### =========================================================================
 ### GmapParam class
 ### -------------------------------------------------------------------------
 ###
 ### High-level interface to gmap.
 ###
 
 setClassUnion("GmapSnpsORNULL", c("GmapSnps", "NULL"))
 
 setClass("GmapAlignerParam",
          representation(genome = "GmapGenome",
                         part = "characterORNULL",
                         batch = "character",
                         snps = "GmapSnpsORNULL",
                         mode = "character",
                         nthreads = "integer",
                         npaths = "integer",
                         quiet_if_excessive = "logical",
                         nofails = "logical", 
                         split_output = "logical",
                         extra = "list"))
 
 setClass("GmapParam",
          representation(suboptimal_score = "integer",
                         splicing = "logical",
                         format = "character"),
          contains="GmapAlignerParam")
 
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 ### Constructor
 ###
 
 GmapParam <- function(genome, unique_only = FALSE,
                       suboptimal_score = 0L, mode = "standard",
                       snps = NULL,
                       npaths = if (unique_only) 1L else 100L,
                       quiet_if_excessive = unique_only, nofails = unique_only,
                       split_output = !unique_only,
                       splicing = TRUE, 
                       nthreads = 1L, part = NULL, batch = "2",
                       format = c("gff3_gene", "gff3_match_cdna",
                           "gff3_match_est", "sampe", "samse", "psl",
                           "splicesites", "introns",
                           "map_exons", "map_ranges", "coords"),
                       ...)
 {
     format <- match.arg(format)
     newGmapAlignerParam("GmapParam", genome, snps)
 }
 
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 ### Coercion
 ###
 
 setAs("GmapParam", "list", function(from) {
           to <- GmapAlignerParam_asList(from)
           to$nosplicing <- !to$splicing
           to$splicing <- NULL
           to
       })