attractorSummary	attractorSummary
backupStage	ternaryFitParameters-class
backupStage,ternaryFitParameters-method	ternaryFitParameters-class
backupStage<-	ternaryFitParameters-class
backupStage<-,ternaryFitParameters-method	ternaryFitParameters-class
beta0	ternaryFitParameters-class
beta0,ternaryFitParameters-method	ternaryFitParameters-class
beta0<-	ternaryFitParameters-class
beta0<-,ternaryFitParameters-method	ternaryFitParameters-class
chi0	ternaryFitParameters-class
chi0,ternaryFitParameters-method	ternaryFitParameters-class
chi0<-	ternaryFitParameters-class
chi0<-,ternaryFitParameters-method	ternaryFitParameters-class
class:ternaryFit	ternaryFit-class
class:ternaryFitParameters	ternaryFitParameters-class
class:ternaryPost	ternaryPost-class
degreeObjMin	ternaryFit-class
degreeObjMin,ternaryFit-method	ternaryFit-class
degreeObjMin<-	ternaryFit-class
degreeObjMin<-,ternaryFit-method	ternaryFit-class
degreeObjs	ternaryPost-class
degreeObjs,ternaryPost-method	ternaryPost-class
degreeObjs<-	ternaryPost-class
degreeObjs<-,ternaryPost-method	ternaryPost-class
delta	ternaryFitParameters-class
delta,ternaryFitParameters-method	ternaryFitParameters-class
delta<-	ternaryFitParameters-class
delta<-,ternaryFitParameters-method	ternaryFitParameters-class
dim,ternaryFit-method	ternaryFit-class
dim,ternaryPost-method	ternaryPost-class
edgePenalty	ternaryFitParameters-class
edgePenalty,ternaryFitParameters-method	ternaryFitParameters-class
edgePenalty<-	ternaryFitParameters-class
edgePenalty<-,ternaryFitParameters-method	ternaryFitParameters-class
epsilon	ternaryFitParameters-class
epsilon,ternaryFitParameters-method	ternaryFitParameters-class
epsilon<-	ternaryFitParameters-class
epsilon<-,ternaryFitParameters-method	ternaryFitParameters-class
experimentNames	ternaryFit-class
experimentNames,ternaryFit-method	ternaryFit-class
experimentNames,ternaryPost-method	ternaryPost-class
experimentNames<-	ternaryFit-class
experimentNames<-,ternaryFit-method	ternaryFit-class
experimentNames<-,ternaryPost-method	ternaryPost-class
finalTemperature	ternaryFit-class
finalTemperature,ternaryFit-method	ternaryFit-class
finalTemperature<-	ternaryFit-class
finalTemperature<-,ternaryFit-method	ternaryFit-class
geneNames	ternaryFit-class
geneNames,ternaryFit-method	ternaryFit-class
geneNames,ternaryPost-method	ternaryPost-class
geneNames<-	ternaryFit-class
geneNames<-,ternaryFit-method	ternaryFit-class
geneNames<-,ternaryPost-method	ternaryPost-class
graphObjMin	ternaryFit-class
graphObjMin,ternaryFit-method	ternaryFit-class
graphObjMin<-	ternaryFit-class
graphObjMin<-,ternaryFit-method	ternaryFit-class
graphObjs	ternaryPost-class
graphObjs,ternaryPost-method	ternaryPost-class
graphObjs<-	ternaryPost-class
graphObjs<-,ternaryPost-method	ternaryPost-class
graphPosterior	graphPosterior
initialize,ternaryFit-method	ternaryFit-class
initialize,ternaryFitParameters-method	ternaryFitParameters-class
initialize,ternaryPost-method	ternaryPost-class
inputParams	ternaryFit-class
inputParams,ternaryFit-method	ternaryFit-class
inputParams,ternaryPost-method	ternaryPost-class
inputParams<-	ternaryFit-class
inputParams<-,ternaryFit-method	ternaryFit-class
inputParams<-,ternaryPost-method	ternaryPost-class
m0	ternaryFitParameters-class
m0,ternaryFitParameters-method	ternaryFitParameters-class
m0<-	ternaryFitParameters-class
m0<-,ternaryFitParameters-method	ternaryFitParameters-class
maxDegree	ternaryFitParameters-class
maxDegree,ternaryFitParameters-method	ternaryFitParameters-class
maxDegree<-	ternaryFitParameters-class
maxDegree<-,ternaryFitParameters-method	ternaryFitParameters-class
maxStage	ternaryFitParameters-class
maxStage,ternaryFitParameters-method	ternaryFitParameters-class
maxStage<-	ternaryFitParameters-class
maxStage<-,ternaryFitParameters-method	ternaryFitParameters-class
maxTransition	ternaryFitParameters-class
maxTransition,ternaryFitParameters-method	ternaryFitParameters-class
maxTransition<-	ternaryFitParameters-class
maxTransition<-,ternaryFitParameters-method	ternaryFitParameters-class
minScore	ternaryFit-class
minScore,ternaryFit-method	ternaryFit-class
minScore<-	ternaryFit-class
minScore<-,ternaryFit-method	ternaryFit-class
ne	ternaryFitParameters-class
ne,ternaryFitParameters-method	ternaryFitParameters-class
ne<-	ternaryFitParameters-class
ne<-,ternaryFitParameters-method	ternaryFitParameters-class
neighborDegree	ternaryFitParameters-class
neighborDegree,ternaryFitParameters-method	ternaryFitParameters-class
neighborDegree<-	ternaryFitParameters-class
neighborDegree<-,ternaryFitParameters-method	ternaryFitParameters-class
newScore	ternaryFit-class
newScore,ternaryFit-method	ternaryFit-class
newScore<-	ternaryFit-class
newScore<-,ternaryFit-method	ternaryFit-class
pAddParent	ternaryFitParameters-class
pAddParent,ternaryFitParameters-method	ternaryFitParameters-class
pAddParent<-	ternaryFitParameters-class
pAddParent<-,ternaryFitParameters-method	ternaryFitParameters-class
parallelFit	parallelFit
perturbationObj	ternaryFit-class
perturbationObj,ternaryFit-method	ternaryFit-class
perturbationObj,ternaryPost-method	ternaryPost-class
perturbationObj<-	ternaryFit-class
perturbationObj<-,ternaryFit-method	ternaryFit-class
perturbationObj<-,ternaryPost-method	ternaryPost-class
perturbationType	ternaryFitParameters-class
perturbationType,ternaryFitParameters-method	ternaryFitParameters-class
perturbationType<-	ternaryFitParameters-class
perturbationType<-,ternaryFitParameters-method	ternaryFitParameters-class
pExchangeParent	ternaryFitParameters-class
pExchangeParent,ternaryFitParameters-method	ternaryFitParameters-class
pExchangeParent<-	ternaryFitParameters-class
pExchangeParent<-,ternaryFitParameters-method	ternaryFitParameters-class
plotFit	plotFit
plotPost	plotPost
plotTraces	plotTraces
pNeighborhood	ternaryFitParameters-class
pNeighborhood,ternaryFitParameters-method	ternaryFitParameters-class
pNeighborhood<-	ternaryFitParameters-class
pNeighborhood<-,ternaryFitParameters-method	ternaryFitParameters-class
predictAttractor	predictAttractor
rho	ternaryFitParameters-class
rho,ternaryFitParameters-method	ternaryFitParameters-class
rho<-	ternaryFitParameters-class
rho<-,ternaryFitParameters-method	ternaryFitParameters-class
scores	ternaryPost-class
scores,ternaryPost-method	ternaryPost-class
scores<-	ternaryPost-class
scores<-,ternaryPost-method	ternaryPost-class
scoreType	ternaryFitParameters-class
scoreType,ternaryFitParameters-method	ternaryFitParameters-class
scoreType<-	ternaryFitParameters-class
scoreType<-,ternaryFitParameters-method	ternaryFitParameters-class
show,ternaryFit-method	ternaryFit-class
show,ternaryFitParameters-method	ternaryFitParameters-class
show,ternaryPost-method	ternaryPost-class
simulateSteadyState	simulateSteadyState
stageCount	ternaryFit-class
stageCount,ternaryFit-method	ternaryFit-class
stageCount<-	ternaryFit-class
stageCount<-,ternaryFit-method	ternaryFit-class
steadyStateObj	ternaryFit-class
steadyStateObj,ternaryFit-method	ternaryFit-class
steadyStateObj,ternaryPost-method	ternaryPost-class
steadyStateObj<-	ternaryFit-class
steadyStateObj<-,ternaryFit-method	ternaryFit-class
steadyStateObj<-,ternaryPost-method	ternaryPost-class
tableObjMin	ternaryFit-class
tableObjMin,ternaryFit-method	ternaryFit-class
tableObjMin<-	ternaryFit-class
tableObjMin<-,ternaryFit-method	ternaryFit-class
tableObjs	ternaryPost-class
tableObjs,ternaryPost-method	ternaryPost-class
tableObjs<-	ternaryPost-class
tableObjs<-,ternaryPost-method	ternaryPost-class
ternaryFit	ternaryFit-class
ternaryFit-class	ternaryFit-class
ternaryFit-methods	ternaryFit-class
ternaryFitParameters	ternaryFitParameters-class
ternaryFitParameters-class	ternaryFitParameters-class
ternaryFitParameters-methods	ternaryFitParameters-class
ternaryPost	ternaryPost-class
ternaryPost-class	ternaryPost-class
ternaryPost-methods	ternaryPost-class
tnetfit	tnetfit
tnetpost	tnetpost
traces	ternaryFit-class
traces,ternaryFit-method	ternaryFit-class
traces<-	ternaryFit-class
traces<-,ternaryFit-method	ternaryFit-class
xSeed	ternaryFit-class
xSeed,ternaryFit-method	ternaryFit-class
xSeed<-	ternaryFit-class
xSeed<-,ternaryFit-method	ternaryFit-class
