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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
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