\HeaderA{"checkvars-methods"}{Checks the ranges, dimensions, and names of the metadata based on the
current data of an FCS R-object.}{"checkvars.Rdash.methods"}
\aliasA{checkvars}{"checkvars-methods"}{checkvars}
\aliasA{checkvars-methods}{"checkvars-methods"}{checkvars.Rdash.methods}
\keyword{methods}{"checkvars-methods"}
\keyword{data}{"checkvars-methods"}
\begin{Description}\relax
Any discrepancy between the metadata
and the data of the FCS object is considered as a failure to pass the
check.  The following is a description of the checks:

\item[1. Dimension check] We always check the dimensions (ie, if the data
dimensions match with size ("\$TOT") and
nparam ("\$PAR") that are specified in the metadata).   

\item[2. Parameter Name check] 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. 

\item[3. Column Variable Range Check] We check the paramranges
("\$PnR") specified in the metadata with the column parameter ranges of the
data; if the paramranges
do not exist in the metadata, then it is noted in the debugging
statements.


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{\LinkA{addParameter-methods}{addParameter.Rdash.methods}}, when rows of the data are
extracted using \code{\LinkA{extractGatedData}{extractGatedData}} or if the user decides to
change the value metadata@original.  Using \code{\LinkA{"["-methods}{"[".Rdash.methods}} and
\code{\LinkA{"[<-"-methods}{"[<.Rdash.".Rdash.methods}} on a "FCS" object
will not change the value of metadata@original.
\end{Description}
\begin{Section}{Methods}
\describe{

\item[x = "FCS"] boolean value is returned; TRUE if the check passes
and FALSE if it does not pass the check.


\item[x = "FCS", MY.DEBUG=TRUE, range.max=NULL] Other options in the signature include:

(1) MY.DEBUG : boolean value; if TRUE, then the output statements
are printed, otherwise if FALSE, then the statements are surpressed;
default is TRUE.

(2) 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)
}
\end{Section}

