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getAttractorSequence <- function(attractorInfo, attractorNo)
{
stopifnot(inherits(attractorInfo,"AttractorInfo") || inherits(attractorInfo,"SymbolicSimulation"))
if (inherits(attractorInfo,"SymbolicSimulation"))
{
if (is.null(attractorInfo$attractors))
stop(paste("This SymbolicSimulation structure does not contain attractor information.",
"Please re-run simulateSymbolicModel() with returnAttractors=TRUE!"))
if (missing(attractorNo) || attractorNo <= 0 || attractorNo > length(attractorInfo$attractors))
stop("Please provide a valid attractor number!")
return(attractorInfo$attractors[[attractorNo]])
}
else
{
if (missing(attractorNo) || attractorNo <= 0 || attractorNo > length(attractorInfo$attractors))
stop("Please provide a valid attractor number!")
if (!is.null(attractorInfo$attractors[[attractorNo]]$initialStates))
stop("A sequence can be obtained for synchronous attractors only!")
numGenes <- length(attractorInfo$stateInfo$genes)
# decode binary representation of states involved in the attractors
binMatrix <- t(matrix(apply(attractorInfo$attractors[[attractorNo]]$involvedStates,2,function(state)
dec2bin(state,numGenes)),nrow=numGenes))
colnames(binMatrix) <- attractorInfo$stateInfo$genes
return(as.data.frame(binMatrix))
}
}
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