GenomicCache: Support package for GenomicFeatures

## An IntervalTree for GRanges objects
## setClass("GRangesTree",
##   representation(trees='list'),
##   prototype=list())

## setValidity("GRangesTree", function(object) {
##   if (is.null(names(object@trees))) {
##     return(paste("`trees` list must be names"))
##   }
##   TRUE
## })

## setAs("GRanges", "GRangesTree", function(from) {
##   .seqranges <- split(from, seqnames(from))
##   trees <- lapply(.seqranges, function(seqranges) {
##     if (length(seqranges) == 0L) {
##       return(NULL)
##     }
##     .stranges <- split(seqranges, strand(seqranges))
##     s <- lapply(.stranges, function(stranges) {
##       if (length(stranges) == 0L) {
##         return(NULL)
##       }
##       IntervalTree(ranges(stranges))
##     })
##     names(s) <- names(.stranges)
##     s <- s[!sapply(s, is.null)]
##   })
##   names(trees) <- names(.seqranges)
##   trees <- trees[!sapply(trees, is.null)]
##   new('GRangesTree', trees=trees)
## })

## setAs("CompressedReads", "GRangesTree", function(from) {
##   from <- as(from, "GRanges")
##   as(from, "GRangesTree")
## })

## setMethod("findOverlaps", c("GRanges", "GRangesTree"),
## function(query, subject, maxgap=0L, minoverlap=1L,
##          type=c("any", "start", "end"),
##          select=c("all", "first")) {
##   ##
##   type <- match.arg(type)
##   select <- match.arg(select)
##   stop("Not implemented")
## })

## setMethod("subsetByOverlaps", c("GRangesTree", "GRanges"),
## function(query, subject, maxgap=0L, minoverlap=1L,
##          type=c('any', 'start', 'end')) {
##   .seqranges <- split(subject, seqnames(subject))
##   seqover <- lapply(.seqranges, function(seqranges) {
##     if (length(seqranges) == 0L) {
##       return(NULL)
##     }
##     seqname <- as.character(seqnames(seqranges)[1])
##     chr.tree <- query@trees[[seqname]]
##     if (is.null(chr.tree)) {
##       return(NULL)
##     }
##     .stranges <- split(seqranges, strand(seqranges))
##     s <- lapply(.stranges, function(stranges) {
##       if (length(stranges) == 0L) {
##         return(NULL)
##       }
##       strandname <- as.character(strand(stranges)[1])
##       if (strandname == '*') {
##         .ranges <- c(IRanges(chr.tree[['+']]), IRanges(chr.tree[['-']]),
##                      IRanges(chr.tree[['*']]))
##         str.tree <- IntervalTree(.ranges)
##       } else {
##         str.tree <- chr.tree[[strandname]]
##       }
##       if (is.null(str.tree)) {
##         return(NULL)
##       }
##       o <- findOverlaps(ranges(stranges), str.tree, maxgap=maxgap,
##                         minoverlap=minoverlap)
##       if (length(o) == 0L) {
##         return(NULL)
##       }
##       GRanges(seqnames=seqname,
##               ranges=as(str.tree[subjectHits(o)], 'IRanges'),
##               strand=strandname)
##     })
##     names(s) <- names(.stranges)
##     s <- s[!sapply(s, is.null)]
##   })
##   seqover <- seqover[!sapply(seqover, is.null)]
##   if (length(seqover) == 0L) {
##     GRanges()
##   } else {
##     seqover <- unlist(seqover)
##     names(seqover) <- NULL
##     do.call(c, seqover)
##   }
## })