findLoc: Find Substring Locations Inside A String

In akin: Functional Utilities for Data Processing

Find Substring Locations Inside A String

Description

Finds all locations of a known character substring inside a character string.

Usage

findLoc(
  subchain,
  chain,
  outlist = FALSE,
  named = FALSE,
  all. = FALSE,
  which = min,
  ignore.case = TRUE,
  perl = FALSE,
  fixed = FALSE,
  useBytes = FALSE
)

Arguments

subchain	character, length 1, e.g. a peptide sequence
chain	(named) character, length 1 or a (named) list of such characters such as a list of protein chains obtained from a fasta file
outlist	logical. Default, FALSE, the output is a (named) integer vector of locations. Otherwise, it is a (named) list of location vectors, each corresponding to a chain in a list of chains
named	logical. Default, FALSE. Output is not named. Otherwise, the output is named
all.	logical, default FALSE, returns the leftmost or the rightmost location inside the chain. When TRUE, returns all locations inside the chain for each chain in a list
which	symbol. Location to report. Default, min. Requires all. = FALSE. which = min returns the leftmost location inside the chain, e.g. closest to the N-terminus of a protein chain. which = max returns the rightmost location, e.g. closest to the C-terminus of a protein chain. Overwritten when all. = TRUE
ignore.case, perl, fixed, useBytes	arguments to base::gregexpr

Details

Wrapper to base::gregexpr, the function scans all chains in a list of chains to find subchain locations. The location is defined as the position inside the chain relative to the left end of the chain of the first subchain character.

Value

A (named) integer or a (named) list of integer vectors of subchain locations inside the chain.

See Also

gregexpr

Examples

if (interactive()) {

# 1. List of chains

chain = list(chain1 = 'alpdxoipoyloiekladxoipoylyl',
             chain2  = 'kdxoipoylyydxoipoylopldxoipoylac')
subchain = 'DXOIPOYL'                                                  # ignoring the case

findLoc(subchain, chain, outlist = TRUE, named = TRUE, all. = TRUE)    # named list
findLoc(subchain, chain, named = TRUE, all. = TRUE)                    # named integer
findLoc(subchain, chain, outlist = TRUE, named = TRUE)                 # the leftmost positions
findLoc(subchain, chain, which = max, named = TRUE)                    # the rightmost positions

# 2. Single chain

chain = chain[[1]]

findLoc(subchain, chain, all. = TRUE)
findLoc(subchain, chain, which = max)
findLoc(subchain, chain)                                               # default location
findLoc(subchain, chain, which = max, ignore.case = FALSE)             # not ignoring the case

}

akin documentation built on May 19, 2026, 5:07 p.m.