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Reactor Class Template Reference

#include <reactor.h>

Inheritance diagram for Reactor::

List of all members.

Public Methods
	Reactor (char *recNr)
virtual	~Reactor ()
virtual int	step ()
virtual int	setup ()
int	checkFitness ()
list<Seq*>&	getSequenceList ()
int	getCurrentCapacity ()
Seq*	gettmpSequence ()
char*	getInFileName ()
int	setCurrentCapacity (int nCap)
int	setBonus (int bonus)
Public Attributes
bool	found_target
bool	bInnovation
double	d_currentLogTime
double	d_currentDumpTime
int	n_currentDumpRepl
double	d_currentStopTime
char*	pTarget
Seq*	tmpSequence
Protected Methods
virtual int	initalize ()
virtual int	readTarget ()
virtual int	readInitalPopulation ()
virtual int	writeSequences ()
virtual int	fillPhenoProductionTable ()
virtual int	fillPhenoDiedOutTable ()
virtual int	fillSeqLineageTable (int nSeqNr, int nInstance, int nParentSeqNr, int nParentInst)
virtual int	replication (double d_random)
virtual int	outflow (double d_random)
virtual int	insertSequence (char *pSequence, Seq *pParent, int nInstanceOfParentSeq, int nDistToParent)
virtual int	mutation (char *&sequence)
virtual int	calcSeqFitness ()
virtual int	writeMonitor ()
virtual int	writeMonitorHeader ()
int	writeDump ()
Protected Attributes
char*	reactNr
char	c_monitorFilename [200]
char	c_lineageFilename [200]
char	c_historyFilename [200]
char	c_inFilename [200]
double	d_currentTime
int	n_current_capacity
double	d_sumChannel
long	n_replications
long	n_sequenceInnovations
double	d_currentReactivity
double	d_outflow
int	n_capacity
int	n_dump
PointMut	mutate
RandomWell	rwell
hash_set<const Seq*, hash< const Seq*>, eqSeq<const Seq*> >	seqSet
hash_set<const Seq*, hash< const Seq*>, eqSeq<const Seq*> >::iterator	seqIter
list<Seq*>	list_Sequence
list<Seq*>::iterator	listIter
Friends
ostream&	operator<< (ostream &stream, Reactor< Seq2 > &flowreactor)

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Detailed Description

template<class Seq> class Reactor

The reactor maintains the replication, mutation and outflow of sequences. It is resposible for time advancement and monitor and dumpfile writings. The reactor class is also the base class for all kinds of flow reactors. It performs a genetic algorithm developed by Daniel Gillespie. Since it is a template class, it works with all kinds of sequences <Seq> if the support the following functions: getUnpackedSequence() getPackedSequence addinstance(); removeinstance(nPos) calculate_fitness(char *pTarget);

Definition at line 35 of file reactor.h.

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Constructor & Destructor Documentation

template<class Seq> Reactor<Seq>::Reactor<Seq> ( char * recNr )

template<class Seq> virtual Reactor<Seq>::~Reactor<Seq> ( ) [virtual]

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Member Function Documentation

template<class Seq> virtual int Reactor<Seq>::calcSeqFitness ( ) [protected, virtual]

Reimplemented in BiFitReactor.

template<class Seq> int Reactor<Seq>::checkFitness ( )

template<class Seq> int Reactor<Seq>::fillPhenoDiedOutTable ( ) [inline, protected, virtual]

Definition at line 61 of file reactor.h. {return(1);};

template<class Seq> int Reactor<Seq>::fillPhenoProductionTable ( ) [inline, protected, virtual]

Definition at line 60 of file reactor.h. {return(1);};

template<class Seq> virtual int Reactor<Seq>::fillSeqLineageTable ( int nSeqNr, int nInstance, int nParentSeqNr, int nParentInst ) [protected, virtual]

template<class Seq> int Reactor<Seq>::getCurrentCapacity ( ) [inline]

Definition at line 106 of file reactor.h. {return (n_current_capacity);}

template<class Seq> char * Reactor<Seq>::getInFileName ( ) [inline]

Definition at line 108 of file reactor.h. {return (c_inFilename);}

template<class Seq> list< Seq *> & Reactor<Seq>::getSequenceList<Seq*> ( ) [inline]

Definition at line 105 of file reactor.h. {return(list_Sequence);}

template<class Seq> Seq * Reactor<Seq>::gettmpSequence ( ) [inline]

Definition at line 107 of file reactor.h. {return tmpSequence;}

template<class Seq> virtual int Reactor<Seq>::initalize ( ) [protected, virtual]

template<class Seq> virtual int Reactor<Seq>::insertSequence ( char * pSequence, Seq * pParent, int nInstanceOfParentSeq, int nDistToParent ) [protected, virtual]

Reimplemented in ProtReactor, RelReactor, StructLifeReactor, and ProtReactor.

template<class Seq> int Reactor<Seq>::mutation ( char *& sequence ) [inline, protected, virtual]

Reimplemented in InsDelReactor, JumpReactor, and NoMutReactor. Definition at line 67 of file reactor.h. {return(mutate(sequence));}

template<class Seq> virtual int Reactor<Seq>::outflow ( double d_random ) [protected, virtual]

Reimplemented in ProtReactor, RelReactor, and ProtReactor.

template<class Seq> virtual int Reactor<Seq>::readInitalPopulation ( ) [protected, virtual]

Reimplemented in ProtReactor, StartReactor, StepReactor, and ProtReactor.

template<class Seq> virtual int Reactor<Seq>::readTarget ( ) [protected, virtual]

Reimplemented in BiFitReactor.

template<class Seq> virtual int Reactor<Seq>::replication ( double d_random ) [protected, virtual]

Reimplemented in CrossReactor, MinorReactor, and ReacFactory.

template<class Seq> int Reactor<Seq>::setBonus ( int bonus )

template<class Seq> int Reactor<Seq>::setCurrentCapacity ( int nCap )

template<class Seq> virtual int Reactor<Seq>::setup ( ) [virtual]

Reimplemented in ProtReactor, PseudoReactor, StructLifeReactor, and ProtReactor.

template<class Seq> virtual int Reactor<Seq>::step ( ) [virtual]

Reimplemented in BatchReactor, ReacFactory, NoMutReactor, PopReactor, RelReactor, StartReactor, StepReactor, and StructLifeReactor.

template<class Seq> int Reactor<Seq>::writeDump ( ) [protected]

template<class Seq> virtual int Reactor<Seq>::writeMonitor ( ) [protected, virtual]

Reimplemented in MinorReactor, and ThresholdReactor.

template<class Seq> virtual int Reactor<Seq>::writeMonitorHeader ( ) [protected, virtual]

template<class Seq> virtual int Reactor<Seq>::writeSequences ( ) [protected, virtual]

Reimplemented in ProtReactor, RelReactor, and ProtReactor.

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Friends And Related Function Documentation

template<class Seq> ostream& operator<< ( ostream & stream, Reactor< Seq2 > & flowreactor ) [friend]

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Member Data Documentation

template<class Seq> bool Reactor<Seq>::bInnovation

Definition at line 89 of file reactor.h.

template<class Seq> char Reactor<Seq>::c_historyFilename[200] [protected]

Definition at line 41 of file reactor.h.

template<class Seq> char Reactor<Seq>::c_inFilename[200] [protected]

Definition at line 42 of file reactor.h.

template<class Seq> char Reactor<Seq>::c_lineageFilename[200] [protected]

Definition at line 40 of file reactor.h.

template<class Seq> char Reactor<Seq>::c_monitorFilename[200] [protected]

Definition at line 39 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_currentDumpTime

Definition at line 91 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_currentLogTime

Definition at line 90 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_currentReactivity [protected]

Definition at line 48 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_currentStopTime

Definition at line 93 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_currentTime [protected]

Definition at line 43 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_outflow [protected]

Definition at line 49 of file reactor.h.

template<class Seq> double Reactor<Seq>::d_sumChannel [protected]

Definition at line 45 of file reactor.h.

template<class Seq> bool Reactor<Seq>::found_target

Definition at line 88 of file reactor.h.

template<class Seq> list<Seq*>::iterator Reactor<Seq>::listIter [protected]

Definition at line 79 of file reactor.h.

template<class Seq> list<Seq*> Reactor<Seq>::list_Sequence [protected]

Definition at line 78 of file reactor.h.

template<class Seq> PointMut Reactor<Seq>::mutate [protected]

Reimplemented in InsDelReactor, and JumpReactor. Definition at line 53 of file reactor.h. Referenced by mutation(), and InsDelReactor::mutation().

template<class Seq> int Reactor<Seq>::n_capacity [protected]

Definition at line 50 of file reactor.h.

template<class Seq> int Reactor<Seq>::n_currentDumpRepl

Definition at line 92 of file reactor.h.

template<class Seq> int Reactor<Seq>::n_current_capacity [protected]

Definition at line 44 of file reactor.h.

template<class Seq> int Reactor<Seq>::n_dump [protected]

Definition at line 51 of file reactor.h.

template<class Seq> long Reactor<Seq>::n_replications [protected]

Definition at line 46 of file reactor.h.

template<class Seq> long Reactor<Seq>::n_sequenceInnovations [protected]

Definition at line 47 of file reactor.h.

template<class Seq> char* Reactor<Seq>::pTarget

Definition at line 95 of file reactor.h.

template<class Seq> char* Reactor<Seq>::reactNr [protected]

Definition at line 38 of file reactor.h.

template<class Seq> RandomWell Reactor<Seq>::rwell [protected]

Definition at line 54 of file reactor.h.

template<class Seq> hash_set<const Seq*, hash<const Seq*>, eqSeq<const Seq*> >::iterator Reactor<Seq>::seqIter [protected]

Definition at line 76 of file reactor.h.

template<class Seq> hash_set<const Seq*, hash<const Seq*>, eqSeq<const Seq*> > Reactor<Seq>::seqSet [protected]

Definition at line 75 of file reactor.h.

template<class Seq> Seq* Reactor<Seq>::tmpSequence

Definition at line 96 of file reactor.h.

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The documentation for this class was generated from the following file:

• reactor.h

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