\name{addCon}
\title{Add constraints to an already existing constraint set}
\alias{addCon}
\description{
  Given a constraint set, the addCon command allows to add either interval-specific or global constraints to the constraintSet object.
  The possible interval-specific constraints are: boundCon (for information content bounding constraints), posFreqCon (for position frequency constraints), and shapeCon (for shape constraints).
  The possible global constraints are: subMotifCon (when part of the motif is known), palCon (for palindromic constraints) and shapeDiffCon (for information content differences between interval extremities).
  Each constraint can be built with its associated make-command: makeBoundCon, makePosFreqCon, makeShapeCon, makeSubMotifCon, makePalCon and makeShapeDiffCon.
} 
\usage{
  addCon(conSet, constraint, int=1) 
}
\arguments{
  \item{conSet}{an object of class \code{"constraint set"}}
  \item{constraint}{list of constraints constructed with one of the 6
    make constraint commands. The length of the list should be the same
    as that of the 'int' argument. Instead of a list, this may also be a
    single constraint.}
  \item{int}{vector of the intervals to which the constraints given in the constraint argument should be applied. There should be a one-to-one correspondance between the elements of the list and the interval argument.
  For global constraints, the value of the interval is of no importance but should be present and numeric.}
}
\details{
}
\value{
The output will be an object of class \code{"constraintSet"} resulting of the addition of the constraints to the original constraint set passed as first argument.
}
\author{
Fabian Gallusser, \email{fgallusser@berkeley.edu}
}
\seealso{
  \code{\link{boundCon}}, \code{\link{posFreqCon}}, \code{\link{shapeCon}}, \code{\link{subMotifCon}}, \code{\link{shapeDiffCon}}, \code{\link{palCon}}
  \code{\link{makeBoundCon}}, \code{\link{makePosFreqCon}}, \code{\link{makeShapeCon}}, \code{\link{makeSubMotifCon}}, \code{\link{makeShapeDiffCon}}, \code{\link{makePalCon}}
}
\examples{
set=makeConSet(4,c("B","P","V","B"),c(4,50,NA,4))
con1=makeBoundCon(1,2)
con2=makePalCon(1,4,0.5)
con3=makeSubMotifCon("TATA",0.6)
con4=makePosFreqCon("2","A",0.5)
con5=makePosFreqCon("All","G",0.4)
conSet=addCon(set,list(con1,con2,con3,con4,con5),c(2,NA,NA,1,3))
#Because of the palindromic constraint on intervals 1 and 4, the fourth
#interval will inherit the nucleotide position frequency constraint
#assigned to the first interval.
}
\keyword{misc}