Genotype Class Reference

Genotype class. More...

Inheritance diagram for Genotype:

Classes
class	nObjectiveGreaterThanComparator
	Utility class for generating a function for comparing genotype of an objective. More...

Public Member Functions
	Genotype (unsigned int size=0)
	Construct a un-initialized Genotype.
	Genotype (QString, bool compressed=false)
	Read the values from QString and set the size accordlying to length of QString.
	Genotype (const Genotype &genotype)
	Copy-Constructor (generate a clone of the genoma)
virtual	~Genotype ()
	Destructor.
void	assign (const Genotype *genotype)
	Assign method (it call operator=)
bool	bit (unsigned int i) const
	Return the i-th bit.
virtual unsigned int	bitToGeneIndex (unsigned int bit) const
	Convert the index of the given bit to the index of the gene that this bit is part of.
virtual Genotype *	clone () const
	Create an exact copy of this Genotype.
virtual void	configure (ConfigurationParameters &params, QString prefix)
	Configure the object using the ConfigurationParameters specified.
bool	dominatedBy (const Genotype *genotype)
	Return True if this Genotype is dominated by the Genotype specified by param.
unsigned int	extractUInt (unsigned int startPos, unsigned int stopPos)
	Utility function for extracting an integer value.
double	fitness () const
	Return the fitness of this Genotype.
bool	fromCompressedString (QString str)
	Read from compressed data with toCompressedString()
void	fromString (QString)
	Configure the bits accordlying to its string representation passed.
virtual unsigned int	geneToBitIndex (unsigned int gene) const
	Convert the index of the given gene to the index of the start of the bit(s) that encode this gene.
int	hammingDistance (const Genotype *)
	Calculate the Hamming distance from the Genotype.
void	insertUInt (unsigned int value, unsigned int startPos, unsigned int stopPos)
	Utility function for settings an integer value into Genotype.
QString	notes () const
	Return the notes of this Genotype.
int	numOfObjectives () const
	Return the number of Objectives setted The number of objectives is automatically configured by setObjective method.
double	objective (int i) const
	Return the value of the i-th objective of the fitness.
virtual Genotype &	operator= (const Genotype &genotype)
	Assign operator (performs same operation of Copy-constructor) Due to virtual attribute, Subclasses can customize the behaviour of this operator=, for an easy way to copy Genotype data the protected method copyDataFrom is provided and it behaves like this implementation of operator=.
virtual void	randomize ()
	Randomize the value contained (attention, this method destroys previous data)
double	rank () const
	Return the rank of this Genotype.
virtual void	save (ConfigurationParameters &params, QString prefix)
	Save the actual status of parameters into the ConfigurationParameters object passed.
void	set (unsigned int i)
	Set to One the i-th bit.
void	setFitness (double value)
	Set the fitness value of this Genotype.
void	setNotes (QString notes)
	Set the notes of this Genotype.
void	setObjective (int i, double value)
	Set the i-th objective value of the (multi-objective) fitness.
void	setRank (double rank)
	Set the rank of the genotype.
unsigned int	size () const
	Return the size of Genotype.
QString	toCompressedString () const
	Compress the data; It return a printable String.
void	toggle (unsigned int i)
	toggle the i-th bit
QString	toString () const
	Return a QString representing this Genotype.
void	unset (unsigned int i)
	set to zero the i-th bit
Public Member Functions inherited from ParameterSettableWithConfigureFunction
void	addObserver (RuntimeParameterObserver *obs)
T	getRuntimeParameter (QString paramName)
virtual ParameterSettableUI *	getUIManager ()
	ParameterSettable ()
virtual void	postConfigureInitialization ()
void	removeObserver (RuntimeParameterObserver *obs)
void	setRuntimeParameter (QString paramName, T newvalue)
QString	typeName () const
Public Member Functions inherited from ParameterSettable
void	addObserver (RuntimeParameterObserver *obs)
T	getRuntimeParameter (QString paramName)
void	removeObserver (RuntimeParameterObserver *obs)
void	setRuntimeParameter (QString paramName, T newvalue)
QString	typeName () const

Static Public Member Functions
static void	describe (QString type)
	Add to Factory::typeDescriptions() the descriptions of all parameters and subgroups.
static bool	rankGreaterThanComparator (const Genotype *g1, const Genotype *g2)
	Utility function comparing two genotype pointers on their rank.
Static Public Member Functions inherited from ParameterSettableWithConfigureFunction
static void	describe (QString type)
static QString	fullParameterDescriptionPath (QString type, QString param)
static QString	fullSubgroupDescriptionPath (QString type, QString sub)
Static Public Member Functions inherited from ParameterSettable
static void	describe (QString type)
static QString	fullParameterDescriptionPath (QString type, QString param)
static QString	fullSubgroupDescriptionPath (QString type, QString sub)

Protected Member Functions
void	copyDataFrom (Genotype *source)
	Utility method for copying data among Genotype.
void	resize (unsigned int newsize)
	Resize the Genotype.
Protected Member Functions inherited from ParameterSettableWithConfigureFunction
void	notifyChangesToParam (QString paramName)
Protected Member Functions inherited from ParameterSettable
void	notifyChangesToParam (QString paramName)

Protected Attributes
unsigned int	allocated
	Allocated memory.
unsigned char *	data
	Data represented as a char vector allocated in memory.
QVector< double >	fitnessv
	Objective values of the Fitness.
QString	notesv
	Notes about this Genotype.
double	rankv
	Rank.
unsigned int	sizev
	Size.

Additional Inherited Members
Public Types inherited from ParameterSettableWithConfigureFunction
enum	Property
Public Attributes inherited from ParameterSettableWithConfigureFunction
	AllowMultiple
	Default
	IsList
	IsMandatory
Static Public Attributes inherited from ParameterSettableWithConfigureFunction
static const double	Infinity
static const int	MaxInteger
static const int	MinInteger
Static Protected Member Functions inherited from ParameterSettableWithConfigureFunction
static Descriptor	addTypeDescription (QString type, QString shortHelp, QString longHelp=QString(""))
static void	setGraphicalEditor (QString type)

Detailed Description

Genotype class.

Description

Represent a bit-string

Warnings

Definition at line 38 of file genotype.h.

Constructor & Destructor Documentation

Genotype

(

unsigned int

size = 0

)

Construct a un-initialized Genotype.

Warning

you must explicity call randomize() to get a randomized Genotype

Definition at line 28 of file genotype.cpp.

References Genotype::allocated, Genotype::data, Genotype::fitnessv, Genotype::notesv, Genotype::rankv, Genotype::size(), and Genotype::sizev.

Referenced by Genotype::clone().

~Genotype ( )

virtual

Destructor.

Definition at line 39 of file genotype.cpp.

References Genotype::data.

Genotype	(	QString	str,
		bool	compressed = false
	)

Read the values from QString and set the size accordlying to length of QString.

Definition at line 43 of file genotype.cpp.

References Genotype::allocated, Genotype::data, Genotype::fitnessv, Genotype::notesv, Genotype::rankv, Genotype::sizev, and Genotype::unset().

Genotype

(

const Genotype &

genotype

)

Copy-Constructor (generate a clone of the genoma)

Definition at line 77 of file genotype.cpp.

References Genotype::allocated, Genotype::data, Genotype::fitnessv, Genotype::notesv, Genotype::rankv, and Genotype::sizev.

Member Function Documentation

void assign

(

const Genotype *

genotype

)

Assign method (it call operator=)

Definition at line 144 of file genotype.cpp.

bool bit

(

unsigned int

i

)

const

Return the i-th bit.

Definition at line 213 of file genotype.cpp.

References Genotype::data.

Referenced by SignedRangeGenotype::at(), Genotype::bitToGeneIndex(), OnePoint::crossover(), Genotype::extractUInt(), Genotype::hammingDistance(), Genotype::toCompressedString(), and Genotype::toString().

unsigned int bitToGeneIndex ( unsigned int  bit ) const

virtual

Convert the index of the given bit to the index of the gene that this bit is part of.

Reimplemented in DoubleGenotype.

Definition at line 359 of file genotype.cpp.

References Genotype::bit().

Genotype * clone ( ) const

virtual

Create an exact copy of this Genotype.

Reimplemented in RealGenotype, and SignedRangeGenotype.

Definition at line 149 of file genotype.cpp.

References Genotype::Genotype().

Referenced by Genome::append(), Genome::configure(), StefanoSteadyStateGA::gaStep(), Genome::Genome(), Genome::operator=(), and Genome::set().

void configure ( ConfigurationParameters &  params, QString  prefix  )

virtual

Configure the object using the ConfigurationParameters specified.

Parameters

params	the object with configuration parameters
prefix	the group in which parameters are expected to be (this is terminated by a separator character). We expect to receive as prefix the group with genotype parameters

Implements ParameterSettableWithConfigureFunction.

Reimplemented in RealGenotype, and SignedRangeGenotype.

Definition at line 100 of file genotype.cpp.

References Genotype::fitnessv, Genotype::fromCompressedString(), ConfigurationParameters::getValue(), Genotype::notesv, Genotype::rankv, and Genotype::resize().

void copyDataFrom ( Genotype *  source )

protected

Utility method for copying data among Genotype.

Definition at line 363 of file genotype.cpp.

References Genotype::allocated, Genotype::data, Genotype::fitnessv, Genotype::notesv, Genotype::rankv, and Genotype::sizev.

Referenced by RealGenotype::operator=(), and SignedRangeGenotype::operator=().

void describe ( QString  type )

static

Add to Factory::typeDescriptions() the descriptions of all parameters and subgroups.

Definition at line 136 of file genotype.cpp.

References ParameterSettableWithConfigureFunction::addTypeDescription(), ParameterSettable::IntDescriptor::def(), ParameterSettable::Descriptor::describeInt(), ParameterSettable::Descriptor::describeReal(), ParameterSettable::Descriptor::describeString(), ParameterSettable::StringDescriptor::help(), ParameterSettable::RealDescriptor::help(), ParameterSettable::IntDescriptor::help(), ParameterSettableWithConfigureFunction::IsList, ParameterSettableWithConfigureFunction::IsMandatory, ParameterSettable::IntDescriptor::limits(), ParameterSettable::RealDescriptor::props(), and ParameterSettable::IntDescriptor::props().

bool dominatedBy

(

const Genotype *

genotype

)

Return True if this Genotype is dominated by the Genotype specified by param.

Warning

the two Genotypes should have the same number of objectives; if this constraint is not meet then the number of objectives compared will be the minimum between the two genotypes

Note

Definition of Domination: a Genotype A is dominated by Genotype B iff all objective values of A are less-equal of corresponding objective values of B and for at least one objective the value of A is strictly less that value in B

Definition at line 190 of file genotype.cpp.

References Genotype::fitnessv.

unsigned int extractUInt	(	unsigned int	startPos,
		unsigned int	stopPos
	)

Utility function for extracting an integer value.

Parameters

startPos	is the index of starting position of the bits to decode
stopPos	is the index of end position of the bits to decode +----------------------------+ | 0 1 0 0 1 0 1 1 0 1 0 1 0 | +----------------------------+ if startPos is 4 and stopPos is 8 the bits 1011 is decode and this methods will returns 11 if stopPos is beyond the length of Genotype, ad example startPos 9 and stopPos 15 then the bits 1010 will be decoded and this methods will return 10.

Definition at line 325 of file genotype.cpp.

References Genotype::bit(), and Genotype::sizev.

Referenced by SignedRangeGenotype::at().

double fitness

(

)

const

Return the fitness of this Genotype.

Note

it is the same of objective(0);

Definition at line 173 of file genotype.cpp.

References Genotype::objective().

Referenced by StefanoSteadyStateGA::gaStep().

bool fromCompressedString

(

QString

str

)

Read from compressed data with toCompressedString()

Returns

true on successfull decompression, false otherwise

Definition at line 308 of file genotype.cpp.

References Genotype::sizev, and Genotype::unset().

Referenced by RealGenotype::configure(), SignedRangeGenotype::configure(), and Genotype::configure().

void fromString

(

QString

str

)

Configure the bits accordlying to its string representation passed.

Definition at line 287 of file genotype.cpp.

References Genotype::sizev, and Genotype::unset().

unsigned int geneToBitIndex ( unsigned int  gene ) const

virtual

Convert the index of the given gene to the index of the start of the bit(s) that encode this gene.

Reimplemented in DoubleGenotype.

Definition at line 355 of file genotype.cpp.

int hammingDistance

(

const Genotype *

other

)

Calculate the Hamming distance from the Genotype.

Definition at line 260 of file genotype.cpp.

References Genotype::bit(), and Genotype::sizev.

void insertUInt	(	unsigned int	value,
		unsigned int	startPos,
		unsigned int	stopPos
	)

Utility function for settings an integer value into Genotype.

Parameters

value	is the value to be converted and inserted into genotype
startPos	is the index of starting position of the bits to decode
stopPos	is the index of end position of the bits to decode The parameters has the same meanings of extractUInt, and the behaviour is exactly the opposite.

Definition at line 340 of file genotype.cpp.

References Genotype::sizev, and Genotype::unset().

Referenced by SignedRangeGenotype::set().

QString notes

(

)

const

Return the notes of this Genotype.

Definition at line 252 of file genotype.cpp.

References Genotype::notesv.

Referenced by Genotype::setNotes().

int numOfObjectives

(

)

const

Return the number of Objectives setted The number of objectives is automatically configured by setObjective method.

Definition at line 186 of file genotype.cpp.

References Genotype::fitnessv.

Referenced by GeneticAlgo::updateStats().

double objective

(

int

i

)

const

Return the value of the i-th objective of the fitness.

Note

fitness() return the same value of objective(0)

Definition at line 182 of file genotype.cpp.

References Genotype::fitnessv.

Referenced by Genotype::fitness(), Genotype::nObjectiveGreaterThanComparator::operator()(), and GeneticAlgo::updateStats().

Genotype & operator= ( const Genotype &  genotype )

virtual

Assign operator (performs same operation of Copy-constructor)
Due to virtual attribute, Subclasses can customize the behaviour of this operator=, for an easy way to copy Genotype data the protected method copyDataFrom is provided and it behaves like this implementation of operator=.

Reimplemented in SignedRangeGenotype, and RealGenotype.

Definition at line 87 of file genotype.cpp.

References Genotype::allocated, Genotype::data, Genotype::fitnessv, Genotype::notesv, Genotype::rankv, and Genotype::sizev.

void randomize ( )

virtual

Randomize the value contained (attention, this method destroys previous data)

Reimplemented in RealGenotype.

Definition at line 268 of file genotype.cpp.

References globalRNG, Genotype::sizev, and Genotype::unset().

double rank

(

)

const

Return the rank of this Genotype.

Definition at line 209 of file genotype.cpp.

References Genotype::rankv.

Referenced by StefanoSteadyStateGA::gaStep(), Genotype::rankGreaterThanComparator(), and RouletteWheelSelection::setGenome().

static bool rankGreaterThanComparator ( const Genotype *  g1, const Genotype *  g2  )

inlinestatic

Utility function comparing two genotype pointers on their rank.

Definition at line 182 of file genotype.h.

References Genotype::rank().

Referenced by StefanoSteadyStateGA::finalize(), SimpleGA::gaStep(), ParallelGA::gaStep(), and LaralGA::gaStep().

void resize ( unsigned int  newsize )

protected

Resize the Genotype.

Parameters

newsize

is the number of bits after resizing

Warning

if the new dimension is shorter than the old one, some data will be discarded

The data pointer will be changed after this method execution

Definition at line 157 of file genotype.cpp.

References Genotype::allocated, Genotype::data, and Genotype::sizev.

Referenced by RealGenotype::configure(), SignedRangeGenotype::configure(), and Genotype::configure().

void save ( ConfigurationParameters &  params, QString  prefix  )

virtual

Save the actual status of parameters into the ConfigurationParameters object passed.

Parameters

params	the configuration parameters object on which save actual parameters
prefix	the prefix to use to access the object configuration parameters.

Implements ParameterSettableWithConfigureFunction.

Reimplemented in RealGenotype, and SignedRangeGenotype.

Definition at line 123 of file genotype.cpp.

References ConfigurationParameters::createParameter(), Genotype::fitnessv, Genotype::notesv, Genotype::rankv, Genotype::sizev, and Genotype::toCompressedString().

Referenced by Genome::save().

void set

(

unsigned int

i

)

Set to One the i-th bit.

Definition at line 222 of file genotype.cpp.

References Genotype::data.

Referenced by RandomBit::mutate(), and SignedRangeGenotype::set().

void setFitness

(

double

value

)

Set the fitness value of this Genotype.

Note

it is the same of setObjective( 0, value );

Definition at line 169 of file genotype.cpp.

References Genotype::setObjective().

void setNotes

(

QString

notes

)

Set the notes of this Genotype.

Definition at line 256 of file genotype.cpp.

References Genotype::notes(), and Genotype::notesv.

void setObjective	(	int	i,
		double	value
	)

Set the i-th objective value of the (multi-objective) fitness.

Note

multi-objective fitness are used only with the GeneticAlgo that support them

setFitness( aValue ) correspond to setObjectiveValue( 0, value );

in a single objective fitness, the setObjectiveValue could be used to print out some intermediate values used for calculating the total fitness

Definition at line 177 of file genotype.cpp.

References Genotype::fitnessv.

Referenced by Genotype::setFitness().

void setRank

(

double

rank

)

Set the rank of the genotype.

Note

the rank is a general single value used to order the genotypes inside the genome; it is different from fitness and it is GA-dependent. In simple cases, like SimpleGA, where the GA is driven by only one objective, then tipically the rank correspond to the fitness. But in multi-objective GAs (MOGA), like NSGA2, the rank depends on how the MOGA orders the genotypes

better genotype will have higher rank value

Definition at line 205 of file genotype.cpp.

References Genotype::rankv.

Referenced by StefanoSteadyStateGA::gaStep().

unsigned int size

(

)

const

Return the size of Genotype.

Definition at line 153 of file genotype.cpp.

References Genotype::sizev.

Referenced by RealGenotype::at(), SignedRangeGenotype::at(), OnePoint::crossover(), Genotype::Genotype(), FlipBit::mutate(), RandomBit::mutate(), RealGenotype::set(), and SignedRangeGenotype::set().

QString toCompressedString

(

)

const

Compress the data; It return a printable String.

Definition at line 298 of file genotype.cpp.

References Genotype::bit(), and Genotype::sizev.

Referenced by RealGenotype::save(), SignedRangeGenotype::save(), and Genotype::save().

void toggle

(

unsigned int

i

)

toggle the i-th bit

Definition at line 242 of file genotype.cpp.

References Genotype::data.

Referenced by OnePoint::crossover(), and FlipBit::mutate().

QString toString

(

)

const

Return a QString representing this Genotype.

Definition at line 278 of file genotype.cpp.

References Genotype::bit(), and Genotype::sizev.

void unset

(

unsigned int

i

)

set to zero the i-th bit

Definition at line 232 of file genotype.cpp.

References Genotype::data.

Referenced by Genotype::fromCompressedString(), Genotype::fromString(), Genotype::Genotype(), Genotype::insertUInt(), RandomBit::mutate(), Genotype::randomize(), and SignedRangeGenotype::set().

Member Data Documentation

unsigned int allocated

protected

Allocated memory.

Definition at line 203 of file genotype.h.

Referenced by Genotype::copyDataFrom(), Genotype::Genotype(), Genotype::operator=(), and Genotype::resize().

unsigned char* data

protected

Data represented as a char vector allocated in memory.

Definition at line 199 of file genotype.h.

Referenced by Genotype::bit(), RealGenotype::configure(), Genotype::copyDataFrom(), Genotype::Genotype(), RealGenotype::operator=(), Genotype::operator=(), RealGenotype::RealGenotype(), Genotype::resize(), Genotype::set(), Genotype::toggle(), Genotype::unset(), and Genotype::~Genotype().

QVector<double> fitnessv

protected

Objective values of the Fitness.

Definition at line 205 of file genotype.h.

Referenced by RealGenotype::configure(), SignedRangeGenotype::configure(), Genotype::configure(), Genotype::copyDataFrom(), Genotype::dominatedBy(), Genotype::Genotype(), Genotype::numOfObjectives(), Genotype::objective(), Genotype::operator=(), SignedRangeGenotype::save(), RealGenotype::save(), Genotype::save(), and Genotype::setObjective().

QString notesv

protected

Notes about this Genotype.

Usage is left open.

Definition at line 209 of file genotype.h.

Referenced by RealGenotype::configure(), SignedRangeGenotype::configure(), Genotype::configure(), Genotype::copyDataFrom(), Genotype::Genotype(), Genotype::notes(), Genotype::operator=(), SignedRangeGenotype::save(), RealGenotype::save(), Genotype::save(), and Genotype::setNotes().

double rankv

protected

Rank.

Definition at line 207 of file genotype.h.

Referenced by RealGenotype::configure(), SignedRangeGenotype::configure(), Genotype::configure(), Genotype::copyDataFrom(), Genotype::Genotype(), Genotype::operator=(), Genotype::rank(), SignedRangeGenotype::save(), RealGenotype::save(), Genotype::save(), and Genotype::setRank().

unsigned int sizev

protected

Size.

Definition at line 201 of file genotype.h.

Referenced by Genotype::copyDataFrom(), Genotype::extractUInt(), Genotype::fromCompressedString(), Genotype::fromString(), Genotype::Genotype(), Genotype::hammingDistance(), Genotype::insertUInt(), Genotype::operator=(), Genotype::randomize(), Genotype::resize(), Genotype::save(), Genotype::size(), Genotype::toCompressedString(), and Genotype::toString().

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

• ga/include/core/genotype.h
• ga/src/core/genotype.cpp