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StructSeq Class Reference

#include <structseq.h>

Inheritance diagram for StructSeq::

List of all members.

Public Methods
	StructSeq (char *newSequence, int nRunningNr)
RNAStructure*	getPhenoType () const
int	getPhenoTypeInnovations ()
virtual int	calculate_fitness (char *pTarget)
virtual int	removeinstance (int nPos)
virtual int	addinstance ()
Static Public Attributes
hash_set<const RNAStructure*, hash<const RNAStructure*>, eqRNAStructure>	structSet
hash_set<const RNAStructure*, hash<const RNAStructure*>, eqRNAStructure>::iterator	structIter
Protected Attributes
RNAStructure*	pSecStructure
float	mfe
Static Protected Attributes
int	nPhenoTypes
int	nPhenoTypeInnovations

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Detailed Description

The StructSeq class handles the management of phenoypes (class RNAStructure) in a static hash. The calculate_fitness(..) function inserts new structures. No structure is ever removed to ensure consistent numbering. Packing (compression) is handled in the RNAStructure, the logging of shapes in a history file is done in a reactor class or a inherited class.

Definition at line 29 of file structseq.h.

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Constructor & Destructor Documentation

StructSeq::StructSeq ( char * newSequence, int nRunningNr ) [inline]

Definition at line 40 of file structseq.h. : Sequence(newSequence, nRunningNr){}

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Member Function Documentation

virtual int StructSeq::addinstance ( ) [virtual]

Reimplemented from Sequence.

int StructSeq::calculate_fitness ( char * pTarget ) [virtual]

processes fitness calculation and phenotype handling Reimplemented from Sequence. Reimplemented in EvalSeq.

RNAStructure * StructSeq::getPhenoType ( ) const [inline]

Definition at line 45 of file structseq.h. {return pSecStructure;};

int StructSeq::getPhenoTypeInnovations ( ) [inline]

Definition at line 46 of file structseq.h. {return(nPhenoTypeInnovations);};

virtual int StructSeq::removeinstance ( int nPos ) [virtual]

Reimplemented from Sequence.

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Member Data Documentation

float StructSeq::mfe [protected]

Definition at line 37 of file structseq.h.

int StructSeq::nPhenoTypeInnovations [static, protected]

Definition at line 35 of file structseq.h.

int StructSeq::nPhenoTypes [static, protected]

Definition at line 34 of file structseq.h.

RNAStructure* StructSeq::pSecStructure [protected]

Definition at line 32 of file structseq.h.

hash_set<const RNAStructure*, hash<const RNAStructure*>, eqRNAStructure>::iterator StructSeq::structIter [static]

Definition at line 43 of file structseq.h.

hash_set<const RNAStructure*, hash<const RNAStructure*>, eqRNAStructure> StructSeq::structSet [static]

Definition at line 42 of file structseq.h.

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

• structseq.h

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