## This code is part of the megaptera package
## © C. Heibl 2014 (last update 2016-11-03)
setOldClass("DNAbin")
setClass(Class = "locusRef",
representation = list(
reference = "DNAbin"),
contains = "locus"
)
## SET METHOD: INITIALIZE
## ----------------------
setMethod("initialize", "locusRef",
function(.Object, kind, sql, aliases,
not, adj.gene1, adj.gene2,
search.fields, use.genomes,
align.method,
min.identity, min.coverage,
reference){
if ( !missing(aliases) ){
.Object@kind <- kind
.Object@sql <- sql
.Object@aliases <- aliases
.Object@not <- not
.Object@adj.gene1 <- adj.gene1
.Object@adj.gene2 <- adj.gene2
.Object@search.fields <- search.fields
.Object@use.genomes <- use.genomes
.Object@align.method <- align.method
.Object@min.identity <- min.identity
.Object@min.coverage <- min.coverage
.Object@reference <- reference
}
return(.Object)
}
)
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