SeqId Matching with Rcpp

matchseq.cpp

#include <Rcpp.h>
#include <unordered_map>
using namespace Rcpp;
using namespace std;

/* Trying to speed up matchSeqIds()
Generate a C++ version called matchseq_cpp()
Install inside matchSeqIds() - a wrapper around matchseq_cpp()
*/

// [[Rcpp::export]]
Rcpp::StringVector
  matchseq_cpp(CharacterVector x,          /* string containing SeqId entries */
               CharacterVector y,          /* string containing SeqIds to match x */
               bool order_by_x = true) {.  /* logical on ordering */
  Function getSeqId("getSeqId");           /* import external getSeqId() function */
  Function base_intersect("intersect");    /* cannot use sugar; order differs; small speed cost tho */
  CharacterVector x_seqs = getSeqId(x);    /* get SeqIds; non-seqs are NA */
  x_seqs = Rcpp::na_omit(x_seqs);          /* rm NAs */
  CharacterVector y_seqs = getSeqId(y);    /* get SeqIds from 'y' */
  int L = y.size();
  std::unordered_map< std::string, std::string > hashmap; /* initialize hashmap */
  for(int i = 0; i < L; i++) {
    hashmap.insert(std::make_pair(y_seqs[i], y[i]));  /* populate hashmap */
  }
  CharacterVector ord_seqs(L);                  /* initiate vector for intersect */
  if (order_by_x) {
    ord_seqs = base_intersect(x_seqs, y_seqs);  /* get SeqId intersection of x & y */
  } else {
    ord_seqs = base_intersect(y_seqs, x_seqs);  /* get SeqId intersection of y & x */
  }
  int n = ord_seqs.size();
  Rcpp::StringVector res(n);
  for(int j = 0; j < n; j++) {
    /* get the corresponding 'y' values   */
    res[j] = hashmap[ Rcpp::as< std::string >(ord_seqs[j]) ];
  }
  return res;
}

/***R
x <- c("seq.4554.56", "seq.3714.49", "PlateId")
y <- c("Group", "3714-49", "Assay", "4554-56")
 bench::mark(
   cpp  = matchseq_cpp(x, y),
   orig = matchSeqIds(x, y),
   iterations = 1000
   ) %>% summary(relative = TRUE)
*/