sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f220d9635203085eb519f8377fc639c4d8634ebae742992721107b8ac0b619ee | C/C++ | 3,173 | 83 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
6f8b12dc242e82e22cb6baefc2fa352fedde175016f9278688d76adaa62156b2 | C/C++ | 3,184 | 147 |
/******************************************************************************
*
* file: ValuesConstraint.h
*
* Copyright (c) 2005, Michael E. Smoot
* All rights reverved.
*
* See the file COPYING in the top directory of this distribution for
* more information.
*
* THE SOFTWARE IS PROVIDED _A... |
c30033d9d6be68329c216fa582c08bb5d546190d7855aa0e37c7d9562392e492 | C/C++ | 3,197 | 125 | #ifndef VISITOR_MACROS_H
#define VISITOR_MACROS_H
/** @file visitor_macros.h
* @author David F. Gleich
* @date 2008-09-29
* @copyright Stanford University, 2006-2008
* Macros to define various commands to work with visitors and MatlabBGL.
*/
/** History
* 2006-05-31: Initial version
* 2008-10-02: Modified to... |
8cf1bad78a37cb03721473abac5ee2ad716ca3935f20d7ed985e9945aec503da | C/C++ | 3,203 | 87 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
7666b6941ffd809fc91320519cfdaf05a60c22c443c59898e12c7243b8d9843d | C/C++ | 3,211 | 98 | /*
Copyright (c) 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 list o... |
7a7587b8521514aad6b52735a3ba100805b680f46f1d8dfeee81e59d5688e812 | C/C++ | 3,217 | 87 | namespace internal {
// TODO : once qrsolv2 is removed, use ColPivHouseholderQR or PermutationMatrix instead of ipvt
template <typename Scalar>
void qrsolv(
Matrix< Scalar, Dynamic, Dynamic > &s,
// TODO : use a PermutationMatrix once lmpar is no more:
const VectorXi &ipvt,
const Matrix... |
856fa7a2b3879e61ca9577ead35a6ca04843f8aa9588078c50a9543115a68ee1 | C/C++ | 3,228 | 123 | /*
* Headers for math utility functions.
*/
#ifndef I_MUT_H
#define I_MUT_H
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* use the following #define's for local versions. */
#ifdef DOS
#define erf mut_erf
#define erfc mut_erfc
#define lgamma mut_lgamma
#endif
#define daws(x) mut_... |
be3bcaf9d18188bf3e29eda47dba2d644f2af43b343bdab5651e2d6d85f15670 | C/C++ | 3,239 | 112 | #ifndef PARAMETERSINFO_DEF
#define PARAMETERSINFO_DEF
class ParameterInfoBase {
public:
string nameString; //string that identifies parameter
int inputLevel; //where the parameter was defined
int inputLevelAllowed; //at which input level parameter definition is allowed
virtual void inputValues(istrings... |
8d554cc9ec4a40329b39743e2a226ff5ff1ccfa0fc193ac8f002cf7bb49b60c0 | C/C++ | 3,244 | 114 | /**
* 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 <ostream>
#include <random>
#include <string>
#inclu... |
ce1eb47ea5d5f3e51ba400a1b2fc8276f464d07363112b9339562013d0a0d721 | C/C++ | 3,246 | 129 | /*
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_VERSIONS_H
#define BOOST_PREDEF_HARDWARE_SIMD_X86_VERSIONS_H
#inclu... |
24ae61be831accbec19b46a87e227821b8d704707d0df448025fce0de1e8ca88 | C/C++ | 3,264 | 79 | #ifndef DEF_BAMfunctions
#define DEF_BAMfunctions
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include SAMTOOLS_SAM_H
#include "ErrorWarning.h"
void outBAMwriteHeader (BGZF* fp, const string &samh, const vector <string> &chrn, const vector <uint> &chrl);
int bam_read1_fromArray(char *bamChar, bam1_t *b);
str... |
adda4093704192b61408c6bde96daa5084f4b62a260561a7670a72ecd064656c | C/C++ | 3,283 | 96 | // 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... |
82a61df747c73bdc547804342494501823d09677c41234183b55435608503290 | C/C++ | 3,301 | 97 | // 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... |
cb308a565f5cc56e4272ea7583efe1bb724279eb323a2625ffcb968db76bba2a | C/C++ | 3,309 | 105 | /*
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_VISUALC_H
#define BOOST_PREDEF_COMPILER_VISUALC_H
/* Other compilers that emulate this one need to be d... |
c6acce2bdbe614c3376b99c162614dde91d70a45c3d23c4ec1bf761ea36d4efa | C/C++ | 3,312 | 82 | // 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... |
5554c37504d4ce1c0681fce5a573513212d5e043e1217aca844b2a583465537d | C/C++ | 3,315 | 105 | /*
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... |
8c4b90db219b1d434e027d3dd1a6b5995af736dc9b3d98f23f69b85f888b0351 | C/C++ | 3,317 | 91 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2009 Hauke Heibel <hauke.heibel@googlemail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the G... |
9639a87f6a018d84e578a749dfe2d024df68ec6e1678074b341dc48c18d95064 | C/C++ | 3,327 | 106 | /*
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_VISUALC_H
#define BOOST_PREDEF_COMPILER_VISUALC_H
/* Other compilers that emulate this one need to be d... |
ded3fb17daadcbb4bfa77e335cc93a4f3d297ad7029f6e60b01befe5eef8048f | C/C++ | 3,327 | 128 | /*
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... |
e7522f657abb61b4f624cc5519c98001278d4c13d67f1e15a64a39cd7ebcec1f | C/C++ | 3,334 | 105 | // 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... |
aaef3d71ac5b262aec27335e5d1bac0b3f5c880fe380ad2f58c01740fd7ceb00 | C/C++ | 3,339 | 96 | // 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... |
4a171d7146835bff687f5bc11c67bd8b4056cd6fbb057796f327fe3a10993f35 | C/C++ | 3,363 | 134 | #pragma once
#include <sstream>
#include <plog/Util.h>
#include <plog/Severity.h>
namespace plog
{
namespace detail
{
//////////////////////////////////////////////////////////////////////////
// Stream output operators as free functions
inline void operator<<(util::nstring... |
cb96976d858bc29e025fd5ca74bfa6251a7dc5af7d36cb928f61426b19042951 | C/C++ | 3,381 | 82 | // 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... |
31df9e9d467d2bc3c79e0327ffff5924c8f07507ea19b116abc246d9ec3c2982 | C/C++ | 3,382 | 105 | // 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... |
beae87f24a426851e7d9f5b41bcde14d49c3fb149cbe1bf52436268ce02c38a7 | C/C++ | 3,388 | 127 | // 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 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
a73174a7615e5dfc27fc66c496a10991dada4fdc805320c037b88066afcb87be | C/C++ | 3,391 | 80 | /*
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 ... |
97f89182cfd47a378dc358134b5cbd154544ad087c253321d87a23f40275871d | C/C++ | 3,398 | 105 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2010 Daniel Lowengrub <lowdanie@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Le... |
0ff647a46d8d418db8afe3f80caa22a3105d77f13f5bc3fd6ceb44d5eb0c8851 | C/C++ | 3,399 | 129 | // 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... |
b99161d9fc65a8e7eb8044763863c4fe387bf6717cf6fd439cdd6fba3f326e36 | C/C++ | 3,405 | 76 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Vincent Lejeune
// Copyright (C) 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
//... |
a841e12147ceccb117c5eb575b37bfd2b077caa6ee458be269f25373c2a4c7e9 | C/C++ | 3,411 | 140 | extern int procv_llmix();
/* adap.c */
extern int alocfit();
/* band.c */
extern void band(), kdeselect(), kdecri();
/* density.c */
extern int densinit(), likeden();
extern int fact[];
extern void prodintresp(), prresp();
extern int de_mint, de_itype, de_renorm;
/* dens_haz.c */
extern void haz_init();
extern int ... |
01ee930b0b5ccbbe705140ff90c395a6b61451cc3b1c11859aba252165de91b9 | C/C++ | 3,426 | 70 | /* ************************************************************
HEADER triuaux.h
For use with mex-files in self-dual-minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. St... |
43a2c4a1801222d51bc73c8652a7459620cc5ec86305d073a1fba09949309f42 | C/C++ | 3,443 | 109 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2011 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2010 Daniel Lowengrub <lowdanie@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Le... |
c512a07ca3ddfcb7832c2937591ae3341cb95c72ef2dc88a8612a73fef103227 | C/C++ | 3,455 | 79 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Vincent Lejeune
// Copyright (C) 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
//... |
a0b21a2d95f0a7618594b552c3b7309c7656207512a6a48a590278feb021e8d1 | C/C++ | 3,457 | 71 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
ff05ac79a7985e6ea43a85812a44f9b7f40755d9c6e06f1d590ad7ed9ad86a92 | C/C++ | 3,479 | 68 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 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 Soft... |
10e30fc368e34fef90ba819c7fce84882936b8d9af8a90e18bb62ee4dc4b2042 | C/C++ | 3,489 | 97 | /*
Copyright (c) 2010-2013 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... |
20a45f536bab2cf0440e63d7329e22e7ed21e03029951e2e3954741b459e815c | C/C++ | 3,489 | 96 | // 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... |
57a7629c6e0f7b54ab6c0e35f4d329df9e7fc440b9aa5a38ad17eb9a01ffd642 | C/C++ | 3,497 | 88 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
002d83da1cfb11bb859fcdb8306b1fb9f2c71359db8ffbad14e250de3fc3c5d8 | C/C++ | 3,504 | 182 | // SharedMemory.cpp
// Gery Vessere - gvessere@illumina.com, gery@vessere.com
// An abstraction over both SysV and POSIX shared memory APIs
#ifndef SHAREDMEMORY_H
#define SHAREDMEMORY_H
#include <string>
#include <semaphore.h>
#include <unistd.h>
#include <exception>
#include <iostream>
enum ErrorState {
ENONE,
EN... |
0e725c07424d8ae991e10739e15abaac93e1965c71c57b1f8192bc9e0a7b2e2a | C/C++ | 3,515 | 112 | /*
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... |
03c66f45cbae95abd6914a9df4ae4fd05bc3ce80cbb49e6241976bcb8731cbef | C/C++ | 3,527 | 99 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2009 Hauke Heibel <hauke.heibel@googlemail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the G... |
a33c8db9453f862c869b8704a4703b42d66ffae8f205a0a3aeb4d5fc5fa34f6f | C/C++ | 3,535 | 92 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
70fc91f4844cc7ee3db62a1a7042faa154c5c0fc624e15290fa1e7a58dda4e58 | C/C++ | 3,536 | 75 | /* hfile_internal.h -- internal parts of low-level input/output streams.
Copyright (C) 2013-2014 Genome Research Ltd.
Author: John Marshall <jm18@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), t... |
c9dbf5ad0cfd39e3b7d7061608af6fe07bdb2e1bf6bdd23648beef6c07856a18 | C/C++ | 3,537 | 124 | /*
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_PPC_H
#define BOOST_PREDEF_ARCHITECTURE_PPC_H
#include <boost/predef/version_number.h>
#include <bo... |
d60bd522964a003416345d6fa70bedb12cec6a2e87e8ad7c67d1d8d2b29e9065 | C/C++ | 3,538 | 119 | /*
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)
*/
#include <boost/predef/hardware/simd/x86.h>
#include <boost/predef/hardware/simd/x86_amd.h>
#include <boost... |
36e62cc561e4a6912544431aac262165fc52e9cba0439b5892a51898e804ebac | C/C++ | 3,539 | 141 | #pragma once
#ifndef NODE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#define NODE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
#include "conversion.h"
#include "exceptions.h"
#include "iterator.h"
#include "mark.h"
#include "noncopyable.h"
#include <iostream>
#include <string>
#include <vector>
#include <map>
#include <memory... |
52d2319bf68b34bff4b9780dd74d5ab84b5f43df094309f13ce5125c9e0436e9 | C/C++ | 3,552 | 86 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2010 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 ... |
be621897f9a16d5b1c1af5e8c6900fc98237e1a24b3441def50adaf1505426ee | C/C++ | 3,588 | 79 | /*
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 ... |
8ce423cf000d3269fb4945042fb562c7ccfeb76b9b1e9b9aabcdfa73e7a9ef26 | C/C++ | 3,590 | 135 | /*
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_VERSIONS_H
#define BOOST_PREDEF_HARDWARE_SIMD_X86_VERSIONS_H
#inclu... |
50b6a5321689ad7d3d73c7f9c03683b7fea4d774ce5c3ba649ef80399bef2e3e | C/C++ | 3,595 | 122 | #pragma once
#include <fstream>
#include <vector>
#include <string>
#include "bgmg_log.h"
// reader must know the type
template<typename T>
void save_value(std::ofstream& os, T value) {
os.write(reinterpret_cast<const char*>(&value), sizeof(T));
}
template<>
inline void save_value<std::string>(std::ofstream& os,... |
79fc7975a7af7419c0208fdd9a395a164c71d1278d62f53b562105b15510ce04 | C/C++ | 3,604 | 133 | /*
* Copyright 1996-2006 Catherine Loader.
*/
/*
* Headers for math utility functions.
*/
#ifndef I_MUT_H
#define I_MUT_H
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
typedef int (*prf)();
extern prf mut_printf;
extern void mut_redirect();
typedef struct {
double *Z; /* jac... |
5942a2636ec3d3861b275fe0282d9805113f59fbee7322f242ef720dfda75347 | C/C++ | 3,614 | 111 | #ifndef _MEDAKA_COUNTS_H
#define _MEDAKA_COUNTS_H
// medaka-style feature data
typedef struct _plp_data {
size_t buffer_cols;
size_t num_dtypes;
size_t num_homop;
size_t n_cols;
size_t *matrix;
size_t *major;
size_t *minor;
size_t featlen;
} _plp_data;
typedef _plp_data *plp_data;
// ... |
3dceb4d99e3c90dc005e6a3f5d02c82e4fd7e2587f0c5e81dada353b5f9ee70d | C/C++ | 3,627 | 150 |
/******************************************************************************
*
* file: CmdLineInterface.h
*
* Copyright (c) 2003, Michael E. Smoot .
* Copyright (c) 2004, Michael E. Smoot, Daniel Aarno.
* All rights reverved.
*
* See the file COPYING in the top directory of this distribution for
*... |
7fdfd37877acd939e52077fd33559c9447e764c2b88bfefb1a4070d64259701c | C/C++ | 3,637 | 117 | #pragma once
#include <algorithm>
#include <plog/Util.h>
#include <plog/Converters/UTF8Converter.h>
namespace plog
{
template<class Formatter, class Converter = UTF8Converter>
class RollingFileAppender : public IAppender
{
public:
RollingFileAppender(const util::nchar* fileName, size... |
eda5663a2b826e55be3d6da269a2eecd0fb9a12ee218e93cf7d731a4938148b5 | C/C++ | 3,671 | 125 | /*
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_H
#define BOOST_PREDEF_HARDWARE_SIMD_X86_H
#include <boost/predef/v... |
0331daa41669a1b0dd4b9cab19ed64027ba106f958f4d3c92217758136c62943 | C/C++ | 3,677 | 91 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
1dfbdc474c1bfc62d8d46624d17e4d2f8845f951d56560b02fb7248d02cf8585 | C/C++ | 3,680 | 126 | #ifndef SIMDXORSHIFT128PLUS_H
#define SIMDXORSHIFT128PLUS_H
#include <stdint.h>// life is short, please use a C99-compliant compiler
#ifdef __cplusplus
extern "C" {
#endif
#if defined(_MSC_VER)
/* Microsoft C/C++-compatible compiler */
#include <intrin.h>
#elif defined(__GNUC__) && (defined(__x86_64__) || d... |
00887f8e4759d455343a248e28318ad4a429dd6f613f0e130e3a6f8830aca54d | C/C++ | 3,682 | 86 | // 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... |
4ade06054c008560dd5d18d83c4bd3480bf22919036119ec3cd2e9caf74ed3fc | C/C++ | 3,693 | 103 | #pragma once
#include "common.h"
#include "types.h"
/// @file inlet.h XML functions
/** @defgroup xml_ptr The lsl_xml_ptr object
* @{
*/
// XML Tree Navigation
/** Get the first child of the element. */
extern LIBLSL_C_API lsl_xml_ptr lsl_first_child(lsl_xml_ptr e);
/** Get the last child of the element. */
exte... |
a8130152bc6335bf205d4a272e83308b1aced50bc322843daaf1ea50c9ebc9ae | C/C++ | 3,699 | 105 | // 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... |
f617f16520c0ac65fab5348c784fbba53cacfea8be5750f9f1df75de9526bc9c | C/C++ | 3,700 | 112 | /* The MIT License
Copyright (c) 2008 Genome Research Ltd (GRL).
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... |
1d4bfea2a8d65413a8f145ec5c3c9d885f479adfe00b32d9b76f0daf63ca4173 | C/C++ | 3,715 | 106 | #ifndef TIME_POSTPROCESSOR_H
#define TIME_POSTPROCESSOR_H
#include "common.h"
#include <cstdint>
#include <functional>
#include <mutex>
namespace lsl {
/// A callback function that allows the post-processor to query state from other objects if needed
using postproc_callback_t = std::function<double()>;
using reset_c... |
7780f88b4bcf8183b19e49e6b45f74b3b162df1c8ae026dd99d3bbf7bd01a225 | C/C++ | 3,715 | 95 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
d6c22dfc2096d773b5d6d7bbd4be702529c395326a38afda819fd992d05cdcdc | C/C++ | 3,715 | 92 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2009-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms o... |
13a6a6a64889f27eedb9093aff89c457f2d0a812d2acd7741c5ff35148c9ec34 | C/C++ | 3,717 | 105 | #ifndef TIME_POSTPROCESSOR_H
#define TIME_POSTPROCESSOR_H
#include "common.h"
#include <functional>
#include <mutex>
namespace lsl {
/// A callback function that allows the post-processor to query state from other objects if needed
using postproc_callback_t = std::function<double()>;
using reset_callback_t = std::fu... |
92f707da7a6501d5bc075e742d929649e7ae2bdd37b06cfbb4e38c038d7c184c | C/C++ | 3,730 | 106 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Rohit Garg <rpg.314@gmail.com>
// 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 Gener... |
44edfa4fc499cce2557ee5e3238cc1e393a511952bd2a14b60d96a65b021b4ae | C/C++ | 3,733 | 109 | /*
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 ... |
f6103d00759eb076091b3cbb391239658d95e8a35d3353f5287a7ad01aeed089 | C/C++ | 3,750 | 108 | // 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... |
e0c66a257bf8be4613bd2dd67756ec6e449fbfd37fa2388815f8ac5f0019ebf6 | C/C++ | 3,764 | 112 | // 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... |
7214aaaceb3ae99312a447e29f1c729edf0f55ae0368b14ffa6935d07306c96a | C/C++ | 3,805 | 123 | /*
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_H
#define BOOST_PREDEF_HARDWARE_SIMD_X86_H
#include <boost/predef/v... |
55216f815a45784546b6950f4f56afcc8f419e49fd00c6837c5e6e4ab12a2f86 | C/C++ | 3,827 | 152 | // This file is a modified version of Python 2.2/2.2.1 Python.h. As
// such it is:
//
// Copyright (c) 2001, 2002 Python Software Foundation; All Rights
// Reserved
//
// boostinspect:nolicense (don't complain about the lack of a Boost license)
//
// Changes from the original:
// 1. #includes <unistd.h> for Pyth... |
3be142848ac26f93c739f8f7d252df5e575fca03b1599188980edb037207ded4 | C/C++ | 3,858 | 95 | #pragma once
#include <cstring>
#include <plog/Logger.h>
#include <plog/Formatters/CsvFormatter.h>
#include <plog/Formatters/TxtFormatter.h>
#include <plog/Appenders/RollingFileAppender.h>
namespace plog
{
namespace
{
bool isCsv(const util::nchar* fileName)
{
const util... |
4d4e3e6f893316f0be77bfd642c857a77f1fa2925acb5df9753e543d35aa3a6a | C/C++ | 3,865 | 83 | /* blast.h -- interface for blast.c
Copyright (C) 2003, 2012, 2013 Mark Adler
version 1.3, 24 Aug 2013
This software is provided 'as-is', without any express or implied
warranty. In no event will the author be held liable for any damages
arising from the use of this software.
Permission is granted to any... |
8207e833b82873ed40cc945b2d0c598a93c98875a9d4511bab4784e0d37b970f | C/C++ | 3,872 | 101 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Guillaume Saupin <guillaume.saupin@cea.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... |
b9049c017cc28fe3c2e705ef9d96daa68cc63d3fc50fc975b5ca4fae60073b34 | C/C++ | 3,877 | 99 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2009-2010 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms o... |
d739ab7583ea2da3519af0fb6bc8893e4cd3fdd553ca91cc41080d4a11e68007 | C/C++ | 3,879 | 163 | /**
* 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 <memory>
#include <random>
#include <vector>
#include "matrix.h"
#include "model.h"
#inc... |
c2eb011f6577421383955db9529862fa9ef401aa5716ebd8a30c58851a6adaa7 | C/C++ | 3,898 | 119 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 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 of the... |
c8cb309ec95e3920f1fba0081f8a0dc90d9482bce99a91c5cfea79b41df51a11 | C/C++ | 3,926 | 124 | // 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... |
7c1a7d95eeb1fc502109a016f61348489c70b18f8cbe6cad66d6d638ec87b120 | C/C++ | 3,928 | 143 | #pragma once
#include "boost/utility.hpp"
#include "boost/date_time/posix_time/posix_time.hpp"
#include "boost/algorithm/string.hpp"
#include <fstream>
#include <vector>
#include <chrono>
#define LOG Logger::singleton()
#define MAX_LOG_LINES 10000000
#define BGMG_THROW_EXCEPTION(x) throw (x)
// A timer ... |
175f5b850556f19d9fb74ba4c888f0e4e0c7c82c9fca8a96f60b74f1d16be0dd | C/C++ | 3,930 | 122 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2008 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 of the... |
66c61d33953616ee3cb537dda2ce4e9edf2412f356925d1803d2f4bfce57cc4c | C/C++ | 3,932 | 149 |
#include <Eigen/Sparse>
#include <bench/BenchTimer.h>
#include <set>
using namespace std;
using namespace Eigen;
using 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<Scalar,Dynamic... |
76e49841fbc78d3dde15dd3fb7c6e909d14242159e2f0133a16d90f84f429c9d | C/C++ | 3,952 | 90 | /*
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 ... |
68c83bda88fdf610b2e0a811d53e86b8172025e68d24cca96323331c2322c73d | C/C++ | 3,955 | 95 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Gael Guennebaud <gael.guennebaud@inria.fr>
// Copyright (C) 2010 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 ... |
bd5181dcb504e3431dbaaa86f3c290a48c85b39affe4fcece5904001c2289842 | C/C++ | 3,967 | 156 |
/******************************************************************************
*
* file: XorHandler.h
*
* Copyright (c) 2003, Michael E. Smoot .
* Copyright (c) 2004, Michael E. Smoot, Daniel Aarno.
* All rights reverved.
*
* See the file COPYING in the top directory of this distribution for
* mor... |
9a1d8eb1ed6da19a33f9bfbaa7fbf9481170cfe55e4aee03d6fa766b7a6be717 | C/C++ | 3,969 | 184 | // -*- Mode: c++; c-basic-offset: 4; tab-width: 4; -*-
/******************************************************************************
*
* file: StandardTraits.h
*
* Copyright (c) 2007, Daniel Aarno, Michael E. Smoot .
* All rights reverved.
*
* See the file COPYING in the top directory of this distributio... |
ce2c9215973afc64786825b1c1501e8607f26ffb6c514d72d1425faa67ecd376 | C/C++ | 4,000 | 163 |
/** \returns an expression of the coefficient-wise absolute value of \c *this
*
* Example: \include Cwise_abs.cpp
* Output: \verbinclude Cwise_abs.out
*
* \sa abs2()
*/
EIGEN_STRONG_INLINE const CwiseUnaryOp<ei_scalar_abs_op<Scalar>, Derived>
abs() const
{
return derived();
}
/** \returns an expression... |
4185cb5055d5519c87cf5a68a7f65acc73ae3fa25d31dc428148f645ff4134c7 | C/C++ | 4,028 | 110 | #ifndef H_SoloFeature
#define H_SoloFeature
#include <fstream>
#include <unordered_map>
#include <unordered_set>
#include "IncludeDefine.h"
#include "ReadAlignChunk.h"
#include "Transcriptome.h"
#include "SoloCommon.h"
#include "SoloRead.h"
#include "ReadAlignChunk.h"
#include "SoloFilteredCells.h"
class SoloFeatu... |
9483ed26c8739a4c04cc85856257bb0142a6c66a95666e1b3e5333f3b5ee5112 | C/C++ | 4,051 | 107 | #ifndef H_Genome
#define H_Genome
#include "IncludeDefine.h"
#include "Parameters.h"
#include "PackedArray.h"
#include "SharedMemory.h"
#include "Variation.h"
#include "SuperTranscriptome.h"
class GTF;
class Genome {
private:
key_t shmKey;
char *shmStart;
uint OpenStream(string name, ifstream & stream, u... |
2903df1d1e6643a5f624fe3ea3f931c3410eb1858ac347c5df278273c6c91ca4 | C/C++ | 4,072 | 123 | // 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... |
fe6298788b23baa4e2e73d3d72bd06b6f1ee4b39fb0ebc3a5a39a8b707eb2ba6 | C/C++ | 4,109 | 86 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// 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 General Public
// License as published by the Free Softwar... |
f79f185199880c0a30e5c68b3dec49178d81347b1091f833897027c7112b7f8d | C/C++ | 4,120 | 155 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009-2010 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... |
48942f1622e05128ecc8bc120f1edb9cd710036ff35d4a5ca4384772ab9f55b0 | C/C++ | 4,142 | 89 | /*
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 ... |
38753b64775882d5c29c89ec51870d83b3bb54458e8e3d4d006080f2b43677ac | C/C++ | 4,147 | 130 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Benoit Jacob <jacob.benoit.1@gmail.com>
// 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 ... |
7aa778dfda123348f24e9ab4dcc8a1a8aad84883a2401c242d79160add8812f6 | C/C++ | 4,148 | 108 | #ifndef TCP_SERVER_H
#define TCP_SERVER_H
#include "forward.h"
#include "socket_utils.h"
#include <atomic>
#include <map>
#include <memory>
#include <mutex>
#include <string>
using asio::ip::tcp;
using err_t = const asio::error_code &;
namespace lsl {
/// shared pointer to a socket
using tcp_socket_p = std::shared_... |
ef0f0c8a0ea440f81298d42b09ab77b22fe915acf735806456899b4ac8782ee2 | C/C++ | 4,159 | 130 | // 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 Gael Guennebaud <g.gael@free.fr>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// Licens... |
818e9f28a429993b9c637635a925756c0e847000770f8b14257c46af0af15304 | C/C++ | 4,176 | 96 | // 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... |
22d9c4f4fee7bb35a138fc259197bba480d41d20eba861c112e1bb5b8fe01f60 | C/C++ | 4,196 | 145 | // 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... |
9719e7d331839fc51e3f3e4f3ad9d36f0e215391b6ea19f3f7bb75a8433aa72b | C/C++ | 4,199 | 133 | // 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... |
bd9786876e33f2716531126d37ce4edbeb177e3a3154cd69c1fee1baee94308a | C/C++ | 4,237 | 149 | // 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... |
8539c19aeab01dc565543e4d66cd42a6c8ef68890cfd3012e0a1c8b6dd1ada85 | C/C++ | 4,273 | 133 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2010 Benoit Jacob <jacob.benoit.1@gmail.com>
// 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 ... |
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