fix: update string indexing

src/setriq/_C/PairwiseDistanceComputer.cpp

@@ -10,15 +10,15 @@ double_vector_t PairwiseDistanceComputer::compute_distance(const string_vector_t
      * the method will be multi-threaded.
      *
      * @param input_strings: a vector of input strings
-     * @return a flat (N * (N - 1)) / 2 vector of doubles
+     * @return a flat (n * (n - 1)) / 2 vector of doubles
      */
-    const auto& N = input_strings.size();
-    double_vector_t distance_matrix(N * (N - 1) / 2);
+    const auto& n = input_strings.size();
+    double_vector_t distance_matrix(n * (n - 1) / 2);
 
-    #pragma omp parallel for default(none) shared(input_strings, distance_matrix, N)
-    for (size_t i = 0; i < N - 1; i++) {
-        for (size_t j = i + 1; j < N; j++) {
-            size_t index = (N * (N - 1)) / 2 - (N - i) * ((N - i) - 1) / 2 + j - i - 1;
+#pragma omp parallel for default(none) firstprivate(n) shared(input_strings, distance_matrix)
+    for (size_t i = 0; i < n - 1; i++) {
+        for (size_t j = i + 1; j < n; j++) {
+            size_t index = (n * (n - 1)) / 2 - (n - i) * ((n - i) - 1) / 2 + j - i - 1;
             distance_matrix[index] = (*this->distance_metric_)(input_strings[i], input_strings[j]);
         }
     }

src/setriq/_C/alignment/SmithWaterman.cpp

@@ -119,11 +119,11 @@ double SmithWaterman::identity_score(const std::string &input_string) {
      * @param input_string: an input string to be aligned with itself
      * @return the maximal self-alignment score for an input string
      */
-    const auto& N = input_string.size();
+    const auto* end = &input_string.back() + 1;
 
-    double score {0};
-    for (size_t i = 0; i < N; i++) {
-        score += this->substitution_matrix_(input_string[i], input_string[i]);
+    auto&& score = 0.f;
+    for (auto* ptr = &input_string.front(); ptr != end; ptr++) {
+        score += this->substitution_matrix_(*ptr, *ptr);
     }
     return score;
 }

src/setriq/_C/metrics/TcrDist.cpp

@@ -31,18 +31,24 @@ double metric::TcrDist::forward(const std::string &a, const std::string &b) {
      * @param b: another string to be compared
      * @return TcrDist metric between the two strings
      */
-    const auto& max_distance {4.};
+    constexpr double max_distance = 4;
+    const auto& n = a.size();
 
-    double distance {0}, substitution;
-    for (size_t i = 0; i < a.size(); i++) {
-        if (a[i] == b[i]) continue;
+    const auto* ptr_a = &a.front();
+    const auto* ptr_b = &b.front();
+    auto &&distance = 0.f;
+    for (size_t i = 0; i < n; i++) {
+        const auto& _a = *(ptr_a + i);
+        const auto& _b = *(ptr_b + i);
+        if (_a == _b)
+            continue;
 
-        if (a[i] == this->gap_symbol_ || b[i] == this->gap_symbol_) {
+        if (_a == this->gap_symbol_ || _b == this->gap_symbol_) {
             distance += this->gap_penalty_;
             continue;
         }
 
-        substitution = max_distance - this->substitution_matrix_(a[i], b[i]);
+        const auto& substitution = max_distance - this->substitution_matrix_(_a, _b);
         distance += std::min(max_distance, substitution);
     }
     return distance * this->distance_weight_;