\name{Assays-class}
\docType{class}

\alias{class:Assays}
\alias{Assays-class}
\alias{Assays}
\alias{length,Assays-method}
\alias{names,Assays-method}
\alias{names<-,Assays-method}
\alias{[[,Assays,ANY,ANY-method}
\alias{[[<-,Assays,ANY,ANY-method}
\alias{dim,Assays-method}
\alias{[,Assays,ANY-method}
\alias{[,Assays,ANY,ANY,ANY-method}
\alias{[<-,Assays,ANY,ANY,ANY-method}
\alias{rbind,Assays-method}
\alias{cbind,Assays-method}
\alias{arbind,Matrix-method}
\alias{acbind,Matrix-method}
\alias{updateObject,Assays-method}

\alias{class:SimpleListAssays}
\alias{SimpleListAssays-class}
\alias{SimpleListAssays}

\alias{class:ShallowData}
\alias{ShallowData-class}
\alias{ShallowData}

\alias{class:ShallowSimpleListAssays}
\alias{ShallowSimpleListAssays-class}
\alias{ShallowSimpleListAssays}
\alias{coerce,SimpleList,ShallowSimpleListAssays-method}
\alias{coerce,ShallowSimpleListAssays,SimpleList-method}

\alias{class:AssaysInEnv}
\alias{AssaysInEnv-class}
\alias{AssaysInEnv}
\alias{length,AssaysInEnv-method}
\alias{names,AssaysInEnv-method}
\alias{names<-,AssaysInEnv-method}
\alias{[[,AssaysInEnv,ANY,ANY-method}
\alias{[[<-,AssaysInEnv,ANY,ANY-method}
\alias{coerce,SimpleList,AssaysInEnv-method}
\alias{coerce,AssaysInEnv,SimpleList-method}

\title{Assays objects}

\description{
  The Assays virtual class and its methods provide a formal abstraction
  of the assays slot of \link{SummarizedExperiment} objects.

  SimpleListAssays and ShallowSimpleListAssays are concrete subclasses of
  Assays with the latter being currently the default implementation of Assays
  objects. Other implementations (e.g. disk-based) could easily be added.

  Note that these classes are not meant to be used directly by the end-user
  and the material in this man page is aimed at package developers.
}

\details{
  Assays objects have a list-like semantics with elements having matrix- or
  array-like semantics (e.g., \code{dim}, \code{dimnames}).

  The Assays API consists of:
  \itemize{
    \item (a) The \code{Assays()} constructor function.
    \item (b) Lossless back and forth coercion from/to \link{SimpleList}.
              The coercion method from \link{SimpleList} doesn't need (and
              should not) validate the returned object.
    \item (c) \code{length}, \code{names}, \code{`names<-`},
              \code{[[}, \code{`[[<-`},
              \code{dim}, \code{[}, \code{`[<-`}, \code{rbind}, \code{cbind}.
  }
  An Assays concrete subclass needs to implement (b) (required) plus,
  optionally any of the methods in (c).

  IMPORTANT: Methods that return a modified Assays object (a.k.a.
  endomorphisms), that is, \code{[} as well as replacement methods
  \code{names<-}, \code{[[<-}, and \code{[<-}, must respect the
  \emph{copy-on-change contract}.
  With objects that don't make use of references internally, the developer
  doesn't need to take any special action for that because it's automatically
  taken care of by R itself. However, for objects that do make use of
  references internally (e.g. environments, external pointers, pointer to a
  file on disk, etc...), the developer needs to be careful to implement
  endomorphisms with copy-on-change semantics.
  This can easily be achieved (and is what the default methods for Assays
  objects do) by performaing a full (deep) copy of the object before modifying
  it instead of trying to modify it in-place. Note that the full (deep) copy
  is not always necessary in order to achieve copy-on-change semantics: it's
  enough (and often preferrable for performance reasons) to copy only the
  parts of the objects that need to be modified.

  Assays has currently 3 implementations which are formalized by concrete
  subclasses SimpleListAssays, ShallowSimpleListAssays, and AssaysInEnv.
  ShallowSimpleListAssays is the default. AssaysInEnv is a \emph{broken}
  alternative to ShallowSimpleListAssays that does NOT respect the
  \emph{copy-on-change contract}. It is only provided for illustration
  purposes (see source file Assays-class.R for the details).

  A little more detail about ShallowSimpleListAssays: a small reference
  class hierarchy (not exported from the \pkg{GenomicRanges} name space)
  defines a reference class ShallowData with a single field \code{data}
  of type \code{ANY}, and a derived class ShallowSimpleListAssays
  that specializes the type of \code{data} as \link{SimpleList}, and
  \code{contains=c("ShallowData", "Assays")}. The assays slot of a
  \link{SummarizedExperiment} object contains an instance of
  ShallowSimpleListAssays.
}

\author{Martin Morgan, \url{mtmorgan@fhcrc.org}}

\seealso{
  \itemize{
    \item \link{SummarizedExperiment} objects.

    \item \link[S4Vectors]{SimpleList} objects in the \pkg{S4Vectors} package.
  }
}

\examples{
## ---------------------------------------------------------------------
## DIRECT MANIPULATION OF Assays OBJECTS
## ---------------------------------------------------------------------
m1 <- matrix(runif(24), ncol=3)
m2 <- matrix(runif(24), ncol=3)
a <- Assays(SimpleList(m1, m2))
a

as(a, "SimpleList")

length(a)
a[[2]]
dim(a)

b <- a[-4, 2]
b
length(b)
b[[2]]
dim(b)

names(a)
names(a) <- c("a1", "a2")
names(a)
a[["a2"]]

rbind(a, a)
cbind(a, a)

## ---------------------------------------------------------------------
## COPY-ON-CHANGE CONTRACT
## ---------------------------------------------------------------------

## ShallowSimpleListAssays objects have copy-on-change semantics but not
## AssaysInEnv objects. For example:
ssla <- as(SimpleList(m1, m2), "ShallowSimpleListAssays")
aie <- as(SimpleList(m1, m2), "AssaysInEnv")

## No names on 'ssla' and 'aie':
names(ssla)
names(aie)

ssla2 <- ssla
aie2 <- aie
names(ssla2) <- names(aie2) <- c("A1", "A2")

names(ssla)  # still NULL (as expected)

names(aie)   # changed! (because the names<-,AssaysInEnv method is not
             # implemented in a way that respects the copy-on-change
             # contract)
}
