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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/GenomicRanges-comparison.R
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### method for Vector objects.
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###
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### Unfortunately, the early version of this method was doing overlaps, not
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### equality. We temporarily add the 'match.if.overlap' argument so the old
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### behavior is still available.
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### TODO: Deprecate 'match.if.overlap' arg in BioC 2.13.
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### TODO: Remove 'match.if.overlap' arg in BioC 2.14.
 
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### TODO: Defunct 'match.if.overlap' arg in BioC 2.14.
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setMethod("match", c("GenomicRanges", "GenomicRanges"),
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    function(x, table, nomatch=NA_integer_, incomparables=NULL,
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                       method=c("auto", "quick", "hash"),
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                 "only accepts 'incomparables=NULL'")
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        if (!isTRUEorFALSE(ignore.strand))
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            stop("'ignore.strand' must be TRUE or FALSE")
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        if (missing(match.if.overlap))
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            warning(IRanges:::match.if.overlap.warning.msg("GenomicRanges"))
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        if (!isTRUEorFALSE(match.if.overlap))
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            stop("'match.if.overlap' must be TRUE or FALSE")
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        if (match.if.overlap) {
 
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            msg <- c("  In the near future (starting with BioC 2.14), ",
 
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                     "match() on GRanges objects\n  won't support ",
 
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                     "the 'match.if.overlap' argument anymore. Please use\n\n",
 
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                     "    findOverlaps(x, table, select=\"first\", ",
 
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                     "ignore.strand=ignore.strand)\n\n",
 
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                     "  instead of\n\n",
 
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                     "    match(x, table, ignore.strand=ignore.strand, ",
 
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                     "match.if.overlap=TRUE)")
 
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            .Deprecated(msg=msg)
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            ans <- findOverlaps(x, table,
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                                select="first", ignore.strand=ignore.strand)
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            if (!is.na(nomatch) && anyMissing(ans))
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        ## Calling merge() is the way to check that 'x' and 'table' are based
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        ## on the same reference genome.
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        merge(seqinfo(x), seqinfo(table))
 
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        x_seqnames <- relevelSeqnamesForMatch(x, table)
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        if (ignore.strand) {
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            x_strand <- integer(length(x))
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            table_strand <- integer(length(table))
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        ## Equivalent to (but faster than):
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        ##     findOverlaps(x, table, type="equal", select="first")
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        ## except when 'x' and 'table' both contain empty ranges.
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        IRanges:::matchIntegerQuads(as.factor(seqnames(x)), x_strand,
 
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        IRanges:::matchIntegerQuads(x_seqnames, x_strand,
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                                    start(x), width(x),
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                                    as.factor(seqnames(table)), table_strand,
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                                    start(table), width(table),
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    }
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)
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relevelSeqnamesForMatch <- function(x, table) {
 
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  x_seqnames <- as.factor(seqnames(x))
 
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  if (!hasHead(seqlevels(x), seqlevels(table)) &&
 
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      !hasHead(seqlevels(table), seqlevels(x))) {
 
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    x_seqnames <- factor(x_seqnames,
 
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                         union(seqlevels(table), seqlevels(x)))
 
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  }
 
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  x_seqnames
 
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}
 
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### The only reason for overriding the method for Vector objects is to issue
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### the warning.
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### TODO: Remove this method in BioC 2.14 when the 'match.if.overlap' arg of
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### match() is gone.
 
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### match() is defunct.
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setMethod("%in%", c("GenomicRanges", "GenomicRanges"),
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    function(x, table)
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    {
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        warning(IRanges:::`%in%.warning.msg`("GenomicRanges"))
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        !is.na(match(x, table, match.if.overlap=FALSE))
 
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        !is.na(match(x, table))
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    }
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)
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### that otherwise would be issued when the user calls findMatches() or
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### countMatches() on GenomicRanges objects.
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### TODO: Remove these methods in BioC 2.14 when the 'match.if.overlap' arg
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### of match() is gone.
 
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### of match() is defunct.
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setMethod("findMatches", c("GenomicRanges", "GenomicRanges"),
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    function(x, table, select=c("all", "first", "last"), ...)