@@ -18,9 +18,11 @@ Imports: methods, graph, parallel, BiocGenerics

 Suggests: RUnit, Rsamtools (>= 1.5.53)

 biocViews: Infrastructure, DataImport

 Collate: 

-  generics.R OldClass.R

-  Streamer.R Producer.R  Consumer.R Stream.R

-  ConnectionProducer.R RawInput.R Seq.R

-  Downsample.R Team.R UserFunction-class.R Utility.R

-  ParallelConnector.R TConnector.R YConnector.R

+  AllGenerics.R 

+  Streamer-class.R Producer-class.R Consumer-class.R Stream-class.R

+  ConnectionProducer-classes.R RawInput-class.R Seq-class.R

+  Downsample-class.R Team-class.R FunctionProducerConsumer-classes.R

+  Utility-classes.R ParallelConnector-class.R TConnector-class.R

+  YConnector-class.R

+  lapply-methods.R stream-methods.R

   zzz.R

@@ -4,6 +4,8 @@ import(methods)

 importFrom(BiocGenerics, lapply, sapply)

+importClassesFrom(BiocGenerics, connection)

+

 ## only exported on unix

 ## importFrom(parallel, mccollect, mcparallel)

similarity index 100%

rename from R/generics.R

rename to R/AllGenerics.R

similarity index 100%

rename from R/ConnectionProducer.R

rename to R/ConnectionProducer-classes.R

similarity index 92%

rename from R/Consumer.R

rename to R/Consumer-class.R

@@ -53,9 +53,3 @@

         txt <- sprintf("stream: %s", inp)

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

     })

-

-setMethod(stream, "Consumer",

-    function(x, ..., verbose=FALSE)

-{

-    .stream_set(x, ..., verbose=verbose)

-})

similarity index 100%

rename from R/Downsample.R

rename to R/Downsample-class.R

deleted file mode 100644

@@ -1,3 +0,0 @@

-## old classes, promoted to S4

-

-setOldClass(c("file", "connection"))

similarity index 100%

rename from R/ParallelConnector.R

rename to R/ParallelConnector-class.R

new file mode 100644

@@ -0,0 +1 @@

+.Producer <- setRefClass("Producer", contains="Streamer")

deleted file mode 100644

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

-.Producer <- setRefClass("Producer", contains="Streamer")

-

-setMethod(stream, "Producer",

-    function(x, ..., verbose=FALSE)

-{

-    if (0L == length(list(...)))

-        .stream_set(x, verbose=verbose)

-    else

-        do.call(stream, c(rev(list(..., verbose=verbose)), list(x)))

-})

-

-setMethod(lapply, "Producer",

-    function(X, FUN, ...)

-{

-    FUN <- match.fun(FUN)

-    YIELD <- selectMethod("yield", class(X)) # avoid S4 dispatch

-

-    it <- 0L

-    result <- vector("list", 4096L)     # pre-allocate

-    .partialResult <- function(err) {

-        if (is(err, "simpleError")) {

-            length(result) <- it

-            err$message <- paste0("yield(): ", conditionMessage(err))

-            err$partialResult <- result

-            class(err) <- c("partialResult", class(err))

-        }

-        stop(err)

-    }

-

-    repeat {

-        y <- tryCatch(YIELD(X), error = .partialResult)

-        if (!length(y))

-            break;

-        y <- tryCatch(FUN(y, ...), error = .partialResult)

-        it <- it + 1L

-        if (it == length(result))       # grow

-            length(result) <- 1.6 * length(result)

-        result[[it]] <- y

-    }

-    length(result) <- it

-    result

-})

-

-setMethod(sapply, "Producer",

-    function(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)

-{

-    FUN <- match.fun(FUN)

-    answer <- tryCatch(lapply(X = X, FUN = FUN, ...), error=function(err) {

-        if (is(err, "partialResult"))

-            err$partialResult <- simplify2array(err$partialResult,

-                                                higher = (simplify == "array"))

-        stop(err)

-    })

-    if (!identical(simplify, FALSE) && length(answer))

-        simplify2array(answer, higher = (simplify == "array"))

-    else answer

-})

similarity index 100%

rename from R/RawInput.R

rename to R/RawInput-class.R

similarity index 100%

rename from R/Seq.R

rename to R/Seq-class.R

new file mode 100644

@@ -0,0 +1,35 @@

+.Stream <- setRefClass("Stream", contains = "Consumer")

+

+.Stream$methods(

+    yield=function()

+    {

+        .self$inputPipe$yield()

+    

+    })

+

+setMethod(length, "Stream",

+    function(x)

+{

+    i <- 0L

+    inp <- x

+    while (extends(class(inp), "Consumer")) {

+        inp <- inp$inputPipe

+        i <- i + 1L

+    }

+    i

+})

+

+setMethod("[[", c("Stream", "numeric"),

+    function(x, i, j, ...)

+{

+    i <- as.integer(i)

+    len <- length(x)

+    if (1L != length(i) || 0 >= i || len < i)

+        stop("'i' must be integer(1), 0 < i <= length(x)")

+    inp <- x$inputPipe

+    while (extends(class(inp), "Consumer") && 1L < i) {

+        inp <- inp$inputPipe

+        i <- i - 1L

+    }

+    inp

+})

deleted file mode 100644

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

-.Stream <- setRefClass("Stream", contains = "Consumer")

-

-.Stream$methods(

-    yield=function()

-    {

-        .self$inputPipe$yield()

-    

-    })

-

-.stream_set <- function(x, ..., verbose)

-{

-    ## helper used to construct streams

-    inp <- list(x, ...)

-    use <- sapply(inp, "[[", "inUse")

-    cls <- sapply(inp, class)

-    if(any(use)) {

-        msg <- sprintf("%s : already in use in another stream",

-                       paste(cls[which(use)], sep = " ", collapse = ", "))

-        stop(msg)

-    }

-    x$inUse <- TRUE

-    inputPipe <- Reduce(function(x, y) {

-        x$inputPipe <- y

-        y$inUse <- TRUE

-        if (is(x, "ParallelConnector")) {

-            x$.upstream <- .mc_parallel(quote({

-                while(TRUE) {

-                    prime <- yield(y)

-                    sendMaster(prime)

-            }}))

-        }

-        x

-    }, list(x, ...), right=TRUE)

-    .Stream$new(inputPipe=inputPipe, verbose=verbose)

-}

-

-setMethod(length, "Stream",

-    function(x)

-{

-    i <- 0L

-    inp <- x

-    while (extends(class(inp), "Consumer")) {

-        inp <- inp$inputPipe

-        i <- i + 1L

-    }

-    i

-})

-

-setMethod("[[", c("Stream", "numeric"),

-    function(x, i, j, ...)

-{

-    i <- as.integer(i)

-    len <- length(x)

-    if (1L != length(i) || 0 >= i || len < i)

-        stop("'i' must be integer(1), 0 < i <= length(x)")

-    inp <- x$inputPipe

-    while (extends(class(inp), "Consumer") && 1L < i) {

-        inp <- inp$inputPipe

-        i <- i - 1L

-    }

-    inp

-})

similarity index 100%

rename from R/Streamer.R

rename to R/Streamer-class.R

similarity index 100%

rename from R/TConnector.R

rename to R/TConnector-class.R

similarity index 100%

rename from R/Team.R

rename to R/Team-class.R

similarity index 100%

rename from R/Utility.R

rename to R/Utility-classes.R

similarity index 100%

rename from R/YConnector.R

rename to R/YConnector-class.R

similarity index 81%

rename from man/ConnectionProducer-class.Rd

rename to man/ConnectionProducer-classes.Rd

@@ -1,6 +1,7 @@

-\name{ConnectionProducer-class}

+\name{ConnectionProducer-classes}

 \Rdversion{1.1}

 \docType{class}

+\alias{ConnectionProducer-classes}

 \alias{ConnectionProducer-class}

 \alias{close.ConnectionProducer}

 \alias{ScanProducer-class}

@@ -10,7 +11,7 @@

 \alias{ReadLinesProducer}

 \alias{ReadTableProducer}

-\title{Class "ConnectionProducer"}

+\title{Producer classes to read file connections}

 \description{

@@ -47,10 +48,16 @@ ReadTableProducer(file, ..., fileArgs=list(), readTableArgs=list(...))

 }

-\section{Internal Methods}{

+\section{Methods}{See \code{\link{Producer}} Methods.}

-  Class-based fields and methods are for internal use. See, e.g.,

-  \code{Streamer:::.ScanLinesProducer$help()} for documentation

+\section{Internal Class Fields and Methods}{

+

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("ReadLinesProducer")$fields}.

+

+  Internal methods of this class are described with

+  \code{getRefClass("ReadLinesProducer")$methods()} and

+  \code{getRefClass("ReadLinesProducer")$help()}.

 }

@@ -1,10 +1,11 @@

 \name{Consumer-class}

 \Rdversion{1.1}

 \docType{class}

+\alias{Consumer}

 \alias{Consumer-class}

 \alias{show,Consumer-method}

-\title{Class "Consumer"}

+\title{Class defining methods for all consumers}

 \description{

@@ -19,56 +20,24 @@

 \section{Methods}{

   Methods defined on this class include:

-  \describe{

-    \item{stream}{\code{signature(x = "Consumer", ...)}: see

-      \code{?stream}.}

-    \item{show}{\code{signature(object = "Consumer")}: Display the

-      stream.}

-  }

-}

-\section{Fields}{

   \describe{

-    \item{\code{inputPipe}:}{Object of class \code{Streamer},

-      representing the \code{Producer} or \code{Consumer} connected

-      up-stream to it and from which records are yielded.}

-    

-    The \code{Consumer} class inherits the fields \code{verbose} and

-    \code{inUse} from the virtual \code{Streamer} class.  Please refer

-    to the \code{\link{Streamer}} class for more details.

+    \item{stream}{Construct a stream from one \code{Producer} and one or

+      more \code{Consumer}. See \code{?stream}.}

   }

 }

-\section{Class-Based Methods}{

-  \describe{

-    \item{\code{initialize(..., inputPipe)}:}{A method to

-      initialize the fields of the \code{Consumer} class.

-      \describe{

-	\item{\code{inputPipe}:}{An object of class \code{Streamer}

-          connected up-stream to it. The class could be a

-          \code{Consumer} or \code{Producer} which yields data to the

-          \code{Consumer} class.}

-      }

-    }

-

-    \item{\code{reset()}:}{Return the result of delegating

-      \code{reset()} to the object in the field \code{inputPipe}.}

-

-    \item{\code{yield()}:}{Return the result of delegating

-      \code{yield()} to the object in the field \code{inputPipe}.}

-

-    \item{\code{inputs()}:}{Return a \code{character} vector

-      representing up-stream components.}

-

-    \item{\code{status{}}:}{Reports the status of the \code{Consumer}

-      class. A \code{list} of the status of the length of the object in

-      the \code{.records} field, the classes connected to the

-      \code{inputPipe} field and the status of the fields of the virtual

-      class \code{Streamer} are returned.}

+\section{Internal Class Fields and Methods}{

+

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("Consumer")$fields}.

+

+  Internal methods of this class are described with

+  \code{getRefClass("Consumer")$methods()} and

+  \code{getRefClass("Consumer")$help()}.

-  }

 }

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

@@ -4,16 +4,14 @@

 \alias{Downsample}

 \alias{Downsample-class}

-\title{Class "Downsample"}

+\title{Consumer class to down-sample data}

 \description{

   A \code{\linkS4class{Consumer}}-class to select records with fixed

   probability, returning a yield of fixed size. Successive calls to

   \code{yield} result in sampling of subsequent records in the stream,

-  until the stream is exhausted. Users interact with this class through

-  the constructor \code{Downsample} and methods \code{\link{yield}},

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

+  until the stream is exhausted.

 }

@@ -22,30 +20,29 @@ Downsample(probability=0.1, sampledSize=1e6, ...)

 }

 \arguments{

+

   \item{probability}{A \code{numeric(1)} between 0, 1 indicating the

     probability with which a record should be retained.}

+

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

     the underlying reference class. Currently unused.}

+

   \item{sampledSize}{A \code{integer(1)} indicating the number of

     records to return.}

+

 }

-\section{Fields}{

-  \describe{

-    \item{\code{probability}:}{Object of class \code{numeric}. The

-      probability of including a record in the \code{yield}.}

-    \item{\code{sampledSize}:}{Object of class \code{integer}

-      storing the number of records to produced each time \code{yield}

-      is invoked.}

-    \item{\code{.buffer}:}{Object of class \code{ANY}, used internally

-      to store read but not yet parsed records.}

-  }

-}

+\section{Methods}{See \code{\link{Consumer}} Methods.}

+

+\section{Internal Class Fields and Methods}{

+

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("Downsample")$fields}.

+

+  Internal methods of this class are described with

+  \code{getRefClass("Downsample")$methods()} and

+  \code{getRefClass("Downsample")$help()}.

-\section{Class-Based Methods}{

-  \describe{

-    \item{\code{.sample(x)}:}{Sample from amongst the incoming records.}

-  }

 }

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

@@ -2,21 +2,21 @@

 \Rdversion{1.1}

 \docType{class}

 \alias{Producer-class}

+\alias{Producer}

 \alias{lapply,Producer-method}

 \alias{sapply,Producer-method}

-\alias{show,Producer-method}

-\title{Class "Producer"}

+\title{Class defining methods for all Producers}

 \description{

   A virtual class representing components that can read data from

   connections, and yield records to the user or a \code{Consumer}

   instance. A \code{Producer} represents a source of data, responsible

-  for parsing a file into records to be passed to \code{Consumer}

-  classes. \code{Producer} and \code{Consumer} instances are associated

-  with each other through the \code{\link{stream}} function or using the

-  \code{\link{connect}} function.  

+  for parsing a file or other data source into records to be passed to

+  \code{Consumer} classes. \code{Producer} and \code{Consumer} instances

+  are associated with each other through the \code{\link{stream}}

+  function or using the \code{\link{connect}} function.

 }

@@ -26,6 +26,7 @@

 }

 \arguments{

+

   \item{X}{An instance of class \code{Producer}}

   \item{FUN}{A function to be applied to each successful \code{yield()}

@@ -42,45 +43,36 @@

 \section{Methods}{

-  \code{lapply} and \code{sapply} apply \code{FUN} to each result

-  applied to \code{yield()}. Partial results on error can be recovered

-  using \code{\link{tryCatch}}, as illustrated below. Infinite producers

-  will of course exhaust memory.

+  Methods defined on this class include:

-  Inherited methods defined on this class include:

   \describe{

-    \item{stream}{\code{signature(x = "Producer", ...)}: see

-      \code{?stream}.}

-    \item{show}{\code{signature(object = "Streamer")}: Display the

-      stream.}

-  }

-}

-\section{Fields}{

-  \describe{

+    \item{stream}{Construct a stream from one \code{Producer} and one or

+      more \code{Consumer}. See \code{?stream}.}

+

+    \item{yield}{Yield a single result (e.g., \code{data.frame}) from

+      the Producer.}

-    The \code{Producer} class inherits the fields \code{verbose} and

-    \code{inUse} fields from the \code{Streamer} class. Please refer to

-    the \code{\link{Streamer}} class for more details.

+    \item{reset}{Reset, if possible, the Producer.}

+

+    \item{lapply, sapply}{Apply \code{FUN} to each result applied to

+      \code{yield()}, simplifying (using \code{simplify2array}) if

+      possible for \code{sapply}. Partial results on error can be

+      recovered using \code{\link{tryCatch}}, as illustrated

+      below. Infinite producers will of course exhaust memory.}

   }

 }

-\section{Class-Based Methods}{

-  \describe{

+\section{Internal Class Fields and Methods}{

-    The \code{Producer} class inherits the methods \code{initialize},

-    \code{msg}, \code{reset}, \code{status} and \code{yield} from the

-    \code{Streamer} virtual class. Please refer to the

-    \code{\link{Streamer}} class for more details.

-    

-    Derived classes should implement an appropriate \code{initialize}

-    method to initialize the fields of the derived class. Additionally,

-    a \code{yield} method should be implemented to return the contents

-    of the current stream. The default method for the base virtual

-    \code{Streamer} class returns a \code{list()}

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("Producer")$fields}.

+

+  Internal methods of this class are described with

+  \code{getRefClass("Producer")$methods()} and

+  \code{getRefClass("Producer")$help()}.

-  }

 }

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

deleted file mode 100644

@@ -1,37 +0,0 @@

-\name{RawToChar-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{RawToChar}

-\alias{RawToChar-class}

-

-\title{Class "RawToChar"}

-

-\description{

-

-  A \code{\linkS4class{Consumer}}-class to convert \code{raw} (binary)

-  records to \code{char}, applying \code{rawToChar} to each record.

-

-}

-

-\usage{RawToChar(...)}

-

-\arguments{

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

-    constructors.}

-}

-

-\section{Constructors}{

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

-}

-

-\section{Fields}{There are no fields unique to this class.}

-

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

-

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

-

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

-

-\examples{showClass("RawToChar")}

-

-\keyword{classes}

deleted file mode 100644

@@ -1,37 +0,0 @@

-\name{Rev-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{Rev}

-\alias{Rev-class}

-

-\title{Class "Rev"}

-

-\description{

-

-  A \code{\linkS4class{Consumer}}-class to reverse the order of

-  records. Note that the content of the \code{yield} is reversed, and

-  not the entire stream.

-

-}

-

-\usage{Rev(...)}

-

-\arguments{

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

-    constructors.}

-}

-

-\section{Constructors}{Use \code{Rev} to construct instances of this class.}

-

-\section{Fields}{There are no fields unique to this class.}

-

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

-

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

-

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

-

-\examples{showClass("Rev")}

-

-\keyword{classes}

-

@@ -4,7 +4,7 @@

 \alias{Seq-class}

 \alias{Seq}

-\title{Class "Seq"}

+\title{Producer class to generate (numeric) sequences}

 \description{

@@ -40,6 +40,8 @@ Seq(from = 1L, to=.Machine$integer.max, by = 1L, yieldSize=1L,

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

 }

+\section{Methods}{See \code{\link{Producer}} Methods.}

+

 \section{Internal Class Fields and Methods}{

   Internal fields of this class are are described with

@@ -4,9 +4,10 @@

 \alias{Stream-class}

 \alias{[[,Stream,numeric-method}

 \alias{length,Stream-method}

-\alias{show,Stream-method}

+\alias{lapply,Stream-method}

+\alias{sapply,Stream-method}

-\title{Class "Stream"}

+\title{Class to represent a Producer and zero or more Consumers}

 \description{

@@ -19,45 +20,72 @@

 }

+\usage{

+\S4method{length}{Stream}(x)

+\S4method{[[}{Stream,numeric}(x, i, j, ...)

+\S4method{lapply}{Stream}(X, FUN, ...)

+\S4method{sapply}{Stream}(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)

+}

+

+\arguments{

+

+  \item{x, X}{An instance of class \code{Stream}.}

+ 

+  \item{FUN}{A function to be applied to each successful \code{yield()}

+    of \code{X}.}

+

+  \item{i, j}{Numeric index of the ith stream element (\code{j} is

+    ignored by this method).}

+

+  \item{...}{For \code{lapply}, \code{sapply}, additional arguments to

+    \code{FUN}.}

+

+  \item{simplify}{See \code{?base::sapply}.}

+

+  \item{USE.NAMES}{See \code{?base::sapply} but note that names do not

+    usually make sense for instances of class \code{Producer}.}

+

+}

+

 \section{Constructors}{

   Instances from this class are constructed with calls to \code{stream};

   see \code{?stream}

 }

 \section{Methods}{

-  This class inherits the following methods:

-  \describe{

-    \item{reset}{\code{signature(x = "Streamer", ...)}: see

-      \code{?reset}.}

-    \item{yield}{\code{signature(x = "Streamer", ...)}: see

-      \code{?yield}.}

-  }

+

   Methods defined on this class include:

+

   \describe{

-    \item{length}{\code{signature(x = "Stream")}: the number of

-      components in this stream}

-    \item{[[}{\code{signature(x = "Stream", i = "numeric")}: The

-      \code{i}th component (including inputs) of this stream. }

-    \item{show}{\code{signature(object = "Stream")}: Display the

+

+    \item{length}{The number of components in this stream.}

+

+    \item{[[}{The \code{i}th component (including inputs) of this

       stream.}

-  }

-}

-\section{Fields}{

-  \describe{

-    \item{\code{inputPipe}:}{Object of class \code{ANY} ~~ }

-    \item{\code{verbose}:}{A \code{logical(1)} instance indicating

-      whether methods invoked on the class should be reported to the

-      user.}

+    \item{yield}{Yield a single result (e.g., \code{data.frame}) from

+      the stream.}

+

+    \item{reset}{Reset, if possible, each component of the stream.}

+

+    \item{lapply, sapply}{Apply \code{FUN} to each result applied to

+      \code{yield()}, simplifying (using \code{simplify2array}) if

+      possible for \code{sapply}. Partial results on error can be

+      recovered using \code{\link{tryCatch}}, as illustrated

+      on the help page \code{\link{Producer}}.}

+

   }

+

 }

-\section{Class-Based Methods}{

+\section{Internal Class Fields and Methods}{

+

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("FunctionProducer")$fields}.

-  The following methods are inherited (from the corresponding class):

-  initialize ("Streamer"), yield ("Streamer"), msg ("Streamer"), yield

-  ("Consumer"), initialize ("Consumer"), reset ("Consumer"), reset

-  ("Streamer"), inputs ("Consumer")

+  Internal methods of this class are described with

+  \code{getRefClass("FunctionProducer")$methods()} and

+  \code{getRefClass("FunctionProducer")$help()}.

 }

@@ -3,7 +3,7 @@

 \docType{class}

 \alias{Streamer-class}

-\title{Class "Streamer"}

+\title{Class defining methods shared by all classes}

 \description{

   A virtual base class from which all classes in the Streamer package

@@ -12,42 +12,20 @@

 }

 \section{Methods}{

-  \describe{

-    \item{reset}{\code{signature(x = "Streamer")}: see \code{?reset}.}

-    \item{yield}{\code{signature(x = "Streamer")}: see \code{?yield}.}

-  }

-}

-

-\section{Fields}{

-  \describe{

-      \item{\code{verbose}:}{A \code{logical(1)} instance indicating

-      whether methods invoked on the class should be reported to the

-      user.}

-      \item{\code{inUse}:}{ A \code{logical(1)} instance indicating whether

-      the object instantiated has been used in a stream.}

-  }

-}

-\section{Class-Based Methods}{

-  \describe{

+  See \code{Stream}, \code{Producer}, and \code{Consumer} Methods.

-    \item{\code{initialize(..., verbose = FALSE)}:}{Initialize

-      \code{Streamer}, setting \code{verbose} and \code{inUse} fields,

-      returning \code{.self} invisibly.}

-

-    \item{\code{msg(fmt, ...)}:}{Use \code{msg} to print

-      \code{sprintf(fmt, ...)} messages to user.}

+}

-    \item{\code{reset()}:}{Reset \code{Streamer}; this default method is

-      a no-op.}

+\section{Internal Class Fields and Methods}{

-    \item{\code{yield()}:}{Yield default value \code{list()}.}

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("Streamer")$fields}.

-    \item{\code{status()}:}{Reports the status of the \code{Streamer}

-       class.  A \code{list} of the status of \code{verbose} and

-       \code{inUse} fields is returned.}

+  Internal methods of this class are described with

+  \code{getRefClass("Streamer")$methods()} and

+  \code{getRefClass("Streamer")$help()}.

-    }

 }

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

@@ -2,7 +2,7 @@

 \alias{Streamer-package}

 \alias{Streamer}

 \docType{package}

-\title{Enable stream processing of large files}

+\title{Enable stream processing of large data}

 \description{

   Large data files can be difficult to work with in R, where data

@@ -4,7 +4,7 @@

 \alias{Team-class}

 \alias{Team}

-\title{Class \code{"Team"}}

+\title{Consumer class to enable parallel evaluation}

 \description{

@@ -37,64 +37,17 @@

 \section{Constructors}{

   Use \code{Team} to contruct instances of this class.

 }

-\section{Fields}{

-  Class-specific fields, intended for internal use:

-  \describe{

-    \item{\code{tasks}:}{Object of class \code{list} to contain

-      in-process tasks.}

+\section{Methods}{See \code{\link{Consumer}} Methods.}

-    \item{\code{FUN}:}{Object of class \code{function}, the function to

-      be evaulated.}

+\section{Internal Class Fields and Methods}{

-    \item{\code{mc.set.seed, silent}:}{Object of class \code{logical},

-      see \code{?mcparallel}.}

+  Internal fields of this class are are described with, e.g.,

+  \code{getRefClass("Team")$fields}.

-    \item{\code{.id}:}{Object of class \code{integer}, a sequential

-      identifier indexing tasks that have been consumed.}

-

-    \item{\code{.yid}:}{Object of class \code{integer}, a sequential

-      identifier indexing tasks that have been yielded.}

-

-  }

-