R/AllGeneric.r

#' Generic function for dist_replacement
#' @param x a sequence object
#' @param kmer_summary  a kmer_summary object
#' @param k k-mer length
#' @param ... additional parameters
#'
setGeneric('dist_replacement', function(x, kmer_summary, k, ...) standardGeneric('dist_replacement'))

#' Generic function for dist_weighted_hamming
#' @param x a sequence object
#' @param wVec weight vector
#' @param ... additional parameters
#'
setGeneric('dist_weighted_hamming', function(x, wVec, ...) standardGeneric('dist_weighted_hamming'))

#' Generic function for substr_kmer
#' @param x a kmer object
#' @param ... additional parameters
#'
setGeneric('substr_kmer', function(x, ...) standardGeneric('substr_kmer'))

#' Generic function for summarize_kmer
#' @param x a sequence object
#' @param ... additional parameters
#'
setGeneric('summarize_kmer', function(x, ...) standardGeneric('summarize_kmer'))

#' Generic function for simulate
#' @param config a lineage_tree_config object
#' @param x a sequence object
#' @param ... additional parameters
#'
setGeneric('simulate', function(config, x, ...) standardGeneric('simulate'))

#' Generic function for process_sequence
#' @param x a sequence object
#' @param ... additional parameters
#'
setGeneric('process_sequence', function(x, ...) standardGeneric('process_sequence'))

#' Generic function for as_phylo
#' @param x a graph object
#' @param ... additional parameters
#'
setGeneric('as_phylo', function(x, ...) standardGeneric('as_phylo'))

#' Generic function for as_igraph
#' @param x a phylo object
#' @param ... additional parameters
#'
setGeneric('as_igraph', function(x, ...) standardGeneric('as_igraph'))

#' Generic function for downsample 
#' @param x a data object
#' @param ... additional parameters
#'
setGeneric('downsample', function(x, ...) standardGeneric('downsample'))

#' Generic function for subtree
#' @param x a lineage_tree object
#' @param ... additional parameters
#'
setGeneric('subtree', function(x, ...) standardGeneric('subtree'))

#' Generic function for subtract
#' @param x a lineage_tree object
#' @param y a lineage_tree object
#' @param ... additional parameters
#'
setGeneric('subtract', function(x, y, ...) standardGeneric('subtract'))

#' Generic function for get_leaves
#' @param x a lineage_tree object
#' @param ... additional parameters
#'
setGeneric('get_leaves', function(x, ...) standardGeneric('get_leaves'))

#' Generic function for prune
#' @param x a lineage_tree object
#' @param ... additional parameters
#'
setGeneric('prune', function(x, ...) standardGeneric('prune'))

#' Generic function for as_lineage_tree
#' @param x a phyDat object
#' @param y a phylo object
#' @param config a lineage_tree_config object
#' @param ... additional parameters
#'
setGeneric('as_lineage_tree', function(x, y, config, ...) standardGeneric('as_lineage_tree'))

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DCLEAR documentation built on Sept. 14, 2023, 9:09 a.m.