R/matchLRPatterns.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

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### The "matchLRPatterns" new generic.
###

setGeneric("matchLRPatterns", signature="subject",
    function(Lpattern, Rpattern, max.gaplength, subject,
             max.Lmismatch=0, max.Rmismatch=0,
             with.Lindels=FALSE, with.Rindels=FALSE,
             Lfixed=TRUE, Rfixed=TRUE)
        standardGeneric("matchLRPatterns")
)

### Dispatch on 'subject' (see signature of generic).
setMethod("matchLRPatterns", "XString", 
    function(Lpattern, Rpattern, max.gaplength, subject,
             max.Lmismatch=0, max.Rmismatch=0,
             with.Lindels=FALSE, with.Rindels=FALSE,
             Lfixed=TRUE, Rfixed=TRUE)
    {
        ans_start <- ans_end <- integer(0)
        Lmatches <- matchPattern(Lpattern, subject,
                                 max.mismatch=max.Lmismatch,
                                 with.indels=with.Lindels,
                                 fixed=Lfixed)
        if (length(Lmatches) != 0L) {
            Rmatches <- matchPattern(Rpattern, subject,
                                     max.mismatch=max.Rmismatch,
                                     with.indels=with.Rindels,
                                     fixed=Rfixed)
            if (length(Rmatches) != 0L) {
                for (i in seq_len(length(Lmatches))) {
                    gaplength <- start(Rmatches) - end(Lmatches)[i] - 1L
                    jj <- which(0L <= gaplength & gaplength <= max.gaplength)
                    ans_start <- c(ans_start, rep.int(start(Lmatches)[i], length(jj)))
                    ans_end <- c(ans_end, end(Rmatches)[jj])
                }
            }
        }
        ans_width <- ans_end - ans_start + 1L
        Views(subject, start=ans_start, width=ans_width)
    }
)

### Dispatch on 'subject' (see signature of generic).
### WARNING: Unlike the other "matchLRPatterns" methods, the XStringViews object
### returned by this method is not guaranteed to have its views ordered from
### left to right in general! One important particular case where this is
### guaranteed though is when 'isNormal(subject)' is TRUE (i.e. 'subject' is
### a normal XStringViews object) and 'max.mismatch=0' and 'max.Rmismatch=0'
### (so there are no "out of limits" matches).
setMethod("matchLRPatterns", "XStringViews",
    function(Lpattern, Rpattern, max.gaplength, subject,
             max.Lmismatch=0, max.Rmismatch=0,
             with.Lindels=FALSE, with.Rindels=FALSE,
             Lfixed=TRUE, Rfixed=TRUE)
    {
        ans_start <- ans_width <- integer(0)
        subject <- trim(subject)
        Lcounts <- vcountPattern(Lpattern, subject,
                                 max.mismatch=max.Lmismatch,
                                 with.indels=with.Lindels,
                                 fixed=Lfixed)
        candidates <- which(Lcounts > 0L)
        if (length(candidates) != 0L) {
            subject <- subject[candidates]
            Lcounts <- Lcounts[candidates]
            Lmatches <- matchPattern(Lpattern, subject,
                                     max.mismatch=max.Lmismatch,
                                     with.indels=with.Lindels,
                                     fixed=Lfixed)
            Rranges <- IRanges(start=end(Lmatches) + 1L,
                               width=max.gaplength + nchar(Rpattern))
            Rranges <- pintersect(Rranges,
                                  rep(as(subject, "IRanges"), Lcounts))
            Rsubject <- as(Views(subject(subject), Rranges), "XStringSet")
            Rmatches <- vmatchPattern(Rpattern, Rsubject,
                                      max.mismatch=max.Rmismatch,
                                      with.indels=with.Rindels,
                                      fixed=Rfixed)
            Rcounts <- elementNROWS(Rmatches)
            Roffset <- unlist(endIndex(Rmatches), use.names=FALSE)
            if (length(Roffset) != 0L) {
                ans_start <- rep.int(start(Lmatches), Rcounts)
                ans_width <- rep.int(width(Lmatches), Rcounts) + Roffset
            }
        }
        Views(subject(subject), start=ans_start, width=ans_width)
    }
)

### Dispatch on 'subject' (see signature of generic).
setMethod("matchLRPatterns", "MaskedXString",
    function(Lpattern, Rpattern, max.gaplength, subject,
             max.Lmismatch=0, max.Rmismatch=0,
             with.Lindels=FALSE, with.Rindels=FALSE,
             Lfixed=TRUE, Rfixed=TRUE)
        matchLRPatterns(Lpattern, Rpattern, max.gaplength,
                        toXStringViewsOrXString(subject),
                        max.Lmismatch=max.Lmismatch,
                        max.Rmismatch=max.Rmismatch,
                        with.Lindels=with.Lindels,
                        with.Rindels=with.Rindels,
                        Lfixed=Lfixed, Rfixed=Rfixed)
)