COL
    AABC1
   AAAABD2
  AAAAAABF3

COL         NEW_COL
    AABC1          T1
   AAAABD2         T2
  AAAAAABF3        T3

CLASS       NEW_COL
    BC          T1
    BD          T2
    BF          T3

DF <- data.frame(COL = c("AABC1",
                         "AAAABD2",
                         "AAAAABF3"),
                 stringsAsFactors = FALSE)

lookup_tbl <- data.frame(CLASS = c("BC", "BD", "BF"),
                         NEW_COL = c("T1", "T2", "T3"),
                         stringsAsFactors = FALSE)

library(dplyr)
DF %>%
  mutate(CLASS = gsub(paste0("^.*(",
                            paste0(lookup_tbl[["CLASS"]], collapse = "|"),
                            ").*$"),
                      "\1",
                      lookup_tbl[["CLASS"]])) %>%
  # or inner_join as required
  left_join(lookup_tbl, by = "CLASS")

library(tidyverse)

lookup_table <- data.frame(
                    row.names = c('BC', 'BD', 'BF'),
                    new_col = c('T1', 'T2', 'T3'),
                    stringsAsFactors = FALSE)

lookup <- function(x, table) {
    for (class in rownames(table)) {
        if (grepl(class, x)) {
            return(table[class, 'new_col'])
        }
    }
}

data_frame(col = c('AABC1', 'AAAABD2', 'AAAAAABF3')) %>%
    rowwise %>% mutate(new_col = lookup(col, lookup_table))