kinetics/WriteKkit.cpp File Reference

#include <iomanip>
#include <fstream>
#include "../shell/Shell.h"
#include "../shell/Wildcard.h"
#include "header.h"
#include "../utility/utility.h"
#include "PoolBase.h"
#include "Pool.h"
#include "BufPool.h"
#include "ReacBase.h"
#include "EnzBase.h"
#include "lookupVolumeFromMesh.h"
#include <sstream>
#include <set>

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Functions
void	writeHeader (ofstream &fout, double simdt, double plotdt, double maxtime, double defaultVol)
string	trimPath (Id id, Id comptid)
Id	getEnzCplx (Id id)
Id	getEnzMol (Id id)
void	writeEnz (ofstream &fout, Id id, string colour, string textcolour, double x, double y, Id comptid)
void	writeReac (ofstream &fout, Id id, string colour, string textcolour, double x, double y, Id comptid)
unsigned int	getSlaveEnable (Id id)
void	writePool (ofstream &fout, Id id, string colour, string textcolour, double x, double y, Id comptid, int comptIndex)
void	writePlot (ofstream &fout, Id id, string colour, string textcolour, double x, double y)
void	writeGui (ofstream &fout)
void	writeFooter (ofstream &fout)
void	storeMMenzMsgs (Id enz, vector< string > &msgs, Id comptid)
void	storeCplxEnzMsgs (Id enz, vector< string > &msgs, Id comptid)
void	storeEnzMsgs (Id enz, vector< string > &msgs, Id comptid)
void	storeReacMsgs (Id reac, vector< string > &msgs, Id comptid)
void	storeFunctionMsgs (Id func, vector< string > &msgs, map< double, pair< Id, int > > &compt_vol)
void	storePlotMsgs (Id tab, vector< string > &msgs, Id pool, string bg, Id comptid)
double	estimateSimTimes (double &simDt, double &plotDt)
double	estimateDefaultVol (Id model)
	Returns an estimate of the default volume used in the model.
void	writeMsgs (ofstream &fout, const vector< string > &msgs)
void	writeGroup (ofstream &fout, Id model)
void	writeKkit (Id model, const string &fname)

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Function Documentation

double estimateDefaultVol

(

Id

model

)

Returns an estimate of the default volume used in the model.

References Field< A >::get().

Referenced by writeKkit().

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double estimateSimTimes	(	double &	simDt,
		double &	plotDt
	)

A bunch of heuristics to find good SimTimes to use for kkit. Returns runTime.

References Field< A >::get().

Referenced by writeKkit().

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Id getEnzCplx

(

Id

id

)

Referenced by writeEnz().

Id getEnzMol

(

Id

id

)

Referenced by writeEnz().

unsigned int getSlaveEnable

(

Id

id

)

References Cinfo::findFinfo(), and PoolBase::initCinfo().

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void storeCplxEnzMsgs	(	Id	enz,
		vector< string > &	msgs,
		Id	comptid
	)

References Field< A >::get(), and trimPath().

Referenced by storeEnzMsgs().

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void storeEnzMsgs	(	Id	enz,
		vector< string > &	msgs,
		Id	comptid
	)

References storeCplxEnzMsgs(), and storeMMenzMsgs().

Referenced by writeKkit().

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void storeFunctionMsgs	(	Id	func,
		vector< string > &	msgs,
		map< double, pair< Id, int > > &	compt_vol
	)

References Id::eref(), Neutral::parent(), trimPath(), and Id::value().

Referenced by writeKkit().

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void storeMMenzMsgs	(	Id	enz,
		vector< string > &	msgs,
		Id	comptid
	)

References Field< A >::get(), and trimPath().

Referenced by storeEnzMsgs().

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void storePlotMsgs	(	Id	tab,
		vector< string > &	msgs,
		Id	pool,
		string	bg,
		Id	comptid
	)

References Id::path(), and trimPath().

Referenced by writeKkit().

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void storeReacMsgs	(	Id	reac,
		vector< string > &	msgs,
		Id	comptid
	)

References trimPath().

Referenced by writeKkit().

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string trimPath	(	Id	id,
		Id	comptid
	)

Referenced by storeCplxEnzMsgs(), storeFunctionMsgs(), storeMMenzMsgs(), storePlotMsgs(), storeReacMsgs(), writePool(), and writeReac().

void writeEnz	(	ofstream &	fout,
		Id	id,
		string	colour,
		string	textcolour,
		double	x,
		double	y,
		Id	comptid
	)

References Field< A >::get(), getEnzCplx(), getEnzMol(), and NA.

Referenced by writeKkit().

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void writeFooter

(

ofstream &

fout

)

Referenced by writeKkit().

void writeGroup	(	ofstream &	fout,
		Id	model
	)

References Field< A >::get(), Id::path(), wildcardFind(), and y.

Referenced by writeKkit().

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void writeGui

(

ofstream &

fout

)

Referenced by writeKkit().

void writeHeader	(	ofstream &	fout,
		double	simdt,
		double	plotdt,
		double	maxtime,
		double	defaultVol
	)

Referenced by writeKkit().

void writeKkit	(	Id	model,
		const string &	fname
	)

References estimateDefaultVol(), estimateSimTimes(), Field< A >::get(), Id::path(), storeEnzMsgs(), storeFunctionMsgs(), storePlotMsgs(), storeReacMsgs(), wildcardFind(), writeEnz(), writeFooter(), writeGroup(), writeGui(), writeHeader(), writeMsgs(), writePlot(), writePool(), writeReac(), and y.

Referenced by testWriteKkit().

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void writeMsgs	(	ofstream &	fout,
		const vector< string > &	msgs
	)

Referenced by writeKkit().

void writePlot	(	ofstream &	fout,
		Id	id,
		string	colour,
		string	textcolour,
		double	x,
		double	y
	)

Referenced by writeKkit().

void writePool	(	ofstream &	fout,
		Id	id,
		string	colour,
		string	textcolour,
		double	x,
		double	y,
		Id	comptid,
		int	comptIndex
	)

References Field< A >::get(), NA, and trimPath().

Referenced by writeKkit().

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void writeReac	(	ofstream &	fout,
		Id	id,
		string	colour,
		string	textcolour,
		double	x,
		double	y,
		Id	comptid
	)

References Field< A >::get(), and trimPath().

Referenced by writeKkit().

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