\name{RangesMapping-class}
\docType{class}
\alias{RangesMapping-class}

% generic
\alias{map}

% accessors
\alias{hits}
\alias{ranges,RangesMapping-method}
\alias{space,RangesMapping-method}
\alias{dim,RangesMapping-method}
\alias{length,RangesMapping-method}
\alias{queryHits,RangesMapping-method}
\alias{subjectHits,RangesMapping-method}

% coercion
\alias{coerce,RangesMapping,RangedData-method}

\title{Mapping of ranges to another sequence}

\description{The \code{map} generic converts a set of ranges to the
  equivalent ranges on another sequence, through some sort of alignment
  between sequences, and outputs an \code{RangesMapping} object. There
  are three primary components of that object: the transformed \code{ranges},
  the \code{space} (destination sequence) for the ranges, and
  the \code{hits}, a \code{\linkS4class{Hits}} object of the same length
  that matches each input range to a destination sequence (useful when
  the alignment is one/many to many).}

\usage{map(from, to, ...)}

\arguments{
  \item{from}{Typically an object containing ranges to map.}
  \item{to}{Typically an object representing an alignment.}
  \item{...}{Arguments to pass to methods}
}

\value{
  A \code{RangesMapping} object, as documented here.
}

\section{\code{RangesMapping} Accessors}{
  \describe{
    \item{}{\code{ranges(x)}: Gets the mapped ranges.}
    \item{}{\code{space(x)}: Gets the destination spaces (sequence
      names).}
    \item{}{\code{hits(x)}: Gets the matching between the input ranges
      and the destination sequences (of which there may be more than
      one).}
    \item{}{\code{dim(x)}: Same as \code{dim(hits(x))}.}
    \item{}{\code{length(x)}: Same as \code{length(hits(x))}.}
    \item{}{\code{subjectHits(x)}: Same as \code{subjectHits(hits(x))}.}
    \item{}{\code{queryHits(x)}: Same as \code{queryHits(hits(x))}.}
  }
}

\section{\code{RangesMapping} Coercion}{
  \describe{
    \item{}{\code{as(from, "RangedData")}: Converts
      a \code{RangesMapping} into
      a \code{\linkS4class{RangedData}}. The \code{ranges}/\code{space}
      in the \code{RangedData} are the \code{ranges}/\code{space}
      of \code{from}, and the \code{values} result from the coercion of
      the \code{hits} to a \code{DataFrame}.
    }
  }
}

\author{ Michael Lawrence }

\seealso{
  Methods on the generic \code{map}, which generates an instance of
  this class, are defined in other packages, like GenomicRanges.
}

\keyword{methods}
\keyword{classes}