R/getAttributes.R

In egonw/BridgeDbR: Code for using BridgeDb identifier mapping framework from within R

getAttributes <- function(mapper, source, identifier) {
    datasource <- getDataSource(code = source)
    xref <- .jnew("org/bridgedb/Xref", identifier, datasource)
    attribs <- mapper$getAttributes(xref)
    str <- attribs$keySet()$toString()
    str <- substring(str, 2)
    str <- substring(str, 1, nchar(str) - 1)
    str <- strsplit(str[[1]][1], ", ")
    foo <- unlist(str)
    keys <- sapply(foo, function(x) {
        unlist(substr(x, regexpr(":", x, fixed = TRUE) + 1, nchar(x)))
    })
    names(keys) <- c()
    pairs <- c()
    for (key in keys) {
        val <- attribs$get(key)$toString()
        val <- substring(val, 2)
        val <- substring(val, 1, nchar(val) - 1)
        pairs <- c(pairs, key, val)
    }
    results <- matrix(unlist(pairs), byrow = TRUE, ncol = 2)
    results
}