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# Retrieves the transition table of an AttractorInfo structure
# in a readable way
getTransitionTable <- function(attractorInfo)
{
stopifnot(inherits(attractorInfo,"AttractorInfo") || inherits(attractorInfo,"SymbolicSimulation"))
if (inherits(attractorInfo,"SymbolicSimulation"))
{
if (is.null(attractorInfo$graph))
stop(paste("This SymbolicSimulation structure does not contain transition table information.",
"Please re-run simulateSymbolicModel() with returnGraph=TRUE!"))
return(attractorInfo$graph)
}
else
if (is.null(attractorInfo$stateInfo$table))
stop(paste("This AttractorInfo structure does not contain transition table information.",
"Please re-run getAttractors() with a synchronous search and returnTable=TRUE!"))
return(.internal.getTransitionTable(attractorInfo$stateInfo))
}
# Internally used to extract the information from the <stateInfo> subcomponent
# of AttractorInfo
.internal.getTransitionTable <- function(stateInfo)
{
fixedGenes <- which(stateInfo$fixedGenes != -1)
nonFixedGenes <- which(stateInfo$fixedGenes == -1)
if (!is.null(stateInfo$initialStates))
{
initialStates <- t(apply(stateInfo$initialStates,2,dec2bin,length(stateInfo$genes)))
}
else
{
initialStates <- matrix(ncol=length(stateInfo$genes),nrow=2^length(nonFixedGenes))
# encode the initial states
# first, encode the changing part by calculating all combinations
temp <- allcombn(2,length(nonFixedGenes)) - 1
initialStates[,nonFixedGenes] <- temp[,ncol(temp):1]
if (length(fixedGenes) > 0)
# if there are fixed genes, encode their values
initialStates[,fixedGenes] <- sapply(stateInfo$fixedGenes[fixedGenes],
function(value)rep(value,2^length(nonFixedGenes)))
}
# build return structure of class TransitionTable
res <- data.frame(initialStates,
t(apply(stateInfo$table,2,dec2bin,length(stateInfo$genes))),
stateInfo$attractorAssignment,stateInfo$stepsToAttractor)
colnames(res) <- c(paste("initialState.",stateInfo$genes,sep=""),
paste("nextState.",stateInfo$genes,sep=""),
"attractorAssignment","transitionsToAttractor")
class(res) <- c("TransitionTable","data.frame")
return(res)
}
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