Add SpectrumParser virtual class

NAMESPACE

@@ -2,8 +2,12 @@
 
 export(.massbankParseProcessBuffer)
 export(.massbankParseRecord)
+export(MassbankParser)
 export(parserMassBank)
 export(schema_export)
 export(schema_import)
+exportClasses(MassbankParser)
+exportClasses(SpectrumParser)
+exportMethods(importSpectrum)
 import(MSnbase)
 import(yaml)

R/SpectrumParser.R

@@ -0,0 +1,50 @@
+
+#' @title Spectrum parser
+#'
+#' @name SpectrumParser
+#'
+#' @description
+#' 
+#' Classes extending the base `SpectrumParser` object are supposed to read
+#' spectrum data from a certain input format and return a standardized output
+#' format.
+#'
+#' @md
+#'
+#' @author Johannes Rainer
+#'
+#' @exportClass SpectrumParser
+NULL
+
+setClass("SpectrumParser",
+         slots = c(schema = "list"),
+         prototype = prototype(schema = list()),
+         contains = "VIRTUAL")
+
+#' @description
+#'
+#' `importSpectrum` reads spectrum data from a file, extracted all fields and
+#' maps them to the corresponding *standard* fields using the parser's schema
+#' definition.
+#'
+#' @param file `character(1)` with the name of the file from which spectrum
+#'     data should be imported.
+#'
+#' @param object object extending `SpectrumParser`.
+#'
+#' @return a `Spectra` object - TODO needs to be discussed!
+#' 
+#' @md
+#'
+#' @exportMethod importSpectrum
+#' 
+#' @rdname SpectrumParser
+setGeneric("importSpectrum", function(object, file, ...)
+    standardGeneric("importSpectrum"))
+setMethod("importSpectrum", "SpectrumParser", function(object, file, ...)
+          stop("importSpectrum not implemented for ", class(object)))
+
+setMethod("show", "SpectrumParser", function(object) {
+    cat("Object of class", class(object), "\n")
+})
+

R/massbankParser.R

@@ -211,3 +211,57 @@ parserMassBank <- function()
     "block" = .massbankRuleParseBlock
   )
 )}
+
+#' @title Massbank parser
+#'
+#' @description
+#'
+#' Parser for Massbank spectrum files.
+#'
+#' New objects are supposed to be created with the `MassbankParser` function.
+#'
+#' @author Michele Stravs, Johannes Rainer
+#' 
+#' @name MassbankParser
+#'
+#' @exportClass MassbankParser
+#'
+#' @examples
+#' library(MSnio)
+#'
+#' ## Create and intialize a parser
+#' prs <- MassbankParser()
+#'
+#' ## Spectrum file
+#' fl <- system.file("spectra/massbank/EA016614.txt", package="MSnio")
+#' res <- importSpectrum(prs, fl)
+setClass("MassbankParser",
+         contains = "SpectrumParser")
+
+#' @rdname MassbankParser
+setMethod("importSpectrum", "MassbankParser", function(object, file, ...) {
+    if (!file.exists(file))
+        stop("File ", file, " not found")
+    if (length(object@schema) == 0)
+        stop("Parser does not have any schema")
+    tkns <- .massbankParseRecord(readLines(file))
+    ## map to "standard" fields, return a Spectra/Spectrum/whatever
+    tkns
+})
+
+setValidity("MassbankParser", function(object) {
+    msg <- NULL
+    ## Would be nice to check the schema for correctness or similar.
+    if (length(msg)) msg
+    else TRUE
+})
+
+
+#' @rdname MassbankParser
+#'
+#' @export MassbankParser
+MassbankParser <- function() {
+    new("MassbankParser",
+        schema = yaml.load_file(system.file("schemas/schema_massbank_auto.yaml",
+                                            package="MSnio")))
+}