R/fastMatch.R

In CAMERA: Collection of annotation related methods for mass spectrometry data

fastMatch <- function(x,y,tol=0.001, symmetric=FALSE) {

    if (any(is.na(y)))
        stop("NA's are not allowed in y !\n")
    ok <- !(is.na(x))
    ans <- order(x)
    keep <- seq_along(ok)[ok]
    xidx <- ans[ans %in% keep]
    xs <- x[xidx]
    yidx <- order(y)
    ys <- y[yidx] 
    if (!is.double(xs)) 
      xs <- as.double(xs)
    if (!is.double(ys)) 
      ys<- as.double(ys)
    if (!is.integer(xidx)) 
      xidx <- as.integer(xidx)
    if (!is.integer(yidx)) 
      yidx <- as.integer(yidx)  
    
 fm <- .Call("fastMatch", xs, ys, xidx, yidx, as.integer(length(x)), as.double(tol) , PACKAGE ='CAMERA' ) 
 fm2 <- vector("list", length=length(fm))
    #stop("!")
   if (symmetric){  
       for (a in 1:length(fm)) {
            if (!is.null(fm[[a]][1])){
                tmp<-NULL
                for (b in 1:length(fm[[a]])){
                    if ((abs(x[a]-y[fm[[a]]][b]) == min(abs(x[a]-y[fm[[a]][b]]),
                                                      abs(x[a]  -y[fm[[a]][b]-1]),
                                                      abs(x[a]  -y[fm[[a]][b]+1]),
                                                      abs(x[a-1]-y[fm[[a]][b]]),
                                                      abs(x[a+1]-y[fm[[a]][b]]), na.rm=T)
                       )) {
                       tmp<-c(tmp, fm[[a]][b])
                       }
                    }
               fm2[[a]]<-tmp
               }
           }
        }else {
            fm2 <- fm}
fm2
}