A B C D G H I L M P R S T U

A

AIP - Class in <Unnamed>
object storing data about AIP concentration inside biofilm
AIP(double, double, double, double, double, double) - Constructor for class AIP
 

B

BiofilmStruct - Class in <Unnamed>
object storing data about biofilm structure (basic geometry)
BiofilmStruct(double, double, double, double, double) - Constructor for class BiofilmStruct
 

C

carryCap - Variable in class TotalBiofilmPop
 
convRate - Variable in class TotalBiofilmPop
 

D

Diffusion - Class in <Unnamed>
 
Diffusion(double, double, double, double, double) - Constructor for class Diffusion
 
DspB - Class in <Unnamed>
object storing data about DspB concentration inside biofilm
DspB(double, double) - Constructor for class DspB
 

G

get(String) - Method in class Parameters
accessor methods
getAIP() - Method in class AIP
 
getAIPprev() - Method in class AIP
 
getColLen() - Method in class History
 
getColVal(int) - Method in class History
 
getDepth() - Method in class BiofilmStruct
accessor methods
getDspB() - Method in class DspB
 
getDspBprev() - Method in class DspB
 
getPhageLayer() - Method in class Diffusion
 
getPhageLayerPrev() - Method in class Diffusion
 
getPopCount() - Method in class PhagePop
 
getPopCount() - Method in class TotalBiofilmPop
 
getPopCountPrev() - Method in class PhagePop
accessor methods
getPopCountPrev() - Method in class TotalBiofilmPop
accessor methods
getRate() - Method in class Diffusion
 
getRatePrev() - Method in class Diffusion
accessor methods
getRowLen() - Method in class History
access methods
getRowVal(int) - Method in class History
 
getSuscept() - Method in class BiofilmStruct
 
getTermX(double, double, double, double) - Method in class PhagePop
 
getTermX(double, double, double, double) - Method in class TotalBiofilmPop
 
getTermZ(double, double, double, double) - Method in class DspB
 
getTermZ(double, double, double, double) - Method in class PhagePop
 
getTheta(double, double, double) - Method in class TotalBiofilmPop
term-calculation methods
getWashOffRate() - Method in class Diffusion
 
getWashOffRatePrev() - Method in class Diffusion
 
growthRateI - Variable in class TotalBiofilmPop
 
growthRateU - Variable in class TotalBiofilmPop
 

H

History - Class in <Unnamed>
 
History(int) - Constructor for class History
Constructor for objects of class History

I

InfectedBiofilmPop - Class in <Unnamed>
object storing data about infected biofilm subpopulation
InfectedBiofilmPop(double, double, double, double) - Constructor for class InfectedBiofilmPop
variables and parameters
init() - Method in class PhilmApplet
 

L

LatentBiofilmPop - Class in <Unnamed>
object storing data about infected biofilm subpopulation
LatentBiofilmPop(double, double, double, double, double, double) - Constructor for class LatentBiofilmPop
variables and parameters
lysisRate - Variable in class TotalBiofilmPop
 
LyticBiofilmPop - Class in <Unnamed>
object storing data about biofilm subpopulation infected with phage in lytic cycle
LyticBiofilmPop(double, double, double, double, double, double) - Constructor for class LyticBiofilmPop
variables and parameters

M

main(String[]) - Static method in class Philm
MAIN method

P

Parameters - Class in <Unnamed>
 
Parameters(String) - Constructor for class Parameters
private double growthRateU; private double growthRateI; private double carryCap; private double lysisRate; private double convRate; private double portionLytic; private double halfLife; private double infectRate; private double productRateR; private double rMin; private double rMax; private double rOut; private double Y; private double sigmaRate; private double gammaRate; private double AIPmax; private double AIPthres; private double productRateS; private double occupancy; private double cellDiameter; private double crossArea;
PhagePop - Class in <Unnamed>
object storing data about phage population
PhagePop(double, double, double, double) - Constructor for class PhagePop
 
Philm - Class in <Unnamed>
 
Philm(String) - Constructor for class Philm
Constructor for objects of class Philm
PhilmApplet - Class in <Unnamed>
 
PhilmApplet() - Constructor for class PhilmApplet
 
PhilmGUI - Class in <Unnamed>
Write a description of class PhilmGUI here.
PhilmGUI() - Constructor for class PhilmGUI
Constructor for objects of class PhilmGUI
popCount - Variable in class TotalBiofilmPop
variables and parameters
popCountPrev - Variable in class TotalBiofilmPop
 
portionLytic - Variable in class TotalBiofilmPop
 
printResults(History, String) - Method in class Philm
 

R

run(int) - Method in class Philm
 

S

sampleMethod(int) - Method in class PhilmGUI
An example of a method - replace this comment with your own

T

TotalBiofilmPop - Class in <Unnamed>
object storing data about total biofilm population serves as the parent class to subpop.
TotalBiofilmPop(double, double, double, double, double) - Constructor for class TotalBiofilmPop
 

U

UninfectedBiofilmPop - Class in <Unnamed>
object storing data about uninfected biofilm subpopulation
UninfectedBiofilmPop(double, double, double) - Constructor for class UninfectedBiofilmPop
variables and parameters
updateAIP(double) - Method in class AIP
 
updateDepth(double) - Method in class BiofilmStruct
core methods
updateDspB(double, double, double, double, double) - Method in class DspB
 
updateHistory(double[], int) - Method in class History
 
updatePhageLayer() - Method in class Diffusion
 
updatePopCount(double, double, double, double, double) - Method in class InfectedBiofilmPop
overloads parent method
updatePopCount(double, double, double, double, double) - Method in class LatentBiofilmPop
overloads parent method
updatePopCount(double, double, double, double, double, double, double) - Method in class LyticBiofilmPop
overloads parent method
updatePopCount(double, double, double, double, double, double, double) - Method in class PhagePop
core methods
updatePopCount(double, double) - Method in class TotalBiofilmPop
core methods
updatePopCount(double, double, double, double, double) - Method in class UninfectedBiofilmPop
overloads parent method
updateRate(double) - Method in class Diffusion
core methods
updateSuscept(double) - Method in class BiofilmStruct
 
updateWashOffRate() - Method in class Diffusion
 

A B C D G H I L M P R S T U