.config mods complete

Author: SamStan4

bin/app

@@ -1,4 +1,4 @@
-match 2
+match 1
 mismatch -2
 h -5
 g -2

input/alignment-params.config

@@ -26,15 +26,20 @@ clean:
 
 run-sample: $(TARGET)
 	@if [ -f $(TARGET) ]; then \
-		./$(TARGET) input/base-sample.fasta; \
+		./$(TARGET) \
+		input/alignment-params.config \
+		input/base-sample.fasta \
+		; \
 	else \
 		echo "Error: Executable $(TARGET) not found. Please build it first."; \
 		exit 1; \
 	fi
 
 run-brca2: $(TARGET)
 	@if [ -f $(TARGET) ]; then \
-		./$(TARGET) input/Human-Mouse-BRCA2-cds.fasta; \
+		./$(TARGET) \
+		input/Human-Mouse-BRCA2-cds.fasta \
+		; \
 	else \
 		echo "Error: Executable $(TARGET) not found. Please build it first."; \
 		exit 1; \

makefile

@@ -58,8 +58,8 @@ namespace io_utils {
     std::string& out_string_one,
     std::string& out_string_two,
     std::string& out_string_one_name,
-    std::string& out_string_two_name) {
-  
+    std::string& out_string_two_name
+  ) {
     out_string_one.clear();
     out_string_two.clear();
     out_string_one_name.clear();
@@ -122,4 +122,48 @@ namespace io_utils {
     std::sort(out_string.begin(), out_string.end());
     return true;
   }
+
+  bool load_alignment_params(
+    const char* file_path,
+    int64_t& out_match_score,
+    int64_t& out_mismatch_score,
+    int64_t& out_opening_gap_score,
+    int64_t& out_gap_extension_score
+  ) {
+    std::ifstream input_stream(file_path);
+    if (!input_stream.is_open()) {
+      return false;
+    }
+    std::unordered_map<std::string, int64_t> param_map = {
+      {"match", 0},
+      {"mismatch", 0},
+      {"g", 0},
+      {"h", 0}
+    };
+    std::string buffer;
+    int8_t total_params = 0;
+    while (std::getline(input_stream, buffer)) {
+      if (buffer.empty()) {
+        continue;
+      }
+      try {
+        std::stringstream read_stream(buffer);
+        std::string key;
+        std::string val;
+        read_stream >> key >> val;
+        if (param_map.find(key) != param_map.end()) {
+          param_map[key] = static_cast<int64_t>(std::stoi(val));
+          ++total_params;
+        }
+      } catch (...) {
+        continue;
+      }
+    }
+    input_stream.close();
+    out_match_score = param_map["match"];
+    out_mismatch_score = param_map["mismatch"];
+    out_opening_gap_score = param_map["h"];
+    out_gap_extension_score = param_map["g"];
+    return total_params == 4;
+  }
 }

obj/io/io_utils.o

@@ -4,13 +4,16 @@
 #include <string>
 #include <fstream>
 #include <unordered_set>
+#include <unordered_map>
 #include <algorithm>
+#include <sstream>
 
 namespace io_utils {
   bool load_one_gene(const char*, std::string&, std::string&);
   bool load_one_gene(const char*, std::string&);
   bool load_two_genes(const char*, std::string&, std::string&, std::string&, std::string&);
   bool load_alphabet(const char*, std::string&);
+  bool load_alignment_params(const char*, int64_t&, int64_t&, int64_t&, int64_t&);
 }
 
 #endif

obj/wrapper/program_wrapper.o

@@ -13,19 +13,39 @@ program_wrapper& program_wrapper::get_instance(void) {
 }
 
 void program_wrapper::run_program(const int arg_count, const char* const* arg_vector) {
-  if (arg_count != 2) {
+  if (arg_count != 3) {
     throw std::runtime_error("error, not enough command line args");
   }
   std::string gene_one;
   std::string gene_two;
   std::string gene_one_name;
   std::string gene_two_name;
-  if (!io_utils::load_two_genes(arg_vector[1], gene_one, gene_two, gene_one_name, gene_two_name)) {
+  if (!io_utils::load_two_genes(arg_vector[2], gene_one, gene_two, gene_one_name, gene_two_name)) {
     throw std::runtime_error("error, not able to load genes from file");
   }
-  // TODO: load parameters from .config file
-  int64_t result1 = alignment::execute_global_alignment(gene_one, gene_two, 1, -2, -5, -2);
-  int32_t result2 = alignment::execute_modified_global_alignment(gene_one, gene_two, 1, -2, -5, -2);
+  int64_t match_score;
+  int64_t mismatch_score;
+  int64_t opening_gap_score;
+  int64_t gap_extension_score;
+  if (!io_utils::load_alignment_params(arg_vector[1], match_score, mismatch_score, opening_gap_score, gap_extension_score)) {
+    throw std::runtime_error("error, not able to load alignment parameters from file");
+  }
+  int64_t result1 = alignment::execute_global_alignment(
+    gene_one,
+    gene_two,
+    match_score,
+    mismatch_score,
+    opening_gap_score,
+    gap_extension_score
+  );
+  int32_t result2 = alignment::execute_modified_global_alignment(
+    gene_one,
+    gene_two,
+    match_score,
+    mismatch_score,
+    opening_gap_score,
+    gap_extension_score
+  );
   std::cout << result1 << std::endl;
   std::cout << result2 << std::endl;
 }