mix.R

    ## Throw out the possibly empty members.
    really_okind <- okind[m$qa$ms[irows, ]$qa_pass]
    m$qa$ms[which(qa_pass),ms2_sel:=.(mapply(function (spl,inds,ms1rt) {
        rtdiff <- sapply(spl[inds],function (x) abs(x$rt-ms1rt))
        closest <- which.min(rtdiff)
        inds[[closest]]
    },
    spec,
    really_okind,
    ms1_rt,
    SIMPLIFY=T))]

    m    
}

gen_mz_err_f <- function(entry,msg) {
    eppm <- grab_unit(entry,"ppm")
    eda <- grab_unit(entry,"Da")
    shinyscreen:::assert(xor(is.na(eda), is.na(eppm)), msg = msg)
    if (is.na(eda)) function(mz) eppm*1e-6*mz else function (mz) eda
}


gen_rt_err <- function(entry,msg) {
    em <- grab_unit(entry,"min")
    es <- grab_unit(entry,"s")
    shinyscreen:::assert(xor(is.na(em), is.na(es)), msg = msg)
    if (is.na(em)) es/60. else em
}

fig_path <- function(top,set,group,id,suff,ext="pdf") {
    base <- paste("plot",set,group,id,suff,sep="_")
    fn <- paste0(base,".",ext)
    fn <- gsub("\\[","",fn)
    fn <- gsub("\\]","",fn)
    fn <- gsub("\\+","p",fn)
    fn <- gsub("-","m",fn)
    if (!is.null(top)) file.path(top,fn) else fn
}

get_coord_lim <- function(new,def) {
    if (is.null(new)) return(def)
    res <- new
    if (length(new[[1]])==0) res[[1]]<-def[[1]]
    if (length(new[[2]])==0) res[[2]]<-def[[2]]
    res
}