@@ -64,7 +64,7 @@ smoothSds <- function(BSseqStat, k = 101, qSd = 0.75, mc.cores = 1,

                              rawSds <- as.array(rawSds)

                              smoothSd(rawSds, k = k, qSd = qSd)

                          }, mc.cores = mc.cores))

-    smoothSds <- .DelayedMatrix(as.matrix(smoothSds))

+    smoothSds <- as.matrix(smoothSds)

     if("smoothSds" %in% names(getStats(BSseqStat)))

         BSseqStat@stats[["smoothSds"]] <- smoothSds

     else

@@ -92,12 +92,11 @@ computeStat <- function(BSseqStat, coef = NULL) {

                                      what = "cor.coefficients")[coef,coef]

         # NOTE: classifyTestsF() calls as.matrix(tstats) and so realises this

         #       array

-        stat <- .DelayedMatrix(as.matrix(classifyTestsF(tstats,

-                                                        cor.coefficients,

-                                                        fstat.only = TRUE)))

+        stat <- as.matrix(

+            classifyTestsF(tstats, cor.coefficients, fstat.only = TRUE))

         stat.type <- "fstat"

     } else {

-        stat <- .DelayedMatrix(tstats)

+        stat <- tstats

         stat.type <- "tstat"

     }

     if("stat" %in% names(getStats(BSseqStat))) {

@@ -9,9 +9,6 @@ setValidity("BSseqStat", function(object) {

        anyDuplicated(names(object@stats)))

         msg <- validMsg(msg, "the 'stats' list needs to be named with unique names.")

     for(name in c("rawSds", "smoothsSds", "stat", "rawTstats")) {

-        if(name %in% names(object@stats) &&

-           !is(object@stats[[name]], "DelayedMatrix"))

-            msg <- validMsg(msg, sprintf("component '%s' of slot 'stats' has to be a DelayedMatrix object", name))

         if(name %in% names(object@stats) && isTRUE(nrow(object@stats[[name]]) != length(object@gr)))

             msg <- validMsg(msg, sprintf("component '%s' of slot 'stats' has to have the same number of rows as slot 'gr' is long", name))

     }

@@ -24,17 +21,6 @@ setMethod("show", signature(object = "BSseqStat"),

               cat(" ", length(object), "methylation loci\n")

               cat("based on smoothed data:\n")

               cat(" ", object@parameters$smoothText, "\n")

-              not_delayed_matrices <- c("cor.coefficients", "stat.type")

-              delayed_matrices <- setdiff(names(object@stats),

-                                          not_delayed_matrices)

-              is_HDF5Array_backed <- vapply(object@stats[delayed_matrices],

-                                            .isHDF5ArrayBacked,

-                                            logical(1L))

-              if (any(is_HDF5Array_backed)) {

-                  cat("'stats' slot is HDF5Array-backed\n")

-              } else {

-                  cat("'stats' slot is in-memory\n")

-              }

           })

 setMethod("[", "BSseqStat", function(x, i, ...) {

@@ -48,7 +34,6 @@ setMethod("[", "BSseqStat", function(x, i, ...) {

     x@stats <- lapply(statnames, function(nam) {

         if(nam %in% c("rawTstats", "modelCoefficients", "rawSds", "smoothSds",

                       "stat")) {

-            stopifnot(is(x@stats[[nam]], "DelayedMatrix"))

             return(x@stats[[nam]][i,,drop=FALSE])

         }

         x@stats[[nam]]

@@ -59,26 +44,24 @@ setMethod("[", "BSseqStat", function(x, i, ...) {

 BSseqStat <- function(gr = NULL, stats = NULL, parameters = NULL) {

     out <- new("BSseqStat")

     out@gr <- gr

-    not_delayed_matrices <- c("cor.coefficients", "stat.type")

-    delayed_matrices <- setdiff(names(stats), not_delayed_matrices)

-    stats[delayed_matrices] <- endoapply(stats[delayed_matrices],

-                                         .DelayedMatrix)

     out@stats <- stats

     out@parameters <- parameters

     out

 }

-setMethod("updateObject", "BSseqStat",

-          function(object, ...) {

-              not_delayed_matrices <- c("cor.coefficients", "stat.type")

-              delayed_matrices <- setdiff(names(stats), not_delayed_matrices)

-              stats <- object@stats

-              stats[delayed_matrices] <- endoapply(stats[delayed_matrices],

-                                                   .DelayedMatrix)

-              object@stats <- stats

-              object

-          }

-)

+# TODO: updateObject() to use ordinary matrix instead of DelayedMatrix with

+#       in-memory seed.

+# setMethod("updateObject", "BSseqStat",

+#           function(object, ...) {

+#               not_delayed_matrices <- c("cor.coefficients", "stat.type")

+#               delayed_matrices <- setdiff(names(stats), not_delayed_matrices)

+#               stats <- object@stats

+#               stats[delayed_matrices] <- endoapply(stats[delayed_matrices],

+#                                                    .DelayedMatrix)

+#               object@stats <- stats

+#               object

+#           }

+# )

 ## summary.BSseqStat <- function(object, ...) {

 ##     quant <- quantile(getStats(object)[, "tstat.corrected"],

@@ -1,5 +1,5 @@

 setClass("BSseqTstat", contains = "hasGRanges",

-         representation(stats = "DelayedMatrix",

+         representation(stats = "matrix",

                         parameters = "list")

          )

 setValidity("BSseqTstat", function(object) {

@@ -17,11 +17,6 @@ setMethod("show", signature(object = "BSseqTstat"),

               cat(" ", object@parameters$smoothText, "\n")

               cat("with parameters\n")

               cat(" ", object@parameters$tstatText, "\n")

-              if (.isHDF5ArrayBacked(object@stats)) {

-                  cat("'stats' slot is HDF5Array-backed\n")

-              } else {

-                  cat("'stats' slot is in-memory\n")

-              }

           })

 setMethod("[", "BSseqTstat", function(x, i, ...) {

@@ -37,7 +32,7 @@ setMethod("[", "BSseqTstat", function(x, i, ...) {

 BSseqTstat <- function(gr = NULL, stats = NULL, parameters = NULL) {

     out <- new("BSseqTstat")

     out@gr <- gr

-    out@stats <- .DelayedMatrix(stats)

+    out@stats <- stats

     out@parameters <- parameters

     out

 }

@@ -75,7 +70,7 @@ plot.BSseqTstat <- function(x, y, ...) {

 setMethod("updateObject", "BSseqTstat",

           function(object, ...) {

               stats <- object@stats

-              stats <- .DelayedMatrix(stats)

+              stats <- stats

               object@stats <- stats

               object

           }

@@ -27,19 +27,6 @@

     quantile(x, ...)

 }

-.DelayedMatrix <- function(x) {

-    x_name <- deparse(substitute(x))

-    X <- try(DelayedArray(x), silent = TRUE)

-    if (is(X, "try-error")) {

-        stop("Could not construct DelayedMatrix from '", x_name, "'",

-             call. = FALSE)

-    }

-    if (!is(X, "DelayedMatrix")) {

-        stop("'", x_name, "' must be matrix-like", call. = FALSE)

-    }

-    X

-}

-

 .isSimpleDelayedMatrix <- function(x) {

     is(x@seed, "matrix")

 }