RNAModel.h File Reference

#include "GenModel.h"
#include <string>
#include "bioseq.h"
#include "Coverdepth.h"
#include "strformat.h"
#include <cassert>
#include <cmath>

Go to the source code of this file.

Classes
class	OutsideGenomicSequence
class	RNAModel
class	mRNAModel
class	mRNAModelUpdate
class	InvalidJGIModel
class	JGIModel
class	ESTAssembly
class	ESTAssemblyid
Enumerations
enum	modeltype { RNA, mRNA, EST, JGI }
Functions
bool	useFullORF (int lenfull, int lenpartial)
void	clumpModelIntoGene (set< ESTAssemblyid *, lessByChainDirectionPtr > &mod, list< list< ESTAssemblyid * > > &loci)
	helper method //////////////

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Enumeration Type Documentation

enum modeltype

Enumerator:

RNA
mRNA
EST
JGI

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Function Documentation

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

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

this method is for combest program to build gene relationship. Because the assembler class produced models in set<ESTAssemblyid*, lessByChainDirectionPtr> this method also use this type. The consequence of this method is to reset the geneid.

Parameters:

	loci	contains the models belonging to the same locus. the models from the same gene have no distinction. counter was used to make geneid.
	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().

bool useFullORF	(	int	lenfull,
		int	lenpartial
	)

pick which ever longer without going through cutoff checking.

Referenced by maxFullORF().