\name{applyChanges-methods} \docType{methods} \encoding{utf8} \alias{applyChanges} \alias{applyChanges-methods} \alias{applyChanges,sysBiolAlg-method} \alias{applyChanges,sysBiolAlg_room-method} \title{Generic Function to Apply Changes to Objects of Class sysBiolAlg} \description{ Use method \code{applyChanges} to apply changes in objects of class \code{\linkS4class{sysBiolAlg}}. Changes can be coefficients of the objective function, variable bounds or the optimization direction. } \usage{ \S4method{applyChanges}{sysBiolAlg}(object, del, obj, ld, react = NULL, lb = NULL, ub = NULL, obj_coef = NULL, fldind = TRUE, lpdir = NULL) \S4method{applyChanges}{sysBiolAlg_room}(object, del, obj, ld, react = NULL, lb = NULL, ub = NULL, obj_coef = NULL, fldind = TRUE, lpdir = NULL) } \section{Methods}{ \describe{ \item{\code{signature(object = "sysBiolAlg")}}{ Method used with objects extending class \code{\linkS4class{sysBiolAlg}} } \item{\code{signature(object = "sysBiolAlg_room")}}{ Method used with objects of class \code{\linkS4class{sysBiolAlg_room}} } } } \arguments{ \item{object}{ An object of class \code{\linkS4class{sysBiolAlg}}. } \item{del}{ A logical value indicating whether variable bounds should be altered or not. } \item{obj}{ A logical value indicating whether objective coefficients should be altered or not. } \item{ld}{ A logical value indicating whether the direction of optimization should be altered or not. } \item{react}{ A numeric vector containing indices to reactions which should be changed (in terms of variable bounds or objective coefficients).\cr Default: \code{NULL}. } \item{lb}{ Numeric vector of the same length as \code{react}, containing the new lower variable bounds.\cr Default: \code{NULL}. } \item{ub}{ Numeric vector of the same length as \code{react}, containing the new upper variable bounds.\cr Default: \code{NULL}. } \item{obj_coef}{ Numeric vector of the same length as \code{react}, containing the new objective coefficients.\cr Default: \code{NULL}. } \item{fldind}{ Boolean value. If set to \code{TRUE}, (default) indices in \code{"react"} are used only for reactions. If set to \code{FALSE}, indices in \code{"react"} are used for all variables during optimization, e.g. also for additional variables introduced by the \code{\link{mtf}} algorithm. Currently unused by class \code{\linkS4class{sysBiolAlg_room}}.\cr Default: \code{TRUE}. } \item{lpdir}{ A single character value indicating the new direction of optimization.\cr Default: \code{NULL}. } } \value{ Returns a list containing the original values in order to undo the changes with \code{\link{resetChanges}}: \item{fi}{ A numeric vector containing variable id's to apply changes to. } \item{lb}{ A numeric vector of the same length as \code{react} containing the original variable lower bounds. } \item{ub}{ A numeric vector of the same length as \code{react} containing the original variable upper bounds. } \item{obj_coef}{ A numeric vector of the same length as \code{react} containing the original objective coefficients. } \item{lpdir}{ A single character value giving the original optimization direction. } \item{ri}{ A numeric vector of the same length as \code{react} containing row indices of the stoichiometric matrix required to apply changes in variable bounds when algorithm \code{"room"} is used. (only used by the \code{\linkS4class{sysBiolAlg_room}} method). } \item{ci}{ A numeric vector of the same length as \code{react} containing column indices of the stoichiometric matrix required to apply changes in variable bounds when algorithm \code{"room"} is used. (only used by the \code{\linkS4class{sysBiolAlg_room}} method). } } \author{ Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de> Maintainer: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de> } \seealso{ Class \code{\linkS4class{sysBiolAlg}} and \code{\link{resetChanges}} } \keyword{methods} \keyword{optimize}