@@ -17,7 +17,6 @@ License: Artistic-2.0

 LazyLoad: yes

 Imports: methods, graph, parallel

 Suggests: RUnit, Rsamtools (>= 1.5.53)

-Enhances: multicore

 biocViews: Infrastructure, DataImport

 Collate: 

   generics.R OldClass.R Streamer.R

deleted file mode 100644

@@ -1,106 +0,0 @@

-\name{NetCDFFile-class}

-

-\Rdversion{1.1}

-\docType{class}

-

-\alias{NetCDFFile-class}

-\alias{NetCDFFile}

-\alias{precision}

-\alias{dimensions}

-\alias{precision,NetCDFFile-method}

-\alias{dimensions,NetCDFFile-method}

-

-\title{Class "NetCDFFile"}

-

-\description{

-

-  A \code{\linkS4class{NetCDFFile}}-class to interpret data stored in

-  NetCDF files. Users interact with this class through the constructor

-  \code{\link{NetCDFFile}} and methods \code{\link{precision}}, and

-  \code{\link{dimensions}}.

-

-}

-

-\usage{

-NetCDFFile(file = character(), ...)

-\S4method{dimensions}{NetCDFFile}(x, ...)

-\S4method{precision}{NetCDFFile}(x, ...)

-}

-

-\arguments{

-

-  \item{file}{A character string for the path to the NetCDF file.}

-

-  \item{x}{An insance of the \code{NetCDFFile} class.}

-

-  \item{...}{Additional arguments, passed to the \code{$new} method of

-    this class. Currently ignored.}

-

-}

-

-\section{Class Methods}{

-  \describe{

-

-    \item{\code{precision()}:}{Returns a named character vector

-      corresponding to the storage precision of the variables in the

-      NetCDF file.}

-

-    \item{\code{dimensions()}:}{Returns a named \code{list} containing

-      the names and lengths of the dimensions for each variable in the

-      NetCDF file.}

-

-  }

-}

-

-\section{Class Internal Fields: (For developers)}{

-  \describe{

-

-    \item{\code{con}:}{Object of class \code{ncdf4}. An R ncdf4

-      connection obtained by opening a NetCDF file from which data is to

-      be read using the \code{nc_open} function.}

-

-    \item{\code{dimensions}:}{A named \code{list} corresponding to the

-      names of the variables in the NetCDF file. Each element of the

-      \code{list} is a named integer vector, with names of the

-      dimensions for each variable and values the length of the

-      dimension in the NetCDF file.}

-

-    \item{\code{precision}:}{A named character vector of the number of

-      precision for each variable stored in the NetCDF file.}

-

-  }

-}

-

-\section{Class Internal Methods: (For developers)}{

-  \describe{

-

-    \item{\code{initialize(file=character(), ...)}:}{Called during

-      object creation with \code{file} being the path to a valid NetCDF

-      file.}

-

-    \item{\code{getPath()}:}{Retrive the path to the NetCDF file.}

-

-    \item{\code{getDimensions()}:}{Retrieves a list of variables, with

-      each element in the list containing a named integer vector of

-      dimensions and their lengths.}

-

-    \item{\code{getPrecision()}:}{Retrieves the precision of each

-      variable in the NetCDF file.}

-

-  }

-}

-

-\author{Nishant Gopalakrishnan \url{ngopalak@fhcrc.org}}

-

-\seealso{\code{\link{stream}}}

-

-\examples{

-\dontrun{

-pth <- system.file("extdata", "NetCDFData.nc", package = "Streamer")

-ncFile <- NetCDFFile(pth)

-dimensions(ncFile)

-precision(ncFile)

-ncFile

-}

-}

-\keyword{classes}

deleted file mode 100644

@@ -1,142 +0,0 @@

-\name{NetCDFInput-class}

-

-\Rdversion{1.1}

-\docType{class}

-

-\alias{NetCDFInput-class}

-\alias{NetCDFInput}

-\alias{dimensions,NetCDFInput-method}

-

-\title{Class "NetCDFInput"}

-

-\description{

-

-  A \code{\linkS4class{NetCDFInput}}-class to retrieve data store in

-  NetCDF files. Users interact with this class through the constructor

-  \code{\link{NetCDFInput}} and methods \code{\link{yield}},

-  \code{\link{status}}, and \code{\link{reset}}.

-

-}

-

-\usage{

-NetCDFInput(ncdf, var, slice, ..., verbose = FALSE)

-\S4method{dimensions}{NetCDFInput}(x, ...)

-}

-

-\arguments{

-

-  \item{ncdf}{An object of class \code{NetCDFFile} rrepresenting the

-    file from which data is to be read.}

-

-  \item{var}{A \code{character(1)} string naming the variable to be read

-    from the NetCDF file.}

-

-  \item{slice}{A named integer vector specifying the slice to be

-    iterated over. The names correspond to dimensions of \code{var}, the

-    values to the number of elements to be retrieved with each

-    \code{yield}.}

-

-  \item{...}{Additional arguments, passed to the \code{$new} method of

-    this class. Currently ignored.}

-

-  \item{verbose}{\code{logical(1)} indicating whether class methods

-    should report to the user.}

-

-  \item{x}{An instance of the \code{NetCDFInput} class.}

-

-}

-

-\section{Class Methods}{

-

-  \describe{

-

-    \item{\code{dimensions()}:}{Return the dimensions associated with

-      the variable this object is iterating over.}

-

-    \item{\code{yield()}:}{Processes the NetCDF file and retrieves a

-      matrix of data from the NetCDF file corresponding to the slice

-      size that has been set.  Repeated calls to the \code{yield}

-      function retrieves the next block of data until the end of file

-      has been reached.}

-

-    \item{\code{reset()}:}{Resets the cursor that tracks the next block

-      of data to be read to the start of the file.}

-

-     \item{\code{status()}:}{Returns a named numeric vector for the

-       position of the start of the block from which data will be read

-       for the next call to the \code{yield} function.}

-

-  }

-}

-

-\section{Class Internal Fields: (For developers)}{

-  \describe{

-

-    \item{\code{ncdf}:}{An object of class \code{NetCDFFile} from which

-      data is being read.}

-

-    \item{\code{name}:}{A \code{character(1)} specifying the name of

-      the variable that is being read.}

-

-    \item{\code{slice}:}{A named numeric vector specifying the size of

-      the chunk of data that will be retrived along each dimension using

-      the \code{yield} method.}

-

-    \item{\code{start}:}{A named numeric vector specifying the position

-      along each dimension from which data will start to be read for the

-      next call to the \code{yield} function.}

-

-    \item{\code{verbose}:}{Report messages from evalaution?}

-

-  }

-}

-

-\section{Class Internal Methods: (For developers)}{

-  \describe{

-

-    \item{\code{initialize(ncdf, var, slice, ..., verbose)}:}{Called

-      during object creation with values to initialize fields.}

-

-    \item{\code{yield()}:}{Processes the NetCDF file and retrieves a

-      block of data from the NetCDF file corresponding to the slice size

-      that has been set.  Repeated calls to the \code{yield} function

-      retrieves the next block of data until the end of file has been

-      reached.}

-

-    \item{\code{reset()}:}{Resets the cursor that tracks the next block

-      of data to be read to the start of the file.}

-

-    \item{\code{status()}:}{Retrieves the position of the start of the

-      block from which data will be read for the next call to the

-      \code{yield} function.}

-

-    \item{\code{.getCounts()}:}{Retrieve the dimensions of the next

-      slice.}

-

-    \item{\code{.getNextStart()}:}{Retrieve coordinates at which next

-      yield starts.}

-

-  }

-}

-

-\author{Nishant Gopalakrishnan \url{ngopalak@fhcrc.org}}

-

-\seealso{\code{\link{NetCDFFile}}}

-

-\examples{

-\dontrun{

-    showClass("NetCDFInput")

-

-pth <- system.file("extdata", "NetCDFData.nc", package = "Streamer")

-ncFile <- NetCDFFile(pth)

-dimensions(ncFile)		# variable names and dimensions

-

-ncProd <- NetCDFInput(ncFile, "2dIntData", c(sampleDim=5, snpDim=2))

-yield(ncProd)

-status(ncProd)

-reset(ncProd)

-yield(ncProd)

-}

-

-}

-\keyword{classes}