\name{Ranges-comparison}

\alias{Ranges-comparison}

\alias{==}
\alias{==,Ranges,Ranges-method}
\alias{!=,Ranges,Ranges-method}
\alias{duplicated,Ranges-method}
\alias{unique,Ranges-method}

\alias{<=}
\alias{<=,Ranges,Ranges-method}
\alias{>=}
\alias{>=,Ranges,Ranges-method}
\alias{<}
\alias{<,Ranges,Ranges-method}
\alias{>}
\alias{>,Ranges,Ranges-method}
\alias{order}
\alias{order,Ranges-method}
\alias{sort,Ranges-method}
\alias{rank,Ranges-method}


\title{Ranges comparison}

\description{
  Equality and ordering of ranges, and related methods.
}

\usage{
## ==== Equality and related methods ====
## --------------------------------------

\S4method{==}{Ranges,Ranges}(e1, e2)

\S4method{!=}{Ranges,Ranges}(e1, e2)

\S4method{duplicated}{Ranges}(x, incomparables=FALSE, fromLast=FALSE,
           method=c("auto", "quick", "hash"), ...)

\S4method{unique}{Ranges}(x, incomparables=FALSE, fromLast=FALSE,
       method=c("auto", "quick", "hash"), ...)

## ==== Ordering and related methods ====
## --------------------------------------

\S4method{<=}{Ranges,Ranges}(e1, e2)
\S4method{>=}{Ranges,Ranges}(e1, e2)
\S4method{<}{Ranges,Ranges}(e1, e2)
\S4method{>}{Ranges,Ranges}(e1, e2)

\S4method{order}{Ranges}(..., na.last=TRUE, decreasing=FALSE)

\S4method{sort}{Ranges}(x, decreasing=FALSE, ...)

\S4method{rank}{Ranges}(x, na.last=TRUE,
     ties.method=c("average", "first", "random", "max", "min"))
}

\arguments{
  \item{e1,e2,x}{
    \link{Ranges} objects.
  }
  \item{incomparables}{
    Must be \code{FALSE}.
  }
  \item{fromLast}{
    See default S3 method for \code{\link[base]{duplicated}}.
  }
  \item{method}{
    Use a Quicksort-based (\code{method="quick"})
    or a hash-based (\code{method="hash"}) algorithm.
    The latter tends to give better performance, except maybe for some
    pathological input that we've not been able to determine so far.
    When \code{method="auto"} is specified, the hash-based algorithm
    is used as long as the length of \code{x} is <= 2^29, otherwise the
    Quicksort-based algorithm is used.
  }
  \item{...}{
    \link{Ranges} objects for \code{order}.
  }
  \item{na.last}{
    Ignored.
  }
  \item{decreasing}{
    \code{TRUE} or \code{FALSE}.
  }
  \item{ties.method}{
    A character string specifying how ties are treated. Only \code{"first"}
    is supported for now.
  }
}

\details{
  Two ranges are considered equal iff they share the same start and width.
  Note that with this definition, 2 empty ranges are generally
  not equal (they need to share the same start to be considered equal).
  This means that, when it comes to comparing ranges, an empty range is
  interpreted as a position between its end and start. For example, a
  typical usecase is comparison of insertion points defined along a string
  (like a DNA sequence) and represented as empty ranges.

  Ranges are ordered by starting position first, and then by width.
  This way, the space of ranges is totally ordered.
  The \code{order}, \code{sort} and \code{rank} methods for \link{Ranges}
  objects are consistent with this order.

  \describe{
    \item{}{
      \code{duplicated(x)}:
      Determines which elements of \code{x} are equal to elements
      with smaller subscripts, and returns a logical vector indicating
      which elements are duplicates.
      It is semantically equivalent to \code{duplicated(as.data.frame(x))}.
      See \code{\link[base]{duplicated}} in the base package for more details.
    }
    \item{}{
      \code{unique(x)}:
      Removes duplicate ranges from \code{x}.
      See \code{\link[base]{unique}} in the base package for more details.
    }
    \item{}{
      \code{order(...)}:
      Returns a permutation which rearranges its first argument (a \link{Ranges}
      object) into ascending order, breaking ties by further arguments (also
      \link{Ranges} objects).
      See \code{\link[base]{order}} in the base package for more details.
    }
    \item{}{
      \code{sort(x)}:
      Sorts \code{x}.
      See \code{\link[base]{sort}} in the base package for more details.
    }
    \item{}{
      \code{rank(x, na.last=TRUE, ties.method=c("average", "first", "random", "max", "min"))}:
      Returns the sample ranks of the ranges in \code{x}.
      See \code{\link[base]{rank}} in the base package for more details.
    }
  }
}

\seealso{
  \link{Ranges-class},
  \link{IRanges-class},
  \code{\link[base]{duplicated}},
  \code{\link[base]{unique}},
  \code{\link[base]{order}},
  \code{\link[base]{sort}},
  \code{\link[base]{rank}}
}

\examples{
  x <- IRanges(start=c(20L, 8L, 20L, 22L, 25L, 20L, 22L, 22L),
               width=c( 4L, 0L, 11L,  5L,  0L,  9L,  5L,  0L))
  x
  which(width(x) == 0)  # 3 empty ranges
  x[2] == x[2]  # TRUE
  x[2] == x[5]  # FALSE
  x == x[4]
  duplicated(x)
  unique(x)
  x >= x[3]
  order(x)
  sort(x)
  rank(x, ties.method="first")
}

\keyword{methods}