Class containing methods to create and query the simulation world (bulk and computational domains) More...

Public Member Functions
void	init (Simulator aSim, XMLParser worldRoot)
	Creates and registers the bulks and computationDomains defined in the world mark-up of the protocol file. More...

Domain	getDomain (String cDName)
	Returns a domain from the domain list that matches a specified name. More...

Bulk	getBulk (String bulkName)
	Return a bulk object of the given string name. More...

boolean	containsBulk (String bulkName)
	Determines if a bulk object of a given string name exists. More...

double	getBulkTimeConstraint ()
	Calculates and returns the simulation time required to change 100% of a bulk concentration. More...

double[]	getAllBulkValue (int soluteIndex)
	Returns the Sbulk value for a given solute index from that specified in the protocol file, for all bulks specified. More...

double	getMaxBulkValue (int soluteIndex)
	Return the max value of a particular solute in the bulk. More...

Public Attributes
ArrayList< Domain >	domainList = new ArrayList<Domain>()

LinkedList< Bulk >	bulkList = new LinkedList<Bulk>()

double[]	bulkTime = new double[2]

Detailed Description

Class containing methods to create and query the simulation world (bulk and computational domains)

The simulation world is a description of all bulks and computation domains defined in the simulation. This class is used to create the world specified in the protocol files. The world mark-up in the protocol file collects the description of all bulks and computational domains defined in the simulation. The bulk mark-up defines a bulk solute compartment that is a source or sink for solutes involved in biofilm growth. The computationDomain mark-up defines the spatial region the biofilm will grow in. Only one world may be defined, but this world may contain several bulk compartments and computationDomain domains, each with a different name. Though when simulating a chemostat scenario, the name of the bulk MUST be chemostat, regardless of the corresponding computationalDomain name.

This class is a component class of iDynoMiCS, released under the CECIL license. Please see www.idynomics.bham.ac.uk for more information

Since: June 2006

Version: 1.2

Author: Andreas Dötsch (andre.nosp@m.as.d.nosp@m.oetsc.nosp@m.h@he.nosp@m.lmhol.nosp@m.tz-h.nosp@m.zi.de), Helmholtz Centre for Infection Research (Germany); Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France; Brian Merkey (brim@.nosp@m.env..nosp@m.dtu.d.nosp@m.k, bvm@n.nosp@m.orth.nosp@m.weste.nosp@m.rn.e.nosp@m.du), Department of Engineering Sciences and Applied Mathematics, Northwestern University (USA); Kieran Alden (k.j.a.nosp@m.lden.nosp@m.@bham.nosp@m..ac..nosp@m.uk), Centre for Systems Biology, University of Birmingham, UK

Member Function Documentation

boolean simulator.World.containsBulk ( String bulkName )

Determines if a bulk object of a given string name exists.

Determines if a bulk object of a given string name exists

Parameters

bulkName The name of the bulk that is required

Returns: Boolean stating whether or not this bulk exists

double [] simulator.World.getAllBulkValue ( int soluteIndex )

Returns the Sbulk value for a given solute index from that specified in the protocol file, for all bulks specified.

Parameters

soluteIndex The integer reference of the solute in the solute dictionary

Returns: An array of Sbulk values for this given solute - one for each bulk specified

Bulk simulator.World.getBulk ( String bulkName )

Return a bulk object of the given string name.

Return a bulk object of the given string name

Parameters

bulkName The name of the bulk that is required

Returns: Bulk object of that given name

double simulator.World.getBulkTimeConstraint ( )

Calculates and returns the simulation time required to change 100% of a bulk concentration.

Calculates and returns the simulation time required to change 100% of a bulk concentration

Returns: the time needed to change of 100% a bulk concentration

Domain simulator.World.getDomain ( String cDName )

Returns a domain from the domain list that matches a specified name.

Returns a domain from the domain list that matches a specified name. One example - used to link solute grids to a particular domain

Parameters

cDName The name of the domain to return from domainList

Returns: The domain of the name specified by cDName, from domainList

double simulator.World.getMaxBulkValue ( int soluteIndex )

Return the max value of a particular solute in the bulk.

Return the max value of a particular solute in the bulk

Parameters

soluteIndex The simulation dictionary integer reference for the solute being queried

Returns: Double value representing the max level of concentration in the bulk

void simulator.World.init	(	Simulator	aSim,
		XMLParser	worldRoot
	)

Creates and registers the bulks and computationDomains defined in the world mark-up of the protocol file.

This method, called by the createWorld method of the Simulator class, creates and registers the bulk and computation domains that are defined in the protocol file. The computation domains are stored in an arraylist, with the bulk information stored in a linked list

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
worldRoot	The World mark-up within the specified protocol file

Member Data Documentation

LinkedList<Bulk> simulator.World.bulkList = new LinkedList<Bulk>()

LinkedList of bulk domains specified in a simulation scenario

double [] simulator.World.bulkTime = new double[2]

Holds time constraints that are applicable to this bulk

ArrayList<Domain> simulator.World.domainList = new ArrayList<Domain>()

ArrayList of computation domains specified in a simulation scenario

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/World.java

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation