done?

Author: SamStan4

bin/app

@@ -7,22 +7,12 @@ namespace alignment {
     std::vector<dp_cell> cur_dp_row(col_size, dp_cell());
     std::vector<dp_cell> prev_dp_row(col_size, dp_cell());
 
-    // temp
-    std::ofstream s("./output.txt");
-
-    // prev_dp_row[0].print_scores(s);
-    // s << " ";
-
     for (size_t i = 1; i < col_size; ++i) {
       prev_dp_row[i].set_top_row(i);
-      // prev_dp_row[i].print_scores(s);
-      // s << " ";
     }
 
     for (size_t row_idx = 1; row_idx < row_size; ++row_idx) {
       cur_dp_row[0].set_left_col(row_idx);
-      // cur_dp_row[0].print_scores(s);
-      // s << " ";
       for (size_t col_idx = 1; col_idx < col_size; ++col_idx) {
         cur_dp_row[col_idx].score_cell(
           prev_dp_row[col_idx-1],
@@ -31,21 +21,46 @@ namespace alignment {
           string_one[row_idx-1],
           string_two[col_idx-1]
         );
-        // cur_dp_row[col_idx].print_scores(s);
-        // s << " ";
       }
-      // s << std::endl;
       std::swap(prev_dp_row, cur_dp_row);
     }
+    return prev_dp_row.back().get_max_score();
+  }
 
-    s << prev_dp_row.back().to_string() << std::endl;
+  int32_t execute_modified_global_alignment(const std::string& string_one, const std::string& string_two) {
+    const size_t row_size = string_one.size() + 1;
+    const size_t col_size = string_two.size() + 1;
+    std::vector<dp_cell> cur_dp_row(col_size, dp_cell());
+    std::vector<dp_cell> prev_dp_row(col_size, dp_cell());
 
-    s.close();
+    for (size_t i = 1; i < col_size; ++i) {
+      prev_dp_row[i].set_top_row(i);
+    }
 
-    return prev_dp_row.back().get_max_score();
-  }
+    int64_t max_score = 0;
+    int32_t max_score_matches = 0;
+
+    for (size_t row_idx = 1; row_idx < row_size; ++row_idx) {
+      cur_dp_row[0].set_left_col(row_idx);
+      for (size_t col_idx = 1; col_idx < col_size; ++col_idx) {
+        cur_dp_row[col_idx].score_cell(
+          prev_dp_row[col_idx-1],
+          prev_dp_row[col_idx],
+          cur_dp_row[col_idx-1],
+          string_one[row_idx-1],
+          string_two[col_idx-1]
+        );
+
+        const int64_t temp_max_score = cur_dp_row[col_idx].get_max_score();
 
-  // int32_t execute_modified_global_alignment(const std::string& string_one, const std::string& string_two) {
-  //   throw std::runtime_error("not implemented");
-  // }
+        if (temp_max_score > max_score) {
+          max_score = temp_max_score;
+          max_score_matches = cur_dp_row[col_idx].get_max_score_matches();
+        }
+      }
+      std::swap(prev_dp_row, cur_dp_row);
+    }
+
+    return max_score_matches;
+  }
 }

obj/alignment/alignment.o

@@ -11,7 +11,7 @@
 
 namespace alignment {
   int64_t execute_global_alignment(const std::string&, const std::string&);
-  // int32_t execute_modified_global_alignment(const std::string&, const std::string&);
+  int32_t execute_modified_global_alignment(const std::string&, const std::string&);
 }
 
 #endif

obj/wrapper/program_wrapper.o

@@ -23,6 +23,6 @@ void program_wrapper::run_program(const int arg_count, const char* const* arg_ve
   if (!io_utils::load_two_genes(arg_vector[1], gene_one, gene_two, gene_one_name, gene_two_name)) {
     throw std::runtime_error("error, not able to load genes from file");
   }
-  int64_t result = alignment::execute_global_alignment(gene_one, gene_two);
+  int64_t result = alignment::execute_modified_global_alignment(gene_one, gene_two);
   std::cout << result << std::endl;
 }