RNAModel.cpp File Reference

#include "RNAModel.h"
#include "strformat.h"
#include <cmath>
#include <cstring>
#include <iterator>
#include <list>
#include "hatrees.h"

Functions
int	n2p (int n)
bool	useFullORF (int lenfull, int lenpartial)
int	maxFullORF (bool(*orfinder)(const string &, pair< int, int > &, string &, pair< int, int > &, string &), const string &rna, pair< int, int > &bound, string &pep)
bool	modelFarEnough (const Range &r1, const Range &r2)
bool	CDSFarAndLong (const Range &r1, const Range &r2)
bool	CDSFar (const Range &r1, const Range &r2)
bool	CDSNoStart (const string &rna, const Range &rr)
bool	CDSNoStartReverse (const string &rna, const Range &rr)
void	clumpModelIntoGene (set< ESTAssemblyid *, lessByChainDirectionPtr > &mod, list< list< ESTAssemblyid * > > &loci)
	helper method //////////////

---

Function Documentation

bool CDSFar	(	const Range &	r1,
		const Range &	r2
	)

References Range::distance(), and Range::sameDirection().

bool CDSFarAndLong	(	const Range &	r1,
		const Range &	r2
	)

helper function for deciding whether to break chimera ORF or not These are simply the Range of CDS on RNA. could be on either direction. thise helper no longer used.

References Range::distance(), Range::length(), and Range::sameDirection().

bool CDSNoStart	(	const string &	rna,
		const Range &	rr
	)

References Range::begin().

Referenced by ESTAssemblyid::breakup().

bool CDSNoStartReverse	(	const string &	rna,
		const Range &	rr
	)

References Range::begin().

Referenced by ESTAssemblyid::breakup().

void clumpModelIntoGene	(	set< ESTAssemblyid *, lessByChainDirectionPtr > &	mod,
		list< list< ESTAssemblyid * > > &	loci
	)

helper method //////////////

Parameters:

	mod	input.
	loci.	Output result. If mod has only one model, then deallocate memory, clear mod then return. Case of more than one model: use mRNAModel::sameGene() method to cluster models into genes. This method pick a random modelid as the geneid.

References hatrees< T >::clusterArray(), Range::end(), hatrees< T >::getNodeCount(), and hatrees< T >::keyset().

Referenced by assembleChain().

int maxFullORF	(	bool(*)(const string &, pair< int, int > &, string &, pair< int, int > &, string &)	orfinder,
		const string &	rna,
		pair< int, int > &	bound,
		string &	pep
	)

Returns:

-1 if no ORF found, this is extremely unlikely 0 if only ORF of no start and no stop found, this is more likely with short sequences. 1 if ORF of missing either start or stop 2 if Full ORF found and is the choice when applied to useFullORF() function.

Parameters:

	orfinder	pointer to a program, such as longestNoStopORFPlus
	rna	input RNA
	pep	output peptide sequence string
	bound	the start and end of ORF in mRNA index This is a helper function.

References useFullORF().

Referenced by ESTAssembly::breakPrefixModel(), and ESTAssembly::breakSuffixModel().

bool modelFarEnough	(	const Range &	r1,
		const Range &	r2
	)

References Range::distance(), and Range::sameDirection().

int n2p

(

int

n

)

Referenced by mRNAModel::sfExonsProtein().

bool useFullORF	(	int	lenfull,
		int	lenpartial
	)

pick which ever longer without going through cutoff checking.

Referenced by maxFullORF().