## ----setClass------------------------------------------------------------
.AnnMat <- setClass("AnnMat",
    representation(matData="matrix", rowData="data.frame",
        colData="data.frame"))


## ----generating-function-------------------------------------------------
am0 <- .AnnMat()
am1 <- .AnnMat(
      matData=matrix(1:10, 2, dimnames=list(letters[1:2], LETTERS[1:5])),
      rowData=data.frame(roi_id=1:2),
      colData=data.frame(
          sample_id=1:5,
          treatment=c("A", "A", "B", "B", "B")))


## ----getters-------------------------------------------------------------
setGeneric("rowData", function(x, ...) standardGeneric("rowData"))

setGeneric("colData", function(x, ...) standardGeneric("colData"))

setGeneric("matData", function(x, ...) standardGeneric("matData"))


## ----getter-methods------------------------------------------------------
setMethod("rowData", "AnnMat", function(x, ...) x@rowData)

setMethod("colData", "AnnMat", function(x, ...) x@colData)

setMethod("matData", "AnnMat", function(x, ...) x@matData)


## ----dim-getGeneic-------------------------------------------------------
getGeneric("dim")


## ----dim-setMethod-------------------------------------------------------
setMethod("dim", "AnnMat", function(x) dim(matData(x)))

setMethod("dimnames", "AnnMat", function(x) dimnames(matData(x)))


## ----nrow-for-free-------------------------------------------------------
dim(am1)
nrow(am1)


## ----show----------------------------------------------------------------
setMethod("show", "AnnMat", function(object)
{
      cat("class:", class(object), "\n")
      cat("dim:", dim(object), "\n")
      cat("rowData names():", names(rowData(object)), "\n")
      cat("colData names():", names(colData(object)), "\n")
})
am1


## ----update--------------------------------------------------------------
df <- data.frame(x=1:5, y=5:1)
df[,"x"] <- log(df$x)


## ----subset-assign-df----------------------------------------------------
head(get("[<-.data.frame"))


## ----setter-matData------------------------------------------------------
setGeneric("matData<-", function(x, ..., value)
      standardGeneric("matData<-"))


## ----setter-matData-impl-------------------------------------------------
setReplaceMethod("matData", c("AnnMat", "matrix"),
      function(x, ..., value)
{
      x@matData <- value
      x
})


## ----setter-dimnames-impl------------------------------------------------
setReplaceMethod("dimnames", c("AnnMat", "list"), 
      function(x, value)
{
      dimnames(matData(x)) <- value
      value
})


## ----setValidity---------------------------------------------------------
setValidity("AnnMat", function(object) {
      msg <- NULL
      if (nrow(rowData(object)) != nrow(matData(object)))
          msg <- c(msg, 
              "number of rowData rows and matData rows differ")
      if (nrow(colData(object)) != ncol(matData(object)))
          msg <- c(msg,
              "number of colData rows and matData columns differ")
      if (is.null(msg)) TRUE else msg
})


## ----validity-action-----------------------------------------------------
.AnnMat(matData=matrix(1:10, 2), 
      rowData=data.frame(roi_id=1:2),
      colData=data.frame(sample_id=1:5))
cat(try({
      .AnnMat(matData=matrix(1:10, 2), 
          rowData=data.frame(roi_id=1:5),
          colData=data.frame(sample_id=1:2))
}))


## ----subsetting----------------------------------------------------------
getGeneric("[")


## ----subset-facade-------------------------------------------------------
setMethod("[", c("AnnMat", "ANY", "ANY"),
      function(x, i, j,  ..., drop=TRUE)
{
      ## FIXME: warn user about ignoring 'drop'?
     initialize(x, matData=matData(x)[i, j, drop=FALSE],
          rowData=rowData(x)[i,,drop=FALSE],
          colData=colData(x)[,j,drop=FALSE], ...)
})

setMethod("[", c("AnnMat", "ANY", "missing"),
      function(x, i, j, ..., drop=TRUE)
{
      initialize(x, matData=matData(x)[i,,drop=FALSE],
          rowData=rowData(x)[i,,drop=FALSE])
})

setMethod("[", c("AnnMat", "missing", "ANY"),
      function(x, i, j, ..., drop=TRUE)
{
      initialize(x, matData=matData(x)[,j,drop=FALSE],
          colData=colData(x)[j,,drop=FALSE])
})

setMethod("[", c("AnnMat", "missing", "missing"),
      function(x, i, j, ..., drop=TRUE)
{
      initialize(x, ...)
})