Is there an efficient way to search a subject with a query that finds matches where the pattern is entirely contained in the subject, or the subject is entirely contained within the pattern ? The strings in the subject may be shorter or longer than the query string.

> vcountPattern("ABCD", "ABCDEF")
[1] 1
> vcountPattern("ABCDEF", "ABCD")
[1] 0

I'd like both of these to return 1.

Hi,

I would do something like this:

## A bi-directional vcountPattern().
vcountPattern2 <- function(pattern, subject, ...)
{
    if (!is(subject, "XStringSet"))
        subject <- as(subject, "XStringSet")
    ans <- integer(length(subject))
    swap <- width(pattern) > width(subject)
    swap_idx <- which(swap)
    noswap_idx <- which(!swap)
    if (length(noswap_idx) != 0L) {
        ans[noswap_idx] <- vcountPattern(pattern,
                                         subject[noswap_idx],
                                         ...)
    }
    if (length(swap_idx) != 0L) {
        pattern2 <- subject[swap_idx]
        subject2 <- as(pattern, "XString")
        ans[swap_idx] <- countPDict(pattern2, subject2, ...)
    }
    ans
}

Then:

vcountPattern2("ABcdAB", c("ABcdABef", "DD", "AB"))
# [1] 1 0 2

Cheers,

H.

I have developed a vectorised version which is shorter and simpler.

    queries <- c("ABCD", "ABCDEFG", "BCDE")
    subjects <- c("ABCDEF", "CDE")

    queriesInSubjects <- colSums(sapply(queries, function(query) vcountPattern(query, subjects)))
    queriesContainSubjects <- rowSums(sapply(subjects, function(subject) sapply(vmatchPattern(subject, queries), length)))

    rowSums(matrix(c(queriesInSubjects, queriesContainSubjects), ncol = 2))