deleted file mode 100644

@@ -1,25 +0,0 @@

-.ParallelConnector <-

-    setRefClass("ParallelConnector", contains="Consumer",

-                fields=list(.upstream="ANY"))

-

-.ParallelConnector$methods(

-    yield = function() 

-   {  

-        "Read data from childProcess"

-        if (verbose) msg(".ParallelConnector$yield()")   

-        if(is(.self$inputPipe, "uninitializedField")

-           || is(.self$.upstream, "uninitializedField")) 

-        {

-            stop("ParallelConnector not connected to a valid stream")

-        

-        } else {

-        

-            res <- readChild(.self$.upstream)

-            if(is.raw(res)) unserialize(res) else res 

-        

-        }

-    })

-

-ParallelConnector <- function(...)

-    .ParallelConnector$new(...)

-

deleted file mode 100644

@@ -1,62 +0,0 @@

-## TOut

-

-.TOut <- setRefClass("TOut", 

-    contains="Consumer",

-    fields=list(.start = "numeric"))

-

-.TOut$methods(

-    initialize =function(...) 

-    {  

-       "initialize TOut"

-        callSuper(..., .start = 1L)

-    },

-    yield = function() 

-    {

-        "Calls yield on the inputPipe"

-        if (verbose) msg(".TOut$yield()")

-        inputPipe$.add(inputPipe$yield())

-        dat <- inputPipe$.records

-        inputPipe$.dump()

-        dat

-    })

-

-TOut <- function(...) .TOut$new(...)

-

-## TConnector

-

-.TConnector <- setRefClass("TConnector", 

-    contains = "Consumer",

-    fields = list(

-        .records = "list",

-        .tOuts="list"

-    ))

-    

-.TConnector$methods(

-    initialize = function(...) 

-    {   

-        "initialize TConnector"

-        callSuper(..., .tOuts = list())

-    },   

-    .add = function(input)

-    { 

-        ".add (incomplete) 'input'"

-        if (verbose) msg("TConnector$.add()")

-        .self$.records <- c(.records, input)

-        .self    

-    },

-    .dump = function() 

-    {    

-        "Clear .records that are used"

-        if (verbose) msg("TConnector$.dump()")

-        mn <- min(sapply(.tOuts, function(x) x$.start))

-        if (mn != 1L) {

-            for(i in seq_along(.tOuts))

-                .self$.tOuts[[i]]$.start <- .tOuts[[i]]$.start - mn +1L

-            .self$.records[seq_len(mn - 1L)] <- NULL

-        }

-        .self

-   })

-

-TConnector <- function(...) .TConnector$new(...)

-

-

deleted file mode 100644

@@ -1,32 +0,0 @@

-.YConnector <- setRefClass("YConnector",

-    contains = "Consumer",

-    fields = list(.upstream="list", .fun="function"

-    ))

-    

-.YConnector$methods(

-    initialize = function(..., fun) 

-    {

-        "initialize YConnector"

-        if(missing(fun))

-            fun <- function(...) as.list(...)

-        callSuper(..., .upstream=list(), .fun=fun)

-    },

-    yield = function() 

-    {

-        "yield data from stream"

-        args <- lapply(.self$.upstream, function(k) {

-                       k$yield()

-                   })

-        do.call(.self$.fun, args)

-    },

-    show = function()

-    {

-        callSuper()

-        upstream <- paste(sapply(.upstream, "class"), collapse = " ,")

-        upstream[!nzchar(upstream)] <- "uninitialized field"

-        txt <- sprintf("upstream: %s", upstream)

-        cat(strwrap(txt, exdent=2), sep="\n")

-    })

-

-YConnector <- function(fun, ...)

-    .YConnector$new(fun=fun, ...)

deleted file mode 100644

@@ -1,58 +0,0 @@

-\name{ParallelConnector-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{ParallelConnector-class}

-\alias{ParallelConnector}

-\title{Class "ParallelConnector"}

-

-\description{

-

-  The \code{ParallelConnector} \code{\linkS4class{Consumer}}-class can

-  be used to parallelize the computations done by blocks directly

-  connected to the \code{ParallelConnector} and all blocks down-stream

-  to the \code{ParallelConnector}. i.e Computations performed by the

-  block directly connected up-stream to the \code{ParallelConnector} and

-  all blocks connected down-stream to the \code{ParallelConnector} in a

-  stream happen simultaneously.

-

-}

-

-\usage{ParallelConnector(...)}

-

-\arguments{

-  \item{...}{Additional arguments to be passed to the constructor.}

-}

-

-\section{Constructors}{

-  Use \code{ParallelConnector} to construct instances of this class.

-}

-

-\section{Fields}{

-  \describe{

-    \item{\code{.upstream}:}{Object of class \code{ANY}. The output of a

-      call to the \code{mcparallel} function from the

-      \code{parallel}-package. This field is internal to the

-      \code{ParallelConnector} class and will be populated by a call to

-      the \code{stream} method or the \code{connect} function used to

-      connect the \code{ParallelConnector} to other blocks in a

-      \code{stream}.}

-  }

-}

-

-\section{Methods}{

-  \describe{

-    \item{\code{initialize(...)}:}{Initializes the fields of the

-        \code{ParallelConnector} class.}

-    \item{\code{yield()}:}{Reads data from the child processes and converts the

-        result (which must be a list of \code{raw}) into a vector of

-        \code{character}.}

-  }

-}

-

-\author{Nishant Gopalakrishnan, Martin Morgan}

-

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

-

-\examples{showClass("ParallelConnector")}

-

-\keyword{classes}

deleted file mode 100644

@@ -1,92 +0,0 @@

-\name{TConnector-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{TConnector}

-\alias{TConnector-class}

-

-\title{Class "TConnector"}

-

-\description{

-

-  A \code{\linkS4class{Consumer}}-class that is used to connect the

-  output of one stream to several \code{Consumer} \code{stream}s that

-  perform different operations on the records. The \code{TConnector}

-  manages the records supplied to it to ensure that all streams get

-  access to \emph{all} records passed to the TConnector.

-

-  A \code{TConnector} can be connected to other \code{Producer} and

-  \code{Consumer} objects using the \code{\link{connect}} function.

-}

-

-\usage{TConnector(...)}

-

-\arguments{

-  \item{...}{Arguments passed to the \code{\linkS4class{Consumer}}-class

-    constructors.}

-}

-

-\section{Constructors}{

-  Use \code{TConnector} to construct instances of this class.

-}

-

-\section{Fields}{

-  \describe{

-

-    \item{\code{.records}:}{ A temporary buffer used to save records

-      retrieved from the \code{Producer} or \code{Consumer} class

-      connector up-stream to the \code{TConnector}. This field is used

-      internally by class methods and is not intended to be manipulated

-      directly by the user.}

-

-    \item{\code{.tOuts}:}{A \code{list} of objects of class \code{TOut}

-      of length equal to the number of streams connected down-stream to

-      it. This field is used internally by the \code{TConnector}-class

-      method and not intended to be manipulated directly by the user.}

-

-   }

-}

-

-\section{Methods}{

-  \describe{

-

-    \item{\code{.add()}:}{An internal method to add records to the

-      internal buffer(\code{.records}).}

-

-    \item{\code{.dump()}:}{An internal method to remove records that

-      have been passed down to all the down-stream classes (and are no

-      longer needed) from the internal buffer(\code{.records}).}

-

-  }

-}

-

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

-

-\seealso{\code{\link{stream}},\code{\link{YConnector}}, \code{\link{connect}} }

-

-\examples{

-

-### Two Streams b, c1 and b, c2 connected with a Tconnector t

-fl <- system.file("extdata", "s_1_sequence.txt", package="Streamer")

-b <- RawInput(fl, 100L, reader=rawReaderFactory(1e4))

-### c1 and c2 return different number of records

-c1 <- RawToChar()

-c2 <- RawToChar()

-t <- TConnector()

-

-### Connect the blocks together using the connect function

-blocks <- list(b=b, c1=c1, c2=c2, t=t)

-df <- data.frame(from = c("b", "t", "t"), 

-                 to = c("t", "c1", "c2"))

-res <- connect(blocks, df)

-

-### yield on c2 returns 20 records 

-yield(res$c2)

-### yield on c1 returns the same records as with yield on c2 

-### 10 records at a time

-yield(res$c1)

-yield(res$c1)

-

-}

-

-\keyword{classes}

-

deleted file mode 100644

@@ -1,57 +0,0 @@

-\name{TOut-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{TOut}

-\alias{TOut-class}

-

-\title{Class "TOut"}

-

-\description{

-

-  A \code{\linkS4class{Consumer}}-class that is used internally to connect 

-  several \code{Consumer} streams to a \code{TConnector}-class.

- 

-  This class is only for use by functions internal to the \code{Streamer}

-  package. The \code{TOut}-class is responsible for filing the \code{.records}

-  field of the \code{TConnector} with adequate number of records.

-}

-

-\usage{TOut(...)}

-

-\arguments{

-  \item{...}{Arguments passed to the \code{\linkS4class{Consumer}}-class

-    constructors.}

-}

-

-\section{Constructors}{

-  Use \code{TOut} to construct instances of this class.

-}

-

-\section{Fields}{

-  \describe{

-

-    \item{\code{.start}:}{A \code{integer(1)} indicating the start

-      position of the record to be read next.}

-

-  }

-}

-

-\section{Methods}{

-  \describe{

-

-    \item{\code{.add(input)}:}{Temporarily store records fro sbusequent

-      use.}

-

-    \item{\code{.dump()}:}{Remove records not required for subsequent

-      use.}

-  }

-}

-

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

-

-\seealso{\code{\link{TConnector}}}

-

-\examples{showClass("TOut")}

-

-\keyword{classes}

-

deleted file mode 100644

@@ -1,103 +0,0 @@

-\name{YConnector-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{YConnector}

-\alias{YConnector-class}

-

-\title{Class "YConnector"}

-

-\description{

-

-  The \code{YConnector} \code{\linkS4class{Consumer}}-class can be used to 

-  combine the output of multiple \code{stream}'s together. The output records of

-  the \code{stream}'s are combined using a user supplied function (\code{fun}) 

-  passed to the constructor of the \code{YConnector} class. The output of the

-  \code{YConnector} can then be used to feed a \code{Consumer}-class connected 

-  down-stream to it.

-

-  The \code{YConnector} can be connector to other \code{Producer} and

-  \code{Consumer} objects using the \code{\link{connect}} function.

-

-}

-

-\section{Methods}{

-  Methods defined on this class include:

-  \describe{

-

-      \item{show}{\code{signature(object = "YConnector")}: Displays the

-        names of the up-stream components to which the

-        \code{YConnector}-class has been connected.}

-

-  }

-}

-

-\usage{YConnector(fun, ...)}

-

-\arguments{

-

-   \item{fun}{A \code{function} that is used to combine the output of

-     the streams connected up-stream to the \code{YConnector}. The

-     function \code{fun} takes named arguments. The names correspond to

-     the names of the objects passed to the \code{connect} function used

-     to connect the \code{YConnector} to up-stream \code{Streamer}

-     classes.}

-

-  \item{...}{Arguments passed to the \code{\linkS4class{Consumer}}-class

-    constructors.}

-

-}

-

-

-\section{Constructors}{

-  Use \code{YConnector} to construct instances of this class.

-}

-

-\section{Fields}{

-  \describe{

-

-    \item{\code{.fun}:}{User defined \code{function} to combine the

-      output of several streams. The function is applied on the named

-      outputs obtained by calling the \code{yield} method on the named

-      streams connected upstream to it.}

-

-    \item{\code{.upstream}:}{A named \code{list} of objects connected

-      up-stream to the \code{YConnector}-class. This field is meant to

-      be internal to the class and is only modified by using the

-      \code{connect} function to connect the \code{YConnector} to other

-      \code{Streamer} objects.}

-

-  }

-}

-

-\section{Methods}{There are no methods unique to this class.}

-

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

-

-\seealso{\code{\link{stream}},\code{\link{TConnector}}, \code{\link{connect}} }

-

-\examples{

-

-fl <- system.file("extdata", "s_1_sequence.txt", package="Streamer")

-#### Blocks for stream1 

-b1 <- RawInput(fl, 100L, reader=rawReaderFactory(1e4))

-c1 <- RawToChar()

-

-#### Blocks for stream2

-b2 <- RawInput(fl, 100L, reader=rawReaderFactory(1e4))

-c2 <- RawToChar()

-#### YConnector with function list for combining the blocks

-y <- YConnector(fun=list)

-

-blocks <- structure(list(b1,c1, b2, c2, y), 

-                    names = c("b1", "c1", "b2", "c2","y"))

-df <- data.frame(from =c("b1", "b2", "c1", "c2"), to = c("c1", "c2", "y", "y"))

-#### Connect the blocks using the connect function

-res <- connect(blocks, df)

-y

-

-#### Yield data from the y connector

-yield(res$y)

-}

-

-\keyword{classes}

-

deleted file mode 100644

@@ -1,71 +0,0 @@

-\name{connect}

-\alias{connect}

-

-\title{Function to create a complex stream}

-

-\description{

-

-  The function \code{connect} can be used to connect \code{Producer} and

-  \code{Consumer} components together.

-  

-  For simple streams, it may be more appropriate to use the

-  \code{\link{stream}} method. The \code{connect} function is useful for

-  connecting together more complex \code{stream}s involving classes such

-  as \code{YConnector}, \code{TConnector}, \code{ParallelConnector} etc

-  which cannot be handled by the \code{stream} method.

-

-  The \code{connect} function returns a named list of possible

-  \code{stream}s from the connection information provided by the

-  user. The user can then call \code{yield} on the streams to obtain

-  records.

-

-}

-

-\usage{

-connect(blocks, df)

-}

-

-\arguments{

-

-  \item{blocks}{A named list of instances of classes \code{Consumer} and

-    \code{Producer} to the connected together in a \code{stream}}

-

-  \item{df}{ A \code{data.frame} with two columns: "from" and "to" which

-    are character vectors corresponding to the names of the blocks.

-    Each row of \code{df} describes a connection between \code{Consumer}

-    or \code{Producer} blocks.}

-

-}

-

-\details{

-

-  Arguments \code{blocks} must consist of a named list of a single

-  \code{Producer} and zero or more \code{Consumer} components.

-

-}

-

-\value{A named \code{list} of instances of class \code{\linkS4class{Stream}}.}

-

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

-

-\seealso{\code{\link{yield}},\code{\link{connect}}, 

-    \code{\linkS4class{Stream}-class}.}

-

-\examples{

-###  A simple stream involving a Producer and Consumer class 

-fl <- system.file("extdata", "s_1_sequence.txt", package="Streamer")

-b <- RawInput(fl, 100L, reader=rawReaderFactory(1e4))

-c <- RawToChar()

-

-###  Create a named list of the blocks to be connected together

-blocks <- list(b=b, c=c)

-

-## Create a data.frame that describes the connection between blocks

-df <- data.frame(from ="b", to = "c")

-res <- connect(blocks, df)

-yield(res$c)

-reset(res$c)

-while (length(yield(res$c))) cat("tick\n")

-}

-

-\keyword{manip}