# define mBison classes and methods

setClass("MBnetwork",representation(N="numeric",Names="character",States="numeric",Cpds="matrix",Counts="matrix",Margs="matrix",Pvals="numeric"),prototype=list(N=0,Names=character(),States=integer(),Cpds=matrix(0,2,0),Counts=matrix(0,2,0),Margs=matrix(0,2,0),Pvals=numeric()),sealed=TRUE)
setValidity("MBnetwork",validMBnetwork)

setClass("MBparams",representation(N="numeric",m="numeric",Names="character",Values="matrix",Sim="list"),prototype=list(N=0,m=0,Names=character(),Values=matrix(0,2,0),Sim=list()),sealed=TRUE)
setValidity("MBparams",validMBparams)

setClass("MBdataDE",representation(N="numeric",n="numeric",IDs="character",M="matrix",W="matrix",design="matrix",lmMethod="character",prop="numeric"),prototype=list(N=0,n=0,IDs=character(),M=matrix(0,0,0),W=matrix(0,0,0),design=matrix(0,0,0),lmMethod="ls",prop=0.01),sealed=TRUE)
setValidity("MBdataDE",validMBdataDE)

setClass("MBdataKS",representation(N="numeric",assoc="list",IDs="character",Name="character"),prototype=list(N=0,assoc=list(),IDs=character(),Name=character()),sealed=TRUE)
setValidity("MBdataKS",validMBdataKS)

setClass("MBgibbsPars",representation(chains="numeric",thresh="numeric",burn="list",slice="list",samp="list",KLrepeat="character",method="character"),prototype=list(chains=1,thresh=.1,burn=list("1"=100),slice=list("1"=0),samp=list("1"=1000),KLrepeat="n",method="d"),sealed=TRUE)
setValidity("MBgibbsPars",validMBgibbsPars)

setMethod("addData","MBdataDE",addData.MBdataDE,sealed=TRUE)
setMethod("addGenes",signature(x="MBdataKS",data="MBdataDE"),addGenes.MBdataKS.MBdataDE,sealed=TRUE)
setMethod("addGenes",signature(x="MBdataKS",data="missing"),addGenes.MBdataKS,sealed=TRUE)
setMethod("addNodes","MBnetwork",addNodes.MBnetwork,sealed=TRUE)
setMethod("addParams","MBparams",addParams.MBparams,sealed=TRUE)
setMethod("trimParams",signature(x="MBparams",data="MBdataDE"),trimParams.MBparams.MBdataDE,sealed=TRUE)
setMethod("calcCPDs",signature(x="MBnetwork",data="MBdataDE"),calcCPDs.MBnetwork.MBdataDE,sealed=TRUE)
setMethod("calcLods","MBnetwork",calcLods.MBnetwork,sealed=TRUE)
setMethod("calcMargs","MBnetwork",calcMargs.MBnetwork,sealed=TRUE)
setMethod("calcSim",signature(x="MBparams",meta="missing"),calcSim.MBparams,sealed=TRUE)
setMethod("calcSim",signature(x="MBparams",meta="MBdataKS"),calcSim.MBparams.MBdataKS,sealed=TRUE)
setMethod("calcTruth","MBdataDE",calcTruth.MBdataDE,sealed=TRUE)
setMethod("compatObjects",signature(x="MBnetwork",y="MBparams"),compatObjects.MBnetwork.MBparams,sealed=TRUE)
setMethod("compatObjects",signature(x="MBparams",y="MBnetwork"),compatObjects.MBparams.MBnetwork,sealed=TRUE)
setMethod("compatObjects",signature(x="MBnetwork",y="MBdataDE"),compatObjects.N,sealed=TRUE)
setMethod("compatObjects",signature(x="MBparams",y="MBdataDE"),compatObjects.N,sealed=TRUE)
setMethod("compatObjects",signature(x="MBdataDE",y="MBnetwork"),compatObjects.N,sealed=TRUE)
setMethod("compatObjects",signature(x="MBparams",y="MBdataKS"),compatObjects.N,sealed=TRUE)
setMethod("compatObjects",signature(x="MBdataKS",y="MBparams"),compatObjects.N,sealed=TRUE)
setMethod("CcrossValid",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CcrossValid.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CpermSigMeta",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CpermSigMeta.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CpermSigGene",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CpermSigGene.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CpermSigKnow",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CpermSigKnow.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CpermSigGene",signature(params="MBparams",graph="MBnetwork",data="missing",gibbsPars="MBgibbsPars"),CpermSigGene.MBparams.MBnetwork.MBgibbsPars,sealed=TRUE)
setMethod("CpermSigKnow",signature(params="MBparams",graph="MBnetwork",data="missing",gibbsPars="MBgibbsPars"),CpermSigKnow.MBparams.MBnetwork.MBgibbsPars,sealed=TRUE)
setMethod("CrocAuc",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CrocAuc.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CcorrProf",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CcorrProf.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CcrossValidLik",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CcrossValidLik.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("CpriorEnrich",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CpriorEnrich.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("getAssoc","MBdataKS",getAssoc.MBdataKS,sealed=TRUE)
setMethod("CgibbsSampler",signature(x="MBnetwork",params="MBparams",gibbsPars="MBgibbsPars"),CgibbsSampler.MBnetwork.MBparams.MBgibbsPars,sealed=TRUE)
setMethod("CgreedySearch",signature(params="MBparams",graph="MBnetwork",data="MBdataDE",gibbsPars="MBgibbsPars"),CgreedySearch.MBparams.MBnetwork.MBdataDE.MBgibbsPars,sealed=TRUE)
setMethod("initCounts","MBnetwork",initCounts.MBnetwork,sealed=TRUE)
setMethod("randInit",signature(x="MBnetwork",params="missing"),randInit.MBnetwork,sealed=TRUE)
setMethod("randInit",signature(x="missing",params="MBparams"),randInit.MBparams,sealed=TRUE)
setMethod("CsampleNIter",signature(x="MBnetwork",params="MBparams"),CsampleNIter.MBnetwork.MBparams,sealed=TRUE)
setMethod("setLMmethod","MBdataDE",setLMmethod.MBdataDE,sealed=TRUE)
setMethod("setProp","MBdataDE",setProp.MBdataDE,sealed=TRUE)
setMethod("setChains","MBgibbsPars",setChains.MBgibbsPars,sealed=TRUE)
setMethod("setThresh","MBgibbsPars",setThresh.MBgibbsPars,sealed=TRUE)
setMethod("setBurn","MBgibbsPars",setBurn.MBgibbsPars,sealed=TRUE)
setMethod("setSlice","MBgibbsPars",setSlice.MBgibbsPars,sealed=TRUE)
setMethod("setSamp","MBgibbsPars",setSamp.MBgibbsPars,sealed=TRUE)
setMethod("setKLrepeat","MBgibbsPars",setKLrepeat.MBgibbsPars,sealed=TRUE)
setMethod("setGSmethod","MBgibbsPars",setGSmethod.MBgibbsPars,sealed=TRUE)
setMethod("setValues","MBparams",setValues.MBparams,sealed=TRUE)
setMethod("setValue","MBparams",setValue.MBparams,sealed=TRUE)
setMethod("setZeros","MBparams",setZeros.MBparams,sealed=TRUE)
setMethod("setZero","MBparams",setZero.MBparams,sealed=TRUE)
setMethod("setPrior",signature(x="MBparams",data="missing"),setPrior.MBparams,sealed=TRUE)
setMethod("setPrior",signature(x="MBparams",data="MBdataDE"),setPrior.MBparams.MBdataDE,sealed=TRUE)
setMethod("drawStory",signature(network="MBnetwork",params="MBparams"),drawStory.MBnetwork.MBparams,sealed=TRUE)
setMethod("drawStory",signature(network="missing",params="MBparams"),drawStory.MBparams,sealed=TRUE)

# function run upon loading mBison

.onLoad <- function(lib, pkg)
{
    if(!require(methods)) stop("methods package required for package mBison")
    library.dynam("mBison",pkg)
}

# function run upon unloading mBison

.Last.lib <- function(libpath)
{
    library.dynam.unload("mBison",libpath)
}