Change the package path

R/layers.metabarcoding.R

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+#' @include 02_class_metabarcoding.data.R
+NULL
+
+#
+#
+# Managment of layers
+#
+# Layers a matrix or factors with the same dimension
+# than the read matrix
+#
+
+# get motus data.frames
+
+#' @export
+setGeneric("layer.names", function(obj) {
+  return(standardGeneric("layer.names"))
+})
+
+#' Returns the names of all the layers 
+#' 
+#' \code{layer.names} extracts the list of all the layer
+#' names attached to a \code{\link{metabarcoding.data}} instance.
+#' 
+#' @param   obj a \code{\link{metabarcoding.data}} instance
+#' @return  a vector of type \code{character} containing the
+#'          list of all the layer names.
+#' 
+#' @docType methods
+#' @rdname layer.names-methods
+#' @aliases layer.names-methods,metabarcoding.data
+#' 
+setMethod("layer.names", "metabarcoding.data", function(obj) {
+  return(names(obj@layers))
+})
+
+
+#' Returns the a layer associated to a \code{\link{metabarcoding.data}}
+#' 
+#' [[ operator Extracts a layer
+#' attached to a \code{\link{metabarcoding.data}} instance.
+#' 
+#' @usage \method{[[}{unmutable}(x,i)
+#'
+#' @param   x a \code{\link{metabarcoding.data}} instance
+#' @return  matrix or a factor.
+#' 
+#' @docType methods
+#' @rdname double-open-brace-methods
+#' @aliases double-open-brace-methods,metabarcoding.data
+#' @method [[
+#' @export
+#' 
+setMethod("[[", "metabarcoding.data", 
+          function(x, i, j, ...) {
+            
+            if (! is.character(i))
+              stop('Just named index must be used')  
+            
+            if (i=="reads")
+              return(x@reads)
+            
+            if (i=="samples")
+              return(x@samples)
+            
+            if (i=="motus")
+              return(x@motus)
+            
+            if (i=="reads")
+              return(x@reads)
+            
+            return(x@layers[[i,exact=TRUE]])
+          })
+
+#' @method $
+#' @export
+setMethod("$", "metabarcoding.data", 
+          function(x, name) {
+            return(x[[name]])
+          })
+
+
+# set one data layer data.frames
+
+#' @method [[<-
+#' @export
+setMethod("[[<-","metabarcoding.data", 
+          function(x, i, j, ...,value) {
+            
+            if (any(dim(value)!=c(x@scount,x@mcount)))
+              stop("data dimmension are not coherent with this metabarcoding.data")
+            
+            if (hasArg('j'))
+              stop('Just one dimension must be specified')
+            
+            if (! is.character(i))
+              stop('Just named index must be used')
+            
+            if (i=='reads')
+              stop('you cannot change the reads layer by this way')
+            
+            if (i=='motus' | i=='samples')
+              stop('layers cannot be names motus or samples')
+            
+            value = as.factor.or.matrix(value)
+            rownames(value)=rownames(x@reads)
+            colnames(value)=colnames(x@reads)
+            x@layers[[i]]=value
+            
+            return(x)
+          })
+
+#' @method $<-
+#' @export
+setMethod("$<-","metabarcoding.data", 
+          function(x, name, value) {
+            
+            x[[name]]=value
+            return(x)
+          })