R/compare_strings.R

In hhabra/metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

##This file contains utility functions for matching character string values

#' Ignore Bracketed Strings
#'
#' @description
#' This function is generally used to ignore certain strings that are bracketed
#' for the purposes of string comparisons
#'
#' @param s  a character vector
#'
#' @param brackets  any one or a combination of bracket characters
#'
#' @return character vector with bracketed strings replaced with empty string
#'
#' @noRd
ignore_brackets = function(s, brackets)
{
    if("(" %in% brackets | ")" %in% brackets | "()" %in% brackets)
        s <- gsub("^\\([^&]*\\)$", "", s, perl = TRUE)

    if("[" %in% brackets | "]" %in% brackets | "[]" %in% brackets)
        s <- gsub("^\\[[^&]*\\]$", "", s, perl = TRUE)

    if("{" %in% brackets | "}" %in% brackets | "{}" %in% brackets)
        s <- gsub("^\\{[^&]*\\}$", "", s, perl = TRUE)

    return(s)
}

#' @title remove bracket characters in strings
#'
#' @description This removes bracket characters, usually in conjunction with
#' usage of "grep" for sample & extra column indexing
#'
#' @noRd
rmbrackets <- function(s){
    gsub("\\(|\\[|\\{|\\}|\\]|\\)", "", s)
}


#' Determine Matching Identity Strings
#'
#' @param s1  One of two character vectors to be compared
#'
#' @param s2  One of two character vectors to be compared
#'
#' @param match value to give for matching s1 and s2 strings
#'
#' @param mismatch value to give for mismatching / empty s1 and s2 strings
#'
#' @param brackets  bracketed character strings of these types will be
#' ignored according to this argument
#'
#' @param type Option to assign match-based
#'
#' @return  vector. Indices of matching strings are equal to value of match,
#'          with mismatching strings equal to value of mismatch
#'
#' @noRd
compare_strings <- function(s1,s2, match, mismatch, brackets, type = "m")
{
    s1 <- ignore_brackets(ifelse(is.na(s1), "", s1), brackets)
    s2 <- ignore_brackets(ifelse(is.na(s2), "", s2), brackets)

    if (type == "m")
        return(ifelse(!(s1 == "" | s2 == "") & tolower(s1) == tolower(s2),
                match, mismatch))

    else if (type == "mm")
        return(ifelse(!(s1 == "" | s2 == "") & tolower(s1) != tolower(s2),
                mismatch, match))
}