R/getset.R

In InteractionSet: Base Classes for Storing Genomic Interaction Data

###############################################################
# Simple getters and setters (some of these are exported):

for (siglist in list("GInteractions", "ContactMatrix")) {
    setMethod("regions", siglist, function(x) { x@regions })
}

for (siglist in list("GInteractions", "ContactMatrix")) { 
    # internal, for use with environments and with().
    setMethod("anchor1", siglist, function(x) { x@anchor1 })
    setMethod("anchor2", siglist, function(x) { x@anchor2 })

    setReplaceMethod("unchecked_regions", siglist, function(x, value) {
        x@regions <- value
        return(x)        
    })

    setReplaceMethod("unchecked_anchor1", siglist, function(x, value) {
        x@anchor1 <- value 
        return(x)        
    })

    setReplaceMethod("unchecked_anchor2", siglist, function(x, value) {
        x@anchor2 <- value 
        return(x)        
    })
}

setMethod("interactions", "InteractionSet", function(x) { return(x@interactions) })

setReplaceMethod("unchecked_interactions", "InteractionSet", function(x, value) { 
    x@interactions <- value
    return(x)
}) 

setMethod("as.matrix", "ContactMatrix", function(x) {
    return(x@matrix)
}) 

setReplaceMethod("unchecked_matrix", "ContactMatrix", function(x, value) {
    x@matrix <- value
    return(x)
}) 

###############################################################
# Exported getters for anchors. 

setMethod("anchorIds", "GInteractions", function(x, type="both") {
    type <- match.arg(type, c("both", "first", "second"))
    if (type=="both") {
        out <- list(first=anchor1(x), second=anchor2(x))
        names(out$first) <- names(out$second) <- names(x)
    } else if (type=="first") {
        out <- anchor1(x)
        names(out) <- names(x)
    } else {
        out <- anchor2(x)
        names(out) <- names(x)
    }
    return(out)
}) 

setMethod("anchors", "GInteractions", function(x, type="both", id=FALSE) {
    if (id) { 
        return(anchorIds(x, type=type)) 
    }

    type <- match.arg(type, c("both", "first", "second"))
    if (type=="both") {
        out <- list(first=regions(x)[anchor1(x)], second=regions(x)[anchor2(x)])
        names(out$first) <- names(out$second) <- names(x)
    } else if (type=="first") {
        out <- regions(x)[anchor1(x)]
        names(out) <- names(x)
    } else {
        out <- regions(x)[anchor2(x)]
        names(out) <- names(x)
    }
    return(out)
})

# Defining some convenience methods.
setMethod("first", "GInteractions", function(x) { anchors(x, type="first") })
setMethod("second", "GInteractions", function(x) { anchors(x, type="second") })

# Same again for ContactMatrix objects.
setMethod("anchorIds", "ContactMatrix", function(x, type="both") {
    type <- match.arg(type, c("both", "row", "column"))
    if (type=="both") {
        out <- list(row=anchor1(x), column=anchor2(x))
        names(out$row) <- rownames(x)
        names(out$column) <- colnames(x)
    } else if (type=="row") {
        out <- anchor1(x)
        names(out) <- rownames(x)
    } else {
        out <- anchor2(x)
        names(out) <- colnames(x)
    }
    return(out)
}) 

setMethod("anchors", "ContactMatrix", function(x, type="both", id=FALSE) {
    if (id) { 
        return(anchorIds(x, type=type)) 
    }

    type <- match.arg(type, c("both", "row", "column"))
    if (type=="both") {
        out <- list(row=regions(x)[anchor1(x)], column=regions(x)[anchor2(x)])
        names(out$row) <- rownames(x)
        names(out$column) <- colnames(x)
    } else if (type=="row") {
        out <- regions(x)[anchor1(x)]
        names(out) <- rownames(x)
    } else {
        out <- regions(x)[anchor2(x)]
        names(out) <- colnames(x)
    }
    return(out)
})

###############################################################
# Setters for regions:

for (siglist in c("GInteractions", "ContactMatrix")) { 
    setReplaceMethod("regions", siglist, function(x, value) {
        if (length(value)!=length(regions(x))) { 
            stop("assigned value must be of the same length as 'regions(x)'")
        }
        out <- .resort_regions(anchor1(x), anchor2(x), value)
        unchecked_anchor1(x) <- out$anchor1
        unchecked_anchor2(x) <- out$anchor2
        unchecked_regions(x) <- out$regions
        validObject(x)
        return(x)
    })
}

# Also allow setting of regions of different length.

for (siglist in c("GInteractions", "ContactMatrix")) { 
    setReplaceMethod("replaceRegions", siglist, function(x, value) {
        converter <- match(regions(x), value)
        new.a1 <- converter[anchor1(x)]
        new.a2 <- converter[anchor2(x)]
        if (any(is.na(new.a1)) || any(is.na(new.a2))) { 
            stop("some existing ranges do not exist in replacement GRanges") 
        }

        out <- .resort_regions(new.a1, new.a2, value)
        unchecked_anchor1(x) <- out$anchor1
        unchecked_anchor2(x) <- out$anchor2
        unchecked_regions(x) <- out$regions
        return(x)
    })
}

# Append regions.

for (siglist in c("GInteractions", "ContactMatrix")) {
    setReplaceMethod("appendRegions", siglist, function(x, value) {
        out <- .resort_regions(anchor1(x), anchor2(x), c(regions(x), value)) 
        unchecked_anchor1(x) <- out$anchor1
        unchecked_anchor2(x) <- out$anchor2
        unchecked_regions(x) <- out$regions
        return(x)
    })
}

# Reduce regions.

for (siglist in c("GInteractions", "ContactMatrix")) { 
    setMethod("reduceRegions", siglist, function(x) {
        used <- logical(length(regions(x)))
        used[anchor1(x)] <- TRUE
        used[anchor2(x)] <- TRUE
        new.dex <- integer(length(used))
        new.dex[used] <- seq_len(sum(used))
        unchecked_anchor1(x) <- new.dex[anchor1(x)]
        unchecked_anchor2(x) <- new.dex[anchor2(x)]
        unchecked_regions(x) <- regions(x)[used]
        return(x)
    })
}

###############################################################
# Setters for anchors.

setReplaceMethod("anchorIds", "GInteractions", function(x, type="both", ..., value) {
    type <- match.arg(type, c("both", "first", "second"))
    if (type=="both") { 
        if (length(value)!=2L) { 
            stop("'value' must be a list of 2 numeric vectors")
        }
        unchecked_anchor1(x) <- as.integer(value[[1]])
        unchecked_anchor2(x) <- as.integer(value[[2]])
    } else if (type=="first") {
        unchecked_anchor1(x) <- as.integer(value)
    } else {
        unchecked_anchor2(x) <- as.integer(value)
    }

    validObject(x)
    return(x)
})

setReplaceMethod("anchorIds", "ContactMatrix", function(x, type="both", ..., value) {
    type <- match.arg(type, c("both", "row", "column"))
    if (type=="both") { 
        if (length(value)!=2L) { 
            stop("'value' must be a list of 2 numeric vectors")
        }
        unchecked_anchor1(x) <- as.integer(value[[1]])
        unchecked_anchor2(x) <- as.integer(value[[2]])
    } else if (type=="row") {
        unchecked_anchor1(x) <- as.integer(value)
    } else {
        unchecked_anchor2(x) <- as.integer(value)
    }

    validObject(x)
    return(x)
})

# Specialist methods for enforced classes.
setReplaceMethod("anchorIds", "StrictGInteractions", function(x, type="both", ..., value) {
    x <- as(x, "GInteractions")
    anchorIds(x, type=type, ...) <- value
    x <- swapAnchors(x)
    as(x, "StrictGInteractions")
})

setReplaceMethod("anchorIds", "ReverseStrictGInteractions", function(x, type="both", ..., value) {
    x <- as(x, "GInteractions")
    anchorIds(x, type=type, ...) <- value
    x <- swapAnchors(x, mode="reverse")
    as(x, "ReverseStrictGInteractions")
})

###############################################################
# Methods on InteractionSet that operate on GInteractions.

setReplaceMethod("interactions", "InteractionSet", function(x, value) { 
    unchecked_interactions(x) <- value
    validObject(x)
    return(x)
}) 

setMethod("anchors", "InteractionSet", function(x, type="both", id=FALSE) { 
    anchors(interactions(x), type=type, id=id) 
})

setMethod("anchorIds", "InteractionSet", function(x, type="both") {
    anchorIds(interactions(x), type=type)
})

setMethod("first", "InteractionSet", function(x) { first(interactions(x)) })

setMethod("second", "InteractionSet", function(x) { second(interactions(x)) })

setMethod("regions", "InteractionSet", function(x) { regions(interactions(x)) })

# Modification of regions in GInteractions doesn't affect validity of InteractionSet.

setReplaceMethod("anchorIds", "InteractionSet", function(x, type="both", ..., value) { 
    i <- interactions(x)
    anchorIds(i, type=type, ...) <- value 
    unchecked_interactions(x) <- i
    return(x)
})

setReplaceMethod("regions", "InteractionSet", function(x, value) { 
    i <- interactions(x)
    regions(i) <- value
    unchecked_interactions(x) <- i
    return(x)
})

setReplaceMethod("replaceRegions", "InteractionSet", function(x, value) { 
    i <- interactions(x)
    replaceRegions(i) <- value
    unchecked_interactions(x) <- i
    return(x)
})

setReplaceMethod("appendRegions", "InteractionSet", function(x, value) { 
    i <- interactions(x)
    appendRegions(i) <- value
    unchecked_interactions(x) <- i
    return(x)
})

setMethod("reduceRegions", "InteractionSet", function(x) {
    unchecked_interactions(x) <- reduceRegions(interactions(x))
    return(x)
})

###############################################################
# Defining some other getters and setters.

setMethod("$", "GInteractions", function(x, name) {
    return(mcols(x)[[name]])
})

setReplaceMethod("$", "GInteractions", function(x, name, value) {
    mcols(x)[[name]] <- value
    return(x)
})

setMethod("mcols", "InteractionSet", function(x, use.names=FALSE) {
    mcols(interactions(x), use.names=use.names)
})

setReplaceMethod("mcols", "InteractionSet", function(x, ..., value) {
    i <- interactions(x)                 
    mcols(i, ...) <- value
    unchecked_interactions(x) <- i
    return(x)
})

###############################################################
# Name getting and setting.

setMethod("names", "GInteractions", function(x) { 
    x@NAMES 
})

setReplaceMethod("names", "GInteractions", function(x, value) {
    if (!is.null(value) && !is.character(value)) { value <- as.character(value) }                
    x@NAMES <- value
    validObject(x)
    return(x)
})

setMethod("names", "InteractionSet", function(x) {
    names(interactions(x))
})

setReplaceMethod("names", "InteractionSet", function(x, value) {
    i <- interactions(x)                 
    names(i) <- value
    unchecked_interactions(x) <- i
    return(x)
})

setMethod("dimnames", "ContactMatrix", function(x) {
    dimnames(as.matrix(x))
})

setReplaceMethod("dimnames", "ContactMatrix", function(x, value) {
    m <- as.matrix(x)
    dimnames(m) <- value
    unchecked_matrix(x) <- m
    return(x)
})

###############################################################
# Seqinfo getting and setting.

for (siglist in c("GInteractions", "ContactMatrix")) { 
    setMethod("seqinfo", siglist, function(x) {
        seqinfo(regions(x))
    })
    
    setReplaceMethod("seqinfo", siglist, function(x, new2old = NULL, pruning.mode = c("error", "coarse", "fine", "tidy"), value) {
        r <- regions(x)
        seqinfo(r, new2old=new2old, pruning.mode=pruning.mode) <- value
        unchecked_regions(x) <- r
        return(x)
    })
}

setMethod("seqinfo", "InteractionSet", function(x) {
     seqinfo(interactions(x))
})

setReplaceMethod("seqinfo", "InteractionSet", function(x, new2old = NULL, pruning.mode = c("error", "coarse", "fine", "tidy"), value) {
    i <- interactions(x)                 
    seqinfo(i) <- value
    unchecked_interactions(x) <- i
    return(x)
})

##############################################
# Matrix dimensions

setMethod("dim", "ContactMatrix", function(x) { 
    dim(as.matrix(x))
})

setMethod("length", "ContactMatrix", function(x) { 
    length(as.matrix(x))
})

setReplaceMethod("as.matrix", "ContactMatrix", function(x, value) {
    if (is(value, "Matrix")) {
        if (!identical(dim(x), dim(value))) { 
            stop("replacement Matrix must have same dimensions as 'x'")
        }
        unchecked_matrix(x) <- value
    } else {
        x@matrix[] <- value
    }
    return(x)
}) 

###############################################################
# End