bio.singa.simulation.events

Class EpochUpdateWriter

java.lang.Object

bio.singa.simulation.events.EpochUpdateWriter

All Implemented Interfaces:

UpdateEventListener<UpdatableUpdatedEvent>

public class EpochUpdateWriter
extends Object
implements UpdateEventListener<UpdatableUpdatedEvent>

This class can be used to write the concentration of chemical entities of a node and the changes applied to the node to a file. The updates are written each time a event is received. The events can be scheduled by using the SimulationManager.setUpdateEmissionCondition(Predicate). A node is observed by calling addNodeToObserve(AutomatonNode).

Author:

cl

Constructor Summary

Constructors

Constructor and Description
EpochUpdateWriter(Path workspacePath, Path folder, Set<ChemicalEntity> entitiesToObserve, Set<ConcentrationBasedModule> modulesToObserve) Creates a new EpochUpdateWriter.
EpochUpdateWriter(Path workspacePath, Path folder, Set<ChemicalEntity> entitiesToObserve, Set<ConcentrationBasedModule> modulesToObserve, boolean printHeader) Creates a new EpochUpdateWriter.

Method Summary

Modifier and Type	Method and Description
void	addNodeToObserve(AutomatonNode node) Initializes a node that will be observed during simulation.
void	closeWriters() Close all associated writers.
QuantityFormatter<MolarConcentration>	getConcentrationFormatter()
QuantityFormatter<javax.measure.quantity.Time>	getTimeFormatter()
void	onEventReceived(UpdatableUpdatedEvent event)
void	setConcentrationFormatter(QuantityFormatter<MolarConcentration> concentrationFormatter)
void	setTimeFormatter(QuantityFormatter<javax.measure.quantity.Time> timeFormatter)

Methods inherited from class java.lang.Object

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

Constructor Detail

EpochUpdateWriter

public EpochUpdateWriter(Path workspacePath,
                         Path folder,
                         Set<ChemicalEntity> entitiesToObserve,
                         Set<ConcentrationBasedModule> modulesToObserve)

Creates a new EpochUpdateWriter. A extended header is printed in each file.

Parameters:

workspacePath - The location of the simulation workspace.

folder - The folder, where the files written by this class should be located.

entitiesToObserve - The entities to observe.

modulesToObserve - The modules to record deltas from.

EpochUpdateWriter

public EpochUpdateWriter(Path workspacePath,
                         Path folder,
                         Set<ChemicalEntity> entitiesToObserve,
                         Set<ConcentrationBasedModule> modulesToObserve,
                         boolean printHeader)

Creates a new EpochUpdateWriter.

Parameters:

workspacePath - The location of the simulation workspace.

folder - The folder, where the files written by this class should be located.

entitiesToObserve - The entities to observe.

modulesToObserve - The modules to record deltas from.

printHeader - True, if an extended header should be printed.

Method Detail

getTimeFormatter

public QuantityFormatter<javax.measure.quantity.Time> getTimeFormatter()

setTimeFormatter

public void setTimeFormatter(QuantityFormatter<javax.measure.quantity.Time> timeFormatter)

getConcentrationFormatter

public QuantityFormatter<MolarConcentration> getConcentrationFormatter()

setConcentrationFormatter

public void setConcentrationFormatter(QuantityFormatter<MolarConcentration> concentrationFormatter)

addNodeToObserve

public void addNodeToObserve(AutomatonNode node)
                      throws IOException

Initializes a node that will be observed during simulation. Also prepares the files that will be written during simulation.

Parameters:

node - The node to be observed.

Throws:

IOException - If the file can not be created.

closeWriters

public void closeWriters()

Close all associated writers. Usually called after simulation finishes.

onEventReceived

public void onEventReceived(UpdatableUpdatedEvent event)

Specified by:

onEventReceived in interface UpdateEventListener<UpdatableUpdatedEvent>