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optsol_blockedReact-class.Rd 5.01 KiB
\name{optsol_blockedReact-class}
\Rdversion{1.1}
\docType{class}
\alias{optsol_blockedReact-class}
\alias{blocked,optsol_blockedReact-method}
\alias{blocked<-,optsol_blockedReact-method}
\alias{blocked}
\alias{blocked<-}
\alias{react,optsol_blockedReact-method}
\alias{react<-,optsol_blockedReact-method}
\alias{react<-}
\alias{maxSol,optsol_blockedReact-method}
\alias{minSol,optsol_blockedReact-method}
\alias{maxSol}
\alias{minSol}
\title{Class \code{"optsol_blockedReact"}}
\description{
Structure of the class \code{"optsol_blockedReact"}. Objects of that class are
returned by the function \code{\link{blockedReact}}.
}
\section{Objects from the Class}{
Objects can be created by calls of the form
\code{new("optsol_blockedReact", ...)}.
}
\section{Slots}{
\describe{
\item{\code{blocked}:}{Object of class \code{"logical"}
indicating if a reaction is blocked, or not.
}
\item{\code{react}:}{Object of class \code{"reactId"}
containing the reaction id's of checked reactions.
}
\item{\code{mod_id}:}{Object of class \code{"character"}
containing the model id of the used model.
}
\item{\code{mod_key}:}{Object of class \code{"character"}
containing the model key of the used model.
}
\item{\code{solver}:}{Object of class \code{"character"}
indicating the used solver.
}
\item{\code{method}:}{Object of class \code{"character"}
indicating the used method.
}
\item{\code{algorithm}:}{Object of class \code{"character"}
containing the name of the algorithm used for optimizations.
}
\item{\code{num_of_prob}:}{Object of class \code{"integer"}
indicating the number of optimization problems.
}
\item{\code{lp_num_cols}:}{Object of class \code{"integer"}
indicating the number of columns.
}
\item{\code{lp_num_rows}:}{Object of class \code{"integer"}
indicating the number of rows.
}
\item{\code{lp_obj}:}{Object of class \code{"numeric"}
containing the optimal values of the objective function after
optimization. If no flux distribution is available, slot \code{lp_obj}
contains the cross-product of the objective coefficients in slot
\code{obj_coef} and the part of the flux distribution in slot
\code{fluxdist} containing the values representing fluxes in the entire
metabolic network (slot \code{fldind}).
}
\item{\code{lp_ok}:}{Object of class \code{"integer"}
containing the exit code of the optimization.
}
\item{\code{lp_stat}:}{Object of class \code{"integer"}
containing the solution status of the optimization.
}
\item{\code{lp_dir}:}{Object of class \code{"character"}
indicating the direction of optimization.
}
\item{\code{obj_coef}:}{Object of class \code{"numeric"}
containing the objective coefficients of the used model (slot
\code{obj_coef} of an object of class \code{\linkS4class{modelorg}}).
These are not necessarily the objective coefficients of the used
algorithm.
}
\item{\code{obj_func}:}{Object of class \code{"character"}
containing the objective function of the used model. Usually, it contains
the return value of \code{\link{printObjFunc}}.
}
\item{\code{fldind}:}{Object of class \code{"integer"}
pointers to columns (variables) representing a flux (reaction) in the
original network. The variable \code{fldind[i]} in the problem object
represents reaction \code{i} in the original network.
}
\item{\code{fluxdist}:}{Object of class \code{"fluxDistribution"}
containing the solutions flux distributions.
}
\item{\code{alg_par}:}{Object of class \code{"list"}
containing a named list containing algorithm specific parameters.
}
}
}
\section{Extends}{
Class \code{"\linkS4class{optsol}"}, directly.
}
\section{Methods}{
\describe{
\item{\code{blocked}:}{
\code{signature(object = "optsol_blockedReact")}: gets the \code{blocked} slot.
}
\item{\code{blocked<-}:}{
\code{signature(object = "optsol_blockedReact")} sets the \code{blocked} slot.
}
\item{\code{react}:}{
\code{signature(object = "optsol_blockedReact")}: gets the \code{react} slot.
}
\item{\code{react<-}:}{
\code{signature(object = "optsol_blockedReact")} sets the \code{react} slot.
}
\item{\code{maxSol}:}{
\code{signature(object = "optsol_blockedReact")}(\code{slot}): returns the
values in the slot given in \code{slot} for optimizations in \dQuote{max}
direction.
}
\item{\code{minSol}:}{
\code{signature(object = "optsol_blockedReact")}(\code{slot}): returns the
values in the slot given in \code{slot} for optimizations in \dQuote{min}
direction.
}
}
}
\author{
Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>
Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
}
\seealso{
\code{\link{checkOptSol}} and \code{\linkS4class{optsol}}
}
\examples{
showClass("optsol_blockedReact")
}
\keyword{classes}