A C D F G H I J K L M N O P R S T U V W X Y Z

A

a - Variable in class Medium
Empirical constant van Genucten's alpha (dimensionless).
AboutFrame - class AboutFrame.
 
AboutFrame() - Constructor for class AboutFrame
 
accept(File) - Method in class JpgFilter
 
addSoil(Medium) - Method in class SoilStack
 
addSoil(Medium, String) - Method in class FlowComboPanel
 
addVirus(Operandum) - Method in class VirusStack
 
addVirus(Operandum, String) - Method in class VirusComboPanel
 
alphaz - Variable in class Medium
Vertical dispersivity (meters).
Attenuator - interface Attenuator.
This is the interface that generalizes attenuation of an Operandum (e.g., a solute, colloid, heat) in a Medium (e.g., a lake, stream, porous medium, soil).

C

changeRange(double, double) - Method in class GasDev
Change the range for the deviates from the default of [0., 10000].
clone() - Method in class Medium
Clone method redefinition
clone() - Method in class Normal
 
clone() - Method in class Operandum
Clone method redefinition
clone() - Method in class StringAsChars
 

D

DataBuilder - class DataBuilder.
This class is a surrogate for a forthcoming bona fide XML parser which I have not yet written.
DataBuilder() - Constructor for class DataBuilder
 

F

FlowComboPanel - class FlowComboPanel.
FlowComboPanel class.
FlowComboPanel(Gossiper) - Constructor for class FlowComboPanel
Construct a FlowComboPanel instance.
FlowPanel - class FlowPanel.
FlowPanel class.
FlowPanel(Gossiper) - Constructor for class FlowPanel
Construct an instance of FlowPanel.

G

GasDev - class GasDev.
Merely a Java translation of the popular C program gasdev.c (Press et al.
GasDev() - Constructor for class GasDev
Create one.
getAdvection() - Method in interface Attenuator
This method returns the mean advection rate supplied by the Medium.
getAdvection() - Method in class UnsatVirusAttenuator
Compute the gravity flow water flux.
getAttenuation() - Method in interface Attenuator
This method returns the attenuation factor which is by definition the quantity of Operandum remaining divided by the initial input quantity of Operandum.
getAttenuation() - Method in class UnsatVirusAttenuator
Compute the attenuation factor.
getData() - Method in class FlowPanel
Obtain the current data.
getData() - Method in class VirusPanel
Retrieve the virus data the user has selected.
getData(RandomAccessFile) - Method in class DataBuilder
 
getData(String) - Method in class SoilStack
Retrieve data by soil type descriptor.
getData(String) - Method in class VirusStack
Retrieve the data entered by the user.
getDescription() - Method in class JpgFilter
 
getExtension(File) - Static method in class Utils
 
geth(double) - Method in class UnsatVirusAttenuator
 
getImage() - Method in class HistoPanel
 
getKh(double) - Method in class UnsatVirusAttenuator
 
getLabels() - Method in class FlowPanel
Obtain the labels for the parameter fields as a String array.
getLabels() - Method in class VirusPanel
Retrieve the virus labels as a array of Strings.
getMedium() - Method in interface Attenuator
 
getMedium() - Method in class UnsatVirusAttenuator
 
getNext() - Method in class HspMonteCarlo
 
getOperandum() - Method in interface Attenuator
 
getOperandum() - Method in class UnsatVirusAttenuator
 
getPreferredSize() - Method in class ImageCanvas
 
getSelection() - Method in class FlowComboPanel
 
getUnits() - Method in class FlowPanel
 
getUnits() - Method in class VirusPanel
 
getVarCov(String) - Method in class VarCov
 
getXML() - Method in class MediumXMLWriter
 
Gossiper - class Gossiper.
Subclass of java.util.Observable that acts as the "subject" of the Observer design pattern (Gamma et al.
Gossiper() - Constructor for class Gossiper
Creat a new Gossiper object.

H

HistoPanel - class HistoPanel.
 
HistoPanel(int[], int, int) - Constructor for class HistoPanel
 
HspBasicMath - class HspBasicMath.
HspBasicMath class.
HspBasicMath() - Constructor for class HspBasicMath
 
HspMonteCarlo - class HspMonteCarlo.
Class for generating Monte Carlo simulations.
HspMonteCarlo(Medium, Operandum) - Constructor for class HspMonteCarlo
 

I

ImageCanvas - class ImageCanvas.
This code is by Geary, Mastering the JFC, 3rd Ed.
ImageCanvas(BufferedImage) - Constructor for class ImageCanvas
 
ImageCanvas(String) - Constructor for class ImageCanvas
 
ImagePanel - class ImagePanel.
 
ImagePanel() - Constructor for class ImagePanel
 
is - Variable in class StringAsChars
 

J

JarLoadable - class JarLoadable.
Allows images files to be loaded from a Java Archive (jar) file.
JarLoadable() - Constructor for class JarLoadable
 
jpg - Static variable in class Utils
 
JpgFilter - class JpgFilter.
 
JpgFilter() - Constructor for class JpgFilter
 

K

K0 - Variable in class Medium
Saturated hydraulic conductivity (meter/hr).
kappa0 - Variable in class Operandum
Mass transfer coefficients {liquid-liq/solid, liquid-liq/air} (per hour).
kappa1 - Variable in class Operandum
 
Kd - Variable in class Operandum
Initial concentration or mass (any units).

L

lambda0 - Variable in class Operandum
Inactivation rate coefficients {liquid, solid-sorbed, air-sorbed} (log[per hour]).
lambda1 - Variable in class Operandum
 
loadImage(String) - Method in class JarLoadable
 

M

m - Variable in class NormalF
 
main(String[]) - Static method in class Virulo
 
mean - Variable in class Normal
 
Medium - class Medium.
Medium class.
Medium() - Constructor for class Medium
 
MediumXMLWriter - class MediumXMLWriter.
 
MediumXMLWriter(Medium, String) - Constructor for class MediumXMLWriter
 
Mvn - class Mvn.
This class is for generating multvariate normal deviates.
Mvn(Matrix, double[]) - Constructor for class Mvn
Create one.

N

n - Variable in class Medium
van Genuchten parameter (dimensionless).
name - Variable in class Medium
USDA name of the soil stored as a char[].
name - Variable in class Operandum
The name of this operandum.
nextDeviate() - Method in class GasDev
Obtain the next random deviate ~ N(ll,ul), where by default ll=0, ul=1000.
nextDouble() - Method in class Random
Returns the next random number in the sequence.
nextDoubles(double[]) - Method in class Random
Returns the next N random numbers in the sequence, as a vector.
Normal - class Normal.
Data structure to describe a normally distributed random variable.
Normal() - Constructor for class Normal
 
Normal(double, double) - Constructor for class Normal
 
NormalF - class NormalF.
 
NormalF() - Constructor for class NormalF
 

O

Operandum - class Operandum.
Operandum class.
Operandum() - Constructor for class Operandum
 
OperandumXMLWriter - class OperandumXMLWriter.
 
OperandumXMLWriter(Operandum, String) - Constructor for class OperandumXMLWriter
 
OutputPanel - class OutputPanel.
OutputPanel class.
OutputPanel() - Constructor for class OutputPanel
Construct a OutputPanel object.

P

paint(Graphics) - Method in class ImageCanvas
 
paintComponent(Graphics) - Method in class HistoPanel
 
paintComponent(Graphics) - Method in class ImagePanel
 
permuteDouble(Vector, double[]) - Static method in class VectorParser
Supply a permutation of a native array of doubles of a given Vector of indices
perturb() - Method in class Mvn
Generate the Matrix of Multivariate Normal Deviates where each row corresponds to an event for each random variable.
printOutput(String) - Method in class OutputPanel
Print the outString.
putData(Medium) - Method in class FlowPanel
 
putData(Operandum) - Method in class VirusPanel
 

R

Random - class Random.
 
Random() - Constructor for class Random
Initializes a sequence of uniformly distributed quasi random numbers with a seed based on the system clock.
Random(double, double) - Constructor for class Random
Initializes a sequence of uniformly distributed quasi random numbers on a given half-open interval [left,right) with a seed based on the system clock.
Random(int) - Constructor for class Random
Initializes a sequence of uniformly distributed quasi random numbers with a given seed.
Random(int, double, double) - Constructor for class Random
Initializes a sequence of uniformly distributed quasi random numbers with a given seed on a given half-open interval [left,right).
redraw(int[]) - Method in class HistoPanel
 
replace(Medium, Operandum) - Method in interface Attenuator
A replace is used to replace the data for purposes of a time-series or a Monte Carlo implementation.
replace(Medium, Operandum) - Method in class UnsatVirusAttenuator
 
requestAttention(String) - Method in class FlowPanel
 
requestAttention(String) - Method in class VirusPanel
 
rho - Variable in class Medium
Soil bulk density (g/m^3).
rp - Variable in class Medium
Average radius of soil particles (meter).
rv - Variable in class Operandum
Radius (m)

S

s - Variable in class NormalF
 
sdev - Variable in class Normal
 
setBreak(double) - Method in class HistoPanel
 
setHits(int) - Method in class HistoPanel
 
setRuns(int) - Method in class HistoPanel
 
setTheta_mUniform(boolean) - Method in class HspMonteCarlo
 
SoilStack - class SoilStack.
SoilStack class.
SoilStack() - Constructor for class SoilStack
 
StringAsChars - class StringAsChars.
Data structure for a string in hsp.
StringAsChars() - Constructor for class StringAsChars
 

T

t - Variable in class Medium
Temperature for computing molecular diffusivity (degrees Celsius).
tell(Object) - Method in class Gossiper
Inform Gossiper object of a change in the concrete subjects so that it will notify the designated observers.
theta_m - Variable in class Medium
 
theta_mIsUniform() - Method in class FlowPanel
 
theta_r - Variable in class Medium
 
theta_s - Variable in class Medium
Soil water content parameters: {Residual water content, Water content, Saturated water content} (dimensionless).
toDoubleArray(Vector) - Static method in class VectorParser
Convert Vector to native array.
toFloatArray(Vector) - Static method in class VectorParser
Convert Vector to native array.
toIntArray(Vector) - Static method in class VectorParser
Convert Vector to native array.
toPointArray(Vector) - Static method in class VectorParser
Convert Vector of Points to array of Points.
txt - Static variable in class Utils
 

U

UnsatVirusAttenuator - class UnsatVirusAttenuator.
UnsatVirusAttenuator class.
UnsatVirusAttenuator(Medium, Operandum) - Constructor for class UnsatVirusAttenuator
Construct one.
update(Observable, Object) - Method in class FlowPanel
This method is called by the Gossiper (or other subclass of Observable) and updates the Medium instance.
update(Observable, Object) - Method in class VirusPanel
This method is called by the Gossiper (or other subclass of Observable) and updates the Operandum instance.
Utils - class Utils.
 
Utils() - Constructor for class Utils
 

V

VarCov - class VarCov.
 
VarCov() - Constructor for class VarCov
 
VectorParser - class VectorParser.
VectorParser class.
VectorParser() - Constructor for class VectorParser
 
Virulo - class Virulo.
Virulo class.
Virulo() - Constructor for class Virulo
 
ViruloFrame - class ViruloFrame.
ViruloFrame class.
ViruloFrame() - Constructor for class ViruloFrame
Construct a ViruloFrame.
VirusComboPanel - class VirusComboPanel.
VirusComboPanel class.
VirusComboPanel(Gossiper) - Constructor for class VirusComboPanel
Construct a VirusComboPanel.
VirusPanel - class VirusPanel.
VirusPanel class.
VirusPanel(Gossiper) - Constructor for class VirusPanel
Construct a VirusPanel.
VirusStack - class VirusStack.
VirusStack class.
VirusStack() - Constructor for class VirusStack
 

W

writeXML() - Method in class OperandumXMLWriter
 

X

xml - Static variable in class Utils
 
xSplitPoint(Vector) - Static method in class VectorParser
Convert Vector of Points to native array of the X "coordinates."

Y

ySplitPoint(Vector) - Static method in class VectorParser
Convert Vector of Points to native array of the Y "coordinates."

Z

z - Variable in class Medium
Thickness of the proposed hydrogeologic barrier (meters).

A C D F G H I J K L M N O P R S T U V W X Y Z