\name{replaceLetterAt}

\alias{replaceLetterAt}
\alias{replaceLetterAt,DNAString-method}
\alias{.inplaceReplaceLetterAt}

% Deprecated:
\alias{replaceLetterAtLoc}


\title{Replacing letters in a sequence at some specified locations}

\description{
  \code{replaceLetterAt} first makes a copy of a sequence and then
  replaces the original letters by new letters at some specified locations
  in the copied sequence.

  \code{.inplaceReplaceLetterAt} is the IN PLACE version of
  \code{replaceLetterAt}: it will modify the original
  sequence in place i.e. without copying it first.
  Note that in place modification of a sequence is fundamentally
  dangerous because it alters all objects defined in your session
  that make reference to the modified sequence.
  NEVER use \code{.inplaceReplaceLetterAt}, unless you know what
  you are doing!
}

\usage{
  replaceLetterAt(x, at, letter, if.not.extending="replace", verbose=FALSE)

  ## NEVER USE THIS FUNCTION!
  .inplaceReplaceLetterAt(x, at, letter)
}

\arguments{
  \item{x}{
    A \link{DNAString} object.
  }
  \item{at}{
    An integer vector with no NAs specifying the locations where the
    replacements must occur. Note that locations can be repeated and in
    this case the last replacement to occur at a given location prevails.
  }
  \item{letter}{
    Character vector with no NAs. The total number of letters in \code{letter}
    (\code{sum(nchar(letter))}) must be equal to the number of locations
    (\code{length(at)}).
  }
  \item{if.not.extending}{
    What to do if the new letter is not "extending" the old letter?
    The new letter "extends" the old letter if both are IUPAC letters
    and the new letter is as specific or less specific than the old
    one (e.g. M extends A, Y extends Y, but Y doesn't extend S).
    Possible values are \code{"replace"} (the default) for replacing
    in all cases, \code{"skip"} for not replacing when the new letter
    does not extend the old letter, \code{"merge"} for merging the new
    IUPAC letter with the old one, and \code{"error"} for raising
    an error.

    Note that the gap (\code{"-"}) and hard masking (\code{"+"})
    letters are not extending or extended by any other letter.

    Also note that \code{"merge"} is the only value for the
    \code{if.not.extending} argument that guarantees the final result
    to be independent on the order the replacement is performed (although
    this is only relevant when \code{at} contains duplicated locations,
    otherwise the result is of course always independent on the order,
    whatever the value of \code{if.not.extending} is).
  }
  \item{verbose}{
    When \code{TRUE}, a warning will report the number of skipped or merged
    letters.
  }
}

\details{
  \code{.inplaceReplaceLetterAt} semantic is equivalent to calling
  \code{replaceLetterAt} with \code{if.not.extending="merge"}
  and \code{verbose=FALSE}.

  Never use \code{.inplaceReplaceLetterAt}!
  It is used by the \code{\link[BSgenome]{injectSNPs}} function
  in the BSgenome package, as part of the "lazy sequence loading"
  mechanism, for altering the original sequences of a
  \link[BSgenome]{BSgenome} object at "sequence-load time".
  This alteration consists in injecting the IUPAC ambiguity letters
  representing the SNPs into the just loaded sequence, which is the
  only time where in place modification of the external data of
  an \link{XString} object is safe.
}

\value{
  A \link{DNAString} object of the same length as the orignal object \code{x}
  for \code{replaceLetterAt}.
}

\author{H. Pages}

\seealso{
  \code{\link{IUPAC_CODE_MAP}},
  \code{\link{chartr}},
  \code{\link{injectHardMask}},
  \link{DNAString},
  \code{\link[BSgenome]{injectSNPs}},
  \link[BSgenome]{BSgenome}
}

\examples{
  replaceLetterAt(DNAString("AAMAA"), c(5, 1, 3, 1), "TYNC")
  replaceLetterAt(DNAString("AAMAA"), c(5, 1, 3, 1), "TYNC", if.not.extending="merge")
}

\keyword{utilities}
\keyword{manip}