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# $Id: locus.R 1337 2008-04-30 00:54:56Z warnes $
getlocus <- function(x,...)
{
if(is.locus(x))
return(x)
else if(!is.null(x["locus"]))
return(x["locus"])
else if(!is.null(attr(x,"locus")))
return(attr(x,"locus"))
else
NULL
}
getmarker <- getgene <- getlocus
locus <- function(name, chromosome, arm=c("p","q","long","short",NA),
index.start=NULL, index.end=NULL)
{
object <- list()
if(!missing(name))
object$name <- name
if(!missing(chromosome))
object$chromosome <- chromosome
if(!missing(arm))
{
arm <- match.arg( arm )
object$arm <- switch( arm, p="p", q="q", long="p", short="q")
}
if(!missing(index.start))
object$index.start <- index.start
if(!missing(index.end))
object$index.end <- index.end
class(object) <- "locus"
return(object)
}
gene <- function(name, chromosome, arm=c("p","q","long","short"),
index.start, index.end=NULL)
{
object <- locus(name, chromosome, arm, index.start, index.end)
class(object) <- c("gene","locus")
object
}
marker <- function(name, type,
locus.name, bp.start, bp.end=NULL, relative.to=NULL,
...
)
{
if(is.locus(locus.name))
object <- locus.name
else
object <- locus(locus.name, ...)
if(!missing(name))
object$marker.name <- name
if(!missing(type))
object$type <- type
if(!missing(bp.start))
object$bp.start <- bp.start
if(!missing(bp.end))
object$bp.end <- bp.end
if(!missing(relative.to))
object$relative.to <- relative.to
class(object) <- c("marker","locus")
object
}
is.locus <- function(x)
inherits(x, "locus")
is.gene <- function(x)
inherits(x, "gene")
is.marker <- function(x)
inherits(x, "marker")
as.character.locus <- function(x,...)
{
loc <- paste( x$chromosome, x$arm, x$index.start, sep="" )
if( !is.null(x$index.end ) && x$index.start != x$index.end )
loc <- paste(loc, "-", x$index.end, sep="")
loc
}
as.character.gene <- function(x,...)
as.character.locus(x,...)
as.character.marker <- function(x,...)
{
loc <- as.character.locus(x)
loc <- paste(loc, ":", x$bp.start, sep="")
if(!is.null(x$bp.end)) loc <- paste(loc, "-", x$bp.end, sep="")
loc
}
print.locus <- function(x,...)
{
cat("Locus: ", x$name, " (", as.character.locus(x), ")\n", sep="" )
}
print.gene <- function(x,...)
{
cat("Gene: ", x$name, " (", as.character.locus(x), ")\n", sep="" )
}
print.marker <- function(x,...)
{
cat("Marker: ", paste(x$name,":",x$marker.name,sep=""),
" (", as.character.marker(x), ")\tType: ",x$type,"\n", sep="" )
}
"locus<-" <- function(x,value)
{
attr(x,"locus") <- value
x
}
"marker<-" <- "gene<-" <- get("locus<-")
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