Create the Recombination mutation (to save in the Tree)

src/libaevol/CMakeLists.txt

@@ -94,6 +94,8 @@ set(libaevol_sources
   mutation/SmallInsertion.h
   mutation/Translocation.cpp
   mutation/Translocation.h
+  mutation/Recombination.h
+  mutation/Recombination.cpp
 #  mutation/GeneMutation.cpp
 #  mutation/GeneMutation.h
   legacy/phenotype/fuzzy/Fuzzy.cpp

src/libaevol/mutation/Recombination.cpp

+// ****************************************************************************
+//
+//          Aevol - An in silico experimental evolution platform
+//
+// ****************************************************************************
+//
+// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
+// Web: http://www.aevol.fr/
+// E-mail: See <http://www.aevol.fr/contact/>
+// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ****************************************************************************
+
+// ============================================================================
+//                                   Includes
+// ============================================================================
+#include "Recombination.h"
+
+#include <sstream>
+
+namespace aevol {
+
+// ============================================================================
+//                       Definition of static attributes
+// ============================================================================
+
+// ============================================================================
+//                                Constructors
+// ============================================================================
+
+// ============================================================================
+//                                 Destructor
+// ============================================================================
+
+// ============================================================================
+//                                   Methods
+// ============================================================================
+void Recombination::save(gzFile backup_file) const {
+  int8_t tmp_mut_type = RECOMB;
+  gzwrite(backup_file, &tmp_mut_type, sizeof(tmp_mut_type));
+  gzwrite(backup_file, &posA_, sizeof(posA_));
+  gzwrite(backup_file, &posB_, sizeof(posB_));
+  gzwrite(backup_file, &align_score_, sizeof(align_score_));
+}
+
+void Recombination::load(gzFile backup_file) {
+  gzread(backup_file, &posA_, sizeof(posA_));
+  gzread(backup_file, &posB_, sizeof(posB_));
+  gzread(backup_file, &align_score_, sizeof(align_score_));
+}
+
+std::string Recombination::generic_description_string() const {
+  std::ostringstream stream;
+  stream << mut_type() << ' '
+         << posA() << ' '
+         << posB() << ' '
+         << -1 << ' '
+         << -1 << ' ' << -1 << ' '
+         << align_score() << ' '
+         << -1 << ' '
+         << -1 << ' '
+         << -1;
+  return stream.str();
+}
+
+// ============================================================================
+//                            Non inline accessors
+// ============================================================================
+
+} // namespace aevol

src/libaevol/mutation/Recombination.h

+// ****************************************************************************
+//
+//          Aevol - An in silico experimental evolution platform
+//
+// ****************************************************************************
+//
+// Copyright: See the AUTHORS file provided with the package or <www.aevol.fr>
+// Web: http://www.aevol.fr/
+// E-mail: See <http://www.aevol.fr/contact/>
+// Original Authors : Guillaume Beslon, Carole Knibbe, David Parsons
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+// ****************************************************************************
+
+#ifndef AEVOL_RECOMBINATION_H_
+#define AEVOL_RECOMBINATION_H_
+
+// ============================================================================
+//                                   Includes
+// ============================================================================
+
+#include "sys/types.h"
+#include "Mutation.h"
+
+namespace aevol {
+
+/**
+ *
+ */
+class Recombination : public Mutation {
+ public :
+  // ==========================================================================
+  //                               Constructors
+  // ==========================================================================
+  Recombination() = default; //< Default ctor
+  Recombination(const Recombination&) = default; //< Copy ctor
+  // The move constructor is implicitly deleted.
+  Recombination(int32_t posA, int32_t posB, int16_t align_score = -1) :
+               posA_{posA},  posB_{posB}, align_score_{align_score} {}
+
+  virtual Mutation* Clone() const override { return new Recombination(*this); };
+
+  // ==========================================================================
+  //                                Destructor
+  // ==========================================================================
+  virtual ~Recombination() noexcept = default; //< Destructor
+
+  // ==========================================================================
+  //                                Operators
+  // ==========================================================================
+  // The copy and move operators are implicitly deleted.
+
+  // ==========================================================================
+  //                              Public Methods
+  // ==========================================================================
+  virtual void save(gzFile backup_file) const override;
+  virtual void load(gzFile backup_file) override;
+  std::string generic_description_string() const override;
+
+  // ==========================================================================
+  //                                 Getters
+  // ==========================================================================
+  virtual MutationType mut_type() const override { return RECOMB; };
+  int32_t posA() const { return posA_; }
+  int32_t posB() const { return posB_; }
+  int16_t align_score() const { return align_score_; }
+
+  // ==========================================================================
+  //                                 Setters
+  // ==========================================================================
+
+ protected :
+  // ==========================================================================
+  //                            Protected Methods
+  // ==========================================================================
+
+  // ==========================================================================
+  //                               Attributes
+  // ==========================================================================
+  int32_t posA_, posB_;
+  int16_t align_score_ = -1;
+};
+
+} // namespace aevol
+#endif