\name{"fixvars-methods"}
\docType{methods}
\alias{"fixvars-methods"}
\alias{fixvars-methods}
\alias{fixvars}
\title{Checks and fixes the ranges, dimensions, and names of the
  metadata based on the current data of an FCS R-object.}
\description{
  Any discrepancy between the metadata
  and the data of the FCS object is considered as a failure to pass the
  check and will be updated with the descriptives from the data.
  The following is a description of the checks and fixes:

  \item{1. Dimension check and fix}{We always check the dimensions (ie,
    if the data dimensions match with size (\$TOT) and nparam (\$PAR)
    that are specified in the metadata.  If they are not in check, then
    the metadata parameters are changed to reflect the values of the
    data dimensions.    
  }
  \item{2. Parameter Name check and fix}{We check the names of the metadata with the
    names of the data column parameters.  Either only the longnames (\$PnS)
    or the shortnames (\$PnN) of the metadata are checked against the
    names of the data.  Please take note that
    both (\$PnS) and (\$PnN) ARE NOT BOTH checked.  Depending on the number
    of discrepancies (ie, the one with
    the least number of discrepanices; by default the longnames if there
    is a tie), either the longnames or the shortnames  of the
    metadata are replaced with the column names of the data. 
  }
  \item{3. Column Variable Range Check}{We check the paramranges
    (\$PnR) specified in the metadata with the column parameter ranges of the
    data; if there are any discrepancies, then the paramranges are
    replaced with the maximum values of the data columns.
  }
  
  Please note that if the metadata@original is FALSE, then the metadata
  slotNames have a 
  "RFACSadd$>>$" suffix and are located
  in metadata@fcsinfo in order to store the current data descriptives.
  The original data descriptives can be retrieved/checked
  when metadata@original is set to TRUE; otherwise the current metadata
  information about the data is retrieved/checked even when the "RFACSadd$>>$"
  suffix is not noted in the character index.

  (ie) If metadata@original
  is FALSE, then metadata[["size"]] will return
  metadata[["RFACSadd$>>$\$TOT"]], the current row length of the data,
  while metadata@size will return the number of rows for the original
  data.

  Note that metadata@original is changed only when a parameter column is
  added to the data using \code{\link{addParameter-methods}}, when rows of the data are
  extracted using \code{\link{extractGatedData}} or if the user decides to
  change the value metadata@original.  Using \code{\link{"["-methods}}
  and \code{\link{"[<-"-methods}} on a \code{\link{FCS}} object
  will not change the value of metadata@original.
}
\section{Methods}{
\describe{

  \item{x = "FCS"}{A \code{FCS}object will be returned with any fixes to the
    metadata.}
 \item{x = "FCS", x.name="", MY.DEBUG=TRUE, range.max=NULL}{
    Other options in the signature include:

     (1) x.name : character string of the true object name; default is ""
     (ie, the objectname in the metadata will be regarded as the true
     object name )
     
     (2) MY.DEBUG : boolean value; if TRUE, then the output statements
     are printed, otherwise if FALSE, then the statements are surpressed;
     default is TRUE.
     
     (3) range.max : numeric value describing the true maximum of the
     data that the checks on the ranges will be compared; default is NULL
     (ie, the maximum of each column variable in
     the data is the truth)

   }
}}
\keyword{methods}
\keyword{data}