simulator.geometry.FluctEnv Class Reference

Inheritance diagram for simulator.geometry.FluctEnv:

Public Member Functions
	FluctEnv (Simulator aSim, XMLParser aBulkRoot) throws FileNotFoundException
ArrayList< String >	envDic () throws FileNotFoundException
double[][]	envProb () throws FileNotFoundException
double[][]	envCumProb () throws FileNotFoundException
Matrix	transMatrix () throws FileNotFoundException
double	setEnv () throws FileNotFoundException
ArrayList< Integer >	indexCalc () throws FileNotFoundException
double	transProbVal () throws FileNotFoundException
String	envTransName () throws FileNotFoundException
Public Member Functions inherited from simulator.geometry.Bulk
	Bulk (Simulator aSim, XMLParser aBulkRoot)
	Creates a bulk compartment object with attributes specified in the protocol file. More...
void	updateBulk (SoluteGrid[] soluteGrid, SoluteGrid[] reacGrid, double timeStep)
	Updates the bulk solute concentration if the bulk is not constant. More...
void	updateChemostatBulk (SoluteGrid[] allSol, SoluteGrid[] reacGrid)
	Method to update Bulk solute concentrations during a chemostat setup. More...
void	updateBulkByReaction (SoluteGrid[] reacGrid, double timeStep)
	Update bulk concentration by reaction, determining reaction rate seen from reaction compartments. More...
void	updateBulkByGradient (SoluteGrid[] soluteGrid, double timeStep)
	Update bulk concentration on the basis of the flow passed through the interface with the bulk compartment. More...
void	computeFlow (SoluteGrid aSG, DiscreteVector aDC, ContinuousVector flow)
	Compute massic flow. More...
Boolean	contains (int soluteIndex)
	Determine if a particular solute is in the bulk. More...
double	getValue (int soluteIndex)
	Get the value of a particular solute in the bulk. More...
void	setValue (int soluteIndex, double value)
	Set the value of a particular solute in the bulk. More...
String	getName ()
	Get the name of this bulk. More...
double	getTimeConstraint ()
	Return the time constraint of the bulk. More...
void	writeReport (ResultFile buffer) throws Exception
	Writes a description of the bulk in the result file. More...

Static Public Member Functions
static String	setEnvCycle (int index)

Static Public Attributes
static ArrayList< String >	envName = new ArrayList<String>()
static double[][]	envCumProb
static double[][]	transitions
static ArrayList< Integer >	indices = new ArrayList<Integer>()
static ArrayList< String >	envTrans = new ArrayList<String>()
static double	cumProb =0
static double	transProb = 0
static HashMap< String, Double >	envListTime = new HashMap<String, Double>()
static ArrayList< String >	envNameList = new ArrayList<String>()
static HashMap< String, Integer >	envIter = new HashMap<String, Integer>()
static String	envStatus
static double	counter = 0

Additional Inherited Members
Public Attributes inherited from simulator.geometry.Bulk
Simulator	mySim
double[]	_bulkValue
double	_D
double[]	_sIn
Boolean[]	_isConstant

Detailed Description

This class is intended to randomly change the external environment felt by the agents. The transition between these different states is determined by a transition probability matrix whose values are in probability per hour. The correspondent cumulative probability matrix is used to decide the next state, simply because it avoids the problem of having 2 equal values (and thus having to decide randomly between them...). It has also been implemented the recalculation of the cumulative probability values according to the current time step (as long as it is lower or equal to 1h... since higher values would produce probabilities higher than 1...)

It has also been implemented a method to deterministically change the environmental conditions and their duration.

Author

SoniaMartins

Constructor & Destructor Documentation

simulator.geometry.FluctEnv.FluctEnv	(	Simulator	aSim,
		XMLParser	aBulkRoot
	)		throws FileNotFoundException

public FluctEnv(Simulator aSim, String name) { super(aSim, name);

}

Member Function Documentation

double [][] simulator.geometry.FluctEnv.envCumProb

(

)

throws FileNotFoundException

reads a txt file containing the cumulative probability matrix describing the transitions between environments.

Returns

double 2D array envCumProb

Exceptions

FileNotFoundException

ArrayList<String> simulator.geometry.FluctEnv.envDic

(

)

throws FileNotFoundException

reads a text file containing the names of the environments involved and returns a list with those names

Returns

ArrayList

Exceptions

FileNotFoundException

double [][] simulator.geometry.FluctEnv.envProb

(

)

throws FileNotFoundException

reads a txt file containing a "table" with the transitions probabilities and returns a 2D array of it

Returns

double 2D array transitions

Exceptions

FileNotFoundException

String simulator.geometry.FluctEnv.envTransName

(

)

throws FileNotFoundException

taking into account the retrieved indices, builds a list with the names of the environments involved in the transitions in the correct order

Returns

ArrayList

Exceptions

FileNotFoundException

ArrayList<Integer> simulator.geometry.FluctEnv.indexCalc

(

)

throws FileNotFoundException

knowing the cumpr_val and the which row of probabilities is being used for this iteration, we can infer the indices of the cumulative probability matrix that correspond to the environment transition.

Returns

arrayList indices

Exceptions

FileNotFoundException

double simulator.geometry.FluctEnv.setEnv

(

)

throws FileNotFoundException

this method sets the new environment state according to the condition: 1st cumulative probability>= random number; it returns the cumulative probability value that has been chosen; This is called in the step() in Simulator class and it is by default commented out.

Returns

double cumpr_val

Exceptions

FileNotFoundException

static String simulator.geometry.FluctEnv.setEnvCycle ( int  index )

static

This method is the deterministic version of environment fluctuations, where different environments have defined time durations thus cycling between them at defined time points.

Parameters

index

Returns

the environment Name just set.

Matrix simulator.geometry.FluctEnv.transMatrix

(

)

throws FileNotFoundException

transforms the 2D array containing the transition probabilities into a matrix whose format can be used to perform matrix operations

Returns

Matrix

Exceptions

FileNotFoundException

double simulator.geometry.FluctEnv.transProbVal

(

)

throws FileNotFoundException

we would also like to know to which transition probability value is this transition associated with; that's what is done here. Using the indices we can retrieve the transition probability value.

Returns

Exceptions

FileNotFoundException

Member Data Documentation

double simulator.geometry.FluctEnv.counter = 0

static

double simulator.geometry.FluctEnv.cumProb =0

static

double [][] simulator.geometry.FluctEnv.envCumProb

static

HashMap<String,Integer> simulator.geometry.FluctEnv.envIter = new HashMap<String, Integer>()

static

HashMap<String, Double> simulator.geometry.FluctEnv.envListTime = new HashMap<String, Double>()

static

ArrayList<String> simulator.geometry.FluctEnv.envName = new ArrayList<String>()

static

ArrayList<String> simulator.geometry.FluctEnv.envNameList = new ArrayList<String>()

static

String simulator.geometry.FluctEnv.envStatus

static

ArrayList<String> simulator.geometry.FluctEnv.envTrans = new ArrayList<String>()

static

ArrayList<Integer> simulator.geometry.FluctEnv.indices = new ArrayList<Integer>()

static

double [][] simulator.geometry.FluctEnv.transitions

static

double simulator.geometry.FluctEnv.transProb = 0

static

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

• /home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/geometry/FluctEnv.java