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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-11-26 19:52:13 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20131126195213-1zwbthnie0a7fdns
Tags: 1.14.3-1
http://bugs.debian.org/730574
* New upstream version
  Closes: #730574
* Build-Depends: r-bioc-xvector

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R/GRangesList-class.R
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            paste("'mcols(x)' cannot have columns named \"seqnames\", ",
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                  "\"ranges\", \"strand\", \"start\", \"end\", \"width\", ",
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                  "or \"element\""))
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    if (any(colnames(x_mcols) %in%
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            colnames(x@unlistData@elementMetadata)))
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        msg <-
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          c(msg,
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            paste("'mcols(x)' cannot have columns named as metadata ",
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                  "columns of unlisted GRanges"))
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    if (!is.null(rownames(x_mcols)))
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        msg <- c(msg, "'mcols(x)' cannot have row names")
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    msg
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{
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    if (!is(value, "Seqinfo"))
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        stop("the supplied 'seqinfo' must be a Seqinfo object")
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    unlisted <- x@unlistData
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    dangling_seqlevels <- getDanglingSeqlevels(unlisted,
 
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    dangling_seqlevels <- getDanglingSeqlevels(x,
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                              new2old=new2old, force=force,
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                              seqlevels(value))
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    if (length(dangling_seqlevels) != 0L) {
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        dropme <- which(seqnames(unlisted) %in% dangling_seqlevels)
 
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        dropme <- which(seqnames(x@unlistData) %in% dangling_seqlevels)
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        x <- x[-unique(togroup(x, j=dropme))]
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    }
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    seqinfo(x@unlistData, new2old=new2old) <- value
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{
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    if (!is(value, class(x)[1]))
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        stop(paste0("replacement value must be a ", class(x)[1], " object"))
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    if (!missing(i)) {
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        iInfo <- IRanges:::.bracket.Index(i, length(x), names(x))
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        if (!is.null(iInfo[["msg"]]))
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            stop(iInfo[["msg"]])
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        i <- iInfo[["idx"]]
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    }
 
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    if (!missing(i))
 
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        i <- IRanges:::extractROWS(setNames(seq_along(x), names(x)), i)
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    if (!missing(j)) {
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        if (!is.character(j))
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            stop("'j' must be a character vector")