@@ -6,6 +6,7 @@ export(metaDataBlocks)

 export(spectraVariableMapping)

 exportClasses(MsBackendMassbank)

 exportClasses(MsBackendMassbankSql)

+exportMethods("$<-")

 exportMethods("[")

 exportMethods("intensity<-")

 exportMethods("mz<-")

@@ -56,7 +56,7 @@ MsBackendMassbankSql <- function() {

     if (length(db_cols)) {

         res <- cbind(

-            res, DataFrame(.fetch_spectra_data_sql(x, columns = db_cols)))

+            res, as(.fetch_spectra_data_sql(x, columns = db_cols), "DataFrame"))

         if (any(colnames(res) == "synonym"))

             res$synonym <- CharacterList(res$synonym, compress = FALSE)

     }

@@ -41,6 +41,9 @@

 #'

 #' @param j For `[`: not supported.

 #'

+#' @param name name of the variable to replace for `<-` methods. See individual

+#'     method description or expected data type.

+#'

 #' @param object Object extending `MsBackendMassbankSql`.

 #'

 #' @param spectraVariables For `selectSpectraVariables`: `character` with the

@@ -481,3 +484,12 @@ setMethod("compounds", "MsBackendMassbankSql", function(object, ...) {

     res$name <- vapply(syns, function(z) z[1], character(1))

     res[match(object$compound_id, res$compound_id), ]

 })

+

+#' @rdname MsBackendMassbankSql

+#'

+#' @export

+setReplaceMethod("$", "MsBackendMassbankSql", function(x, name, value) {

+    if (name %in% c("spectrum_id"))

+        stop("Spectra IDs can not be changes.", call. = FALSE)

+    callNextMethod()

+})

@@ -18,6 +18,7 @@

 \alias{[,MsBackendMassbankSql-method}

 \alias{compounds,Spectra-method}

 \alias{compounds,MsBackendMassbankSql-method}

+\alias{$<-,MsBackendMassbankSql-method}

 \title{MS backend accessing the MassBank MySQL database}

 \usage{

 MsBackendMassbankSql()

@@ -47,6 +48,8 @@ MsBackendMassbankSql()

 \S4method{compounds}{Spectra}(object, ...)

 \S4method{compounds}{MsBackendMassbankSql}(object, ...)

+

+\S4method{$}{MsBackendMassbankSql}(x, name) <- value

 }

 \arguments{

 \item{object}{Object extending \code{MsBackendMassbankSql}.}

@@ -76,6 +79,9 @@ total ion current should be (re)calculated on the actual data

 \item{drop}{For \code{[}: not considered.}

+\item{name}{name of the variable to replace for \verb{<-} methods. See individual

+method description or expected data type.}

+

 \item{spectraVariables}{For \code{selectSpectraVariables}: \code{character} with the

 names of the spectra variables to which the backend should be subsetted.}

 }