gregexpr2: A replacement for R standard gregexpr function

In anandhupresannan/biostrings: Efficient manipulation of biological strings

Description

This is a replacement for the standard gregexpr function that does exact matching only. Standard gregexpr() misses matches when they are overlapping. The gregexpr2 function finds all matches but it only works in "fixed" mode i.e. for exact matching (regular expressions are not supported).

Usage

gregexpr2(pattern, text)

Arguments

pattern	character string to be matched in the given character vector
text	a character vector where matches are sought

Value

A list of the same length as text each element of which is an integer vector as in gregexpr, except that the starting positions of all (even overlapping) matches are given. Note that, unlike gregexpr, gregexpr2 doesn't attach a "match.length" attribute to each element of the returned list because, since it only works in "fixed" mode, then all the matches have the length of the pattern. Another difference with gregexpr is that with gregexpr2, the pattern argument must be a single (non-NA, non-empty) string.

Author(s)

H. Pagès

See Also

gregexpr, matchPattern

Examples

    gregexpr("aa", c("XaaaYaa", "a"), fixed=TRUE)
    gregexpr2("aa", c("XaaaYaa", "a"))

anandhupresannan/biostrings documentation built on Nov. 2, 2019, 1:47 p.m.