useDynLib(BoolNet)

import("igraph", "XML")
importFrom("graphics", "abline", "arrows", "axis", "hist", "legend", "lines", "par", "plot", "rect", "text")
importFrom("grDevices", "dev.interactive")
importFrom("stats", "dist", "kmeans", "quantile", "rnorm", "rpois", "runif")
importFrom("utils", "installed.packages", "tail")
importFrom("grDevices", "adjustcolor")

S3method(print, AttractorInfo)
S3method(print, SymbolicSimulation)
S3method(print, BooleanNetwork)
S3method(print, SymbolicBooleanNetwork)
S3method(print, BooleanNetworkCollection)
S3method(print, ProbabilisticBooleanNetwork)
S3method(print, BooleanStateInfo)
S3method(print, TransitionTable)
S3method(print, MarkovSimulation)

export(
loadNetwork,
loadBioTapestry,
loadSBML,
saveNetwork,
getAttractors,
plotAttractors,
plotSequence,
plotStateGraph,
plotNetworkWiring,
plotPBNTransitions,
attractorsToLaTeX,
sequenceToLaTeX,
stateTransition,
getAttractorSequence,
getTransitionTable,
getStateSummary,
getBasinOfAttraction,
getPathToAttractor,
getTransitionProbabilities,
toPajek,
toSBML,
generateRandomNKNetwork,
generateCanalyzing,
generateNestedCanalyzing,
generateState,
generateTimeSeries,
perturbNetwork,
perturbTrajectories,
simplifyNetwork,
simulateSymbolicModel,
reconstructNetwork,
chooseNetwork,
fixGenes,
binarizeTimeSeries,
markovSimulation,
testNetworkProperties,
testAttractorRobustness,
testTransitionRobustness,
testIndegree,
truthTableToSymbolic,
symbolicToTruthTable)