org.simulator.sbml

Class SBMLinterpreter

java.lang.Object

org.simulator.sbml.EquationSystem

org.simulator.sbml.SBMLinterpreter

All Implemented Interfaces:

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

public class SBMLinterpreter
extends EquationSystem

This differential equation system (DESystem) takes a model in SBML format and maps it to a data structure that is understood by the AbstractDESSolver. Therefore, this class implements all necessary functions expected by SBML.

Since:

0.9

Version:

$Rev$

Author:

Alexander Dörr, Andreas Dräger, Roland Keller, Dieudonné Motsou Wouamba

See Also:

Serialized Form

Field Summary

Fields inherited from class org.simulator.sbml.EquationSystem

changeRate, TEMP_VALUE

Constructor Summary

Constructors

Constructor and Description
SBMLinterpreter(org.sbml.jsbml.Model model) This constructs a new DESystem for the given SBML Model.
SBMLinterpreter(org.sbml.jsbml.Model model, double defaultSpeciesValue, double defaultParameterValue, double defaultCompartmentValue)
SBMLinterpreter(org.sbml.jsbml.Model model, double defaultSpeciesValue, double defaultParameterValue, double defaultCompartmentValue, Map<String,Boolean> amountHash) Creates a new SBMLinterpreter

Method Summary

Modifier and Type	Method and Description
double	compileReaction(int reactionIndex)
void	computeDerivatives(double time, double[] Y, double[] changeRate)
void	computeDerivativeWithChangingCompartment(org.sbml.jsbml.Species sp, double[] changeRate)
double[]	getAdditionalValues(double t, double[] Y) Computes and/or delivers the intermediate results at the given time and for the given results from the previous time step.
EventInProgress	getNextEventAssignments(double t, double previousTime, double[] Y) Returns a list with event assignments for the events triggered either by the time t or by the concentrations of the species stored in Y.
void	init() This method initializes the differential equation system for simulation.
void	init(boolean refreshTree) This method initializes the differential equation system for simulation.
void	init(boolean renewTree, double defaultSpeciesValue, double defaultParameterValue, double defaultCompartmentValue) This method initializes the differential equation system for simulation.
void	init(boolean renewTree, double defaultSpeciesValue, double defaultParameterValue, double defaultCompartmentValue, Map<String,Boolean> amountHash) This method initializes the differential equation system for simulation.
boolean	processAssignmentRules(double t, double[] Y) Calculates the changes or assignments that are defined by all rules in the system at the given simulation time point.
void	processInitialAssignments(double time, double[] Y) Processes the initial assignments
boolean	processRules(double time, double[] changeRate, double[] Y, boolean initialCalculations) Processes the rules
void	setParameters(double[] params) This method allows us to set the parameters of the model to the specified values in the given array.
void	updateSpeciesConcentration(AmountManager amountManager) Updates the species concentration as per the updated values in the AmountManager.

Methods inherited from class org.simulator.sbml.EquationSystem

addConstraintListener, computeDelayedValue, containsEventsOrRules, containsFastProcesses, copyAST, getAdditionalValueCount, getAdditionalValueIds, getChangeRate, getConstantHash, getConstraintListenerCount, getCurrentCompartmentSize, getCurrentCompartmentValueOf, getCurrentParameterValue, getCurrentSpeciesValue, getCurrentStoichiometry, getCurrentTime, getCurrentValueOf, getCurrentValueOf, getDimension, getEventCount, getIdentifiers, getInitialValues, getModel, getNoDerivatives, getParameterCount, getPositionOfParameters, getPositiveValueCount, getRateRulesRoots, getRuleCount, getSymbolHash, getY, propertyChange, registerDelayValueHolder, removeConstraintListener, removeConstraintListener, setCurrentTime, setDelaysIncluded, setFastProcessComputation, setPreviousTimePoint

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLinterpreter

public SBMLinterpreter(org.sbml.jsbml.Model model)
                throws org.sbml.jsbml.validator.ModelOverdeterminedException,
                       org.sbml.jsbml.SBMLException

This constructs a new DESystem for the given SBML Model. Note that only a maximum of Integer.MAX_VALUE Species can be simulated. If the model contains more Species, this class is not applicable.

Note that currently, units are not considered.

Parameters:

model -

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

SBMLinterpreter

public SBMLinterpreter(org.sbml.jsbml.Model model,
                       double defaultSpeciesValue,
                       double defaultParameterValue,
                       double defaultCompartmentValue)
                throws org.sbml.jsbml.SBMLException,
                       org.sbml.jsbml.validator.ModelOverdeterminedException

Parameters:

model -

defaultSpeciesValue -

defaultParameterValue -

defaultCompartmentValue -

Throws:

org.sbml.jsbml.SBMLException

org.sbml.jsbml.validator.ModelOverdeterminedException

SBMLinterpreter

public SBMLinterpreter(org.sbml.jsbml.Model model,
                       double defaultSpeciesValue,
                       double defaultParameterValue,
                       double defaultCompartmentValue,
                       Map<String,Boolean> amountHash)
                throws org.sbml.jsbml.SBMLException,
                       org.sbml.jsbml.validator.ModelOverdeterminedException

Creates a new SBMLinterpreter

Parameters:

model - the model to interpret

defaultSpeciesValue - the default value for species, if no value is given

defaultParameterValue - the default value for parameters, if no value is given

defaultCompartmentValue - the default value for compartments, if no value is given

amountHash - a hash that states for the species in the model, whether their amount or their concentration should be computed

Throws:

org.sbml.jsbml.SBMLException

org.sbml.jsbml.validator.ModelOverdeterminedException

Method Detail

getAdditionalValues

public double[] getAdditionalValues(double t,
                                    double[] Y)
                             throws org.apache.commons.math.ode.DerivativeException

Computes and/or delivers the intermediate results at the given time and for the given results from the previous time step.

Parameters:

t - The time point for which intermediate results are to be computed.

Y - The result vector from the previous time step.

Returns:

An array of intermediate results. Simulators should call this method after computation of the next time point to avoid unnecessary re-computation. Implementing classes should store interesting intermediate results to be accessible in case time and Y are the same values than those just used for the actual computation.

Throws:

org.apache.commons.math.ode.DerivativeException - If the system cannot be solved for the given configuration or no intermediate results can be computed in this step.

getNextEventAssignments

public EventInProgress getNextEventAssignments(double t,
                                               double previousTime,
                                               double[] Y)
                                        throws org.apache.commons.math.ode.DerivativeException

Returns a list with event assignments for the events triggered either by the time t or by the concentrations of the species stored in Y.

Parameters:

t - The current simulation time.

Y - The current change of the system.

Returns:

Returns a list with event assignments for the events triggered

Throws:

org.apache.commons.math.ode.DerivativeException

computeDerivatives

public void computeDerivatives(double time,
                               double[] Y,
                               double[] changeRate)
                        throws org.apache.commons.math.ode.DerivativeException

Throws:

org.apache.commons.math.ode.DerivativeException

init

public void init()
          throws org.sbml.jsbml.validator.ModelOverdeterminedException,
                 org.sbml.jsbml.SBMLException

This method initializes the differential equation system for simulation. In more detail: the initial amounts or concentration will be assigned to every Species or InitialAssignments if any are executed.

To save computation time the results of this method should be stored in an array. Hence this method must only be called once. However, if the SBML model to be simulated contains initial assignments, this can lead to wrong simulation results because initial assignments may depend on current parameter values.

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

See Also:

init(boolean, double, double, double)

init

public void init(boolean refreshTree)
          throws org.sbml.jsbml.validator.ModelOverdeterminedException,
                 org.sbml.jsbml.SBMLException

This method initializes the differential equation system for simulation. The user can tell whether the tree of ASTNodes has to be refreshed.

Parameters:

refreshTree -

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

init

public void init(boolean renewTree,
                 double defaultSpeciesValue,
                 double defaultParameterValue,
                 double defaultCompartmentValue)
          throws org.sbml.jsbml.validator.ModelOverdeterminedException,
                 org.sbml.jsbml.SBMLException

This method initializes the differential equation system for simulation. The user can tell whether the tree of ASTNodes has to be refreshed and give some default values.

Parameters:

renewTree -

defaultSpeciesValue -

defaultParameterValue -

defaultCompartmentValue -

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

init

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

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.

Overrides:

init in class EquationSystem

Parameters:

renewTree -

defaultSpeciesValue -

defaultParameterValue -

defaultCompartmentValue -

amountHash -

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

org.sbml.jsbml.SBMLException

processAssignmentRules

public boolean processAssignmentRules(double t,
                                      double[] Y)
                               throws org.apache.commons.math.ode.DerivativeException

Calculates the changes or assignments that are defined by all rules in the system at the given simulation time point.

Parameters:

t - The current simulation time.

Y - The current change of the system.

Returns:

flag that is true if there has been a change in the Y vector caused by the rules.

Throws:

org.apache.commons.math.ode.DerivativeException

processInitialAssignments

public void processInitialAssignments(double time,
                                      double[] Y)
                               throws org.sbml.jsbml.SBMLException

Processes the initial assignments

Parameters:

time - the ASTNode time

Y - the Y vector

Throws:

org.sbml.jsbml.SBMLException

processRules

public boolean processRules(double time,
                            double[] changeRate,
                            double[] Y,
                            boolean initialCalculations)
                     throws org.sbml.jsbml.SBMLException

Processes the rules

Parameters:

time - the current time

changeRate - the changeRate vector

Y - the Y vector

initialCalculations -

Returns:

flag that is true if there has been some change caused by any rule

Throws:

org.sbml.jsbml.SBMLException

computeDerivativeWithChangingCompartment

public void computeDerivativeWithChangingCompartment(org.sbml.jsbml.Species sp,
                                                     double[] changeRate)

setParameters

public void setParameters(double[] params)

This method allows us to set the parameters of the model to the specified values in the given array.

Parameters:

params - An array of parameter values to be set for this model. If the number of given parameters does not match the number of model parameters, an exception will be thrown.

updateSpeciesConcentration

public void updateSpeciesConcentration(AmountManager amountManager)

Updates the species concentration as per the updated values in the AmountManager.

Parameters:

amountManager -

compileReaction

public double compileReaction(int reactionIndex)

Parameters:

reactionIndex - index of the reaction

Returns:

the current reaction velocity of a specific reaction