#What are the minimum specifications needed to
#a) massage an ExpressionSet+formula+parms model spec
#into input to an arbitrary machine learning function
#in some R package
#b) massage the output of an arbitrary machine learning
#function in some R package into an MLOutput instance
#

library(MLInterfaces)
library(MASS)
data(crabs)

setClass("MLIschema", representation(
 mlpackageName="character",
 mlfunctionName="character",
 usesFormula="logical",
 retObjectBuilder="function",
 predictMethodName="character",
 predictParms="list",
 tuningParms="list"))

classifOutBuilder = function(mlfunctionName, rans, call, ...) {
 new("classifOutput", method=mlfunctionName, predLabels=
     newPredClass(do.call(predictMethodName, list(rans, ...))),
     call=call, RObject=rans) }


makeMLIschema = function( mlpackageName,
  mlfunctionName, usesFormula,
  predictMethodName, predictParms=list(), retObjectBuilder=NULL, ... ) {
  extra = list(...)
 # cc = match.call()
 # ars = cc[-1]
 # opt = ars[-c(1:4)]
 # anames = names(ars)
 # if (!("predictParms" %in% names(anames))) predictParms=list()
  if (missing(predictParms)) predictParms=list()
  if (is.null(retObjectBuilder)) {
    retObjectBuilder=function(mlfunctionName, rans, call, ...) {
     new("MLOutput", method=mlfunctionName, RObject=rans, call=call,
		distMat=as.dist(matrix(0,1,1))) 
    }}
  new("MLIschema", 
    mlpackageName=mlpackageName,
    mlfunctionName=mlfunctionName,
    usesFormula=usesFormula,
    predictMethodName=predictMethodName, 
    retObjectBuilder=retObjectBuilder,
    predictParms=predictParms,
    tuningParms=extra) }
    

setMethod("MLearn", c("formula", "data.frame",
   "MLIschema" , "numeric"), function( formula,
     data, method, trainInd, mlSpecials = NULL) {
#
# step 1 -- get the function to be called from the schema object
#
    learnFunNm = paste(method@mlpackageName,
      method@mlfunctionName, sep="::")
    if (method@usesFormula==FALSE) stop("method does not accept formula")
#
# can't just use do.call("nnet::nnet" ... it seems; instead, build
# the function using an initial call to resolution operator
#
    thefun = do.call("::", list(method@mlpackageName, method@mlfunctionName))
#
# step 2 -- now build the parms to the call
#
    callParms = list(formula=formula, data=data[trainInd,])
    if (length(method@tuningParms)>0) {
       pn = names(method@tuningParms)
       for (i in 1:length(pn))
         callParms[[pn[i]]] = method@tuningParms[[i]]
       }
#
# step 3 -- execute and get the original object
#
    RANS = do.call( thefun, callParms )
#
# step 4 --  transform value to something we can work with
#
#    new("MLOutput", method=learnFunNm, distMat=as.dist(as.matrix(0,1,1)),
#      RObject=RANS, call=match.call())
     method@retObjectBuilder(learnFunNm, RANS, call=match.call())
})

randomForestI = function(...) makeMLIschema(
     "randomForest", "randomForest",
     TRUE, "predict", predictParms=list(), ... )

#debugMethod("MLearn", c("formula", "data.frame",
#   "MLIschema" , "numeric"))


d1 = MLearn(sp~CW, crabs, randomForestI(), c(1:40,101:140) )
#d2 = MLearn(sp~CW, crabs, randomForestI(ntree=20) , c(1:40,101:140))