\name{generateFunctionMap}
\alias{generateFunctionMap}
\title{Create java wrapper functions for a list of R functions}
\description{
  The \code{generateFunctionMap} function generates java wrapper functions for a list of R functions. It also generates java beans and R--Java data type conversions for any R data types that are related to the function but unavailable in the environment \code{lookup}. This function also updates environments \code{lookup} and \code{cvtImport} (see arguments below) as a side effect.  
}
\usage{
generateFunctionMap(rTypeInfo, genTest = TRUE, workDir = getwd(),
                    verbose = FALSE,
                    deployModeName = "jms", typeModeName = "javalib",
                    wsdlStyle = "WRAPPED", wsdlUse = "LITERAL",
                    extraClasses = "", pkgRoot="org.bioconductor", ...)
}
\arguments{
  \item{rTypeInfo}{a list, each component is an instance of \code{\link{RJavaSignature-class}} and represents the signature of a R function.}
  \item{genTest}{logical, TRUE if want to generate a java program to test the java wrapper functions generated by \code{generateFunctionMap}, FALSE otherwise.} 
  \item{workDir}{a character string, the path of the directory where this function generates all its outputs.}
  \item{verbose}{logical, TRUE if want to print out debug information, FALSE otherwise.}
  \item{deployModeName}{Character, either "demo" or "jms". How the service
    will be deployed. "demo" is no longer supported.}
  \item{typeModeName}{Character, either "robject" or
    "javalib". How Java objects should be generated; see
    \code{\link{generateDataMap}} and \code{\link{converters}}}
  \item{wsdlStyle}{}
  \item{wsdlUse}{}
  \item{extraClasses}{character. Extra classes requied to convert
	function argument or return values, e.g., an argument of type
	\code{list} might require information about the classes present in
	the list. Usually this argument is not required, as S4 classes are
	parsed to their constituent parts}
  \item{pkgRoot}{character. Root package name of the java classes
	classes being created. It should be a sequence of one or 
	more character strings delimited by dot, and no dot after the last
	string}
  \item{\dots}{Additional arguments, to be compatiable with
	\code{\link{createMap}}.}
}
\details{
  The java mappings generated under \code{workDir} are organized as following:
  \item{biocJavaMap}{the base directory}
  \item{biocJavaMap/\code{package1}}{java mappings for functions and data types defined in R \code{package1}}
  \item{biocJavaMap/\code{package1}/data}{java beans and java <-> R mapping functions (in R) for data types defined in \code{pacakge1}}
  \item{biocJavaMap/\code{package1}/function}{java wrapper functions for functions defined in \code{package1}}
  \item{biocJavaMap/\code{package2}}{java mappings for functions and data types defined in \code{package2}}
  \item{biocJavaMap/\code{mainService}}{main java API, which invokes the java mapping functions for \code{package1}, \code{package2}, etc. \code{mainService} value is provided by user as input.}
}
\value{
  A list, each component is an instance of \code{\link{RJavaSignature-class}} and represents the signature of a java wrapper function. The return value has a one-to-one mapping relation with input parameter \code{rTypeInfo}, i.e. the java wrapper function that is represented by the ith component in the return list, is the wrapper for the R function that is represend by the ith component in \code{rTypeInfo}.
}
\author{Nianhua Li}
\examples{
##  This function is usually invoked by \code{\link{createMap}}.
}
\keyword{interface}