checkpoint

Author: SamStan4

bin/app

@@ -24,9 +24,9 @@ $(OBJDIR)/%.o: $(SRCDIR)/%.cpp
 clean:
 	rm -rf $(OBJDIR)/* $(BINDIR)/*
 
-run: $(TARGET)
+run-sample: $(TARGET)
 	@if [ -f $(TARGET) ]; then \
-		./$(TARGET) inputs/alphabets/English_alphabet.txt inputs/genes/banana.txt; \
+		./$(TARGET) input/base-sample.fasta; \
 	else \
 		echo "Error: Executable $(TARGET) not found. Please build it first."; \
 		exit 1; \

makefile

@@ -1,5 +1,28 @@
 #include "./alignment.hpp"
 
 namespace alignment {
+  int64_t execute_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);
+    std::vector<dp_cell> prev_dp_row(col_size);
 
+    for (size_t i = 1; i < col_size; ++i) {
+      prev_dp_row[i].set_top_row(i);
+    }
+
+    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[col_idx-1], string_two[row_idx-1]);
+      }
+      std::swap(prev_dp_row, cur_dp_row);
+    }
+
+    return prev_dp_row.back().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");
+  }
 }

obj/alignment/alignment.o

@@ -1,3 +1,15 @@
+#ifndef __ALIGNMENT_HPP__
+#define __ALIGNMENT_HPP__
+
+#include <string>
+#include <vector>
+#include <cstdint>
+#include <stdexcept>
+#include "./dp_cell.hpp"
+
 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&);
+}
+
+#endif

obj/alignment/de_cell.o

@@ -29,6 +29,7 @@ class dp_cell {
 public:
   dp_cell();
   ~dp_cell();
+  
   int64_t get_max_score(void) const;
   int32_t get_max_score_matches(void) const;
   void score_cell(const dp_cell&, const dp_cell&, const dp_cell&, const char, const char);

obj/io/io_utils.o

@@ -13,5 +13,14 @@ program_wrapper& program_wrapper::get_instance(void) {
 }
 
 void program_wrapper::run_program(const int arg_count, const char* const* arg_vector) {
-  std::cout << "here" << std::endl;
+  if (arg_count != 2) {
+    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)) {
+    throw std::runtime_error("error, not able to load genes from file");
+  }
 }