Reduce number of comparisons in fastquant_max

[sgibb]

This PR is more or less just for documentation. It reduce the number of comparisons via <= and saves some time (if the peaks are already in memory speed gain is nearly two fold; for on disk objects it is just around 10%); see also #130.

library("msdata")
library("MSnbase")
library("microbenchmark")
f <- msdata::proteomics(full.names = TRUE,
                        pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

fastquant_max2 <- function(f, pk, spi, wd = 0.5) {
    ramp <- MSnbase:::.openMSfile(f)
    on.exit(close(ramp))
    pks <- peaks(ramp, spi)
    if (length(spi) == 1)
        pks <- list(pks)
    mzs <- res <- matrix(NA_real_,
                         ncol = length(pk),
                         nrow = length(pks))
    for (i in seq_along(pks)) {
        for (ii in seq_along(pk)) {
            k <- abs(pks[[i]][, 1L] - pk[ii]) <= wd
            if (any(k)) {
                j <- which.max(pks[[i]][k, 2])
                res[i, ii] <- pks[[i]][k, , drop = FALSE][j, 2]
                mzs[i, ii] <- pks[[i]][k, , drop = FALSE][j, 1]
            }
        }
    }
    list(exprs = res,
         mzs = mzs)
}

all.equal(MSnbase:::fastquant_max(f, mz(TMT6), spi=1:509, wd=0.5),
          fastquant_max2(f, mz(TMT6), spi=1:509, wd=0.5))
# [1] TRUE

microbenchmark(MSnbase:::fastquant_max(f, mz(TMT6), spi=1:509, wd=0.5),
               fastquant_max2(f, mz(TMT6), spi=1:509, wd=0.5), times=10)

# MSnbase:::fastquant_max(f, mz(TMT6), spi = 1:509, wd = 0.5) 739.2620 746.6394
#          fastquant_max2(f, mz(TMT6), spi = 1:509, wd = 0.5) 682.8757 687.2723
#     mean   median       uq      max neval
# 765.8628 757.8052 760.7415 879.4974    10
# 718.0008 692.4549 700.9097 829.5581    10