareChainAndFix().

int compareMinusChainMinusIdenticalRight	(	Noschain &	c1,
		Noschain &	c2
	)

left ends are the same

References Range::begin(), Range::end(), FUZZYMARGIN, I, Noschain::numberOfRanges(), and Noschain::setEnd().

Referenced by Noschain::compareChainAndFix().

int comparePlusChainFirstBefore	(	Noschain &	c1,
		Noschain &	c2
	)

several helper functions. The noschain compare function is very hard to implement. I have not figured out a simple way to implement this function.

return 0, 1, 2, -2 These are non-member function.

all use a common value fuzzymargin as static constant. I should use a common value in the Range::margin The the caller will have to set this value. The Range::margin has a default of 20. Which should be set to 16. I will use a global constant FUZZYMARGIN. This value can be changed by the user.

References Range::begin(), Range::end(), FUZZYMARGIN, I, Noschain::numberOfRanges(), Noschain::setBegin(), and Noschain::setEnd().

Referenced by Noschain::compareChainAndFix().

int comparePlusChainIdenticalLeft	(	Noschain &	c1,
		Noschain &	c2
	)

left ends are the same

References Range::begin(), Range::end(), FUZZYMARGIN, I, Noschain::numberOfRanges(), and Noschain::setEnd().

Referenced by Noschain::compareChainAndFix().

void errorMessageFix1	(	Noschain &	c1,
		Noschain &	c2,
		int	status,
		int	end
	)

for debuging

References Noschain::show().

bool nondecreasingVector

(

const vector< int > &

v

)

numbers goes from small to large

Referenced by Noschain::Noschain().

bool nonincreasingVector

(

const vector< int > &

v

)

numbers go from large to small

Referenced by Noschain::Noschain().

Noschain operator-	(	int	c,
		const Noschain &	chain
	)

Each Range of the chain becomes (c-exons[i])

References Noschain::exons.

ostream& operator<<	(	ostream &	ous,
		const Noschain &	nc
	)

References Noschain::exonLength(), Noschain::exons, Noschain::intronLength(), Noschain::isNull(), and Noschain::numberOfRanges().

void string2Vector	(	vector< int > &	v,
		const string &	str
	)

Referenced by Noschain::Noschain().

bool tilingMinus	(	const Noschain &	A,
		const Noschain &	B
	)

helper function A is to the right Condition is A<B and both on - direction possible overlap B i ===<---==<----===<-----= A j =<----===<-----===<-----====

Special case

B i ===<---==<----===<-----===== A j =====<----===<-----===<-----====

References Range::begin(), Range::end(), Noschain::exonIndex(), and Noschain::numberOfRanges().

Referenced by Noschain::exonOverlap().

bool tilingPlus	(	const Noschain &	A,
		const Noschain &	B
	)

helper function A on the left Condition is A<B and both on + direction possible overlap A j ===--->==---->===----->= B i =---->===----->===---->==== overlap at ends A j ===--->==---->===----->==== B i ===---->===----->===---->====

References Range::begin(), Range::end(), Noschain::exonIndex(), and Noschain::numberOfRanges().

Referenced by Noschain::exonOverlap().

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Variable Documentation

int FUZZYMARGIN = 21

Referenced by compareMinusChainFirstBefore(), compareMinusChainMinusIdenticalRight(), comparePlusChainFirstBefore(), comparePlusChainIdenticalLeft(), and main().