mix.R

vald_comp_tab<-function(df,ndf,checkSMILES=F,checkMz=F,checkNames=F) {
    ## Fields.
    if (is.null(df$ID)) stop("Column ID missing in ",ndf," .")
    if (checkMz && is.null(df$mz)) stop("Column mz missing in ", ndf, " .")
    if (checkSMILES && is.null(df$SMILES)) stop("Column SMILES missing in", ndf, " .")
    
    if (checkNames && is.null(df$Name)) warning("Column Name missing in ", ndf," , continuing without.")
    if (is.null(df$RT) && is.null(df$rt)) {
        warning("Column RT (alternatively, rt) missing in ", ndf, ", continuing without.")
    } else {
        if (is.null(df$rt)) {
            df$rt<-df$RT
            df$RT<-NULL
        }
    }

    ## Missing IDs?
    ind<-which(is.na(df$ID))
    if (length(ind)>0) {
        for (i in ind) {
            warning("ID missing at row: ",i," .")
        }
        stop("Missing IDs found.")
    }
    
    ## Unique IDs?
    luids<-length(unique(df$ID))
    if (length(df$ID) > luids) stop("Duplicate IDs in ", ndf, " are not allowed.")

    ## Missing SMILES?
    if (checkSMILES) {
        ind<-which(is.na(df$SMILES))
        if (length(ind)>0) {
            for (i in ind) {
                warning("SMILES missing at row: ",i, "; ID: ",df$ID[[i]]," .")
            }
            stop("Missing SMILES found.")
        }
    }

    ## Missing mz?
    if (checkMz) {
        ind<-which(is.na(df$mz))
        if (length(ind)>0) {
            for (i in ind) {
                warning("mz missing at row: ",i, "; ID: ",df$ID[[i]]," .")
            }
            stop("Missing mz-s found.")
        }
    }

    df
}