R/AllClasses.R

Defines functions CustomTrack OverlayTrack HighlightTrack AlignmentsTrack RNASequenceTrack SequenceTrack .SequenceTrack AlignedReadTrack UcscTrack clearSessionCache .cacheMartData .cacheGenomes .cacheTracks .doCache IdeogramTrack DataTrack GenomeAxisTrack BiomartGeneRegionTrack .bmGuid .fetchBMData .getBMFeatureMap GeneRegionTrack DetailsAnnotationTrack AnnotationTrack .updateDp DisplayPars ImageMap

Documented in AlignedReadTrack AlignmentsTrack AnnotationTrack BiomartGeneRegionTrack clearSessionCache CustomTrack DataTrack DetailsAnnotationTrack DisplayPars GeneRegionTrack GenomeAxisTrack HighlightTrack IdeogramTrack OverlayTrack RNASequenceTrack SequenceTrack UcscTrack

## All class definitions and constructors/initializers for the
## package. Note that some methods have to be defined in here as well
## because they are used as part of the initializers.  Constructors
## and definitions that are exported in the name space are marked with



## Class unions --------------------------------------------------------------------------------------------------------
##
## Some useful class unions to allow for NULL values in certain slots
setClassUnion("DfOrNULL", c("data.frame", "NULL"))
setClassUnion("MartOrNULL", c("Mart", "NULL"))
setClassUnion("FactorOrCharacterOrNULL", c("factor", "character", "NULL"))
setClassUnion("NumericOrNULL", c("numeric", "NULL"))
setClassUnion("ListOrEnv", c("list", "environment"))
setClassUnion("GRangesOrIRanges", c("GRanges", "IRanges"))
setClassUnion("NULLOrMissing", c("NULL", "missing"))
setClassUnion("BSgenomeOrNULL", c("BSgenome", "NULL"))




## ImageMap ------------------------------------------------------------------------------------------------------------
##
## ImageMap - A class to hold HTML image map information
##
## Slots :
##    o coords: a numeric matrix of rectangular image map coordinates, in the order x bl, y bl, x tr, y tr.
##      Rownames are mandatory for the matrix and have to be unique
##    o tags: a list of tags that are to be added to the <map> tag, where the name of the list item is used as the
##      tagname. The value of each list item has to be a named character vector, where the names must match back into
##      the rownames of the 'coords' matrix

setClass("ImageMap", representation(coords = "matrix", tags = "list"),
    prototype = prototype(coords = matrix(1, ncol = 4, nrow = 0), tags = list())
)

## Constructor
ImageMap <- function(coords, tags) {
    if (!(is.matrix(coords) && is.numeric(coords) && ncol(coords) == 4)) {
        stop("'coords' must be a numeric matrix with 4 columns")
    }
    rn <- rownames(coords)
    if (is.null(rn)) {
        stop("Rownames must be set for the matrix in 'coords'")
    }
    if (!is.list(tags) || is.null(names(tags)) || any(names(tags) == "") || !all(vapply(tags, is.character, logical(1)))) {
        stop("'tags' must be a named list with character vector items.")
    }
    n <- unique(unlist(lapply(tags, names)))
    if (is.null(n) || any(n == "")) {
        stop("All items in the 'tags' list must be named character vectors.")
    }
    m <- n %in% rn
    if (!all(m)) {
        stop(
            "The following values in the 'tags' list could not be mapped to the 'coords' matrix:\n",
            paste(n[!m], sep = "", collapse = ", ")
        )
    }
    new("ImageMap", coords = coords, tags = tags)
}

## Allow for NULL value slots
setClassUnion("ImageMapOrNULL", c("ImageMap", "NULL"))




## DisplayPars ---------------------------------------------------------------------------------------------------------
##
## DisplayPars: A class to control the plotting parameters for GdObjects
##
## Slots :
##    o pars: an environment or a list containing parameter key value pairs
##       The initial idea was for the class to uses pass by reference semantic, allowing to update the object
##       without reassigning to a symbol. However this turned out to be problematic whenever a GdObject was
##       copied and to avoid confusion with the users about unwanted side-effects we decided to deprecate this
##       feature.

setClass("DisplayPars", representation(pars = "ListOrEnv"))

## The initializer needs to create the environment, we can't take this
## directly from the class prototype since this would result in using
## the same environment all the time
setMethod("initialize", "DisplayPars", function(.Object, ...) {
    e <- new.env(hash = TRUE)
    args <- list(...)
    n <- names(args)
    if ((is.null(n) & length(args) == 1) || any(n == "")) {
        stop("All supplied arguments must be named.")
    }
    .Object@pars <- args
    return(.Object)
})

## Constructor, all supplied arguments are added to the environment.
DisplayPars <- function(...) {
    return(new("DisplayPars", ...))
}

## Update function and deprecation message to show that an old environment-based
## DisplayParameter object has been updated to a list-based object.
.updateDp <- function(x, interactive = TRUE) {
    if (interactive) {
        message(
            "Note that the behaviour of the 'setPar' method has changed. You need to reassign the result to an ",
            "object for the side effects to happen. Pass-by-reference semantic is no longer supported."
        )
    }
    if (is.environment(x@pars)) {
        x@pars <- as.list(x@pars)
        message("The DisplayPars object has been updated to a list-based representation.")
    }
    return(x)
}

## The accessor methods for the DisplayPars class. (they need to be in
## here because they are being called in the prototypes). For the
## setter method, the input can either be a named list, or a single
## keyword/value pair. The DisplayPars class was first implemented as
## an environment, so we essentially had pass by reference semantic here,
## and the object could be modified without the need to reassign to a
## symbol. However this somewhat broke the the R paradigm, and 'setPar'
## has been deprecated in favour of the more standard 'DisplayPars<-'
## replacement method. The getter methods either return the list
## of all parameters, or a subset of parameters if their names are
## provided as a character vector.  Please note that for convenience
## the result is unlisted if only a single parameter is queried.
## Since version 1.7.3 we have introduced an alias table for display
## parameters in order to harmomize parameter names without loosing
## backwards compatability.
setMethod(
    "setPar", signature("DisplayPars", "list"),
    function(x, value, interactive = TRUE) {
        x <- .updateDp(x, interactive)
        aliasRes <- .dpAliasReverseTable[names(value)]
        new <- is.na(aliasRes)
        aliasRes[new] <- names(value)[new]
        x@pars[aliasRes] <- value
        return(x)
    }
)

setMethod(
    "setPar", signature("DisplayPars", "character"),
    function(x, name, value, interactive = TRUE) {
        if (!(length(name) == 1 && is.null(value)) && length(name) != length(value)) {
            stop("'name' and 'value' must be of equal length")
        }
        x <- .updateDp(x, interactive)
        for (i in seq_along(name)) {
            aliasRes <- .dpAliasReverseTable[name[i]]
            if (is.na(aliasRes)) {
                aliasRes <- name[i]
            }
            x@pars[[aliasRes]] <- value[[i]]
        }
        return(x)
    }
)

setReplaceMethod("displayPars", signature("DisplayPars", "list"), function(x, recursive = FALSE, value) {
    x <- setPar(x, value, interactive = FALSE)
    return(x)
})

setMethod(
    "getPar", c("DisplayPars", "character"),
    function(x, name, asIs = FALSE) {
        aliasRes <- .dpAliasReverseTable[name]
        new <- is.na(aliasRes)
        aliasRes[new] <- name[new]
        if (is.environment(x@pars)) {
            name <- intersect(aliasRes, base::ls(x@pars, all.names = TRUE))
            tmp <- mget(name, x@pars)
        } else {
            name <- intersect(aliasRes, names(x@pars))
            tmp <- x@pars[name]
        }
        if (!asIs) {
            tmp <- if (is.list(tmp) && length(tmp) == 1) tmp[[1]] else tmp
        }
        return(if (length(tmp)) tmp else NULL)
    }
)

setMethod("getPar", c("DisplayPars", "missing"), function(x, hideInternal = TRUE) {
    pars <- as.list(x@pars)
    if (hideInternal) {
        pars <- pars[!grepl("^\\.__", names(pars))]
    }
    return(pars)
})

setMethod("displayPars", c("DisplayPars", "missing"), function(x, hideInternal = TRUE) getPar(x, hideInternal = hideInternal))

setMethod("displayPars", c("DisplayPars", "character"), function(x, name) getPar(x, name))

setMethod("as.list", "DisplayPars", function(x) as(x, "list"))

setAs("DisplayPars", "list", function(from, to) if (!is.null(from)) as.list(from@pars) else list())

## An alias table to define display parameter synonyms. Essentially this is a simple named list,
## where the element names represent the preferred parameter name under which the actual value is
## stored, and the element content is a character vector of synonyms. Please note that this structure
## is also turned into a reverse lookup table for fast access.
.dpAliasTable <- list(
    "fontcolor.title" = "col.title",
    "rotation.title" = c("rot.title", "rotate.title"),
    "fontcolor.group" = "col.group",
    "fontcolor.item" = "col.item",
    "just.group" = c("labelJust", "labelJustification"),
    "transcriptAnnotation" = "geneSymbols",
    "fontcolor.item" = c("fontcolor.exon", "fontcolor.feature"),
    "fontsize.item" = c("fontsize.exon", "fontsize.feature"),
    "fontfamily.item" = c("fontfamily.exon", "fontfamily.feature"),
    "fontface.item" = c("fontface.exon", "fontface.feature"),
    "lineheight.item" = c("lineheight.exon", "lineheight.feature"),
    "alpha.item" = c("alpha.exon", "alpha.feature"),
    "cex.item" = c("cex.exon", "cex.feature"),
    "col.mate" = c("col.mate", "col.mates", "col.pair", "col.pairs"),
    "lty.mate" = c("lty.mate", "lty.mates", "lty.pair", "lty.pairs"),
    "lwd.mate" = c("lwd.mate", "lwd.mates", "lwd.pair", "lwd.pairs"),
    "alpha.mate" = c("alpha.mate", "alpha.mates", "alpha.pair", "alpha.pairs"),
    "col.gap" = "col.gaps",
    "lwd.gap" = "lwd.gaps",
    "lty.gap" = "lty.gaps",
    "alpha.gap" = "alpha.gaps"
)
.dpAliasReverseTable <- character()
.dpAliasReverseTable[names(.dpAliasTable)] <- names(.dpAliasTable)
.dpAliasReverseTable[unlist(.dpAliasTable, use.names = FALSE)] <- rep(names(.dpAliasTable), listLen(.dpAliasTable))
.dpAliasReverseTable <- .dpAliasReverseTable[order(names(.dpAliasReverseTable))]

## InferredDisplayPars -------------------------------------------------------------------------------------------------
##
## InferredDisplayPars: A class to allow for querying of available display parameters.
##                      Essentially this is a normal list with a bit of a fancyfied show method.
## Slots :
##    o name: the name of the class
##    o inheritance: a character vector indicating the inheritance structure
setClass("InferredDisplayPars", representation(name = "character", inheritance = "character"), contains = "list")

setMethod("as.list", "InferredDisplayPars", function(x) as(x, "list"))

setAs(
    "InferredDisplayPars", "list",
    function(from, to) {
        ll <- from@.Data
        names(ll) <- names(from)
        ll
    }
)



##  GdObject ------------------------------------------------------------------------------------------------------------
##
## The GdObject is the parent of all Gviz objects in the system.
## This class is virtual.
## Slots:
##    o dp: object of class DisplayPars to fine-tune the drawing.
##    o name: the object name, used in the title panel if needed.
##    o imageMap: an ImageMap object holding relevant image map information, or NULL
## A bunch of DisplayPars are set during object instantiation:
##    o fontface, fontcolor, fontsize, fontfamily, lineheight, cex: default settings for
##       all text unless specified someplace else.
##    o col, lwd, lty, fill: default settings for all plotting elements unless specified
##       somewhere else.
##    o col.line, col.symbol: default colors for plot symbols and plot lines. The default is
##       to take the value of the global col parameter.
##    o col.frame: the color of the panel frame, if frame==TRUE
##    o col.grid, lwd.grid, lty.grid, v and h: the default parameters for the grid plotting,
##       both when type=="g" in DataTracks and when grid==TRUE
##    o alpha: the transparancy for all track items.
##    o background.title: the fill color for the title panel. Defaults to lightgray.
##    o col.title: the font color for the title panel. Defaults to white.
##    o cex.title: the expansion factor for the title panel. This effects the fontsize
##       of both the title and the axis, if any. Defaults to NULL, which means that the
##       text size is automatically adjusted to the available space.
##    o fontfamily.title, fontface.title: the font family and font face for the title panel.
##       Defaults to bold sans serif.
##    o col.axis: the font and line color for the y axis, if any. Defaults to white.
##    o cex.axis: the expansion factor for the axis annotation. Defaults to NULL, in which case
##       it is computed based on the available space.
##    o background.panel: the background color of the content panel. Defaults to transparent.
##    o showTitle: boolean, controlling whether to plot a title panel. Although this can be
##       set individually for each track, in multi-track plots there will still
##       be an empty placeholder in case any of the other tracks include a title. The
##       same holds true for axes. Note that the background color could be set to
##       transparent in order to completely hide the title/axis panel.
##    o showAxis: boolean, controlling whether to plot a y axis (only track types where axes
##     are implemented).
##    o grid: boolean, switching on/off the plotting of a grid.
##    o collapse: collapse the content of the track to accomodate the minimum current
##     device resolution
##    o min.width, min.height: the minimum width and height in pixels to display. All ranges are expanded
##       to this size in order to avoid rendering issues.
##    o min.distance: the minimum pixel distance before collapsing range items, only if collapse==TRUE
##    o frame: draw a frame around the track
##    o size: the relative size of the track
##    o ...: additional DisplayPars are allowed. Unless specified in one of the subclasses,
##       those should take the value of a valid R color descriptors. The parameter names will
##     later be matched to optional track item types as defined in the 'feature' range
##     attribute, and all tracks of the matched types are colored accordingly. See the
##     documentation of the 'GeneRegion' and 'AnnotationTrack' classes for details.
setClass("GdObject",
    representation = representation("VIRTUAL",
        dp = "DisplayPars",
        name = "character",
        imageMap = "ImageMapOrNULL"
    ),
    prototype = prototype(
        dp = DisplayPars(
            alpha = 1,
            alpha.title = NULL,
            background.panel = "transparent",
            background.title = "lightgray",
            background.legend = "transparent",
            cex.axis = NULL,
            cex.title = NULL,
            cex = 1,
            col.axis = "white",
            col.border.title = "white",
            col.frame = "lightgray",
            col.grid = .DEFAULT_SHADED_COL,
            col.line = NULL,
            col.symbol = NULL,
            col.title = "white",
            col = .DEFAULT_SYMBOL_COL,
            collapse = TRUE,
            fill = .DEFAULT_FILL_COL,
            fontcolor = "black",
            fontface.title = 2,
            fontface = 1,
            fontfamily.title = "sans",
            fontfamily = "sans",
            fontsize = 12,
            frame = FALSE,
            grid = FALSE,
            h = -1,
            lineheight = 1,
            lty.grid = "solid",
            lty = "solid",
            lwd.border.title = 1,
            lwd.title = 1,
            lwd.grid = 1,
            lwd = 1,
            min.distance = 1,
            min.height = 3,
            min.width = 1,
            reverseStrand = FALSE,
            rotation.title = 90,
            rotation = 0,
            showAxis = TRUE,
            showTitle = TRUE,
            size = 1,
            v = -1
        ),
        name = "GdObject",
        imageMap = NULL
    )
)

## We need to set and query DisplayPars in the the initializer, hence
## the appropriate methods have to be defined here first.
setMethod("setPar", signature("GdObject", "character"), function(x, name, value, interactive = TRUE) {
    newDp <- setPar(x@dp, name, value, interactive = interactive)
    x@dp <- newDp
    return(x)
})

setMethod("setPar", signature("GdObject", "list"), function(x, value, interactive = TRUE) {
    newDp <- setPar(x@dp, value, interactive = interactive)
    x@dp <- newDp
    return(x)
})

setReplaceMethod("displayPars", signature("GdObject", "list"), function(x, recursive = FALSE, value) {
    x <- setPar(x, value, interactive = FALSE)
    return(x)
})

setMethod("getPar", c("GdObject", "character"), function(x, name, asIs = FALSE) getPar(x@dp, name, asIs = asIs))

setMethod("getPar", c("GdObject", "missing"), function(x, hideInternal = TRUE) getPar(x@dp, hideInternal = hideInternal))

setMethod("displayPars", c("GdObject", "character"), function(x, name) getPar(x, name))

setMethod("displayPars", c("GdObject", "missing"), function(x, hideInternal = TRUE) getPar(x, hideInternal = hideInternal))

## We add everything that hasn't been clobbered up so far as
## additional DisplayParameters.  Also, the dp slot must be
## re-initiated here in order to get a fresh environment for each
## instance of the class.
setMethod("initialize", "GdObject", function(.Object, name, ...) {
    ## update the default parameters first
    .makeParMapping()
    .Object <- .updatePars(.Object, "GdObject")
    ## now rebuild the slot to get a new environment
    pars <- getPar(.Object, hideInternal = FALSE)
    .Object@dp <- DisplayPars()
    .Object <- setPar(.Object, pars, interactive = FALSE)
    if (!missing(name)) {
        .Object@name <- if (is.null(name)) "" else name
    }
    ## Finally clobber up everything that's left
    .Object <- setPar(.Object, list(...), interactive = FALSE)
    return(.Object)
})



## RangeTrack ----------------------------------------------------------------------------------------------------------
##
## RangeTrack: Parent class for all region-like annotation tracks, storing information
## about start, end, strand, chromosome and the associated genome.
## Slots:
##    o range: object of class GRangesOrIRanges containing all the necessary information
##       for plotting. The content of the metadata columns may vary between
##     subclasses. The strand information may be provided in the form '+' for
##     the Watson strand, '-' for the Crick strand or '*' for any of the two.
##    o chromosome: a character vector giving the active chromosome for which the
##     track is defined. Valid chromosome names are:
##          - a single numeric character
##        - a string, starting with 'chr', followed by any additional characters
##    o genome: character giving the reference genome for which the track is defined.

setClass("RangeTrack",
    representation = representation("VIRTUAL",
        range = "GRangesOrIRanges",
        chromosome = "character",
        genome = "character"
    ),
    contains = "GdObject",
    prototype = prototype(
        chromosome = "chr1",
        dp = DisplayPars(),
        genome = "ANY",
        name = "RangeTrack",
        range = GRanges()
    )
)

## Coercing all input to the appropriate form
setMethod("initialize", "RangeTrack", function(.Object, range, chromosome, genome, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "RangeTrack")
    if (!missing(chromosome) && !is.null(chromosome)) {
        .Object@chromosome <- .chrName(chromosome)[1]
    }
    if (!missing(genome) && !is.null(genome)) {
        .Object@genome <- genome
    }
    if (!missing(range) && is(range, "GRanges")) {
        .Object@range <- range
    }
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})



## ReferenceTrack ------------------------------------------------------------------------------------------------------
##
##
## ReferenceTrack: Parent class for all tracks that provide a reference to data somewhere on the file system.
##                 This class is virtual and only exists for the purpose of dispatching
## Slots:
##   o stream: the import function to stream data off the disk. Needs to be able to handle the two mandatory arguments
##      'file' (a character containing a valid file path) and 'selection' (a GRanges object with the genomic region to plot)
##   o reference: the path to the file containing the data
##   o mapping: a default mapping between the metadata columns of the returned GRanges object from the import function
##      and the metadata columns that make up the final track object
##   o args: a list with the passed in constructor arguments during object instantiation. Those will be needed when
##     fetching the data in order to fill all necessary slots
##   o defaults: a list with the relevant default values to be used when neither 'mapping' nor 'args' provides the
##     necessary information

setClass("ReferenceTrack",
    representation = representation("VIRTUAL",
        stream = "function",
        reference = "character",
        mapping = "list",
        args = "list",
        defaults = "list"
    ),
    prototype = prototype(
        stream = function(x, selection) {},
        reference = "~",
        mapping = list()
    ),
    validity = function(object) {
        msg <- NULL
        if (!all(c("file", "selection") %in% names(formals(object@stream)))) {
            msg <- "The streaming function in the 'stream' slot needs to define two arguments, 'file' and 'selection'"
        }
        if (!file.exists(object@reference)) {
            msg <- c(msg, sprintf("The referenced file '%s' does not exist", object@reference))
        }
        return(if (is.null(msg)) TRUE else msg)
    }
)
setMethod("initialize", "ReferenceTrack", function(.Object, stream, reference, mapping = list(),
                                                   args = list(), defaults = list()) {
    .Object@stream <- stream
    .Object@reference <- reference
    .Object@mapping <- mapping
    .Object@args <- args
    .Object@defaults <- defaults
    validObject(.Object)
    return(.Object)
})



## NumericTrack --------------------------------------------------------------------------------------------------------
##
## NumericTrack: Parent class for all annotation tracks that include numeric values.
##               This is for dispatching purpose only.

setClass("NumericTrack",
    representation = representation("VIRTUAL"),
    prototype = prototype(
        name = "NumericTrack",
        dp = DisplayPars()
    ),
    contains = "RangeTrack"
)



## StackedTrack --------------------------------------------------------------------------------------------------------
##
## StackedTrack: Parent class for all tracks that involve stacking.
##               This is for dispatching purpose only.
## Slots:
##    o stacking: character controlling the stacking of overlapping items on the final plot.
##       One in 'hide', 'dense', 'squish', 'pack' or 'full'.
##    o stacks: a numeric vector holding the current stacking information. Not usually set by the user.
## This is part of the prototype only
##    o stackingValues: possible values of the stacking slot
##     [c("hide", "dense", "squish", "pack", "full")]

setClass("StackedTrack",
    representation = representation("VIRTUAL",
        stacking = "character",
        stacks = "numeric"
    ),
    prototype = prototype(
        name = "StackedTrack",
        stacking = "squish",
        stackingValues = c("hide", "dense", "squish", "pack", "full"),
        dp = DisplayPars(
            stackHeight = 0.75,
            reverseStacking = FALSE
        )
    ),
    contains = "RangeTrack"
)

## Need to fill the stacks slot here, don't want to recompute all the time
setMethod("initialize", "StackedTrack", function(.Object, stacking, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "StackedTrack")
    pt <- getClass("StackedTrack")@prototype
    if (!missing(stacking)) {
        if (!all(stacking %in% pt@stackingValues)) {
            stop(
                sprintf("Problem initializing %s, accepts the following values for 'stacking': ", class(.Object)),
                paste(pt@stackingValues, collapse = ", "), "\n"
            )
        }
        .Object@stacking <- stacking
        r <- list(...)$range
        ## stacks <- if(length(r)>0) disjointBins(ranges(r)) else 0
        ## .Object@stacks <- stacks
        .Object@stacks <- numeric()
    }
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})



## AnnotationTrack -----------------------------------------------------------------------------------------------------
##
## AnnotationTrack: A generic Annotation track, storing information about start, end, chromosome,
##                  strand and the associated genome.
##
## Slots: no additional formal slots are defined, but the following are part of the prototype
##    o columns: column names that are allowed as part of the internal GRanges object in
##       the ranges slot [c("feature", "group")]
##    o featureColumnName: the column in the internal RangedData object identifying the
##       feature type ["feature"]. If a display parameter of the same name is specified
##     the software will use its value for the coloring.
## A bunch of DisplayPars are set during object instantiation:
##    o fill: the fill color for untyped items. Defaults to lightblue.
##    o col: the border color for all track items. This is also used to connect grouped items.
##    o lty, lwd: the line type and width for all track items. This is also used to connect grouped items.
##    o lex: the line expansion factor
##    o fontsize, fontfamily, fontface, fontcolor: the face, size, family and color for the
##       annotation text (i.e., the track item IDs)
##    o cex: the font expansion factor.
##    o size: the relative size of the track, if not explicitely set in the plotTracks function.
##    o lineheight: the text lineheight
##    o showId: boolean controlling whether to plot track item identifiers
##    o showFeatureId: boolean controlling whether to annotate individual exons
##    o col.group, cex.group=0.7, fontface.group=2: the font color, size and face for the
##       group-level annotation
##    o shape: the shape used for the annotation items. Currently only 'box' and 'arrow' are implemented.
##    o rotation: the rotation of the item annotation in degrees.

setClass("AnnotationTrack",
    contains = "StackedTrack",
    prototype = prototype(
        columns = c("feature", "group", "id"),
        stacking = "squish",
        name = "AnnotationTrack",
        dp = DisplayPars(
            arrowHeadWidth = 30,
            arrowHeadMaxWidth = 40,
            cex.group = 0.6,
            cex = 1,
            col.line = "darkgray",
            col = "transparent",
            featureAnnotation = NULL,
            fill = "lightblue",
            fontfamily.group = "sans",
            fontcolor.group = .DEFAULT_SHADED_COL,
            fontcolor.item = "white",
            fontface.group = 2,
            fontsize.group = 12,
            groupAnnotation = NULL,
            just.group = "left",
            lex = 1,
            lineheight = 1,
            lty = "solid",
            lwd = 1,
            mergeGroups = FALSE,
            min.height = 3,
            min.width = 1,
            rotation = 0,
            rotation.group = 0,
            rotation.item = 0,
            shape = "arrow",
            showFeatureId = FALSE,
            showId = FALSE,
            showOverplotting = FALSE,
            size = 1
        )
    )
)

## Essentially we just check for the correct GRanges columns here
setMethod("initialize", "AnnotationTrack", function(.Object, ...) {
    if (is.null(list(...)$range) && is.null(list(...)$genome) && is.null(list(...)$chromosome)) {
        return(.Object)
    }
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "AnnotationTrack")
    range <- list(...)$range
    if (!is.null(range) && length(.Object)) {
        if (!all(.Object@columns %in% colnames(values(range)))) {
            stop(paste(
                "Problem initializing AnnotationTrack need the following columns:",
                paste(.Object@columns, collpase = ", ")
            ), "\n")
        }
        grp <- if (is(.Object, "GeneRegionTrack")) values(range)$transcript else values(range)$group
        if (any(vapply(split(as.character(strand(range)), grp), function(x) length(unique(x)), numeric(1)) != 1)) {
            stop("Grouped elments of a RangeTrack can not be on opposing strands")
        }
    }
    .Object <- callNextMethod()
    return(.Object)
})

## The file-based version of the AnnotationTrack class. This will mainly provide a means to dispatch to
## a special 'subset' method which should stream the necessary data from disk.
setClass("ReferenceAnnotationTrack", contains = c("AnnotationTrack", "ReferenceTrack"))

## This just needs to set the appropriate slots that are being inherited from ReferenceTrack because the
## multiple inheritance has some strange features with regards to method selection
setMethod("initialize", "ReferenceAnnotationTrack", function(.Object, stream, reference, mapping = list(),
                                                             args = list(), defaults = list(), ...) {
    .Object <- selectMethod("initialize", "ReferenceTrack")(.Object = .Object, reference = reference, stream = stream,
        mapping = mapping, args = args, defaults = defaults)
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o range: a data.frame or a GRanges object containing the information
##       about the track items. If a data.frame, it needs to be coerceable
##     to a GRanges object, i.e., it needs at least the mandatory 'start', 'stop' and
##     'strand' columns. Additional optional columns are:
##        - feature: the type of the item. Can be mapped to colors via the DisplayPars.
##        - group: a grouping factor to connect track items.
##        - id: a unique identifier for a feature. This will be plotted if showId==TRUE
##             Note that internally we use the value of ID as the seqnames slot in the
##             internal GRanges object. Defaults for all missing columns are generated.
##    Instead of using the 'range' parameter, all these values can also be passed as
##    individual vectors, in which case they need to be of similar length.
##    o start, end, width: numeric vectors of the item start and end coordinates
##    o strand: the strand information may be provided in the form '+' for
##       the Watson strand, '-' for the Crick strand or '*' for any of the two.
##    o feature, group, id: individual vectors of equal length as described above.
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o stacking: character controlling the stacking of overlapping items. One in 'hide',
##       'dense', 'squish', 'pack' or 'full'.
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as further DisplayParameters

AnnotationTrack <- function(range = NULL, start = NULL, end = NULL, width = NULL, feature, group, id, strand, chromosome,
                            genome, stacking = "squish", name = "AnnotationTrack", fun, selectFun, importFunction,
                            stream = FALSE, ...) {
    ## Some defaults
    covars <- .getCovars(range)
    isStream <- FALSE
    if (!is.character(range)) {
        n <- max(c(length(start), length(end), length(width)), nrow(covars))
        if (is.null(covars[["feature"]]) && missing(feature)) {
            feature <- rep("unknown", n)
        }
        if (is.null(covars[["id"]]) && missing(id)) {
            id <- make.unique(rep(if (!is.null(feature)) as.character(feature) else covars[["feature"]], n)[seq_len(n)])
        }
        if (is.null(covars[["group"]]) && missing(group)) {
            group <- seq_len(n)
        }
    }
    ## Build a GRanges object from the inputs
    .missingToNull(c("feature", "group", "id", "strand", "chromosome", "importFunction", "genome"))
    args <- list(feature = feature, group = group, id = id, strand = strand, chromosome = chromosome, genome = genome)
    defs <- list(feature = "unknown", group = "unknown", id = "unknown", strand = "*", density = 1, chromosome = "chrNA", genome = NA)
    range <- .buildRange(
        range = range, groupId = "group", start = start, end = end, width = width,
        args = args, defaults = defs, chromosome = chromosome, trackType = "AnnotationTrack",
        importFun = importFunction, stream = stream
    )
    if (is.list(range)) {
        isStream <- TRUE
        slist <- range
        range <- GRanges()
    }
    ## Pipes have a special meaning for merged groups, so we can't have them in the initial group vector
    mcols(range)[["group"]] <- gsub("|", "", mcols(range)[["group"]], fixed = TRUE)
    ## If no chromosome was explicitely asked for we just take the first one in the GRanges object
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    ## And finally the object instantiation, we have to distinguish between DetailsAnnotationTracks and normal ones
    genome <- .getGenomeFromGRange(range, ifelse(is.null(genome), character(), genome[1]))
    if (missing(fun)) {
        if (!isStream) {
            return(new("AnnotationTrack",
                chromosome = as.character(chromosome[1]), range = range,
                name = name, genome = genome, stacking = stacking, ...
            ))
        } else {
            ## A bit hackish but for some functions we may want to know which track type we need but at the
            ## same time we do not want to enforce this as an additional argument
            e <- new.env()
            e[["._trackType"]] <- "AnnotationTrack"
            environment(slist[["stream"]]) <- e
            return(new("ReferenceAnnotationTrack",
                chromosome = as.character(chromosome[1]), range = range,
                name = name, genome = genome, stacking = stacking, stream = slist[["stream"]], reference = slist[["reference"]],
                mapping = slist[["mapping"]], args = args, defaults = defs, ...
            ))
        }
    } else {
        if (!is.function(fun)) {
            stop("'fun' must be a function")
        }
        if (missing(selectFun)) {
            selectFun <- function(...) {
                return(TRUE)
            }
        }
        if (!is.function(selectFun)) {
            stop("'selectFun' must be a function")
        }
        return(new("DetailsAnnotationTrack",
            chromosome = as.character(chromosome[1]), range = range,
            name = name, genome = genome, stacking = stacking, fun = fun, selectFun = selectFun, ...
        ))
    }
}


## DetailsAnnotationTrack ----------------------------------------------------------------------------------------------
##
## DetailsAnnotationTrack: is an AnnotationTrack for which each feature (annotation)
## has a detail plot (e.g. a scatter plot e.g. using lattice). The details plot
## is generated by a user defined function that gets called internally with
## arguments start, end and chromosome for the feature. The details plots are placed
## on top of the AnnotationTrack. As details plots can take relatively much space
## compared to features of an AnnotationTrack it only make sense to prove details
## for an AnnotationTrack with few features. The details plots are distributed evenly
## on top of the annotation and can be connected to their corresponding features (they're
## providing details for) with lines for better readability.
##
## The function must have the '...' arguments. All items from the list in
## detailsFunArgs get added as arguments to the function call as well as the
## arguments, start, end, chromosome and identifier.
##
## foo = function(...) {
##    plot(densityplot(rnorm(1000), xlab=NA, ylab=NA), newpage=FALSE, prefix="foo")
## }
##
## Note, use plot with newpage=FALSE and an explicit prefix (otherwise plotting
## get more and more slow the more trellis plots you create!). See '?plot.trellis'
## for details.

setClass("DetailsAnnotationTrack",
    contains = "AnnotationTrack",
    representation = representation(fun = "function", selectFun = "function"),
    prototype = prototype(
        fun = function(...) {},
        selectFun = function(...) {
            return(TRUE)
        },
        dp = DisplayPars(
            details.minWidth = 100,
            details.ratio = Inf,
            details.size = 0.5,
            detailsBorder.col = "darkgray",
            detailsBorder.fill = "transparent",
            detailsBorder.lty = "solid",
            detailsBorder.lwd = 1,
            detailsConnector.cex = 1,
            detailsConnector.col = "darkgray",
            detailsConnector.lty = "dashed",
            detailsConnector.lwd = 1,
            detailsConnector.pch = 20,
            detailsFunArgs = list(),
            groupDetails = FALSE
        )
    )
)

DetailsAnnotationTrack <- function(...) AnnotationTrack(...)

setMethod("initialize", "DetailsAnnotationTrack", function(.Object, fun, selectFun, ...) {
    ## the diplay parameter defaults
    .Object <- .updatePars(.Object, "DetailsAnnotationTrack")
    .makeParMapping()
    .Object@fun <- fun
    .Object@selectFun <- selectFun
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})



## GeneRegionTrack -----------------------------------------------------------------------------------------------------
##
## GeneRegionTrack:
## A track containing all genes in a particular region. The data are usually fetched dynamically
## from an online data store. Of course it would
## also be possible to manually construct an object from local data. Particular data sources
## should be implemented as sub-classes, this is just the common denominator that is being
## used for plotting later on. There are several levels of data associated to a GeneRegionTrack:
##   - exon level: identifiers are stored in the exon column of the GRanges object. Data may be extracted
##          using the 'exons' method.
##   - transcript level: identifiers are stored in the transcript column of the GRanges object.
##          Data may be extracted using the 'transcripts' method.
##   - gene level: identifiers are stored in the gene column of the GRanges object, more human-readable
##          versions in the symbol column. Data may be extracted using the 'genes' or the 'symbols' methods.
##   - transcript-type level: information is stored in the feature column of the GRanges object.
##      If a display parameter of the same name is specified the software will use its value for the coloring.
## Slots: no additional formal slots are defined, but the following are part of the prototype
##    o columns: column names that are allowed as part of the internal GRanges object in
##       the ranges slot [c("feature", "transcript", "symbol", "gene")]
## A bunch of DisplayPars are set during object instantiation:
##    o fill: the fill color for untyped items. Defaults to lightblue.
##    o col: the border color for all track items. This is also used to connect grouped items.
##    o alpha: the transparency for all track items.
##    o lty, lwd: the line type and width for all track items. This is also used to connect grouped items.
##    o lex: the line expansion factor
##    o fontsize, fontfamily, fontface, fontcolor: the face, size, family and color for the
##       annotation text (i.e., the track item IDs)
##    o cex: the font expansion factor.
##    o lineheight: the text lineheight
##    o showId: boolean controlling whether to plot group identifiers, e.g, gene symbols or transcript IDs.
##    o shape: the shape used for the annotation items. Currently only 'box' and 'arrow' are implemented.
##    o rotation: the rotation of the exon annotation in degrees.

setClass("GeneRegionTrack",
    contains = "AnnotationTrack",
    representation = representation(start = "NumericOrNULL", end = "NumericOrNULL"),
    prototype = prototype(
        columns = c("feature", "transcript", "symbol", "gene", "exon"),
        stacking = "squish",
        stacks = 0,
        start = 0,
        end = 0,
        name = "GeneRegionTrack",
        dp = DisplayPars(
            arrowHeadWidth = 10,
            arrowHeadMaxWidth = 20,
            col = NULL,
            collapseTranscripts = FALSE,
            exonAnnotation = NULL,
            fill = "orange",
            min.distance = 0,
            shape = c("smallArrow", "box"),
            showExonId = NULL,
            thinBoxFeature = .THIN_BOX_FEATURES,
            transcriptAnnotation = NULL
        )
    )
)


## Making sure all the display parameter defaults are being set
setMethod("initialize", "GeneRegionTrack", function(.Object, start, end, ...) {
    if (is.null(list(...)$range) && is.null(list(...)$genome) && is.null(list(...)$chromosome)) {
        return(.Object)
    }
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "GeneRegionTrack")
    .Object@start <- ifelse(is.null(start), 0, start)
    .Object@end <- ifelse(is.null(end), 0, end)
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## The file-based version of the GeneRegionTrack class. This will mainly provide a means to dispatch to
## a special 'subset' method which should stream the necessary data from disk.
setClass("ReferenceGeneRegionTrack", contains = c("GeneRegionTrack", "ReferenceTrack"))

## This just needs to set the appropriate slots that are being inherited from ReferenceTrack because the
## multiple inheritence has some strange features with regards to method selection
setMethod("initialize", "ReferenceGeneRegionTrack", function(.Object, stream, reference, mapping = list(),
                                                             args = list(), defaults = list(), ...) {
    .Object <- selectMethod("initialize", "ReferenceTrack")(.Object = .Object, reference = reference, stream = stream,
        mapping = mapping, args = args, defaults = defaults)
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o range: one in a whole number of different potential inputs upon which the .buildRanges method will dispatch
##    o start, end: numeric vectors of the track start and end coordinates.
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o rstarts, rends, rwidths: integer vectors of exon start and end locations or widths, or a character vector of
##      comma-delimited exon locations, one vector element for each transcript
##    o strand, feature, exon, transcript, gene, symbol, chromosome: vectors of equal length containing
##       the exon strand, biotype, exon id, transcript id, gene id, human-readable gene symbol and chromosome information
##    o stacking: character controlling the stacking of overlapping items. One in 'hide',
##       'dense', 'squish', 'pack' or 'full'.
##    o name: the name of the track. This will be used for the title panel.
##    o exonList: boolean, causing the values in starts, rends or rwidths to be interpreted as delim-separated
##       lists that have to be exploded. All other annotation arguments will be repeated accordingly.
##    o delim: the delimiter if coordinates are in a list
## All additional items in ... are being treated as DisplayParameters

GeneRegionTrack <- function(range = NULL, rstarts = NULL, rends = NULL, rwidths = NULL, strand, feature, exon,
                            transcript, gene, symbol, chromosome, genome, stacking = "squish",
                            name = "GeneRegionTrack", start = NULL, end = NULL, importFunction, stream = FALSE, ...) {
    ## Some defaults
    covars <- if (is.data.frame(range)) range else if (is(range, "GRanges")) as.data.frame(mcols(range)) else data.frame()
    isStream <- FALSE
    if (!is.character(range)) {
        n <- if (is.null(range)) max(c(length(start), length(end), length(width))) else if (is(range, "data.frame")) nrow(range) else length(range)
        if (is.null(covars[["feature"]]) && missing(feature)) {
            feature <- paste("exon", seq_len(n), sep = "_")
        }
        if (is.null(covars[["exon"]]) && missing(exon)) {
            exon <- make.unique(rep(if (!missing(feature) && !is.null(feature)) as.character(feature) else covars[["feature"]], n)[seq_len(n)])
        }
        if (is.null(covars[["transcript"]]) && missing(transcript)) {
            transcript <- paste("transcript", seq_len(n), sep = "_")
        }
        if (is.null(covars[["gene"]]) && missing(gene)) {
            gene <- paste("gene", seq_len(n), sep = "_")
        }
    }
    ## Build a GRanges object from the inputs
    .missingToNull(c("feature", "exon", "transcript", "gene", "symbol", "strand", "chromosome", "importFunction", "genome"))
    args <- list(
        feature = feature, id = exon, exon = exon, transcript = transcript, gene = gene, symbol = symbol, strand = strand,
        chromosome = chromosome, genome = genome
    )
    defs <- list(
        feature = "unknown", id = "unknown", exon = "unknown", transcript = "unknown", genome = NA,
        gene = "unknown", symbol = "unknown", strand = "*", density = 1, chromosome = "chrNA"
    )
    range <- .buildRange(
        range = range, groupId = "transcript", start = rstarts, end = rends, width = rwidths, args = args, defaults = defs,
        chromosome = chromosome, tstart = start, tend = end, trackType = "GeneRegionTrack", importFun = importFunction,
        genome = genome
    )
    if (is.list(range)) {
        isStream <- TRUE
        slist <- range
        range <- GRanges()
    }
    if (is.null(start)) {
        start <- if (!length(range)) NULL else min(start(range))
    }
    if (is.null(end)) {
        end <- if (!length(range)) NULL else max(end(range))
    }
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    genome <- .getGenomeFromGRange(range, ifelse(is.null(genome), character(), genome[1]))
    if (!isStream) {
        return(new("GeneRegionTrack",
            start = start, end = end, chromosome = chromosome[1], range = range,
            name = name, genome = genome, stacking = stacking, ...
        ))
    } else {
        return(new("ReferenceGeneRegionTrack",
            start = start, end = end, chromosome = chromosome[1], range = range,
            name = name, genome = genome, stacking = stacking, stream = slist[["stream"]],
            reference = slist[["reference"]], mapping = slist[["mapping"]], args = args, defaults = defs, ...
        ))
    }
}




## BiomartGeneRegionTrack ----------------------------------------------------------------------------------------------
##
## BiomartGeneRegionTrack:
##
## A GeneRegionTrack that fetches its information from Biomart
## Slots:
##    o biomart: a biomaRt object providing the connection to the data source.
##        currently we assume that this connects to a ensembl_gene source for
##        a particular organism.
##    o filter: a named list of additional filters that are passed on to the Biomart query.
## This is defined only in the prototype:
##    o columns: column names that are allowed as part of the internal GRanges object in
##        the ranges slot [c("feature", "transcript", "symbol", "gene")]
## A bunch of DisplayPars are set during object instantiation, all of which are
## transcript types as returned from Biomart in the 'gene_biotype' field.
## This class mainly exists for dispatching purpose and to keep things as flexible
## as possible, the actual plottable information is all contained in the parent
## class definition.

setClass("BiomartGeneRegionTrack",
    contains = "GeneRegionTrack",
    representation = representation(biomart = "MartOrNULL", filter = "list"),
    prototype = prototype(
        biomart = NULL,
        filter = list(),
        columns = c("feature", "transcript", "symbol", "gene", "rank"),
        name = "BiomartGeneRegionTrack",
        dp = DisplayPars(
            C_segment = "burlywood4",
            D_segment = "lightblue",
            J_segment = "dodgerblue2",
            Mt_rRNA = "yellow",
            Mt_tRNA = "darkgoldenrod",
            Mt_tRNA_pseudogene = "darkgoldenrod1",
            V_segment = "aquamarine",
            miRNA = "cornflowerblue",
            miRNA_pseudogene = "cornsilk",
            misc_RNA = "cornsilk3",
            misc_RNA_pseudogene = "cornsilk4",
            protein_coding = "#FFD58A",
            pseudogene = "brown1",
            rRNA = "darkolivegreen1",
            rRNA_pseudogene = "darkolivegreen",
            retrotransposed = "blueviolet",
            scRNA = "gold4",
            scRNA_pseudogene = "darkorange2",
            snRNA = "coral",
            snRNA_pseudogene = "coral3",
            snoRNA = "cyan",
            snoRNA_pseudogene = "cyan2",
            tRNA_pseudogene = "antiquewhite3",
            utr3 = "#FFD58A",
            utr5 = "#FFD58A",
            verbose = FALSE
        )
    )
)

## Helper to return the default biomart to feature mapping
.getBMFeatureMap <- function() {
    return(list(
        gene_id = "ensembl_gene_id", transcript_id = "ensembl_transcript_id", exon_id = "ensembl_exon_id",
        start = "exon_chrom_start", end = "exon_chrom_end", rank = "rank", strand = "strand",
        symbol = c("external_gene_name", "external_gene_id"), feature = "gene_biotype", chromosome = "chromosome_name",
        u5s = "5_utr_start", u5e = "5_utr_end", u3s = "3_utr_start", u3e = "3_utr_end", cdsl = c("cds_length", "cds_start"),
        phase = "phase"
    ))
}

## Helper to do the actual fetching of data from Biomart
.fetchBMData <- function(object, chromosome_name = NULL, staged = FALSE) {
    if (!is.null(chromosome_name)) {
        chromosome_name <- gsub("^chr", "", chromosome_name)
    }
    ## The map between Biomart DB fields and annotation features. The individual values can be vectors for cases where there is
    ## ambiguity between different marts. This will be dynamically evaluated against available filters.
    origFeatureMap <- .getBMFeatureMap()
    featureMap <- modifyList(origFeatureMap, as.list(.dpOrDefault(object, ".__featureMap", list())))
    needed <- c(
        "gene_id", "transcript_id", "exon_id", "start", "end", "rank", "strand", "symbol", "feature",
        "chromosome", "u5s", "u5e", "u3s", "u3e", "cdsl", "phase"
    )
    if (!all(needed %in% names(featureMap))) {
        stop("'featureMap' needs to include items '", paste(setdiff(needed, names(featureMap)), collapse = ", "), "'")
    }
    avail <- listAttributes(object@biomart)[, 1]
    ambig <- names(featureMap)[listLen(featureMap) > 1]
    for (i in ambig) {
        mt <- match(featureMap[[i]], avail)
        if (!all(is.na(mt))) {
            featureMap[[i]] <- featureMap[[i]][min(which(!is.na(mt)))]
        } else {
            featureMap[[i]] <- NA
        }
    }
    featureMap <- unlist(featureMap)
    ## Deal with the filters
    filterValues <- as.list(object@filter)
    start <- object@start
    end <- object@end
    for (i in c("start", "end", "chromosome_name")) {
        if (!is.null(get(i)) && length(get(i)) > 0) {
            filterValues[[i]] <- get(i)
        }
    }
    ens <- getBM(as.vector(featureMap),
        filters = names(filterValues),
        values = filterValues, bmHeader = FALSE,
        mart = object@biomart, uniqueRows = TRUE
    )
    colnames(ens) <- names(featureMap)
    if (staged && nrow(ens) > 0) {
        filterValues <- list(start = min(ens$start), end = max(ens$end), chromosome_name = ens[1, "chromosome"])
        ens <- getBM(as.vector(featureMap),
            filters = names(filterValues),
            values = filterValues, bmHeader = FALSE,
            mart = object@biomart, uniqueRows = TRUE
        )
        colnames(ens) <- names(featureMap)
    }
    ## Only those transcripts that have a CDS length will be considered protein_coding
    ens$feature <- ifelse(is.na(ens$cdsl) & ens$feature == "protein_coding", "non_coding", ens$feature)
    ## We may have to split exons if they contain UTRs
    hasUtr <- !is.na(ens$u5s) | !is.na(ens$u3s)
    ensUtr <- ens[hasUtr, , drop = FALSE]
    ensUtr$ffeature <- ifelse(is.na(ensUtr$u5s), "utr3", "utr5")
    ensUtr$us <- ifelse(ensUtr$ffeature == "utr3", ensUtr$u3s, ensUtr$u5s)
    ensUtr$ue <- ifelse(ensUtr$ffeature == "utr3", ensUtr$u3e, ensUtr$u5e)
    ensUtr$u5e <- ensUtr$u5s <- ensUtr$u3e <- ensUtr$u3s <- NULL
    allUtr <- ensUtr$us == ensUtr$start & ensUtr$ue == ensUtr$end
    utrFinal <- ensUtr[allUtr, , drop = FALSE]
    ensUtr <- ensUtr[!allUtr, , drop = FALSE]
    ensUtrS <- split(ensUtr, ifelse(ensUtr$start == ensUtr$us, "left", "right"))
    utrFinal <- rbind(utrFinal, do.call(rbind, lapply(names(ensUtrS), function(i) {
        y <- ensUtrS[[i]]
        if (nrow(y) == 0) {
            return(NULL)
        }
        yy <- y[rep(seq_len(nrow(y)), each = 2), ]
        sel <- seq(1, nrow(yy), by = 2)
        yy[sel, "end"] <- if (i == "left") yy[sel, "ue"] else yy[sel, "us"] - 1
        yy[sel, "ffeature"] <- yy[sel, ifelse(i == "left", "ffeature", "feature")]
        yy[sel, "phase"] <- if (i == "left") -1 else 0
        sel <- seq(2, nrow(yy), by = 2)
        yy[sel, "start"] <- if (i == "left") yy[sel, "ue"] + 1 else yy[sel, "us"]
        yy[sel, "ffeature"] <- yy[sel, ifelse(i == "left", "feature", "ffeature")]
        yy[sel, "phase"] <- if (i == "left") yy[sel, "phase"] else -1
        yy
    })))
    utrFinal$feature <- utrFinal$ffeature
    keep <- c(
        "gene_id", "transcript_id", "exon_id", "start",
        "end", "rank", "strand", "symbol", "feature",
        "chromosome", "phase"
    )
    ens <- rbind(ens[!hasUtr, keep, drop = FALSE], utrFinal[, keep])
    ens$chromosome <- .chrName(ens$chromosome, force = TRUE)
    range <- GRanges(
        seqnames = ens$chromosome,
        ranges = IRanges(start = ens$start, end = ens$end),
        strand = ens$strand, feature = as.character(ens$feature),
        gene = as.character(ens$gene_id), exon = as.character(ens$exon_id),
        transcript = as.character(ens$transcript_id), symbol = as.character(ens$symbol),
        rank = as.numeric(ens$rank), phase = as.integer(ens$phase)
    )
    suppressWarnings(genome(range) <- unname(genome(object)[1]))
    range <- sort(range)
    return(range)
}


## Create an MD5 hash for a BiomartGeneRegion track taking into account the Biomart details for caching
.bmGuid <- function(bmtrack) {
    digest(list(
        genome = genome(bmtrack), host = bmtrack@biomart@host, mart = bmtrack@biomart@biomart, schema = bmtrack@biomart@vschema,
        dataset = bmtrack@biomart@dataset, filters = bmtrack@filter
    ))
}


## Retrieving information from Biomart.
setMethod("initialize", "BiomartGeneRegionTrack", function(.Object, start = NULL, end = NULL, biomart, filter = list(), range, genome = NULL, chromosome = NULL, strand = NULL,
                                                           featureMap = NULL, symbol = NULL, gene = NULL, transcript = NULL, entrez = NULL, ...) {
    if ((missing(range) || is.null(range)) && is.null(genome) && is.null(chromosome)) {
        return(.Object)
    }
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "BiomartGeneRegionTrack")
    verb <- list(...)$verbose
    displayPars(.Object) <- list(!is.null(verb) && verb == TRUE)
    ## preparing filters
    strand <- .strandName(strand, extended = TRUE)
    if (strand %in% 0:1) {
        filter$strand <- c(1, -1)[strand + 1]
    }
    filterOrig <- filter
    idFilters <- list(
        symbol = c("external_gene_name", "external_gene_id", "hgnc_symbol", "wikigene_name", "dbass3_name"),
        gene = "ensembl_gene_id",
        transcript = "ensembl_transcript_id",
        entrez = "entrezgene"
    )
    staged <- FALSE
    for (i in names(idFilters)) {
        if (!is.null(get(i))) {
            mt <- match(idFilters[[i]], listFilters(biomart)[, 1])
            sfilt <- listFilters(biomart)[mt[!is.na(mt)], 1]
            if (length(sfilt) > 0) {
                staged <- TRUE
                filter[[sfilt[1]]] <- get(i)
                if (!is.null(filter$strand)) {
                    warning(sprintf("Cannot combine %s filter with a strand filter. Strand filtering is ignored.", i))
                    filter$strand <- NULL
                }
                if (!is.null(start) || !is.null(end) || !is.null(chromosome)) {
                    warning(sprintf("Cannot combine %s filter with a range restriction. Ignoring start and end coordinates.", i))
                    start <- end <- chromosome <- NULL
                }
            } else {
                stop(sprintf("Unable to automatically map the %s filter. Manually provide adequate filter list.", i))
            }
        }
    }
    ## We can't have only one in start or end
    if (!is.null(end) && is.null(start)) {
        start <- 1
    } else if (!is.null(start) && is.null(end)) {
        end <- 10e8
    }
    ## filling slots
    .Object@filter <- filter
    .Object@biomart <- biomart
    ## Extending start and end positions to capture genes on the edges. We also need both coordinates set, or none.
    extend <- if (is.null(start) || is.null(end)) 10000 else max(10000, abs(diff(c(end, start))))
    .Object@start <- if (!is.null(start)) max(1, start - extend) else NULL
    .Object@end <- if (!is.null(end)) end + extend else NULL
    displayPars(.Object) <- list(".__featureMap" = featureMap)
    genome(.Object) <- ifelse(is.null(genome), "ANY", genome)
    ## fetching data from Biomart
    range <- if (!is.null(.Object@biomart) && (!is.null(.Object@start) || !is.null(.Object@end) || length(.Object@filter) != 0)) {
        .cacheMartData(.Object, chromosome, staged)
    } else {
        tmp <- GRanges()
        values(tmp) <- DataFrame(feature = "a", gene = "a", exon = "a", transcript = "a", symbol = "a", rank = 0, phase = as.integer(1))[0, ]
        suppressWarnings(genome(tmp) <- unname(genome[1]))
        displayPars(.Object) <- list(".__streamOnly" = TRUE)
        tmp
    }
    .Object@filter <- filterOrig
    if (length(range) == 0) {
        .Object <- setPar(.Object, "size", 0, interactive = FALSE)
    } else {
        chromosome <- if (is.null(chromosome)) seqlevels(range)[1] else chromosome
        rr <- range(range, ignore.strand = TRUE)
        s <- start(rr[seqnames(rr) == chromosome])
        e <- end(rr[seqnames(rr) == chromosome])
        start <- min(s, start)
        end <- max(e, end)
    }
    .Object <- callNextMethod(
        .Object = .Object, range = range, start = start, end = end,
        genome = genome, chromosome = chromosome, strand = strand, ...
    )
    ## We want to warn if searching was performed based on an identifier and now values have been returned
    if ((!is.null(symbol) || !is.null(gene) || !is.null(transcript) || !is.null(entrez)) && length(range) == 0) {
        warning("Search by identifier did not yield any values", call. = FALSE)
    }
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o start, end: numeric vectors of the item start and end coordinates
##    o biomart: a biomaRt object used to to query for gene annotations
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o strand: character, search for gene models on the plus strand ("+" or 0), the
##       minus strand ("-" or 1) or both strands ("+-" or "-+" or 2)
##    o stacking: character controlling the stacking of overlapping items. One in 'hide',
##       'dense', 'squish', 'pack' or 'full'.
##    o filters: list of additional filters for the biomaRt query, where the item names
##          are the filter identifiers and the item values are the filter values.
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as DisplayParameters

BiomartGeneRegionTrack <- function(start = NULL, end = NULL, biomart, chromosome = NULL, strand, genome = NULL,
                                   stacking = "squish", filters = list(), featureMap = NULL, name = "BiomartGeneRegionTrack",
                                   symbol = NULL, gene = NULL, entrez = NULL, transcript = NULL, ...) {
    ## Some default checking
    .missingToNull(c("genome"))
    if (missing(strand)) {
        strand <- "*"
    }
    if ((!is.null(start) || !is.null(end)) && is.null(chromosome)) {
        stop("Also need to specify a chromsome when initializing a BiomartGeneRegionTrack with start or end coordinates")
    }
    if (!is.null(chromosome)) {
        chromosome <- .chrName(chromosome)[1]
    }
    if (missing(biomart)) {
        if (is.null(genome)) {
            stop("Need either a valid Mart connection object as 'biomart' argument or a UCSC genome identifier as the 'genome' argument.")
        }
        biomart <- .genome2Dataset(genome)
    } else if (is.null(genome)) {
        genome <- biomart@dataset
    }
    new("BiomartGeneRegionTrack",
        start = start, end = end, chromosome = chromosome, strand = strand,
        biomart = biomart, name = name, genome = genome, stacking = stacking, filter = filters, featureMap = featureMap,
        symbol = symbol, gene = gene, transcript = transcript, entrez = entrez, ...
    )
}


## This filters for genes with refseq IDs only
.refseqFilter <- list("with_refseq_dna" = TRUE)



## GenomeAxisTrack -----------------------------------------------------------------------------------------------------
##
## GenomeAxisTrack: A track for the genome axis
##
## Slots:
##    o range: an object of class GRanges containing ranges to be highlighted along the axis.
## A bunch of DisplayPars are set during object instantiation:
##    o col: the color for the axis text, lines and tickmarks
##    o fill.range: the fill color for the optional range annotation
##    o col.range: the border color for the optional range annotation
##    o fontsize: the font size for the axis annotation
##    o showTitle: boolean, show or hide the title panel text
##    o background.title: the background color of the title panel
##    o cex: the cex value for the axis text
##    o exponent: the exponent for the axis coordinates. E.g., 3 means mb, 6 means gb, etc.
##    o distFromAxis: numeric, distance of text from the axis
##    o labelPos: character giving the position of axis labels, one in "alternating", "revAlternating",
##       "above" or "below"
##    o add53: boolean, add a 5'->3' indicator
##    o add35: boolean, add a 3'->5' indicator
##    o littleTicks: boolean, add second level of smaller tick marks
##    o size: the relative size of the track
##    o col.id, cex.id: text settings for the optional range annotation
##    o showId: boolean, show range annotation
##    o scale: numeric, if not NULL a small scale is drawn instead of the full axis,
##      if between 0 and 1 it is interpreted as a fraction of the region (otherwise absolute).

setClass("GenomeAxisTrack",
    contains = "GdObject",
    representation = representation(range = "GRanges"),
    prototype(
        range = GRanges(),
        name = "GenomeAxisTrack",
        dp = DisplayPars(
            add35 = FALSE,
            add53 = FALSE,
            background.title = "transparent",
            cex.id = 0.7,
            cex = 0.8,
            col.border.title = "transparent",
            lwd.border.title = 1,
            col.id = "white",
            col.range = "cornsilk4",
            distFromAxis = 1,
            exponent = NULL,
            fill.range = "cornsilk3",
            fontcolor = "#808080",
            fontsize = 10,
            labelPos = "alternating",
            littleTicks = FALSE,
            lwd = 2,
            scale = NULL,
            showId = FALSE,
            showTitle = FALSE,
            ticksAt = NULL,
            size = NULL,
            col = "darkgray"
        )
    )
)

## Only pass on the stuff to the GdObject initializer
setMethod("initialize", "GenomeAxisTrack", function(.Object, range, ids, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "GenomeAxisTrack")
    if (missing(range) || is.null(range)) {
        range <- GRanges()
    }
    if (is(range, "IRanges")) {
        range <- GRanges(ranges = range, seqnames = "dummy", id = ids)
    }
    .Object@range <- range
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o range: an object of class 'GRanges' containing regions to be highlighted on the axis by colored boxes
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as DisplayParameters
## (N)
GenomeAxisTrack <- function(range = NULL, name = "Axis", id, ...) {
    if (missing(id)) {
        id <- names(range)
    }
    new("GenomeAxisTrack", name = name, range = range, id = id, ...)
}




## DataTrack -----------------------------------------------------------------------------------------------------------
##
## DataTrack: A track for all sorts of quantitative values
##
## Slots:
##    o data: a numeric matrix containing the data values
## A bunch of DisplayPars are set during object instantiation:
##    o jitter.x, jitter.y, amount, factor: parameters controlling the jittering in xy-type plots.
##    o span, degree, family, evaluation: parameters controlling the loess calculation.
##    o col.mountain, fill.mountain, col.baseline, lwd.baseline, lty.baseline, baseline:
##       parameters controlling the colors and the baseline position in mountain-type plots.
##    o fill.histogram, col.histogram: fill and line colors for the histogram-type plots
##    o box.ratio, box.width, varwidth, notch, notch.frac, levels.fos, stats, coef, do.out:
##       parameters controlling the boxplot appearance
##    o size: the relative size of the track
##    o type: the plot type, one or several in c("p", "l", "b", "a", "s", "g", "r", "S", "smooth",
##       "histogram", "mountain", "h", "boxplot", "gradient", "heatmap", "polygon")
##    o cex: the default pixel size
##    o ncolor, gradient: the number of colors and the base colors for the gradient type
##    o collpase: collapse overlapping ranges
##    o min.distance: the minimum distance in pixel below which to collapse
##    o window: average the rows of the data matrix to 'window' slices on the data range
##    o separator: number of pixels used to separate individual samples in heatmap-type plots
##    o transformation: a function applied on the data matrix prior to plotting. The function
##         should accept exactly one argument and the return value needs to be a numeric vector
##         which can be coerced back into a data matrix of identical dimensionality as the input
##         data.
##    o aggregation: a function to aggregate values in windows or for collapsed items. Either a
##      function that collapses a numeric vector into a single number, or one of the predefined
##      options "mean", "median", "sum" "min", "max" or "extreme". Defaults to "mean"
##    o stackedBars: logical, draw stacked histograms if groups!=NULL. Else show grouped data as
##         side-by-side bars.
##    o na.rm: remove NA values before plotting


setClass("DataTrack",
    contains = "NumericTrack",
    representation = representation(data = "matrix", strand = "character"),
    prototype = prototype(
        columns = c("score"),
        name = "DataTrack",
        dp = DisplayPars(
            aggregateGroups = FALSE,
            aggregation = "mean",
            missingAsZero = TRUE,
            alpha.confint = 0.3,
            amount = NULL,
            baseline = NULL,
            box.legend = FALSE,
            box.ratio = 1,
            box.width = NULL,
            grid = FALSE,
            cex.legend = 0.8,
            cex.sampleNames = NULL,
            cex = 0.7,
            coef = 1.5,
            col.baseline = NULL,
            col.confint = NA,
            col.boxplotFrame = .DEFAULT_SHADED_COL,
            col.histogram = .DEFAULT_SHADED_COL,
            col.horizon = NA,
            col.mountain = NULL,
            col.sampleNames = "white",
            col = trellis.par.get("superpose.line")[["col"]],
            collapse = FALSE,
            degree = 1,
            do.out = TRUE,
            evaluation = 50,
            factor = 0.5,
            family = "symmetric",
            fill.confint = NULL,
            fill.histogram = NULL,
            fill.horizon = c("#B41414", "#E03231", "#F7A99C", "#9FC8DC", "#468CC8", "#0165B3"),
            fill.mountain = c("#CCFFFF", "#FFCCFF"),
            fontface.legend = NULL,
            fontfamily.legend = NULL,
            fontsize.legend = NULL,
            fontcolor.legend = .DEFAULT_SHADED_COL,
            gradient = brewer.pal(9, "Blues"),
            groups = NULL,
            horizon.origin = 0,
            horizon.scale = NULL,
            jitter.x = FALSE,
            jitter.y = FALSE,
            levels.fos = NULL,
            legend = TRUE,
            lineheight.legend = NULL,
            lty.baseline = NULL,
            lty.mountain = NULL,
            lwd.baseline = NULL,
            lwd.mountain = NULL,
            min.distance = 0,
            na.rm = FALSE,
            ncolor = 100,
            notch.frac = 0.5,
            notch = FALSE,
            pch = 20,
            separator = 0,
            showColorBar = TRUE,
            showSampleNames = FALSE,
            size = NULL,
            span = 1 / 5,
            stackedBars = TRUE,
            stats = boxplot.stats,
            transformation = NULL,
            type = "p",
            varwidth = FALSE,
            window = NULL,
            windowSize = NULL,
            ylim = NULL,
            yTicksAt = NULL
        )
    )
)

## Only pass on the stuff to the GdObject initializer
setMethod("initialize", "DataTrack", function(.Object, data = matrix(), strand, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "DataTrack")
    .Object@data <- data
    if (!missing(strand)) {
        .Object@strand <- unique(strand)
    }
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## The file-based version of the DataTrack class. This will mainly provide a means to dispatch to
## a special 'subset' method which should stream the necessary data from disk.
setClass("ReferenceDataTrack", contains = c("DataTrack", "ReferenceTrack"))

## This just needs to set the appropriate slots that are being inherited from ReferenceTrack because the
## multiple inheritance has some strange features with regards to method selection
setMethod("initialize", "ReferenceDataTrack", function(.Object, stream, reference, mapping = list(),
                                                       args = list(), defaults = list(), ...) {
    .Object <- selectMethod("initialize", "ReferenceTrack")(.Object = .Object, reference = reference, stream = stream,
        mapping = mapping, args = args, defaults = defaults)
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o range: an object of class 'GRanges' containing the data coordinates, or an object of class data.frame
##       with the two mandatroy columns 'start' and 'end'. The coordinates (i.e., the length of the GRanges object)
##       have to match the columns of the data matrix (see below).
##    o data: a numeric matrix of data points with number of columns equal to the number of coordinates in 'range',
##      or a numeric vector of appropriate length that will be coerced in such a one-row matrix.
##    o start, end, width: numeric vectors of the item start and end coordinates, have to match the columns in 'data'
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o strand: character, display data on the plus strand ("+" or 0), the minus strand ("-" or 1) or both
##      strands ("+-" or "-+" or 2). Currently has to be unique for the whole track.
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as DisplayParameters

DataTrack <- function(range = NULL, start = NULL, end = NULL, width = NULL, data, chromosome, strand, genome,
                      name = "DataTrack", importFunction, stream = FALSE, ...) {
    ## Build a GRanges object from the inputs
    wasGR <- is(range, "GRanges") || is.character(range)
    fromFile <- is.character(range)
    isStream <- FALSE
    .missingToNull(c("strand", "chromosome", "importFunction", "genome"))
    args <- list(strand = strand, chromosome = chromosome, genome = genome)
    defs <- list(strand = "*", chromosome = "chrNA")
    range <- .buildRange(
        range = range, start = start, end = end, width = width, args = args, defaults = defs,
        asIRanges = FALSE, chromosome = chromosome, genome = NA, trackType = "DataTrack",
        importFun = importFunction, stream = stream
    )
    if (is.list(range)) {
        isStream <- TRUE
        slist <- range
        range <- GRanges()
    }
    ## Some default checking
    if (length(unique(strand(range))) > 1) {
        stop("The strand has to be unique for all ranges in a DataTrack object.")
    }
    if (!missing(data) && length(range) > 0) {
        if (is.character(data)) {
            if (!wasGR) {
                stop("Columns indices for the data section are only allowed when 'range' is of class 'GRanges'")
            }
            mt <- is.na(match(data, colnames(values(range))))
            if (any(mt)) {
                warning("Unable to match data columns: ", paste(data[mt], collapse = ","))
            }
            data <- as.data.frame(values(range)[, data[!mt], drop = FALSE])
        }
        if (is.null(dim(data))) {
            dim(data) <- c(1, length(data))
        }
        if (is.matrix(data)) {
            data <- as.data.frame(t(data))
        }
    } else {
        data <- if (ncol(values(range))) as.data.frame(values(range)) else matrix(nrow = 0, ncol = 0)
    }
    data <- .prepareDtData(data, len = length(range))
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    genome <- .getGenomeFromGRange(range, ifelse(is.null(genome), character(), genome[1]))
    values(range) <- NULL
    if (!isStream) {
        return(new("DataTrack",
            chromosome = chromosome, strand = as.character(strand(range)), range = range,
            name = name, genome = genome, data = data, ...
        ))
    } else {
        ## A bit hackish but for some functions we may want to know which track type we need but at the
        ## same time we do not want to enforce this as an additional argument
        e <- new.env()
        e[["._trackType"]] <- "DataTrack"
        environment(slist[["stream"]]) <- e
        return(new("ReferenceDataTrack",
            chromosome = chromosome, strand = as.character(strand(range)), range = range,
            name = name, genome = genome, data = data, stream = slist[["stream"]], reference = slist[["reference"]],
            mapping = slist[["mapping"]], args = args, defaults = defs, ...
        ))
    }
}




## IdeogramTrack --------------------------------------------------------------------------------------------------------
##
## IdeogramTrack: A track for chromosome ideograms
##
## A bunch of DisplayPars are set during object instantiation:
##    o size: the relative size of the track
##    o col, fill: the border and fill color used for the highlighted currently displayed region on the chromosome
##    o fontcolor, fontface, fontfamily, fonsize, lineheight, cex : the color, family, face, size, lineheight and
##       expansion factor for the chromosome name text
##    o showId: indicate the chromosome name next to the ideogram
##    o showBandId: show the identifiers of the chromosome bands
##    o cex.bands: character expansion factor for the chromosome band information
##    o bevel: the amount of beveling at the ends of the ideogram. A number between 0 and 1.

setClass("IdeogramTrack",
    contains = "RangeTrack",
    representation = representation(bandTable = "data.frame"),
    prototype = prototype(
        name = "IdeogramTrack",
        bandTable = data.frame(),
        dp = DisplayPars(
            background.title = "transparent",
            bevel = 0.45,
            centromereShape = "triangle",
            cex.bands = 0.7,
            cex = 0.8,
            col = "red",
            col.border.title = "transparent",
            lwd.border.title = 1,
            fill = "#FFE3E6",
            fontface = 1,
            fontfamily = "sans",
            fontcolor = .DEFAULT_SHADED_COL,
            fontsize = 10,
            outline = FALSE,
            showBandId = FALSE,
            lty = 1,
            lwd = 1,
            showId = TRUE,
            showTitle = FALSE,
            size = NULL
        )
    )
)

## Grab the chromosome band and length information from UCSC and fill the ranges slot.
setMethod("initialize", "IdeogramTrack", function(.Object, genome, chromosome, bands, name, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "IdeogramTrack")
    if (missing(bands)) {
        bands <- NULL
    }
    if (is.null(bands) && (missing(genome) || missing(chromosome))) {
        return(callNextMethod(.Object = .Object, range = GRanges(), genome = NULL, chromosome = NULL, ...))
    }
    if (is.null(bands)) {
        sessionInfo <- .cacheGenomes(genome = genome)
        .Object@bandTable <- sessionInfo$bands
        bands <- sessionInfo$bands
    } else {
        .checkClass(bands, "data.frame")
        cols <- c("chrom", "chromStart", "chromEnd", "name", "gieStain")
        miss <- !cols %in% colnames(bands)
        if (any(miss)) {
            stop(sprintf(
                "The following column%s missing from the bands table: %s",
                ifelse(sum(miss) > 1, "s are", " is"), paste(cols[miss], collapse = ", ")
            ))
        }
        .Object@bandTable <- bands
    }
    chromosome <- if (is.null(chromosome)) as.character(bands[1, "chrom"]) else .chrName(chromosome)[1]
    bands <- bands[bands$chrom == chromosome, ]
    if (nrow(bands) == 0) {
        stop("Chromosome '", chromosome, "' does not exist on UCSC genome '", genome, "'")
    }
    if (is.null(name)) {
        name <- .chrName(chromosome)[1]
    }
    bnames <- as.character(bands$name)
    sel <- is.na(bnames)
    if (any(sel)) {
        bnames[sel] <- paste("band", seq_len(sum(sel)), sep = "_")
    }
    if (any(bnames == "")) {
        bnames[bnames == ""] <- sprintf("band_%i", which(bnames == ""))
    }
    ranges <- GRanges(
        seqnames = bnames, ranges = IRanges(start = bands$chromStart, end = bands$chromEnd),
        name = bnames, type = as.character(bands$gieStain)
    )
    .Object <- callNextMethod(.Object = .Object, range = ranges, genome = genome, chromosome = chromosome, name = name, ...)
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as DisplayParameters
## (N)
IdeogramTrack <- function(chromosome = NULL, genome, name = NULL, bands = NULL, ...) {
    if (missing(genome)) stop("Need to specify genome for creating an IdeogramTrack")
    new("IdeogramTrack", chromosome = chromosome, genome = genome, name = name, bands = bands, ...)
}



## UcscTrack -----------------------------------------------------------------------------------------------------------
##
## UcscTrack:
##
## Strictly speaking this is not a class, but rather some sort of meta-constructor for several of the previously
## defined track types directly from UCSC data. It will fetch online data from a particular track (or a sub-table of
## a track) and feed it to one of the original constructors with user-provided argument mappings.
## ----------------------------------------------------------------------------------------------------------------------
## Constructor. The following arguments are supported:
##    o track: a character of one of the available UCSC tracks
##    o table: a character of one one of the sub-tables of the track, or NULL to fetch all
##    o trackType: a character giving the name of the constructor to pass the data to, one in
##       c("AnnotationTrack", "GeneRegionTrack", "DataTrack", "GenomeAxisTrack")
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o from: the starting and end coordinates of the track data
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as DisplayParameters

## A simple caching mechanism for UCSC session information. The overhead for establishing a connection to UCSC is
## quite significant and we can shave off 5 to 10 seconds here by caching sessions and associated information
## for a particular genome and chromosome.
.ucscCache <- new.env()
.ensemblCache <- new.env()
.martCache <- new.env()
.doCache <- function(token, expression, env, callEnv = environment()) {
    if (!token %in% base::ls(env)) {
        res <- eval(expression, envir = callEnv)
        assign(x = token, value = res, envir = env)
        res
    } else {
        env[[token]]
    }
}
.cacheTracks <- function(genome, chromosome, track, env = .ucscCache) {
    genomes <- .doCache("availableGenomes", expression(ucscGenomes()), env)
    if (!genome %in% as.character(genomes[, "db"])) {
        stop("'", genome, "' is not a valid UCSC genome.")
    }
    sessionToken <- paste("session", genome, sep = "_")
    tracksToken <- paste("tracks", genome, sep = "_")
    tablesToken <- paste("tables", track, genome, sep = "_")
    cenv <- environment()
    session <- .doCache(
        sessionToken,
        expression({
            myUcscUrl <- getOption("Gviz.ucscUrl")
            tmp <- if (is.null(myUcscUrl)) browserSession() else browserSession(url = myUcscUrl)
            genome(tmp) <- genome
            tmp
        }), env, cenv
    )
    availTracks <- .doCache(tracksToken, expression(trackNames(ucscTableQuery(session))), env, cenv)
    track <- match.arg(track, sort(c(availTracks, names(availTracks))))
    if (!is.na(availTracks[track])) {
        track <- availTracks[track]
    }
    availTables <- .doCache(tablesToken, expression({
        query <- ucscTableQuery(session, track)
        sort(tableNames(query))
    }), env, cenv)
    chrInfo <- seqlengths(session)
    return(list(
        session = session, availTracks = availTracks, availTables = availTables, track = track,
        chrInfo = chrInfo
    ))
}
.cacheGenomes <- function(genome = NULL, env = .ucscCache) {
    availToken <- "availableGenomes"
    genomesToken <- paste("genomeBands", genome, sep = "_")
    genomes <- .doCache(availToken, expression(ucscGenomes()), env)
    bands <- NULL
    if (!is.null(genome)) {
        cenv <- environment()
        bands <- .doCache(genomesToken, expression({
            if (!genome %in% as.character(genomes[, "db"])) {
                stop("'", genome, "' is not a valid UCSC genome.")
            }
            sessionToken <- paste("session", genome, sep = "_")
            session <- .doCache(
                sessionToken,
                expression({
                    myUcscUrl <- getOption("Gviz.ucscUrl")
                    tmp <- if (is.null(myUcscUrl)) browserSession() else browserSession(url = myUcscUrl)
                    genome(tmp) <- genome
                    tmp
                }), env, cenv
            )
            query <- tryCatch(ucscTableQuery(session, "cytoBandIdeo"), error = function(e) {
                warning(
                    "There doesn't seem to be any cytoband data available for genome '", genome,
                    "' at UCSC or the service is temporarily down. Trying to fetch the chromosome length data."
                )
                tryCatch(ucscTableQuery(session, table = "chromInfo"), error = function(e) {
                    stop(
                        "There doesn't seem to be any chromosome length data available for genome '", genome,
                        "' at UCSC or the service is temporarily down."
                    )
                })
            })
            out <- getTable(query)
            if (all(c("chrom", "size") %in% colnames(out))) {
                out <- data.frame(chrom = out$chrom, chromStart = 0, chromEnd = out$size, name = "", gieStain = "gneg", stringsAsFactors = F)
            }
            out
        }), env, cenv)
    }

    return(list(availableGenomes = genomes, bands = bands))
}
.cacheMartData <- function(bmtrack, chromosome = NULL, staged = FALSE) {
    uid <- .bmGuid(bmtrack)
    req <- if (!is.null(bmtrack@start) && !is.null(bmtrack@end)) GRanges(seqnames = chromosome[1], IRanges(start = bmtrack@start, bmtrack@end)) else NULL
    if (is.null(chromosome) || is.null(.martCache[[uid]])) {
        data <- .fetchBMData(bmtrack, chromosome, staged)
        if (!is.null(req)) {
            .martCache[[uid]] <- list(data = data, ranges = req)
        } else {
            req <- range(data)
        }
        if (length(data) && .dpOrDefault(bmtrack, "verbose", FALSE)) {
            message("Loaded data from Biomart for region ", paste(sprintf("%s:%i-%i(%s)", seqnames(req), start(req), end(req), strand(req)), collapse = " and "))
        }
    } else {
        rr <- .martCache[[uid]][["ranges"]]
        dd <- .martCache[[uid]][["data"]]
        if (!is.null(req) && suppressWarnings(req %within% rr)) {
            genes <- unique(subsetByOverlaps(dd, req)$gene)
            data <- dd[seqnames(dd) == chromosome[1] & dd$gene %in% genes]
            if (.dpOrDefault(bmtrack, "verbose", FALSE)) {
                message(sprintf("Retrieved data from cache for region %s:%i-%i(%s)", chromosome, start(req), end(req), strand(req)))
            }
        } else {
            data <- .fetchBMData(bmtrack, chromosome, staged)
            if (is.null(req)) {
                req <- range(data)
            }
            .martCache[[uid]][["data"]] <- suppressWarnings(c(.martCache[[uid]][["data"]], data[!(seqnames(data) == chromosome[1] & data$gene %in% dd$gene)]))
            .martCache[[uid]][["ranges"]] <- suppressWarnings(union(rr, req))
            if (length(req) && .dpOrDefault(bmtrack, "verbose", FALSE)) {
                message("Loaded data from Biomart for region ", paste(sprintf("%s:%i-%i(%s)", seqnames(req), start(req), end(req), strand(req)), collapse = " and "))
            }
        }
    }
    return(data)
}

## empty the session cache
clearSessionCache <- function() {
    assignInNamespace(".ucscCache", new.env(), ns = "Gviz")
    assignInNamespace(".ensemblCache", new.env(), ns = "Gviz")
    assignInNamespace(".martCache", new.env(), ns = "Gviz")
}


## Constructor
UcscTrack <- function(track, table = NULL, trackType = c(
                          "AnnotationTrack", "GeneRegionTrack",
                          "DataTrack", "GenomeAxisTrack"
                      ),
                      genome, chromosome, name = NULL, from, to, ...) {
    trackType <- match.arg(trackType)
    if (missing(genome) || !isSingleString(genome)) stop("Need to specify genome for creating a UcscTrack")
    if (missing(chromosome)) stop("Need to specify chromosome for creating a UcscTrack")
    chromosome <- .chrName(chromosome)[1]
    sessionInfo <- .cacheTracks(genome = genome, chromosome = chromosome, track = track, env = .ucscCache)
    if (missing(from)) {
        from <- 1
    }
    if (missing(to)) {
        to <- sessionInfo$chrInfo[chromosome]
    }
    gr <- GRanges(ranges = IRanges(start = from, end = to), seqnames = chromosome)
    suppressWarnings(genome(gr) <- unname(genome))[1]
    query <- ucscTableQuery(sessionInfo$session, sessionInfo$track, gr)
    if (!is.null(table)) {
        table <- match.arg(table, sessionInfo$availTables)
        tableName(query) <- table
    }
    if (is.null(name)) {
        name <- if (is.null(table)) track else paste(sessionInfo$track, table)
    }
    tableDat <- if (trackType == "DataTrack") {
        tmp <- try(track(query), silent = TRUE)
        if (is(tmp, "try-error")) {
            warning(tmp)
            data.frame()
        } else {
            as.data.frame(tmp)
        }
    } else {
        tmp <- try(getTable(query), silent = TRUE)
        if (is(tmp, "try-error")) {
            warning(tmp)
            data.frame()
        } else {
            tmp
        }
    }
    if (is(tmp, "try-error") && nrow(tableDat) == 0) {
        stop("Error fetching data from UCSC")
    }
    args <- lapply(list(...), function(x) {
        if (is.character(x) && length(x) == 1) {
            if (!x %in% colnames(tableDat)) x else tableDat[, x]
        } else {
            x
        }
    })
    if (trackType == "GeneRegionTrack") {
        args$start <- from
        args$end <- to
    }
    args <- lapply(args, function(x) if (!length(x)) NULL else x)
    trackObject <- do.call(trackType, args = c(list(chromosome = chromosome, genome = genome, name = name), args))
    return(trackObject)
}



## AlignedReadTrack ----------------------------------------------------------------------------------------------------
##
## AlignedReadTrack: A track to visualize sequence reads, as typically produced by NGS experiments
##
## Slots: no additional formal slots are defined
## A bunch of DisplayPars are set during object instantiation:
##    o detail: the amount of plotting details to show for the aligned reads, one in c("reads", "coverage")

setClass("AlignedReadTrack",
    representation = representation(
        coverage = "list",
        coverageOnly = "logical"
    ),
    contains = "StackedTrack",
    prototype = prototype(
        stacking = "squish",
        name = "AlignedReadTrack",
        coverageOnly = FALSE,
        dp = DisplayPars(
            detail = "coverage",
            type = "histogram",
            fill = "#0080ff",
            size = NULL,
            collapse = FALSE
        )
    )
)

## Recompute coverage on plus and minus strand and combined strands for AlignedRead tracks
## and update the respective slot to hold this information
setMethod("setCoverage", signature("AlignedReadTrack"),
    definition = function(GdObject) {
        if (length(GdObject)) {
            str <- factor(strand(GdObject), levels = c("+", "-"))
            gdSplit <- as.list(split(range(GdObject), str))
            covs <- lapply(gdSplit, coverage)
            covs[["*"]] <- coverage(range(GdObject))
            GdObject@coverage <- covs
        }
        return(GdObject)
    }
)

## Essentially we just update the display parameters here and precompute the coverage
setMethod("initialize", "AlignedReadTrack", function(.Object, coverageOnly = FALSE, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "AlignedReadTrack")
    .Object <- callNextMethod(.Object, ...)
    .Object <- setCoverage(.Object)
    if (coverageOnly) {
        ## from <- min(unlist(lapply(.Object@coverage, function(y) if(length(y)) min(start(y)))))
        ## to <- max(unlist(lapply(.Object@coverage, function(y) if(length(y)) max(end(y)))))
        from <- min(start(range(.Object)))
        to <- max(end(range(.Object)))
        .Object@range <- GRanges(
            ranges = IRanges(start = from, end = to),
            strand = names(.Object@coverage), seqnames = .Object@chromosome
        )
        .Object@coverageOnly <- coverageOnly
    }
    return(.Object)
})

## Constructor. The following arguments are supported:
##    o range: a data.frame or a GRanges object containing the information
##       about the track items. If a data.frame, it needs to be coerceable
##     to a GRanges object, i.e., it needs at least the mandatory 'start', 'stop' and
##     'strand' columns.
##    Instead of using the 'range' parameter, all these values can also be passed as
##    individual vectors, in which case they need to be of similar length.
##    o start, end, width: numeric vectors of the item start and end coordinates, or their widths
##    o strand: the strand information needs to be provided in the form '+' for
##       the Watson strand, '-' for the Crick strand.
##    o genome, chromosome: the reference genome and active chromosome for the track.
##    o stacking: character controlling the stacking of overlapping items. One in 'hide',
##       'dense', 'squish', 'pack' or 'full'.
##    o name: the name of the track. This will be used for the title panel.
## All additional items in ... are being treated as further DisplayParameters
## (N)
AlignedReadTrack <- function(range = NULL, start = NULL, end = NULL, width = NULL, chromosome, strand, genome, stacking = "squish",
                             name = "AlignedReadTrack", coverageOnly = FALSE, ...) {
    .Deprecated("AlignmentsTrack")
    .missingToNull(c("strand", "chromosome", "genome"))
    ## Build a GRanges object from the inputs
    range <- .buildRange(
        range = range, start = start, end = end, width = width,
        args = list(strand = strand, genome = genome, chromosome = chromosome),
        defaults = list(strand = "+", genome = NA, chromosome = "chrNA"), chromosome = chromosome,
        trackType = "AlignedReadTrack"
    )
    str <- unique(as.character(GenomicRanges::strand(range)))
    if ("*" %in% str) {
        stop("Only '+' and '-' strand information is allowed for AlignedReadTrack objects.")
    }
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    ## And finally the object instantiation
    return(new("AlignedReadTrack",
        chromosome = chromosome, range = range, name = name, genome = genome(range)[1],
        stacking = stacking, coverageOnly = coverageOnly, ...
    ))
}




## SequenceTrack -------------------------------------------------------------------------------------------------------
##
## SequenceTrack: A generic track to visualize nucleotide sequences. This class is virtual.
##
## Slots:
##    o chromosome: a character vector giving the active chromosome for which the
##     track is defined. Valid chromosome names are:
##          - a single numeric character
##        - a string, starting with 'chr', followed by any additional characters
##    o genome: character giving the reference genome for which the track is defined.
## A bunch of DisplayPars are set during object instantiation:
##    o foo: bar

setClass("SequenceTrack",
    representation = representation("VIRTUAL",
        chromosome = "character",
        genome = "character"
    ),
    contains = "GdObject",
    prototype = prototype(
        name = "Sequence",
        dp = DisplayPars(
            add53 = FALSE,
            background.title = "transparent",
            col = "darkgray",
            complement = FALSE,
            fontface = 2,
            fontsize = 10,
            lwd = 2,
            min.width = 2,
            noLetters = FALSE,
            showTitle = FALSE,
            size = NULL
        ),
        genome = as.character(NA),
        chromosome = "chrNA"
    )
)

## Essentially we just update the display parameters here and set the chromosome and the genome
setMethod("initialize", "SequenceTrack", function(.Object, chromosome, genome, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "SequenceTrack")
    if (!missing(chromosome) &&
        !is.na(chromosome) &&
        !is.null(chromosome)) {
        if (!is.null(names(sequence))) {
            .Object@chromosome <- .chrName(names(sequence)[1])[1]
        } else {
            .Object@chromosome <- .chrName(chromosome)[1]
        }
    }
    if (missing(genome) || is.na(genome) || is.null(genome)) {
        genome <- as.character(NA)
    }
    .Object@genome <- genome
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

## We want the following behaviour in the constructor:
##   a) sequence is missing (NULL) => build SequenceDNAStringSetTrack with chromosome NA and genome as supplied or NA if missing
##   b) sequence is DNAStringSet => build SequenceDNAStringSetTrack where chromosome is names(sequence)[1] or the supplied
##      chromosome if available, and genome as supplied or NA if missing
##   c) sequence is BSgenome => build SequenceBSgenomeTrack where chromosome is seqnames(sequence)[1] or the supplied
##      chromosome if available, and genome is the supplied genome or the one extracted from the BSgenome object
.SequenceTrack <- function(SeqTrackType, seqtype, sequence, chromosome, genome, name = "SequenceTrack", importFunction, stream = FALSE, ...) {
    .missingToNull(c("chromosome", "genome", "sequence"))
    if (is.null(sequence)) {
        return(new(SeqTrackType, chromosome = chromosome, genome = genome, name = name, ...))
    }
    if (is(sequence, "BSgenome")) {
        if (is.null(genome)) {
            genome <- .providerVersion(sequence)
        }
        if (is.null(chromosome)) {
            chromosome <- seqnames(sequence)[1]
        }
        obj <- new("SequenceBSgenomeTrack", sequence = sequence, chromosome = chromosome, genome = genome, name = name, ...)
    } else if (is(sequence, "XStringSet")) {
        if (seqtype(sequence) != seqtype) {
            seqtype(sequence) <- seqtype
        }
        if (is.null(names(sequence))) {
            stop("The sequences in the ", seqtype, "StringSet must be named")
        }
        if (any(duplicated(names(sequence)))) {
            stop("The sequence names in the ", seqtype, "StringSet must be unique")
        }
        if (is.null(chromosome)) {
            chromosome <- names(sequence)[1]
        }
        obj <- new(SeqTrackType, sequence = sequence, chromosome = chromosome, genome = genome, name = name, ...)
    } else if (is.character(sequence)) {
        sequence <- sequence[1]
        if (!file.exists(sequence)) {
            stop(sprintf("'%s' is not a valid file.", sequence))
        }
        ext <- .fileExtension(sequence)
        obj <- if (missing(importFunction) && ext %in% c("fa", "fasta")) {
            if (!file.exists(paste(sequence, "fai", sep = "."))) {
                new("SequenceDNAStringSetTrack",
                    sequence = readDNAStringSet(sequence), chromosome = chromosome,
                    genome = genome, name = name, ...
                )
            } else {
                new("ReferenceSequenceTrack",
                    chromosome = chromosome, genome = genome, name = name,
                    stream = .import.fasta, reference = path.expand(sequence), ...
                )
            }
        } else if (missing(importFunction) && ext == "2bit") {
            new("ReferenceSequenceTrack",
                chromosome = chromosome, genome = genome, name = name,
                stream = .import.2bit, reference = path.expand(sequence), ...
            )
        } else {
            if (missing(importFunction)) {
                stop(sprintf(
                    "No predefined import function exists for files with extension '%s'. Please manually provide an import function.",
                    ext
                ))
            } else {
                if (!stream) {
                    seq <- importFunction(file = sequence)
                    if (!is(seq, "DNAStringSet")) {
                        stop(
                            "The import function did not provide a valid DNAStringSet object. Unable to build track from file '",
                            sequence, "'"
                        )
                    }
                    new("SequenceDNAStringSetTrack",
                        sequence = importFunction(file = sequence), chromosome = chromosome,
                        genome = genome, name = name, ...
                    )
                } else {
                    new("ReferenceSequenceTrack",
                        chromosome = chromosome, genome = genome, name = name,
                        stream = importFunction, reference = path.expand(sequence), ...
                    )
                }
            }
        }
    } else {
        stop("Argument sequence must be of class 'BSgenome', 'XStringSet' or 'character'")
    }
    return(obj)
}

SequenceTrack <- function(sequence, chromosome, genome, name = "SequenceTrack", importFunction, stream = FALSE, ...) {
    .SequenceTrack(
        "SequenceDNAStringSetTrack",
        "DNA",
        sequence,
        chromosome,
        genome,
        ...
    )
}

RNASequenceTrack <- function(sequence, chromosome, genome, name = "SequenceTrack", importFunction, stream = FALSE, ...) {
    .SequenceTrack(
        "SequenceRNAStringSetTrack",
        "RNA",
        sequence,
        chromosome,
        genome,
        ...
    )
}




## SequenceDNAStringSetTrack -------------------------------------------------------------------------------------------
##
## SequenceDNAStringSetTrack: A track to visualize nucleotide sequences that are stored in a DNAStringSet
##
## Slots:
##    o sequence: a DNAStringSet object that contains all the sequence data

setClass("SequenceDNAStringSetTrack",
    representation = representation(sequence = "DNAStringSet"),
    contains = "SequenceTrack",
    prototype = prototype(
        sequence = DNAStringSet(),
        dp = DisplayPars(fontcolor = getBioColor("DNA_BASES_N"))
    )
)

setMethod("initialize", "SequenceDNAStringSetTrack", function(.Object, sequence, ...) {
    if (missing(sequence) || is.null(sequence)) {
        sequence <- DNAStringSet()
    }
    .Object@sequence <- sequence
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})


## SequenceRNAStringSetTrack -------------------------------------------------------------------------------------------
##
## SequenceRNAStringSetTrack: A track to visualize nucleotide sequences that are stored in a RNAStringSet
## Slots:
##    o sequence: a RNAStringSet object that contains all the sequence data

setClass("SequenceRNAStringSetTrack",
    representation = representation(sequence = "RNAStringSet"),
    contains = "SequenceTrack",
    prototype = prototype(
        sequence = RNAStringSet(),
        dp = DisplayPars(fontcolor = getBioColor("RNA_BASES_N"))
    )
)

setMethod("initialize", "SequenceRNAStringSetTrack", function(.Object, sequence, ...) {
    if (missing(sequence) || is.null(sequence)) {
        sequence <- RNAStringSet()
    }
    .Object@sequence <- sequence
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})



## SequenceBSgenomeTrack -----------------------------------------------------------------------------------------------
##
## SequenceBSgenomeTrack: A track to visualize nucleotide sequences that are stored in a BSgenome package
##
## Slots:
##    o sequence: a DNAStringSet object that contains all the sequence data
##    o pointerCache: an environment to hold pointers to the BSgenome sequences to prevent garbage collection. This
##       will only be filled once the individual sequences have been accessed for the first time

setClass("SequenceBSgenomeTrack",
    representation = representation(sequence = "BSgenomeOrNULL", pointerCache = "environment"),
    contains = "SequenceTrack",
    prototype = prototype(
        sequence = NULL,
        dp = DisplayPars(fontcolor = getBioColor("DNA_BASES_N"))
    )
)

setMethod("initialize", "SequenceBSgenomeTrack", function(.Object, sequence = NULL, ...) {
    .Object@sequence <- sequence
    .Object@pointerCache <- new.env()
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})



## ReferenceSequenceTrack ----------------------------------------------------------------------------------------------
##
## ReferenceSequenceTrack: The file-based version of the ReferenceTrack class.
##                         This will mainly provide a means to dispatch to a special 'subseq' method
##                         which should stream the necessary data from disk.

setClass("ReferenceSequenceTrack", contains = c("SequenceDNAStringSetTrack", "ReferenceTrack"))

## This just needs to set the appropriate slots that are being inherited from ReferenceTrack because the
## multiple inheritance has some strange features with regards to method selection
setMethod("initialize", "ReferenceSequenceTrack", function(.Object, stream, reference, ...) {
    .Object <- selectMethod("initialize", "ReferenceTrack")(.Object = .Object, reference = reference, stream = stream)
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})




## AlignmentsTrack------------------------------------------------------------------------------------------------------
##
## AlignmentsTrack: A track that represents aligned NGS reads on a genome. This supports gapped and paired alignments.

setClassUnion("SequenceTrackOrNULL", c("SequenceTrack", "NULL"))
setClass("AlignmentsTrack",
    representation = representation(
        stackRanges = "GRanges",
        sequences = "DNAStringSet",
        referenceSequence = "SequenceTrackOrNULL"
    ),
    contains = "StackedTrack",
    prototype = prototype(
        stacking = "squish",
        name = "AlignmentsTrack",
        coverageOnly = FALSE,
        stackRanges = GRanges(),
        sequences = DNAStringSet(),
        referenceSequence = NULL,
        dp = DisplayPars(
            alpha.reads = 0.5,
            alpha.mismatch = 1,
            cex = 0.7,
            cex.mismatch = NULL,
            col.coverage = NULL,
            col.gap = .DEFAULT_SHADED_COL,
            col.mates = .DEFAULT_BRIGHT_SHADED_COL,
            col.deletion = "#000000",
            col.insertion = "#984EA3",
            col.mismatch = .DEFAULT_SHADED_COL,
            col.reads = NULL,
            col.sashimi = NULL,
            col = .DEFAULT_SHADED_COL,
            collapse = FALSE,
            coverageHeight = 0.1,
            fill.coverage = NULL,
            fill.reads = NULL,
            fill = "#BABABA",
            fontface.mismatch = 2,
            lty.coverage = NULL,
            lty.gap = NULL,
            lty.mates = NULL,
            lty.deletion = NULL,
            lty.insertion = NULL,
            lty.mismatch = NULL,
            lty.reads = NULL,
            lty = 1,
            lwd.coverage = NULL,
            lwd.gap = NULL,
            lwd.mates = NULL,
            lwd.deletion = NULL,
            lwd.insertion = NULL,
            lwd.mismatch = NULL,
            lwd.reads = NULL,
            lwd.sashimiMax = 10,
            lwd = 1,
            max.height = 10,
            min.height = 5,
            minCoverageHeight = 50,
            minSashimiHeight = 50,
            noLetters = FALSE,
            sashimiFilter = NULL,
            sashimiFilterTolerance = 0L,
            sashimiHeight = 0.1,
            sashimiScore = 1,
            sashimiStrand = "*",
            sashimiTransformation = NULL,
            showIndels = FALSE,
            showMismatches = TRUE,
            size = NULL,
            transformation = NULL,
            type = c("coverage", "pileup")
        )
    )
)

setMethod("initialize", "AlignmentsTrack", function(.Object, stackRanges = GRanges(), stacks = numeric(), sequences = DNAStringSet(),
                                                    referenceSequence = NULL, ...) {
    ## the diplay parameter defaults
    .makeParMapping()
    .Object <- .updatePars(.Object, "AlignmentsTrack")
    .Object@stackRanges <- stackRanges
    .Object <- callNextMethod(.Object, ...)
    .Object@stacks <- stacks
    .Object@sequences <- sequences
    .Object@referenceSequence <- referenceSequence
    return(.Object)
})



setClass("ReferenceAlignmentsTrack", contains = c("AlignmentsTrack", "ReferenceTrack"))

## This just needs to set the appropriate slots that are being inherited from ReferenceTrack because the
## multiple inheritence has some strange features with regards to method selection
setMethod("initialize", "ReferenceAlignmentsTrack", function(.Object, stream, reference, mapping = list(),
                                                             args = list(), defaults = list(), stacks = numeric(),
                                                             stackRanges = GRanges(), sequences = DNAStringSet(),
                                                             referenceSequence = NULL, ...) {
    .Object <- selectMethod("initialize", "ReferenceTrack")(.Object = .Object, reference = reference, stream = stream,
        mapping = mapping, args = args, defaults = defaults)
    .Object <- callNextMethod(.Object, ...)
    .Object@referenceSequence <- referenceSequence
    return(.Object)
})


## Constructor
AlignmentsTrack <- function(range = NULL, start = NULL, end = NULL, width = NULL, strand, chromosome, genome,
                            stacking = "squish", id, cigar, mapq, flag = scanBamFlag(isUnmappedQuery = FALSE), isize, groupid, status, md, seqs,
                            name = "AlignmentsTrack", isPaired = TRUE, importFunction, referenceSequence, ...) {
    ## Some defaults
    if (missing(importFunction)) {
        importFunction <- .import.bam.alignments
    }
    covars <- .getCovars(range)
    isStream <- FALSE
    if (!is.character(range)) {
        n <- max(c(length(start), length(end), length(width)), nrow(covars))
        id <- .covDefault(id, covars[["id"]], paste("read", seq_len(n), sep = "_"))
        cigar <- .covDefault(cigar, covars[["cigar"]], paste(if (is(range, "GRangesOrIRanges")) width(range) else width, "M", sep = ""))
        mapq <- .covDefault(mapq, covars[["mapq"]], rep(as.integer(NA), n))
        flag <- .covDefault(flag, covars[["flag"]], rep(as.integer(NA), n))
        isize <- .covDefault(isize, covars[["isize"]], rep(as.integer(NA), n))
        groupid <- .covDefault(groupid, covars[["groupid"]], seq_len(n))
        md <- .covDefault(md, covars[["md"]], rep(as.character(NA), n))
        status <- .covDefault(status, covars[["status"]], ifelse(groupid %in% groupid[duplicated(groupid)], "mated", "unmated"))
    }
    ## Build a GRanges object from the inputs
    .missingToNull(c(
        "strand", "chromosome", "importFunction", "genome", "id", "cigar", "mapq", "flag", "isize", "groupid", "status",
        "md", "seqs", "referenceSequence"
    ))
    args <- list(
        id = id, cigar = cigar, mapq = mapq, flag = flag, isize = isize, groupid = groupid, status = status, strand = strand, md = md,
        chromosome = chromosome, genome = genome
    )
    defs <- list(
        strand = "*", chromosome = "chrNA", genome = NA, id = as.character(NA), cigar = as.character(NA), mapq = as.integer(NA),
        flag = as.integer(NA), isize = as.integer(NA), groupid = as.character(NA), status = as.character(NA), md = as.character(NA)
    )
    range <- .buildRange(
        range = range, start = start, end = end, width = width,
        args = args, defaults = defs, chromosome = chromosome, trackType = "AlignmentsTrack",
        importFun = importFunction, stream = TRUE, autodetect = TRUE
    )
    ## This is going to be a list if we have to stream data from a file, otherwise we can compute some additional values
    if (is.list(range)) {
        isStream <- TRUE
        slist <- range
        range <- GRanges()
        stackRanges <- GRanges()
        stacks <- NULL
        seqs <- DNAStringSet()
    } else {
        if (is.null(seqs)) {
            seqs <- DNAStringSet(vapply(width(range), function(x) paste(rep("N", x), collapse = ""), character(1)))
        }
        addArgs <- list(...)
        if ("showIndels" %in% names(addArgs)) {
            showIndels <- addArgs$showIndels
        } else {
            showIndels <- FALSE
        }
        tmp <- .computeAlignments(range, drop.D.ranges = showIndels)
        range <- tmp$range
        stackRanges <- tmp$stackRange
        stacks <- tmp$stacks
    }
    ## If no chromosome was explicitly asked for we just take the first one in the GRanges object
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    ## And finally the object instantiation
    genome <- .getGenomeFromGRange(range, ifelse(is.null(genome), character(), genome[1]))
    if (!isStream) {
        return(new("AlignmentsTrack",
            chromosome = chromosome[1], range = range, stacks = stacks,
            name = name, genome = genome, stacking = stacking, stackRanges = stackRanges, sequences = seqs,
            referenceSequence = referenceSequence, ...
        ))
    } else {
        ## A bit hackish but for some functions we may want to know which track type we need but at the
        ## same time we do not want to enforce this as an additional argument
        e <- new.env()
        e[["._trackType"]] <- "AlignmentsTrack"
        e[["._isPaired"]] <- isPaired
        e[["._flag"]] <- flag
        environment(slist[["stream"]]) <- e
        return(new("ReferenceAlignmentsTrack",
            chromosome = chromosome[1], range = range, stackRanges = stackRanges,
            name = name, genome = genome, stacking = stacking, stream = slist[["stream"]], reference = slist[["reference"]],
            mapping = slist[["mapping"]], args = args, defaults = defs, stacks = stacks, referenceSequence = referenceSequence, ...
        ))
    }
}



## HighlightTrack ------------------------------------------------------------------------------------------------------
##
## HighlightTrack: A collection container for several track objects for which a particular area needs to be highlighted.

setClass("HighlightTrack",
    representation = representation(trackList = "list"),
    contains = c("RangeTrack"),
    prototype = prototype(dp = DisplayPars(
        col = "red",
        fill = "#FFE3E6",
        inBackground = TRUE
    ))
)

setMethod("initialize", "HighlightTrack", function(.Object, trackList, ...) {
    .Object <- .updatePars(.Object, "HighlightTrack")
    .Object@trackList <- trackList
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

HighlightTrack <- function(trackList = list(), range = NULL, start = NULL, end = NULL, width = NULL, chromosome, genome,
                           name = "HighlightTrack", ...) {
    ## Some defaults
    covars <- .getCovars(range)
    n <- max(c(length(start), length(end), length(width)), nrow(covars))
    ## Build a GRanges object from the inputs
    .missingToNull(c("strand", "chromosome", "genome"))
    args <- list(chromosome = chromosome, genome = genome)
    defs <- list(strand = "*", density = 1, chromosome = "chrNA", genome = NA)
    range <- .buildRange(
        range = range, start = start, end = end, width = width,
        args = args, defaults = defs, chromosome = chromosome, trackType = "HighlightTrack"
    )
    if (is.list(range)) {
        range <- GRanges()
    }
    if (!is.list(trackList)) {
        trackList <- list(trackList)
    }
    if (!all(vapply(trackList, is, class2 = "GdObject", FUN.VALUE = logical(1)))) {
        stop("All elements in 'trackList' must inherit from 'GdObject'")
    }
    ## If no chromosome was explicitly asked for we just take the first one in the GRanges object
    if (missing(chromosome) || is.null(chromosome)) {
        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"
    }
    ## And finally the object instantiation
    genome <- .getGenomeFromGRange(range, ifelse(is.null(genome), character(), genome[1]))
    return(new("HighlightTrack", trackList = trackList, chromosome = chromosome[1], range = range, name = name, genome = genome, ...))
}
setReplaceMethod("displayPars", signature("HighlightTrack", "list"), function(x, recursive = FALSE, value) {
    x <- setPar(x, value, interactive = FALSE)
    if (recursive) {
        x@trackList <- lapply(x@trackList, function(y) {
            displayPars(y) <- value
            return(y)
        })
    }
    return(x)
})



## OverlayTrack --------------------------------------------------------------------------------------------------------
##
## OverlayTrack: A collection container for several track objects which will all be plotted on top of each other

setClass("OverlayTrack",
    representation = representation(trackList = "list"),
    contains = c("GdObject"),
    prototype = prototype(dp = DisplayPars())
)

setMethod("initialize", "OverlayTrack", function(.Object, trackList, ...) {
    .Object <- .updatePars(.Object, "OverlayTrack")
    .Object@trackList <- trackList
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})

OverlayTrack <- function(trackList = list(), name = "OverlayTrack", ...) {
    if (!is.list(trackList)) {
        trackList <- list(trackList)
    }
    if (!all(vapply(trackList, is, class2 = "GdObject", FUN.VALUE = logical(1)))) {
        stop("All elements in 'trackList' must inherit from 'GdObject'")
    }
    return(new("OverlayTrack", trackList = trackList, name = name, ...))
}
setReplaceMethod("displayPars", signature("OverlayTrack", "list"), function(x, recursive = FALSE, value) {
    x <- setPar(x, value, interactive = FALSE)
    if (recursive) {
        x@trackList <- lapply(x@trackList, function(y) {
            displayPars(y) <- value
            return(y)
        })
    }
    return(x)
})



## CustomTrack ---------------------------------------------------------------------------------------------------------
##
## CustomTrack: A track class to allow for user-defined plotting functions

setClass("CustomTrack",
    contains = c("GdObject"),
    representation = representation(
        plottingFunction = "function",
        variables = "list"
    ),
    prototype = prototype(dp = DisplayPars())
)

setMethod("initialize", "CustomTrack", function(.Object, plottingFunction, variables, ...) {
    .Object <- .updatePars(.Object, "CustomTrack")
    .Object@plottingFunction <- plottingFunction
    .Object@variables <- variables
    .Object <- callNextMethod(.Object, ...)
    return(.Object)
})


CustomTrack <- function(plottingFunction = function(GdObject, prepare = FALSE, ...) {}, variables = list(), name = "CustomTrack", ...) {
    return(new("CustomTrack", plottingFunction = plottingFunction, variables = variables, name = name, ...))
}

Try the Gviz package in your browser

Any scripts or data that you put into this service are public.

Gviz documentation built on Nov. 8, 2020, 7:15 p.m.