commit 4e3edc050e131f044e5947fa78fff2bfbd3c2925
parent 404bb0bd592a4a21cbf0dafe32785cb847c25a68
Author: luxdosugi <luxdotsugi@gmail.com>
Date: Sun, 8 Jul 2018 11:36:35 +1000
Added the Codons
Diffstat:
| A | Codon.cpp | | | 80 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | Codon.h | | | 38 | ++++++++++++++++++++++++++++++++++++++ |
2 files changed, 118 insertions(+), 0 deletions(-)
diff --git a/Codon.cpp b/Codon.cpp
@@ -0,0 +1,80 @@
+/**
+ * Codon.cpp - DNA_sim
+ * Author: Cody Lewis
+ * Date: 2018-07-07
+ * Last Modified: 2018-07-07
+ * Description:
+ * A Class for A codon (a collection of three mRNA bases)
+ */
+#include <cstdlib>
+#include "Codon.h"
+namespace DNA_sim {
+ // Constructors
+ Codon::Codon() {
+ bases.resize(3);
+ }
+ Codon::Codon(std::string input) {
+ Codon();
+ set_bases(input);
+ }
+ // Destructor
+ Codon::~Codon() {}
+ // Queries
+ std::string Codon::get_bases() const {
+ std::string base_string;
+ for(std::size_t i = 0; i < bases.size(); ++i) {
+ switch (bases[i]) {
+ case Base::adenine:
+ base_string += 'A';
+ break;
+ case Base::uracil:
+ base_string += 'U';
+ break;
+ case Base::cytosine:
+ base_string += 'C';
+ break;
+ case Base::guanine:
+ base_string += 'G';
+ break;
+ default:
+ base_string += '_';
+ }
+ }
+ return base_string;
+ }
+ // Mutators
+ bool Codon::set_bases(std::string input) {
+ int j = 0;
+ for(std::string::iterator it = input.begin(); it != input.end(); ++it) {
+ switch (*it) {
+ case 'A':
+ bases[j] = Base::adenine;
+ break;
+ case 'U':
+ bases[j] = Base::uracil;
+ break;
+ case 'C':
+ bases[j] = Base::cytosine;
+ break;
+ case 'G':
+ bases[j] = Base::guanine;
+ break;
+ default:
+ bases[j] = Base::adenine;
+ }
+ j++;
+ }
+ return true;
+ }
+ // Operator overloads
+ std::istream& operator>>(std::istream& in, Codon& cod) {
+ std::string input;
+ in >> input;
+ cod.set_bases(input);
+ return in;
+ }
+ std::ostream& operator<<(std::ostream& out, const Codon& cod) {
+ out << cod.get_bases();
+ return out;
+ }
+}
diff --git a/Codon.h b/Codon.h
@@ -0,0 +1,38 @@
+/**
+ * Codon.h - DNA_sim
+ * Author: Cody Lewis
+ * Date: 2018-07-07
+ * Last Modified: 2018-07-07
+ * Description:
+ * A Class for A codon (a collection of three mRNA bases)
+ */
+#ifndef CODON_h
+#define CODON_h
+#include <string>
+#include <vector>
+#include <iostream>
+namespace DNA_sim {
+ class Codon {
+ private:
+ /* enum Base
+ * The invidual bases of mRNA
+ */
+ enum Base { adenine, uracil, cytosine, guanine };
+ std::vector<Base> bases; // 3 bases per codon
+ public:
+ Codon(); // Default constructor
+ Codon(std::string input); // Input constructor
+ ~Codon(); // Destructor
+
+ // Queries
+ std::string get_bases() const;
+
+ // Mutators
+ bool set_bases(std::string input);
+ // TODO: Add crossover
+ };
+ // Operator Overloads
+ std::istream& operator>>(std::istream& in, Codon& cod); // input
+ std::ostream& operator<<(std::ostream& out, const Codon& cod); // output
+}
+#endif /* ifndef CODON_h */
