man/ExperimentPath-class.Rd
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 \name{ExperimentPath-class}
 \docType{class}
 \alias{ExperimentPath-class}
 % constructors
 \alias{ExperimentPath}
 % etc
 \alias{show,ExperimentPath-method}
 \alias{detail,ExperimentPath-method}
 
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 \title{(Legacy) "ExperimentPath" class representing a file hierarchy of data
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   files}
 
 \description{
 
   Short read technologies often produce a hierarchy of output files. The
   content of the hierarchy varies. This class represents the root of the
   file hierarchy. Specific classes (e.g.,
   \code{\linkS4class{SolexaPath}}) represent different technologies.
 
 }
 \section{Objects from the Class}{
 
   Objects from the class are created by calls to the constructor:
   
   \code{ExperimentPath(experimentPath)}
 
   \describe{
     \item{experimentPath}{\code{character(1)} object pointing to the
       top-level directory of the experiment; see specific technology
       classes for additional detail.}
     \item{verbose=FALSE}{(optional) logical vector which, when
       \code{TRUE} results in warnings if paths do not exist.}
   }
   All paths must be fully-specified.
 }
 \section{Slots}{
   \code{ExperimentPath} has one slot, containing a fully
   specified path to the corresponding directory (described above).
   \describe{
     \item{\code{basePath}}{See above.}
   }
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   The slot is accessed with \code{experimentPath}.
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 }
 \section{Extends}{
   Class \code{"\linkS4class{.ShortReadBase}"}, directly.
 }
 \section{Methods}{
   Methods include:
   \describe{
 
     \item{show}{\code{signature(object = "ExperimentPath")}: briefly
       summarize the file paths of \code{object}.}
 
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     \item{detail}{\code{signature(x = "ExperimentPath")}: summarize
       file paths of \code{x}.}
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   }
 }
 
 \author{Michael Lawrence}
 \examples{
 showClass("ExperimentPath")
 }
 \keyword{classes}