Return matrix M with two columns. For each element in row i and column j M[i,j] => distance between pattern(i) and data(j) sequences equal to or less than .max.errors. This function will uppercase .data and remove all strings, which have anything than A-Z letters.
find.similar.sequences(.data, .patterns = c(), .method = c('exact', 'hamm', 'lev'),
.max.errors = 1, .verbose = T, .clear = F)exact.match(.data, .patterns = c(), .verbose = T)
hamming.match(.data, .patterns = c(), .max.errors = 1, .verbose = T)
levenshtein.match(.data, .patterns = c(), .max.errors = 1, .verbose = T)
Vector of strings.
Character vector of sequences, which will be used for searching for neighbours.
Which method use: 'exact' for exact matching, 'hamm' for Hamming Distance, 'lev' for Levenshtein distance.
Max Hamming or Levenshtein distance between strings. Doesn't use in 'exact' setting.
Should function print progress or not. // DON'T USE IT
if T then remove all sequences with character "*" or "~".
Matrix with two columns [i,j], dist(data(i), data(j)) <= .max.errors.