R/class-01-SpliceSites.R

In splicegear: splicegear

setClass("SpliceSites",
         representation(
                        seq = "character",   # the genomic sequence (if available)
                        seq.length = "integer", 
                        spsiteIpos = "matrix", # a two-columns matrix (window for type I splice site),
                          spsiteIIpos = "integer", # position for type II splice site
                        spsiteIIIpos = "matrix", # a two-columns matrix (window for type III splice site),
                        spsiteIpos.pData = "AnnotatedDataFrame",
                        spsiteIIpos.pData = "AnnotatedDataFrame",
                        spsiteIIIpos.pData = "AnnotatedDataFrame"
                        ))


  setMethod("show", signature(object = "SpliceSites"),
            function(object) {
              cat("Alternative splicing sites (SpliceSites):\n")
              cat("\tseq is ", object@seq.length, " bp long", sep="")
              if (object@seq == "")
                cat(" (warning: sequence not included).\n")
              else
                cat(".\n")
              cat("\t", nrow(object@spsiteIpos), " type I splice site(s)\n", sep="")
              show(object@spsiteIpos.pData)
              cat("\t", length(object@spsiteIIpos), " type II splice site(s)\n", sep="")
              show(object@spsiteIIpos.pData)
              cat("\t", nrow(object@spsiteIIIpos), " type III splice site(s)\n", sep="")
            })


if( !isGeneric("plot") )
  setGeneric("plot", function(x, y, ...)
             standardGeneric("plot"))


setMethod("plot",
          signature(x="SpliceSites", y="missing"),
          function(x, ...) {
              plot.SpliceSites(x, ...)
            })


if( !isGeneric("grid.plot") )
  setGeneric("grid.plot", function(x, y, ...)
             standardGeneric("grid.plot"))

setMethod("grid.plot",
          signature(x="SpliceSites", y="missing"),
          function(x, ...) {
              grid.plot.SpliceSites(x, ...)
            })