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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Soft...
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// Guy Shechter // June 2004 // // Uncomment one of these includes depending on your architecture. // Your installation location may vary. // // // For Linux use this line: // //#include "/usr/local/matlab/extern/include/mex.h" // // // For Windows systems use this line: // #include "mex.h" // // // For Mac Os X syste...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_PLAT_MINGW_H #define BOOST_PREDEF_PLAT_MINGW_H #include <boost/predef/version_number.h> #include <boost/predef/m...
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/** * Copyright (c) 2016-present, Facebook, Inc. * All rights reserved. * * This source code is licensed under the MIT license found in the * LICENSE file in the root directory of this source tree. */ #pragma once #include <istream> #include <memory> #include <random> #include <thread> #include <vector> #inclu...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_SUPERH_H #define BOOST_PREDEF_ARCHITECTURE_SUPERH_H #include <boost/predef/version_number.h> #inclu...
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// Copyright 2008, Google Inc. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions ...
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/** * Copyright (c) 2016-present, Facebook, Inc. * All rights reserved. * * This source code is licensed under the MIT license found in the * LICENSE file in the root directory of this source tree. */ #pragma once #include <assert.h> #include <cstdint> #include <istream> #include <ostream> #include <stdexcept> ...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Soft...
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/* Copyright (c) 2012-2013 Genome Research Ltd. Author: James Bonfield <jkb@sanger.ac.uk> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this l...
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/* Copyright (c) 2012-2013 Genome Research Ltd. Author: James Bonfield <jkb@sanger.ac.uk> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this l...
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#ifndef KSTDINT_H #define KSTDINT_H #include <limits.h> /* Basic assumptions: 1) "char" is 8-bit; 2) there is a 8-bit, 16-bit, 32-bit * and 64-bit integer type, respectively; 3) "short" is no less than "char", * "int" is no less than "short", "long" is no less than "int" and "long long" * is no less than "long"; 4...
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/* Copyright (c) 2010 Genome Research Ltd. Author: Andrew Whitwham <aw7@sanger.ac.uk> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list ...
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// Copyright 2006, Google Inc. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions ...
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#ifndef LSL_TYPES #define LSL_TYPES /** * @class lsl_streaminfo * Handle to a stream info object. * * Stores the declaration of a data stream. * Represents the following information: * * - stream data format (number of channels, channel format) * - core information (stream name, content type, sampling rate) ...
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// Copyright 2008, Google Inc. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions ...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_SUNPRO_H #define BOOST_PREDEF_COMPILER_SUNPRO_H #include <boost/predef/version_number.h> #include <boos...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_SUNPRO_H #define BOOST_PREDEF_COMPILER_SUNPRO_H #include <boost/predef/version_number.h> #include <boos...
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/* Copyright Rene Ferdinand Rivera Morell 2020-2021 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_OTHER_WORD_SIZE_H #define BOOST_PREDEF_OTHER_WORD_SIZE_H #include <boost/predef/architecture.h>...
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#ifndef CODE_Transcriptome #define CODE_Transcriptome #include <set> #include "IncludeDefine.h" #include "Parameters.h" #include "Transcript.h" #include "Quantifications.h" #include "AlignVsTranscript.h" #include "ReadAnnotations.h" class Transcriptome { public: string trInfoDir; vector <string> trID, geID,...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2011 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Softwar...
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#ifndef COMMON_H #define COMMON_H extern "C" { #include "api_types.hpp" // api_types.h defines LSL_TYPES so it needs to be included before the next header #include "../include/lsl/common.h" } #include <boost/version.hpp> #include <stdexcept> #include <string> #include <vector> #ifdef _WIN32 #define LIBLSL_CPP_API __d...
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/** Copyright (C) powturbo 2013-2018 GPL v2 License 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. ...
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#ifdef __cplusplus // If this is a C++ compiler, use C linkage extern "C" { #endif // this definition needs to be here bc the robot and the modules need it and the kilogrid imports // this h file. We take all values so we do not overwrite by accident typedef enum { // Kilobot to Kilobot range MSG_T_NORMAL_IR ...
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#ifndef __KHASH_UTILS_H__ #define __KHASH_UTILS_H__ #include <htslib/khash.h> KHASH_MAP_INIT_STR(str2int, int) /* * Wrappers for khash dictionaries used by mpileup. */ static inline void *khash_str2int_init(void) { return kh_init(str2int); } /* * Destroy the hash structure, but not the keys */ static i...
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/* Copyright Rene Rivera 2008-2015 Copyright Franz Detro 2014 Copyright (c) Microsoft Corporation 2014 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_ARM_H #define BOOST_PREDEF_ARCHI...
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#ifndef zfstream_h #define zfstream_h #include <fstream.h> #include "zlib.h" class gzfilebuf : public streambuf { public: gzfilebuf( ); virtual ~gzfilebuf(); gzfilebuf *open( const char *name, int io_mode ); gzfilebuf *attach( int file_descriptor, int io_mode ); gzfilebuf *close(); int setcompression...
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/* * Most of the changes formerly needed here are handled through * the Makefiles and #ifdef's. */ #ifndef I_LF_H #define I_LF_H /* * DIRSEP: '/' for unix; '\\' for DOS */ #ifdef DOS #define DIRSEP '\\' #else #define DIRSEP '/' #endif /* * Some older math libraries have no lgamma() function, and gamma(arg)...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_MIPS_H #define BOOST_PREDEF_ARCHITECTURE_MIPS_H #include <boost/predef/version_number.h> #include <...
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// Copyright 2008 Google Inc. // All Rights Reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions a...
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#pragma once #include <cstdlib> #include <new> #ifdef _MSC_VER // Ensure _HAS_EXCEPTIONS is defined #include <vcruntime.h> #include <malloc.h> #endif #if !((defined(_MSC_VER) && !defined(__clang__)) ? (_HAS_EXCEPTIONS) : (__EXCEPTIONS)) #include <cstdlib> #endif // Aligned simple vector. namespace intgemm { templat...
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// -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*- /****************************************************************************** * * file: ArgTraits.h * * Copyright (c) 2007, Daniel Aarno, Michael E. Smoot . * All rights reverved. * * See the file COPYING in the top directory of this distribution for...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr> // Copyright (C) 2011 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser Gen...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr> // Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms o...
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/** * Copyright (c) 2016-present, Facebook, Inc. * All rights reserved. * * This source code is licensed under the MIT license found in the * LICENSE file in the root directory of this source tree. */ #pragma once #include <unordered_map> #include <vector> #include "dictionary.h" #include "real.h" #include "ut...
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/* Copyright Rene Rivera 2012-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_OS_BSD_NET_H #define BOOST_PREDEF_OS_BSD_NET_H #include <boost/predef/os/bsd.h> /*` [heading `BOOST_OS_BSD_NET`...
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#ifndef EIGEN_BENCH_UTIL_H #define EIGEN_BENCH_UTIL_H #include <Eigen/Core> #include "BenchTimer.h" using namespace std; using namespace Eigen; #include <boost/preprocessor/repetition/enum_params.hpp> #include <boost/preprocessor/repetition.hpp> #include <boost/preprocessor/seq.hpp> #include <boost/preprocessor/arr...
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/* Copyright Rene Rivera 2012-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_OS_BSD_NET_H #define BOOST_PREDEF_OS_BSD_NET_H #include <boost/predef/os/bsd.h> /* tag::reference[] = `BOOST_OS...
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#ifndef _MEDAKA_COMMON_H #define _MEDAKA_COMMON_H #include <stdint.h> #include "khash.h" #include "kvec.h" // bam tag used for datatypes static const char datatype_tag[] = "DT"; /** Simple integer min/max * @param a * @param b * * @returns the min/max of a and b * */ static inline int max ( int a, int b ) {...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_METROWERKS_H #define BOOST_PREDEF_COMPILER_METROWERKS_H #include <boost/predef/version_number.h> #inclu...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_METROWERKS_H #define BOOST_PREDEF_COMPILER_METROWERKS_H #include <boost/predef/version_number.h> #inclu...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_M68K_H #define BOOST_PREDEF_ARCHITECTURE_M68K_H #include <boost/predef/version_number.h> #include <...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free...
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#ifndef COMMON_H #define COMMON_H extern "C" { #include "api_types.hpp" // api_types.h defines LSL_TYPES so it needs to be included before the next header #include "../include/lsl/common.h" } #include <boost/version.hpp> #include <stdexcept> #include <string> #include <vector> #ifdef _WIN32 #define LIBLSL_CPP_API __d...
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#pragma once #ifndef NODEIMPL_H_62B23520_7C8E_11DE_8A39_0800200C9A66 #define NODEIMPL_H_62B23520_7C8E_11DE_8A39_0800200C9A66 #include "nodeutil.h" namespace YAML { // implementation of templated things template <typename T> inline const T Node::Read() const { T value; *this >> value; return value; } te...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free...
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#ifndef EIGEN2_GEOMETRY_MODULE_H #define EIGEN2_GEOMETRY_MODULE_H #include <limits> #ifndef M_PI #define M_PI 3.14159265358979323846 #endif #if EIGEN2_SUPPORT_STAGE < STAGE20_RESOLVE_API_CONFLICTS #include "RotationBase.h" #include "Rotation2D.h" #include "Quaternion.h" #include "AngleAxis.h" #include "Transform.h" ...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_M68K_H #define BOOST_PREDEF_ARCHITECTURE_M68K_H #include <boost/predef/version_number.h> #include <...
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/* Copyright Charly Chevalier 2015 Copyright Joel Falcou 2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_HARDWARE_SIMD_X86_AMD_H #define BOOST_PREDEF_HARDWARE_SIMD_X86_AMD_H #include <boost/...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Softwar...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free...
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr> // Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms o...
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/* Copyright Rene Rivera 2008-2017 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_INTEL_H #define BOOST_PREDEF_COMPILER_INTEL_H #include <boost/predef/version_number.h> #include <boost/...
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/* Copyright Charly Chevalier 2015 Copyright Joel Falcou 2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_HARDWARE_SIMD_X86_AMD_H #define BOOST_PREDEF_HARDWARE_SIMD_X86_AMD_H #include <boost/...
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#ifndef SEND_BUFFER_H #define SEND_BUFFER_H #include "common.h" #include "forward.h" #include <condition_variable> #include <memory> #include <mutex> #include <vector> namespace lsl { /** * A thread-safe single-producer multiple-consumer queue where each consumer gets every pushed * sample. If the bounded capacity...
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_X86_32_H #define BOOST_PREDEF_ARCHITECTURE_X86_32_H #include <boost/predef/version_number.h> #inclu...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. Eigen itself is part of the KDE project. // // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public //...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr> // Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms o...
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C/C++
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#ifndef FILTER_RESULT_H #define FILTER_RESULT_H #include <iostream> #include <stdio.h> #include <stdlib.h> #include <string> #include <vector> #include "common.h" #include "options.h" #include <fstream> #include <map> struct classcomp { bool operator() (const string& lhs, const string& rhs) const { if (lh...
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C/C++
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/* Copyright Rene Rivera 2008-2017 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_INTEL_H #define BOOST_PREDEF_COMPILER_INTEL_H #include <boost/predef/version_number.h> #include <boost/...
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C/C++
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/* * sparsefa.h * peer * Sparse Factor analysis variant of VBFA * * Created by Oliver Stegle on 3/25/11. * Copyright 2011 __MyCompanyName__. All rights reserved. * */ #ifndef __SPARSEFA_H__ #define __SPARSEFA_H__ #include "vbfa.h" #include "bayesnet.h" #include "ossolog.h" namespace PEER { /*Sparse F...
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C/C++
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/* * Structures, typedefs etc used in Locfit */ typedef struct { double *wk, *coef, *xbar, *f; jacobian xtwx; int lwk, haspc; } paramcomp; #define haspc(pc) ((pc)->haspc) typedef struct { double *x[MXDIM]; double *y; double *w; double *b; double *c; double sca[MXDIM]; double xl[2*MXDIM]; int...
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C/C++
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/*** * Code from Percy "Dragontamer" Tiglao ***/ #ifndef AESDRAGONTAMER_H #define AESDRAGONTAMER_H #if defined( __AES__) && defined(__AVX__) #include <stddef.h> #include <stdint.h> #include <string.h> #include <immintrin.h> typedef struct { __m128i state; __m128i increment; } aesdragontamer_state; static inli...
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C/C++
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//============================================================================= // File : utilities.h // Created : mar jun 19 13:18:14 CEST 2001 // Author : Antoine YESSAYAN, Paul RASCLE, EDF // Project : SALOME // Copyright : EDF 2001 // $Header$ //==========================================================...
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C/C++
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/* Copyright Benjamin Worpitz 2018 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_NVCC_H #define BOOST_PREDEF_COMPILER_NVCC_H #include <boost/predef/version_number.h> #include <boost/pr...
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C/C++
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#include <Eigen/Array> #include <Eigen/Sparse> #include <bench/BenchTimer.h> using namespace std; using namespace Eigen; USING_PART_OF_NAMESPACE_EIGEN #ifndef SIZE #define SIZE 1024 #endif #ifndef DENSITY #define DENSITY 0.01 #endif #ifndef SCALAR #define SCALAR double #endif typedef SCALAR Scalar; typedef Matrix...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Gael Guennebaud <g.gael@free.fr> // Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser Gen...
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C/C++
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_ARCHITECTURE_X86_32_H #define BOOST_PREDEF_ARCHITECTURE_X86_32_H #include <boost/predef/version_number.h> #inclu...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2010 Jitse Niesen <jitse@maths.leeds.ac.uk> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software...
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C/C++
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/* Copyright Benjamin Worpitz 2018 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_COMPILER_NVCC_H #define BOOST_PREDEF_COMPILER_NVCC_H #include <boost/predef/version_number.h> #include <boost/pr...
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C/C++
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#ifndef CANCELLATION_H #define CANCELLATION_H #include <mutex> #include <set> #include <stdexcept> namespace lsl { /// Exception class that indicates that an operation was performed on an registry that is being shut /// down. class shutdown_error : public std::runtime_error { public: explicit shutdown_error(const st...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Softwar...
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C/C++
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#ifndef CODE_Transcript #define CODE_Transcript #include "IncludeDefine.h" #include "Parameters.h" #include "Variation.h" #include "Genome.h" #include <set> class Transcript { public: uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length vector <array<uint32,2>> cigar; //new w...
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C/C++
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/* Time will show if this module will be merged into others or perhaps removed completely. */ #ifndef VCF_UTILS_H #define VCF_UTILS_H #include "vcf.h" /** * bcf_trim_alleles() - remove ALT alleles unused in genotype fields * @header: for access to BCF_DT_ID dictionary * @line: VCF line obtain from...
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C/C++
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/* The MIT License Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation ...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr> // Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com> // // Eigen is free software; you can redistribute it and/or // modify it under the terms o...
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C/C++
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#ifndef CANCELLATION_H #define CANCELLATION_H #include <mutex> #include <set> #include <stdexcept> #include <string> namespace lsl { class cancellable_object; /// Exception class that indicates that an operation was performed on an registry that is being shut /// down. class shutdown_error : public std::runtime_erro...
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C/C++
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/* Copyright (c) 2011, Intel Corporation. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the ...
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C/C++
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/* inftree9.h -- header to use inftree9.c * Copyright (C) 1995-2008 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. Applicati...
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C/C++
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//--------------------------------------------------------- // Copyright 2015 Ontario Institute for Cancer Research // Written by Jared Simpson (jared.simpson@oicr.on.ca) //--------------------------------------------------------- // // nanopolish_variant -- tools for calling variants // #ifndef NANOPOLISH_VARIANT_H #d...
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C/C++
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/* Copyright Rene Rivera 2017 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_WORKAROUND_H #define BOOST_PREDEF_WORKAROUND_H /* tag::reference[] = `BOOST_PREDEF_WORKAROUND` [source] ---- BOOST_...
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C/C++
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/* MIT License Copyright (c) 2021 Shifu Chen <chen@haplox.com> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, m...
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C/C++
2,928
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/* inftrees.h -- header to use inftrees.c * Copyright (C) 1995-2005, 2010 Mark Adler * For conditions of distribution and use, see copyright notice in zlib.h */ /* WARNING: this file should *not* be used by applications. It is part of the implementation of the compression library and is subject to change. App...
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C/C++
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// heap.h /**************************************************************************/ /* This class implements a binary min heap data structure to support the */ /* fast marching algorithm. A min heap is a list which has the property */ /* that the smallest element is always the first element. */ /*...
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C/C++
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/* Copyright (c) 2005-2006, 2008-2009 Genome Research Ltd. Author: James Bonfield <jkb@sanger.ac.uk> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright noti...
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C/C++
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// Copyright 2005, Google Inc. // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions ...
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C/C++
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namespace internal { template <typename Scalar> void r1updt( Matrix< Scalar, Dynamic, Dynamic > &s, const Matrix< Scalar, Dynamic, 1> &u, std::vector<JacobiRotation<Scalar> > &v_givens, std::vector<JacobiRotation<Scalar> > &w_givens, Matrix< Scalar, Dynamic, 1> &v, Matri...
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C/C++
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#ifndef STATS_H #define STATS_H #include <stdio.h> #include <stdlib.h> #include <string> #include <vector> #include <map> #include "read.h" #include "options.h" using namespace std; class Stats{ public: // this @guessedCycles parameter should be calculated using the first several records Stats(Options* opt, ...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2011 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Soft...
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C/C++
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// gcc -I/mnt/seagate10/gsl/include -L/mnt/seagate10/gsl/lib -Wall -O2 -ffast-math -fopenmp -lgsl -lgslcblas -lm -o _cmmcost_omp _cmmcost_omp.c // time ./_cmmcost_omp // gcc on Abel: // gcc -I/cluster/software/VERSIONS/gsl-1.16/include -L/cluster/software/VERSIONS/gsl-1.16/lib -Wall -O2 -ffast-math -fopenmp -lgsl -lgsl...
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C/C++
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#ifndef UDP_SERVER_H #define UDP_SERVER_H #include "forward.h" #include "socket_utils.h" #include <asio/ip/udp.hpp> #include <cstdint> #include <exception> #include <memory> #include <string> using asio::ip::udp; using err_t = const asio::error_code &; namespace lsl { /// shared pointer to a socket using udp_socket_...
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C/C++
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_OS_BSD_H #define BOOST_PREDEF_OS_BSD_H /* Special case: OSX will define BSD predefs if the sys/param.h * header...
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C/C++
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//base_marcher.h #pragma once const unsigned int MaximumDimension = 12; const char Far = 0; const char Narrow = 1; const char Frozen = 2; const char Mask = 3; #include <limits> #include <memory> #include <vector> #define doubleEpsilon std::numeric_limits<double>::epsilon() #define maxDouble ...
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C/C++
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/* Copyright Rene Rivera 2008-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_OS_BSD_H #define BOOST_PREDEF_OS_BSD_H /* Special case: OSX will define BSD predefs if the sys/param.h * header...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Soft...
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C/C++
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#pragma once #ifndef SCANNER_H_62B23520_7C8E_11DE_8A39_0800200C9A66 #define SCANNER_H_62B23520_7C8E_11DE_8A39_0800200C9A66 #include <ios> #include <string> #include <queue> #include <stack> #include <set> #include <map> #include "stream.h" #include "token.h" namespace YAML { class Node; class RegEx; class Scann...
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C/C++
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#ifndef UDP_SERVER_H #define UDP_SERVER_H #include "forward.h" #include <boost/asio/ip/udp.hpp> #include <memory> using lslboost::asio::ip::udp; using lslboost::system::error_code; namespace asio = lslboost::asio; namespace lsl { /// shared pointer to a string using string_p = std::shared_ptr<std::string>; /// shar...
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C/C++
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// This file is part of Eigen, a lightweight C++ template library // for linear algebra. // // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr> // // Eigen is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free...
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C/C++
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#pragma once #include "ConsoleAppender.h" namespace plog { template<class Formatter> class ColorConsoleAppender : public ConsoleAppender<Formatter> { public: #ifdef _WIN32 ColorConsoleAppender() : m_isatty(!!_isatty(_fileno(stdout))), m_stdoutHandle(), m_originalAttr() { ...
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C/C++
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namespace internal { template <typename Scalar> void dogleg( const Matrix< Scalar, Dynamic, Dynamic > &qrfac, const Matrix< Scalar, Dynamic, 1 > &diag, const Matrix< Scalar, Dynamic, 1 > &qtb, Scalar delta, Matrix< Scalar, Dynamic, 1 > &x) { typedef DenseIndex Index; ...
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C/C++
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/* Copyright Rene Rivera 2011-2015 Distributed under the Boost Software License, Version 1.0. (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */ #ifndef BOOST_PREDEF_LANGUAGE_STDCPP_H #define BOOST_PREDEF_LANGUAGE_STDCPP_H #include <boost/predef/version_number.h> #include <boos...