org.simulator.sbml

Class EquationSystem

java.lang.Object

org.simulator.sbml.EquationSystem

All Implemented Interfaces:

PropertyChangeListener, Serializable, EventListener, org.apache.commons.math.ode.FirstOrderDifferentialEquations, DelayedDESystem, DelayValueHolder, DESystem, EventDESystem, FastProcessDESystem, RichDESystem, SBMLValueHolder

Direct Known Subclasses:

SBMLinterpreter

public abstract class EquationSystem
extends Object
implements SBMLValueHolder, DelayedDESystem, EventDESystem, FastProcessDESystem, RichDESystem, PropertyChangeListener

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
double[]	changeRate An array that stores derivatives of each species in the model system at current time.
static String	TEMP_VALUE Key to memorize user objects in ASTNode

Constructor Summary

Constructors

Constructor and Description
EquationSystem(org.sbml.jsbml.Model model)

Method Summary

Modifier and Type	Method and Description
boolean	addConstraintListener(ConstraintListener listener) Adds the given ConstraintListener to this interpreter's list of listeners.
double	computeDelayedValue(double time, String id, DESystem DES, double[] initialValues, int yIndex) Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.
boolean	containsEventsOrRules() This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.
boolean	containsFastProcesses()
org.sbml.jsbml.ASTNode	copyAST(org.sbml.jsbml.ASTNode node, boolean mergingPossible, FunctionValue function, List<org.sbml.jsbml.ASTNode> inFunctionNodes) Creates a copy of an ASTNode or returns an ASTNode that is equal to the presented node.
int	getAdditionalValueCount() Gives the number of intermediate results that are computed by this class.
String[]	getAdditionalValueIds() This provides the column/row identifiers of all intermediate results: one identifier per result.
double[]	getChangeRate()
Map<String,Boolean>	getConstantHash()
int	getConstraintListenerCount()
double	getCurrentCompartmentSize(String id) Returns the size of the compartment with the given id.
double	getCurrentCompartmentValueOf(String speciesId) Returns the size of the compartment of the species with the given id.
double	getCurrentParameterValue(String id) Returns the value of the parameter with the given id.
double	getCurrentSpeciesValue(String id) Returns the value of the species with the given id.
double	getCurrentStoichiometry(String id) Returns the value of the stoichiometry of the species reference with the given id.
double	getCurrentTime() Returns the current simulation time.
double	getCurrentValueOf(int position) Returns the current value of the Y vector at the given position.
double	getCurrentValueOf(String id) Returns the current value of the SBase with the given id.
int	getDimension()
int	getEventCount() Counts the number of events in this system.
String[]	getIdentifiers() Delivers an array of Strings that describe the content of each dimension of the resulting array of this DESystem.
double[]	getInitialValues() Returns the initial values of the model to be simulated.
org.sbml.jsbml.Model	getModel() Returns the model that is used by this object.
boolean	getNoDerivatives()
int	getParameterCount() This method tells you the complete number of parameters within the model.
int	getPositionOfParameters()
int	getPositiveValueCount()
List<RateRuleValue>	getRateRulesRoots()
int	getRuleCount() Counts the number of rules to be evaluated in each time point.
Map<String,Integer>	getSymbolHash()
double[]	getY() Get state array.
void	init(boolean renewTree, double defaultSpeciesValue, double defaultParameterValue, double defaultCompartmentValue, Map<String,Boolean> amountHash) This method initializes the differential equation system for simulation.
void	propertyChange(PropertyChangeEvent propertyChangeEvent)
void	registerDelayValueHolder(DelayValueHolder dvh)
boolean	removeConstraintListener(ConstraintListener listener) Removes the given ConstraintListener from this interpreter.
ConstraintListener	removeConstraintListener(int index) Removes the ConstraintListener with the given index from this interpreter.
void	setCurrentTime(double currentTime)
void	setDelaysIncluded(boolean delaysIncluded)
void	setFastProcessComputation(boolean isProcessing)
void	setPreviousTimePoint(double previousTimePoint)

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.simulator.math.odes.EventDESystem

getNextEventAssignments, processAssignmentRules

Methods inherited from interface org.simulator.math.odes.RichDESystem

getAdditionalValues

Methods inherited from interface org.apache.commons.math.ode.FirstOrderDifferentialEquations

computeDerivatives

Field Detail

TEMP_VALUE

public static final String TEMP_VALUE

Key to memorize user objects in ASTNode

See Also:

Constant Field Values

changeRate

public double[] changeRate

An array that stores derivatives of each species in the model system at current time.

Constructor Detail

EquationSystem

public EquationSystem(org.sbml.jsbml.Model model)

Method Detail

init

public void init(boolean renewTree,
                 double defaultSpeciesValue,
                 double defaultParameterValue,
                 double defaultCompartmentValue,
                 Map<String,Boolean> amountHash)
          throws org.sbml.jsbml.validator.ModelOverdeterminedException

This method initializes the differential equation system for simulation. The user can tell whether the tree of ASTNodes has to be refreshed, give some default values and state whether a Species is seen as an amount or a concentration.

Parameters:

renewTree -

defaultSpeciesValue -

defaultParameterValue -

defaultCompartmentValue -

amountHash -

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

copyAST

public org.sbml.jsbml.ASTNode copyAST(org.sbml.jsbml.ASTNode node,
                                      boolean mergingPossible,
                                      FunctionValue function,
                                      List<org.sbml.jsbml.ASTNode> inFunctionNodes)

Creates a copy of an ASTNode or returns an ASTNode that is equal to the presented node.

Parameters:

node - the node to copy

mergingPossible - flag that is true if it is allowed to return a node that is equal to the given node

function - the function that is currently processed (if any) or null

inFunctionNodes - the nodes that already belong to the function

Returns:

the found node

getCurrentCompartmentSize

public double getCurrentCompartmentSize(String id)

Returns the size of the compartment with the given id.

Specified by:

getCurrentCompartmentSize in interface SBMLValueHolder

Returns:

compartmentSize

getCurrentCompartmentValueOf

public double getCurrentCompartmentValueOf(String speciesId)

Returns the size of the compartment of the species with the given id.

Specified by:

getCurrentCompartmentValueOf in interface SBMLValueHolder

Returns:

compartmentValue

getCurrentParameterValue

public double getCurrentParameterValue(String id)

Returns the value of the parameter with the given id.

Specified by:

getCurrentParameterValue in interface SBMLValueHolder

Returns:

parameterValue

getCurrentSpeciesValue

public double getCurrentSpeciesValue(String id)

Returns the value of the species with the given id.

Specified by:

getCurrentSpeciesValue in interface SBMLValueHolder

Returns:

speciesValue

getCurrentStoichiometry

public double getCurrentStoichiometry(String id)

Returns the value of the stoichiometry of the species reference with the given id.

Specified by:

getCurrentStoichiometry in interface SBMLValueHolder

Returns:

stoichiometry

getCurrentTime

public double getCurrentTime()

Returns the current simulation time.

Specified by:

getCurrentTime in interface SBMLValueHolder

Returns:

time

getCurrentValueOf

public double getCurrentValueOf(String id)

Returns the current value of the SBase with the given id.

Specified by:

getCurrentValueOf in interface SBMLValueHolder

Returns:

value

getCurrentValueOf

public double getCurrentValueOf(int position)

Returns the current value of the Y vector at the given position.

Specified by:

getCurrentValueOf in interface SBMLValueHolder

Returns:

value

computeDelayedValue

public double computeDelayedValue(double time,
                                  String id,
                                  DESystem DES,
                                  double[] initialValues,
                                  int yIndex)

Description copied from interface: DelayValueHolder

Returns the value for the element with the given id at a time point in the past, where the time gives the amount of time in the past.

Specified by:

computeDelayedValue in interface DelayValueHolder

Parameters:

time - the time point (in the past) at which the value is to be computed for the element with the given id.

id - the id of the delayed value

DES - the DESystem

initialValues - the initialValues of the DES

yIndex - the index corresponding to the id in the vector of the DES

Returns:

the computed value for the element with the given identifier at the time point in the past.

registerDelayValueHolder

public void registerDelayValueHolder(DelayValueHolder dvh)

Specified by:

registerDelayValueHolder in interface DelayedDESystem

Parameters:

dvh - the delay value holder to be registered

getIdentifiers

public String[] getIdentifiers()

Delivers an array of Strings that describe the content of each dimension of the resulting array of this DESystem.

Specified by:

getIdentifiers in interface DESystem

Returns:

An array of Strings which has the same length than the number given by FirstOrderDifferentialEquations.getDimension(). Each String describes the content of the given dimension.

containsEventsOrRules

public boolean containsEventsOrRules()

This method is used to check if this differential equation system contains any events or rules that would require a special treatment by the numerical solver.

Specified by:

containsEventsOrRules in interface DESystem

Returns:

flag that is true if any events or rules are contained in the differential equation system.

getPositiveValueCount

public int getPositiveValueCount()

Specified by:

getPositiveValueCount in interface DESystem

Returns:

the number of values in Y that have to be positive.

setDelaysIncluded

public void setDelaysIncluded(boolean delaysIncluded)

Specified by:

setDelaysIncluded in interface DESystem

Parameters:

delaysIncluded - Determines whether delay expression should be included in the calculation.

getDimension

public int getDimension()

Specified by:

getDimension in interface org.apache.commons.math.ode.FirstOrderDifferentialEquations

getEventCount

public int getEventCount()

Counts the number of events in this system.

Specified by:

getEventCount in interface EventDESystem

Returns:

The number of events that are to be checked and potentially evaluated in each time point.

getModel

public org.sbml.jsbml.Model getModel()

Returns the model that is used by this object.

Returns:

Returns the model that is used by this object.

getRuleCount

public int getRuleCount()

Counts the number of rules to be evaluated in each time point.

Specified by:

getRuleCount in interface EventDESystem

Returns:

The number of rules in the system.

getNoDerivatives

public boolean getNoDerivatives()

Specified by:

getNoDerivatives in interface EventDESystem

Returns:

flag that is true, if the change vector is always zero in the system.

containsFastProcesses

public boolean containsFastProcesses()

Specified by:

containsFastProcesses in interface FastProcessDESystem

Returns:

flag that is true if fast processes are contained.

getAdditionalValueIds

public String[] getAdditionalValueIds()

This provides the column/row identifiers of all intermediate results: one identifier per result. This means, the length of the returned String array must equal the length of the array returned by RichDESystem.getAdditionalValues(double, double[]).

Specified by:

getAdditionalValueIds in interface RichDESystem

Returns:

The identifiers of all intermediate results computed during evaluation.

getAdditionalValueCount

public int getAdditionalValueCount()

Gives the number of intermediate results that are computed by this class. The number returned here must equal the length of the arrays returned by the methods RichDESystem.getAdditionalValueIds() and RichDESystem.getAdditionalValues(double, double[]).

Specified by:

getAdditionalValueCount in interface RichDESystem

Returns:

The number of intermediate values that are computed in each time step.

getInitialValues

public double[] getInitialValues()

Returns the initial values of the model to be simulated.

Returns:

Returns the initial values of the model to be simulated.

propertyChange

public void propertyChange(PropertyChangeEvent propertyChangeEvent)

Specified by:

propertyChange in interface PropertyChangeListener

addConstraintListener

public boolean addConstraintListener(ConstraintListener listener)

Adds the given ConstraintListener to this interpreter's list of listeners.

Parameters:

listener - the element to be added.

Returns:

true if this operation was successful, false otherwise.

Throws:

NullPointerException

See Also:

List.add(Object)

removeConstraintListener

public boolean removeConstraintListener(ConstraintListener listener)

Removes the given ConstraintListener from this interpreter.

Parameters:

listener - the element to be removed.

Returns:

true if this operation was successful, false otherwise.

Throws:

NullPointerException

See Also:

List.remove(Object)

removeConstraintListener

public ConstraintListener removeConstraintListener(int index)

Removes the ConstraintListener with the given index from this interpreter.

Parameters:

index - of the ConstraintListener to be removed.

Returns:

true if this operation was successful, false otherwise.

Throws:

IndexOutOfBoundsException

See Also:

List.remove(int)

getConstraintListenerCount

public int getConstraintListenerCount()

Returns:

the number of ConstraintListeners currently assigned to this interpreter.

setPreviousTimePoint

public void setPreviousTimePoint(double previousTimePoint)

setCurrentTime

public void setCurrentTime(double currentTime)

getRateRulesRoots

public List<RateRuleValue> getRateRulesRoots()

getSymbolHash

public Map<String,Integer> getSymbolHash()

getConstantHash

public Map<String,Boolean> getConstantHash()

getY

public double[] getY()

Get state array.

Returns:

the state array

setFastProcessComputation

public void setFastProcessComputation(boolean isProcessing)

Specified by:

setFastProcessComputation in interface FastProcessDESystem

Parameters:

isProcessing - Should there be a splitting of fast and slow reactions in the simulation?

getChangeRate

public double[] getChangeRate()

Returns:

the array of derivatives of each species of the model system at the current time.

getPositionOfParameters

public int getPositionOfParameters()

getParameterCount

public int getParameterCount()

This method tells you the complete number of parameters within the model. It counts the global model parameters and all local parameters (parameters within a kinetic law).

Returns:

The total number of model parameters. Note that this number is limited to an int value, whereas the SBML model may contain int values.