org.gcn.plinguacore.util.psystem

Class Psystem

java.lang.Object

org.gcn.plinguacore.util.psystem.Psystem

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

CellLikePsystem, SpikingPsystem, TissueLikePsystem

public abstract class Psystem
extends java.lang.Object
implements java.io.Serializable

An abstract class for a P System

Author:

Research Group on Natural Computing (http://www.gcn.us.es)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Collection<? extends Membrane>	emptyMembranes

Constructor Summary

Constructors

Constructor and Description
Psystem() The constructor

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addRule(IRule r) adds a rule to the existing rule set
java.util.Iterator<AlphabetObject>	alphabetIterator() Returns an iterator over the alphabet
ISimulator	createSimulator(boolean stepBackSupported, boolean alternativeStepsSupported) Creates a simulator to simulate this P-system.
ISimulator	createSimulator(boolean stepBackSupported, boolean alternativeStepsSupported, java.lang.String id) Creates a simulator to simulate this P-system.
IPsystemFactory	getAbstractPsystemFactory() Gets the current AbstractPsystemFactory instance
java.util.SortedSet<AlphabetObject>	getAlphabet() Returns the P-system alphabet
Configuration	getFirstConfiguration()
MultiSet<java.lang.String>	getFirstMultiSet()
java.util.Map<java.lang.String,MultiSet<java.lang.String>>	getInitialMultiSets() Returns the initial P-system multisets
MembraneStructure	getMembraneStructure()
RulesSet	getRules()
MultiSet<java.lang.String>	getSecondMultiSet()
java.util.Iterator<java.lang.String>	getSimulatorsIDs() Gets an iterator on all possible simulators IDs for the Psystem
void	setAbstractPsystemFactory(IPsystemFactory apf) Sets an specific instance of PsystemFactotyInterface as the current factory to be used
void	setFirstMultiSet(MultiSet<java.lang.String> firstMultiSet)
void	setMembraneStructure(MembraneStructure membraneStructure)
void	setRules(RulesSet rules)
void	setSecondMultiSet(MultiSet<java.lang.String> secondMultiSet)
boolean	supportsAlternativeStep(java.lang.String id) Returns a boolean representing if the simulator related to id could be created capable of performing alternative steps
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

emptyMembranes

public static final transient java.util.Collection<? extends Membrane> emptyMembranes

Constructor Detail

Psystem

public Psystem()

The constructor

Method Detail

setAbstractPsystemFactory

public void setAbstractPsystemFactory(IPsystemFactory apf)
                               throws PlinguaCoreException

Sets an specific instance of PsystemFactotyInterface as the current factory to be used

Parameters:

apf - the PsystemFactoryInterface instance to be held

Throws:

PlinguaCoreException - if any error ocurred during the instantiation of the CreateSimulator instance

getFirstMultiSet

public MultiSet<java.lang.String> getFirstMultiSet()

setFirstMultiSet

public void setFirstMultiSet(MultiSet<java.lang.String> firstMultiSet)

getSecondMultiSet

public MultiSet<java.lang.String> getSecondMultiSet()

setSecondMultiSet

public void setSecondMultiSet(MultiSet<java.lang.String> secondMultiSet)

setRules

public void setRules(RulesSet rules)

getAbstractPsystemFactory

public IPsystemFactory getAbstractPsystemFactory()

Gets the current AbstractPsystemFactory instance

Returns:

the AbstractPsystemFactory instance currently held

getInitialMultiSets

public java.util.Map<java.lang.String,MultiSet<java.lang.String>> getInitialMultiSets()

Returns the initial P-system multisets

Returns:

the initial P-system multisets

getAlphabet

public java.util.SortedSet<AlphabetObject> getAlphabet()

Returns the P-system alphabet

Returns:

the current alphabet

alphabetIterator

public java.util.Iterator<AlphabetObject> alphabetIterator()

Returns an iterator over the alphabet

Returns:

an iterator on the current P-system alphabet

getRules

public RulesSet getRules()

Returns:

The rules set of the p system

addRule

public boolean addRule(IRule r)

adds a rule to the existing rule set

Parameters:

r - the rule to be added

Returns:

if the rule has been successfully added

getFirstConfiguration

public Configuration getFirstConfiguration()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createSimulator

public ISimulator createSimulator(boolean stepBackSupported,
                         boolean alternativeStepsSupported,
                         java.lang.String id)
                           throws PlinguaCoreException

Creates a simulator to simulate this P-system. The parameters specify if this simulator will be able to take steps back, take alternative steps (among different, possible steps) and which specific class will implement the simulator, specified by ID

Parameters:

stepBackSupported - sets if the simulator created supports steps back

alternativeStepsSupported - sets if the simulator created supports alternate steps

id - the Simulator id which references the specific Simulator class to be instantiated

Returns:

a simulator which complies with the parameter conditions

Throws:

PlinguaCoreException - if there are rules which doesn't match the model specification previously defined by setting the AbstractPsystemFactory instance

createSimulator

public ISimulator createSimulator(boolean stepBackSupported,
                         boolean alternativeStepsSupported)
                           throws PlinguaCoreException

Creates a simulator to simulate this P-system. The parameters specify if this simulator will be able to take steps back and/or take alternative steps (among different, possible steps). As no ID is passed as parameter the class implemented by the simulator will be the first available one, taken by default

Parameters:

stepBackSupported - sets if the simulator created supports steps back

alternativeStepsSupported - sets if the simulator created supports alternate steps

Returns:

a simulator which complies with the parameter conditions

Throws:

PlinguaCoreException - if there are rules which doesn't match the model specification previously defined by setting the AbstractPsystemFactory instance

getSimulatorsIDs

public java.util.Iterator<java.lang.String> getSimulatorsIDs()
                                                      throws PlinguaCoreException

Gets an iterator on all possible simulators IDs for the Psystem

Returns:

an iterator on all possible simulators IDs for the Psystem

Throws:

PlinguaCoreException - if the simulators IDs provider hasn't set yet

supportsAlternativeStep

public boolean supportsAlternativeStep(java.lang.String id)
                                throws PlinguaCoreException

Returns a boolean representing if the simulator related to id could be created capable of performing alternative steps

Parameters:

id - the simulator identifier

Returns:

if the simulator related to id could be created capable of performing alternative steps

Throws:

PlinguaCoreException - if the simulators IDs provider hasn't set yet

getMembraneStructure

public MembraneStructure getMembraneStructure()

setMembraneStructure

public void setMembraneStructure(MembraneStructure membraneStructure)