modified_writeMgfData.R

##
## MODIFIED the original writeMgfData
## from https://github.com/lgatto/MSnbase/blob/master/R/readWriteMgfData.R
## 
## by Nathalia Graf Grachet
##
## Now, this function write the correct polarity of the features 
## (original automatically added positive), and 
## the title of the features are now the actual feature identification instead of 
## the long description

# Based on the code contributed by Guangchuang Yu <guangchuangyu@gmail.com>
# Modified by Sebastian Gibb <mail@sebastiangibb.de>
# setMethod("mod_writeMgfData",
#           signature = signature("Spectrum"),
#           function(object,
#                    con = "spectrum.mgf",
#                    COM = NULL,
#                    TITLE = NULL) {
#               mod_writeMgfDataFile(list(object), con = con, COM = COM, TITLE = TITLE, 
#                                verbose = isMSnbaseVerbose())
#           })
# 
# setMethod("mod_writeMgfData",
#           signature = signature("MSnExp"),
#           function(object,
#                    con = "experiment.mgf",
#                    COM = NULL,
#                    verbose = isMSnbaseVerbose()) {
#               mod_writeMgfDataFile(spectra(object), con = con, COM = COM,
#                                verbose = verbose)
#           })

#' @param addFields `data.frame` or `matrix` with optional additional
#'     fields to be added to each spectrum (each column one field).
#'
#' @noRd
mod_writeMgfDataFile <- function(splist, con, COM = NULL, TITLE = NULL,
                             verbose = isMSnbaseVerbose(), addFields = NULL) {
    
    if (class(con) == "character" && file.exists(con)) {
        message("Overwriting ", con, "!")
        unlink(con)
    }
    
    if (length(addFields)) {
        if (length(dim(addFields)) != 2)
            stop("'addFields' has to be a matrix or data.frame.")
        if (!is.matrix(addFields))
            addFields <- do.call(cbind, lapply(addFields, as.character))
        if (is.null(colnames(addFields)))
            stop("Column names required on 'addFields'.")
        if (nrow(addFields) != length(splist))
            stop("nrow of 'addFields' has to match length of 'splist'")
    }
    
    if (class(con)[1] == "character") {
        con <- file(description = con, open = "at")
        on.exit(close(con))
    }
    
    if (is.null(COM)) {
        COM <- paste0(ifelse(length(splist) <= 1, "Spectrum", "Experiment"),
                      "exported by MSnbase on ", date())
    }
    cat(paste0("COM=",COM), file = con, sep = "")
    
    verbose <- verbose & length(splist) > 1
    
    if (verbose)
        pb <- txtProgressBar(min = 0, max = length(splist), style = 3)
    
    for (i in seq(along=splist)) {
        if (verbose)
            setTxtProgressBar(pb, i)
        
        mod_writeMgfContent(splist[[i]], TITLE = splist@elementMetadata@listData[["feature_id"]][[i]], con = con,
                        addFields = addFields[i, ])  
    }
    if (verbose)
        close(pb)
}

mod_writeMgfContent <- function(sp, TITLE = NULL, con, addFields = NULL) {
    .cat <- function(..., file = con, sep = "", append = TRUE) {
        cat(..., file = file, sep = sep, append = append)
    }
    
    .cat("\nBEGIN IONS\n",
         "SCANS=", acquisitionNum(sp))
    
    if (is.null(TITLE)) {
        .cat("\nTITLE=msLevel ", msLevel(sp),
             "; retentionTime ", rtime(sp),
             "; scanNum ", acquisitionNum(sp))
        
        if (length(scanIndex(sp))) {
            .cat("; scanIndex ", scanIndex(sp))
        }
        
        if (msLevel(sp) > 1) {
            .cat("; precMz ", precursorMz(sp),
                 "; precCharge ", precursorCharge(sp))
        }
    } else {
        .cat("\nTITLE=", TITLE)
    }
    
    signal = ""
    
    if(polarity(sp) == 1){
        signal = "+"
    } else signal = "-"
    
    if (msLevel(sp) > 1) {
        .cat("\nRTINSECONDS=", rtime(sp), "\nPEPMASS=", precursorMz(sp))
        if (length(precursorCharge(sp)) && !is.na(precursorCharge(sp))) {
            .cat("\nCHARGE=", precursorCharge(sp), signal)
        }
    } else .cat("\nRTINSECONDS=", rtime(sp))
    
    if (length(addFields) && !is.null(names(addFields)))
        .cat("\n", paste(toupper(names(addFields)),
                         addFields, sep = "=", collapse = "\n"))
    
    .cat("\n", paste(mz(sp), intensity(sp), collapse = "\n"))
    .cat("\nEND IONS\n")
}