R/locus-class.R

In heibl/megaptera: MEGAPhylogeny Techniques in R

## This code is part of the megaptera package
## © C. Heibl 2014 (last update 2016-11-03)

setClass("locus", 
         representation = list(
           kind = "character",
           sql = "character", 
           aliases = "character", 
           not = "character",
           adj.gene1 = "character",
           adj.gene2 = "character",
           search.fields = "character",
           use.genomes = "logical",
           align.method = "character",
           min.identity = "numeric",
           min.coverage = "numeric")
)

## SET METHOD: INITIALIZE
## ----------------------
setMethod("initialize", "locus",
          function(.Object, kind, sql, aliases, 
                   not, adj.gene1, adj.gene2,
                   search.fields, use.genomes,
                   align.method,
                   min.identity, min.coverage){
            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
            }
            return(.Object)
          }
)