Changeset 4346
- Timestamp:
- Apr 24, 2023, 5:39:47 AM (5 months ago)
- Location:
- trunk/yat
- Files:
-
- 32 edited
-
omic/DnaComplementer.cc (modified) (1 diff)
-
omic/DnaComplementer.h (modified) (1 diff)
-
omic/Fasta.cc (modified) (1 diff)
-
omic/Fasta.h (modified) (1 diff)
-
omic/config_bam.h (modified) (1 diff)
-
utility/BFGS.cc (modified) (1 diff)
-
utility/BFGS.h (modified) (1 diff)
-
utility/BFGS2.cc (modified) (1 diff)
-
utility/BFGS2.h (modified) (1 diff)
-
utility/BasicQueue.h (modified) (1 diff)
-
utility/Bisection.cc (modified) (1 diff)
-
utility/Brent.cc (modified) (1 diff)
-
utility/BrentMinimizer.cc (modified) (1 diff)
-
utility/FalsePosition.cc (modified) (1 diff)
-
utility/FletcherReevesConjugate.cc (modified) (1 diff)
-
utility/FletcherReevesConjugate.h (modified) (1 diff)
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utility/GoldenSection.cc (modified) (1 diff)
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utility/MultiMinimizerDerivative.cc (modified) (1 diff)
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utility/MultiMinimizerDerivative.h (modified) (1 diff)
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utility/Newton.cc (modified) (1 diff)
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utility/PolakRibiereConjugate.cc (modified) (1 diff)
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utility/PolakRibiereConjugate.h (modified) (1 diff)
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utility/PriorityQueue.h (modified) (1 diff)
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utility/QuadGolden.cc (modified) (1 diff)
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utility/Queue.h (modified) (1 diff)
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utility/Secant.cc (modified) (1 diff)
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utility/SteepestDescent.cc (modified) (1 diff)
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utility/SteepestDescent.h (modified) (1 diff)
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utility/Steffenson.cc (modified) (1 diff)
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utility/mNeedlemanWunsch.h (modified) (1 diff)
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utility/mSemiLocalAligner.h (modified) (1 diff)
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utility/mSmithWaterman.h (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
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trunk/yat/omic/DnaComplementer.cc
r4089 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2016, 2018, 2021 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with yat. If not, see <http://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2016, 2018, 2021, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/omic/DnaComplementer.h
r3792 r4346 2 2 #define _theplu_yat_omic_dna_complementer 3 3 4 // $Id$ 5 // 6 // Copyright (C) 2016, 2017, 2018 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 4 /* 5 Copyright (C) 2016, 2017, 2018, 2023 Peter Johansson 6 7 This file is part of the yat library, https://dev.thep.lu.se/yat 8 9 The yat library is free software; you can redistribute it and/or 10 modify it under the terms of the GNU General Public License as 11 published by the Free Software Foundation; either version 3 of the 12 License, or (at your option) any later version. 13 14 The yat library is distributed in the hope that it will be useful, 15 but WITHOUT ANY WARRANTY; without even the implied warranty of 16 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 17 General Public License for more details. 18 19 You should have received a copy of the GNU General Public License 20 along with yat. If not, see <https://www.gnu.org/licenses/>. 21 */ 20 22 21 23 namespace theplu { -
trunk/yat/omic/Fasta.cc
r4207 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2016, 2018, 2020, 2021, 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with yat. If not, see <http://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2016, 2018, 2020, 2021, 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/omic/Fasta.h
r4019 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2016, 2017, 2018, 2020 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2016, 2017, 2018, 2020, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include <htslib/faidx.h> -
trunk/yat/omic/config_bam.h
r4207 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2012, 2013, 2014, 2015, 2016, 2018, 2020, 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2012, 2013, 2014, 2015, 2016, 2018, 2020, 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 /* -
trunk/yat/utility/BFGS.cc
r4175 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/BFGS.h
r4175 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "MultiMinimizerDerivative.h" -
trunk/yat/utility/BFGS2.cc
r4175 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/BFGS2.h
r4175 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "MultiMinimizerDerivative.h" -
trunk/yat/utility/BasicQueue.h
r4043 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2017, 2018, 2020, 2021 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2017, 2018, 2020, 2021, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "config_public.h" -
trunk/yat/utility/Bisection.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/Brent.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/BrentMinimizer.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/FalsePosition.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/FletcherReevesConjugate.cc
r4175 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/FletcherReevesConjugate.h
r4175 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "MultiMinimizerDerivative.h" -
trunk/yat/utility/GoldenSection.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/MultiMinimizerDerivative.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/MultiMinimizerDerivative.h
r4338 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "multivariable/df.h" -
trunk/yat/utility/Newton.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/PolakRibiereConjugate.cc
r4175 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/PolakRibiereConjugate.h
r4175 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "MultiMinimizerDerivative.h" -
trunk/yat/utility/PriorityQueue.h
r3999 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2015, 2016, 2017, 2018, 2019, 2020 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2015, 2016, 2017, 2018, 2019, 2020, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "BasicQueue.h" -
trunk/yat/utility/QuadGolden.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/Queue.h
r3999 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2013, 2014, 2016, 2017, 2018, 2020 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with yat. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2013, 2014, 2016, 2017, 2018, 2020, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "BasicQueue.h" -
trunk/yat/utility/Secant.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/SteepestDescent.cc
r4175 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/SteepestDescent.h
r4175 r4346 3 3 4 4 // $Id$ 5 // 6 // Copyright (C) 2022 Peter Johansson 7 // 8 // This program is free software; you can redistribute it and/or modify 9 // it under the terms of the GNU General Public License as published by 10 // the Free Software Foundation; either version 3 of the License, or 11 // (at your option) any later version. 12 // 13 // This program is distributed in the hope that it will be useful, but 14 // WITHOUT ANY WARRANTY; without even the implied warranty of 15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 // General Public License for more details. 17 // 18 // You should have received a copy of the GNU General Public License 19 // along with this program. If not, see <https://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2022, 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 20 24 21 25 #include "MultiMinimizerDerivative.h" -
trunk/yat/utility/Steffenson.cc
r4252 r4346 1 1 // $Id$ 2 // 3 // Copyright (C) 2022 Peter Johansson 4 // 5 // This program is free software; you can redistribute it and/or modify 6 // it under the terms of the GNU General Public License as published by 7 // the Free Software Foundation; either version 3 of the License, or 8 // (at your option) any later version. 9 // 10 // This program is distributed in the hope that it will be useful, but 11 // WITHOUT ANY WARRANTY; without even the implied warranty of 12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 // General Public License for more details. 14 // 15 // You should have received a copy of the GNU General Public License 16 // along with this program. If not, see <https://www.gnu.org/licenses/>. 2 3 /* 4 Copyright (C) 2022, 2023 Peter Johansson 5 6 This file is part of the yat library, https://dev.thep.lu.se/yat 7 8 The yat library is free software; you can redistribute it and/or 9 modify it under the terms of the GNU General Public License as 10 published by the Free Software Foundation; either version 3 of the 11 License, or (at your option) any later version. 12 13 The yat library is distributed in the hope that it will be useful, 14 but WITHOUT ANY WARRANTY; without even the implied warranty of 15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 16 General Public License for more details. 17 18 You should have received a copy of the GNU General Public License 19 along with yat. If not, see <https://www.gnu.org/licenses/>. 20 */ 17 21 18 22 #include <config.h> -
trunk/yat/utility/mNeedlemanWunsch.h
r4344 r4346 2 2 #define _theplu_yat_utility_mneedleman_wunsch_ 3 3 // $Id$ 4 // 5 // Copyright (C) 2023 Peter Johansson 6 // 7 // This program is free software; you can redistribute it and/or modify 8 // it under the terms of the GNU General Public License as published by 9 // the Free Software Foundation; either version 3 of the License, or 10 // (at your option) any later version. 11 // 12 // This program is distributed in the hope that it will be useful, but 13 // WITHOUT ANY WARRANTY; without even the implied warranty of 14 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 15 // General Public License for more details. 16 // 17 // You should have received a copy of the GNU General Public License 18 // along with this program. If not, see <http://www.gnu.org/licenses/>. 4 5 /* 6 Copyright (C) 2023 Peter Johansson 7 8 This file is part of the yat library, https://dev.thep.lu.se/yat 9 10 The yat library is free software; you can redistribute it and/or 11 modify it under the terms of the GNU General Public License as 12 published by the Free Software Foundation; either version 3 of the 13 License, or (at your option) any later version. 14 15 The yat library is distributed in the hope that it will be useful, 16 but WITHOUT ANY WARRANTY; without even the implied warranty of 17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 18 General Public License for more details. 19 20 You should have received a copy of the GNU General Public License 21 along with yat. If not, see <https://www.gnu.org/licenses/>. 22 */ 19 23 20 24 #include "mAligner.h" -
trunk/yat/utility/mSemiLocalAligner.h
r4344 r4346 2 2 #define _theplu_yat_utility_msemi_local_aligner_ 3 3 // $Id$ 4 // 5 // Copyright (C) 2023 Peter Johansson 6 // 7 // This program is free software; you can redistribute it and/or modify 8 // it under the terms of the GNU General Public License as published by 9 // the Free Software Foundation; either version 3 of the License, or 10 // (at your option) any later version. 11 // 12 // This program is distributed in the hope that it will be useful, but 13 // WITHOUT ANY WARRANTY; without even the implied warranty of 14 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 15 // General Public License for more details. 16 // 17 // You should have received a copy of the GNU General Public License 18 // along with this program. If not, see <http://www.gnu.org/licenses/>. 4 5 /* 6 Copyright (C) 2023 Peter Johansson 7 8 This file is part of the yat library, https://dev.thep.lu.se/yat 9 10 The yat library is free software; you can redistribute it and/or 11 modify it under the terms of the GNU General Public License as 12 published by the Free Software Foundation; either version 3 of the 13 License, or (at your option) any later version. 14 15 The yat library is distributed in the hope that it will be useful, 16 but WITHOUT ANY WARRANTY; without even the implied warranty of 17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 18 General Public License for more details. 19 20 You should have received a copy of the GNU General Public License 21 along with yat. If not, see <https://www.gnu.org/licenses/>. 22 */ 19 23 20 24 #include "mAligner.h" -
trunk/yat/utility/mSmithWaterman.h
r4344 r4346 1 1 #ifndef _theplu_yat_utility_msmith_waterman 2 2 #define _theplu_yat_utility_msmith_waterman 3 3 4 // $Id$ 4 // 5 // Copyright (C) 2023 Peter Johansson 6 // 7 // This program is free software; you can redistribute it and/or modify 8 // it under the terms of the GNU General Public License as published by 9 // the Free Software Foundation; either version 3 of the License, or 10 // (at your option) any later version. 11 // 12 // This program is distributed in the hope that it will be useful, but 13 // WITHOUT ANY WARRANTY; without even the implied warranty of 14 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 15 // General Public License for more details. 16 // 17 // You should have received a copy of the GNU General Public License 18 // along with this program. If not, see <http://www.gnu.org/licenses/>. 5 6 /* 7 Copyright (C) 2023 Peter Johansson 8 9 This file is part of the yat library, https://dev.thep.lu.se/yat 10 11 The yat library is free software; you can redistribute it and/or 12 modify it under the terms of the GNU General Public License as 13 published by the Free Software Foundation; either version 3 of the 14 License, or (at your option) any later version. 15 16 The yat library is distributed in the hope that it will be useful, 17 but WITHOUT ANY WARRANTY; without even the implied warranty of 18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 19 General Public License for more details. 20 21 You should have received a copy of the GNU General Public License 22 along with yat. If not, see <https://www.gnu.org/licenses/>. 23 */ 19 24 20 25 #include "mAligner.h"
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