added dp cell logic

Author: SamStan4

.vscode/settings.json

@@ -0,0 +1,60 @@
+{
+  "files.associations": {
+    "algorithm": "cpp",
+    "atomic": "cpp",
+    "bit": "cpp",
+    "cctype": "cpp",
+    "charconv": "cpp",
+    "clocale": "cpp",
+    "cmath": "cpp",
+    "compare": "cpp",
+    "concepts": "cpp",
+    "cstddef": "cpp",
+    "cstdint": "cpp",
+    "cstdio": "cpp",
+    "cstdlib": "cpp",
+    "cstring": "cpp",
+    "ctime": "cpp",
+    "cwchar": "cpp",
+    "exception": "cpp",
+    "format": "cpp",
+    "fstream": "cpp",
+    "initializer_list": "cpp",
+    "ios": "cpp",
+    "iosfwd": "cpp",
+    "iostream": "cpp",
+    "istream": "cpp",
+    "iterator": "cpp",
+    "limits": "cpp",
+    "list": "cpp",
+    "locale": "cpp",
+    "memory": "cpp",
+    "new": "cpp",
+    "optional": "cpp",
+    "ostream": "cpp",
+    "stdexcept": "cpp",
+    "streambuf": "cpp",
+    "string": "cpp",
+    "system_error": "cpp",
+    "tuple": "cpp",
+    "type_traits": "cpp",
+    "typeinfo": "cpp",
+    "unordered_set": "cpp",
+    "utility": "cpp",
+    "vector": "cpp",
+    "xfacet": "cpp",
+    "xhash": "cpp",
+    "xiosbase": "cpp",
+    "xlocale": "cpp",
+    "xlocbuf": "cpp",
+    "xlocinfo": "cpp",
+    "xlocmes": "cpp",
+    "xlocmon": "cpp",
+    "xlocnum": "cpp",
+    "xloctime": "cpp",
+    "xmemory": "cpp",
+    "xstring": "cpp",
+    "xtr1common": "cpp",
+    "xutility": "cpp"
+  }
+}

src/alignment/alignment.cpp

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+#include "./alignment.hpp"
+
+namespace alignment {
+
+}

src/alignment/alignment.hpp

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+namespace alignment {
+  
+}

src/alignment/de_cell.cpp

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+#include "./dp_cell.hpp"
+
+// MARK: public methods
+
+dp_cell::dp_cell() :
+  m_s_score(0),
+  m_d_score(0),
+  m_i_score(0),
+  m_s_matches(0),
+  m_d_matches(0),
+  m_i_matches(0) {
+}
+
+int64_t dp_cell::get_max_score(void) {
+  return std::max(this->m_s_score, std::max(this->m_d_score, this->m_i_score));
+}
+
+int32_t dp_cell::get_max_score_matches(void) {
+  const int64_t max_score = std::max(this->m_s_score, std::max(this->m_d_score, this->m_i_score));
+  if (max_score == this->m_s_score) {
+    return this->m_s_matches;
+  } else if (max_score == this->m_d_score) {
+    return this->m_d_matches;
+  }
+  return this->m_i_matches;
+}
+
+void dp_cell::score_cell(const dp_cell& cell_s, const dp_cell& cell_d, const dp_cell& cell_i) {
+  throw std::runtime_error("not implemented");
+}
+
+void dp_cell::reset_cell(void) {
+  this->m_s_score = 0;
+  this->m_d_score = 0;
+  this->m_i_score = 0;
+  this->m_s_matches = 0;
+  this->m_d_matches = 0;
+  this->m_i_matches = 0;
+}
+
+// MARK: getters
+
+int64_t dp_cell::get_s_score(void) const {
+  return this->m_s_score;
+}
+
+int64_t dp_cell::get_d_score(void) const {
+  return this->m_d_score;
+}
+
+int64_t dp_cell::get_i_score(void) const {
+  return this->m_i_score;
+}
+
+int32_t dp_cell::get_s_matches(void) const {
+  return this->m_s_matches;
+}
+
+int32_t dp_cell::get_d_matches(void) const {
+  return this->m_d_matches;
+}
+
+int32_t dp_cell::get_i_matches(void) const {
+  return this->m_i_matches;
+}
+
+// MARK: setters
+
+void dp_cell::set_s_score(int64_t _s_score) {
+  this->m_s_score = _s_score;
+}
+
+void dp_cell::set_d_score(int64_t _d_score) {
+  this->m_d_score = _d_score;
+}
+
+void dp_cell::set_i_score(int64_t _i_score) {
+  this->m_i_score = _i_score;
+}
+
+void dp_cell::set_s_matches(int32_t _s_matches) {
+  this->m_s_matches = _s_matches;
+}
+
+void dp_cell::set_d_matches(int32_t _d_matches) {
+  this->m_d_matches = _d_matches;
+}
+
+void dp_cell::set_i_matches(int32_t _i_matches) {
+  this->m_i_matches = _i_matches;
+}

src/alignment/dp_cell.hpp

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+#ifndef __DP_CELL_HPP__
+#define __DP_CELL_HPP__
+
+#include <cstdint>
+#include <algorithm>
+#include <stdexcept>
+
+class dp_cell {
+private:
+  int64_t m_s_score;
+  int64_t m_d_score;
+  int64_t m_i_score;
+
+  int32_t m_s_matches;
+  int32_t m_d_matches;
+  int32_t m_i_matches;
+public:
+  dp_cell();
+  int64_t get_max_score(void);
+  int32_t get_max_score_matches(void);
+  void score_cell(const dp_cell&, const dp_cell&, const dp_cell&);
+  void reset_cell(void);
+
+  int64_t get_s_score(void) const;
+  int64_t get_d_score(void) const;
+  int64_t get_i_score(void) const;
+
+  int32_t get_s_matches(void) const;
+  int32_t get_d_matches(void) const;
+  int32_t get_i_matches(void) const;
+
+  void set_s_score(int64_t _s_score);
+  void set_d_score(int64_t _d_score);
+  void set_i_score(int64_t _i_score);
+
+  void set_s_matches(int32_t _s_matches);
+  void set_d_matches(int32_t _d_matches);
+  void set_i_matches(int32_t _i_matches);
+};
+
+#endif