Commit ba7195b6 authored by edrezen's avatar edrezen
Browse files

Modify headers of *.hpp and *.cpp => Affero GPL

parent 91a62421
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Copyright (c) 2013 *
* *
* GATB is free software; you can redistribute it and/or modify it under *
* the CECILL version 2 License, that is compatible with the GNU General *
* Public License *
* *
* 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 *
* CECILL version 2 License for more details. *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/**\page design_page Design of the library
*
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Copyright (c) 2013 *
* *
* GATB is free software; you can redistribute it and/or modify it under *
* the CECILL version 2 License, that is compatible with the GNU General *
* Public License *
* *
* 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 *
* CECILL version 2 License for more details. *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/**\page download_page Download
*
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Copyright (c) 2013 *
* *
* GATB is free software; you can redistribute it and/or modify it under *
* the CECILL version 2 License, that is compatible with the GNU General *
* Public License *
* *
* 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 *
* CECILL version 2 License for more details. *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \mainpage GATB Core Documentation
*
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Copyright (c) 2013 *
* *
* GATB is free software; you can redistribute it and/or modify it under *
* the CECILL version 2 License, that is compatible with the GNU General *
* Public License *
* *
* 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 *
* CECILL version 2 License for more details. *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/**\page snippets_page How to use the library ?
*
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Copyright (c) 2013 *
* *
* GATB is free software; you can redistribute it and/or modify it under *
* the CECILL version 2 License, that is compatible with the GNU General *
* Public License *
* *
* 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 *
* CECILL version 2 License for more details. *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/**\page tests_page Unit tests for the library
*
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file IAlphabet.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file IBank.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file Sequence.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file AbstractBank.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file Alphabet.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
#include <gatb/bank/impl/BankBinary.hpp>
#include <gatb/tools/misc/api/StringsRepository.hpp>
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file BankBinary.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
#include <gatb/bank/impl/BankConverterAlgorithm.hpp>
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file BankConverterAlgorithm.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
#include <gatb/bank/impl/BankFasta.hpp>
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file BankFasta.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
#include <gatb/system/impl/System.hpp>
#include <gatb/bank/impl/BankHelpers.hpp>
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file BankHelpers.hpp
* \date 01/03/2013
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
#include <gatb/bank/impl/BankRandom.hpp>
#include <gatb/tools/misc/api/StringsRepository.hpp>
......
/*****************************************************************************
* GATB : Genome Assembly Tool Box *
* Authors: [R.Chikhi, G.Rizk, E.Drezen] *
* Based on Minia, Authors: [R.Chikhi, G.Rizk], CeCILL license *
* Copyright (c) INRIA, CeCILL license, 2013 *
*****************************************************************************/
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file BankRandom.hpp
* \date 01/03/2013
......
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