Esambl.cpp File Reference

#include "Esambl.h"
#include <iomanip>
#include <list>
#include <iterator>
#include <set>
#include <queue>
#include "RNAModel.h"

Functions
ostream &	operator<< (ostream &ous, const HeadNode &hn)
void	breakExtraModel (ESTAssembly *est, queue< ESTAssembly * > &extra)
ostream &	operator<< (ostream &ous, const Graph &gr)
void	breakExtraModel (ESTAssemblyid *est, queue< ESTAssemblyid * > &extra) throw (PointOutChain)
ostream &	operator<< (ostream &ous, const Graphid &gr)

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Function Documentation

void breakExtraModel	(	ESTAssemblyid *	est,
		queue< ESTAssemblyid * > &	extra
	)			throw (PointOutChain)

helper function works for ESTAssemblyid version used by assemble not in header

Parameters:

est

is the input model pointer is a queue of models produced by braking prefix or suffix models.

References ESTAssemblyid::breakPrefixModel(), ESTAssemblyid::breakSuffixModel(), ESTAssembly::checkIntronBound(), Range::length(), and PointOutChain::what().

void breakExtraModel	(	ESTAssembly *	est,
		queue< ESTAssembly * > &	extra
	)

References ESTAssembly::breakPrefixModel(), ESTAssembly::breakSuffixModel(), ESTAssembly::checkIntronBound(), and Range::length().

Referenced by Graphid::assemble(), and Graph::assemble().

ostream& operator<<	(	ostream &	ous,
		const Graphid &	gr
	)

References Graphid::input, Graphid::showMatrix(), and Graphid::vertices.

ostream& operator<<	(	ostream &	ous,
		const Graph &	gr
	)

Firt it shows input chains, then show matrix. This is only used for debug.

References Graph::input, Graph::showMatrix(), and Graph::vertices.

ostream& operator<<	(	ostream &	ous,
		const HeadNode &	hn
	)

References HeadNode::idx, and Valence::show().