sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9a9e44d974d1660ea5dd3c573f04b36a214dc662f4e75495d7fe32ccf5970e2d | C++ | 35,414 | 1,020 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
9fe2241600d96ab3efba97d753230bddeb9535396c0272dd8e2654f2d48e8f1e | C++ | 35,588 | 963 | // survival_analysis.cpp : �R���\�[�� �A�v���P�[�V�����̃G���g�� �|�C���g���`���܂��B
//
#ifdef _WIN32
#include "stdafx.h"
#endif
#include <iostream>
#include <fstream>
#include <sstream>
#include <cmath>
#include <string>
#ifdef _OPENMP
#include <omp.h>
#endif
#include <time.h>
#include "labeling.h... |
68a1acff23178c755c0c5f1b5355d5d870cc48e8856e9c9cc59caded80b46080 | C++ | 35,720 | 702 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
01221a500785ed06d145e09a4c530f054ea67993eef175acce5ed259d4c35b9a | C++ | 35,992 | 807 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
c37ac097e5937f2b1516033da1fbcc096d8bceb7c99e76bdc90eb969a826bc8f | C++ | 36,331 | 1,033 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
03d9ae39cbd3dbd172d86297b64cfefafb15045cb9fd800b84f04834f668b9a0 | C++ | 36,746 | 1,098 | // ***************************************************************************
// BamStandardIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 25 May 2012 (DB)
// -------------------------... |
d88d8a823691ffb7dc8c23e5538a5b1a605f9e49b7f7bc611427fdb4ec92d203 | C++ | 37,173 | 1,107 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
c2813eb8e9363070fb611d07a619c6cdfb06b75f9721cfbf5dd10acd5838c898 | C++ | 38,552 | 1,346 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
f5832b5c7495a4cb61a6cd6633af3b717e64f6596431232e67e5e202757e8764 | C++ | 40,063 | 1,154 | // ***************************************************************************
// BamAlignment.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 4 December 2012 (DB)
// -------------------------... |
382cce23e2e06daa13343b8ff954c670b93d42201330422c26703c7d757f5a5a | C++ | 40,198 | 1,419 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <algorithm>
#include <unordered_map>
#include <utility>
#include <math.h>
#include <stdint.h>
#include <string.h>
#include "../src/meshoptimizer.h"
static float inverseTranspose(float* result, const float* tr... |
c0c7a3c628d49bf05b2bda6c60711d63abfab295be5f281bf44608dc333e8d60 | C++ | 40,248 | 1,327 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
95328294bdb133e687e28be61878c2037508bc640ba7a8dce4059b0e44ca5dc1 | C++ | 40,567 | 906 | #include "diffusion_operator.hpp"
#include <Omega_h_defines.hpp>
#include <algorithm>
#include <limits>
#include <numeric>
#include <random>
#include <Omega_h_for.hpp>
#include <stdexcept>
#include "geom/dist/distmesh.hpp"
#include "rng/rng.hpp"
#include "util/flat_multimap.hpp"
#include "util/profile/profiler_inter... |
40c4dd69dc2ebe76608544dc6831370f82ad78a40e8be21eceec62a303ec3f6e | C++ | 40,988 | 1,311 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
f5399a5c7f51f291b083c01cf6b92d121034501c5e9d513fe6f9ba26d223a776 | C++ | 41,222 | 1,304 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
c78439414d46f2dc63064789963e3383a4f0e3a613e3f6d983b4ddd21186faf4 | C++ | 41,250 | 1,307 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
017725d3db736387ddccfdd7a5a52c8f75637f11d7024870a2979950dcbe1df8 | C++ | 41,433 | 1,222 | // ***************************************************************************
// bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 December 2012
// ----------... |
574840c2b19f78551f2ed9dedbcdb462c722cfaf20d9d8968643840fe9853022 | C++ | 43,563 | 1,101 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
6b107e86d37ba9d0ac32566ee6570a4827ee4e4c5b10fdf275fb1fd97b33cab7 | C++ | 43,709 | 1,094 | // ***************************************************************************
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 3 May 2013
// -----------------... |
6d86dc6d7a20f6c18cff60d5b5778f13997aed02a4354e3b4f765de50eaa0d0a | C++ | 43,833 | 1,144 | /*
Bayesian Functional GWAS --- MCMC (BFGWAS:MCMC)
Copyright (C) 2018 Jingjing Yang
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 3 of the License, or
(at your ... |
198f7b873858ca11852498bbf2f0c78c13ffa3062b547007a07461d193d4d712 | C++ | 44,017 | 1,244 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
e410cd419d6513a33e80701e170e212055ea9dde47e5e1d576e3fe7bbd819a63 | C++ | 44,056 | 1,446 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
226f8813dc13796f451b9ab776b948771f5a6bd57450365250a4d40abe03296e | C++ | 44,464 | 976 | #include "surface_reactions.hpp"
#include <cassert>
#include <functional>
#include <Omega_h_map.hpp>
#include <Omega_h_mark.hpp>
#include <Omega_h_shape.hpp>
#include <stdexcept>
#include <string>
#include "geom/dist/distmesh.hpp"
#include "math/constants.hpp"
#include "model/complex.hpp"
#include "mpi/dist/tetopspl... |
a7a7225a6bea8cd1cbecf37d5c0bbe7bde63f14cc472ff2d54955ed789971955 | C++ | 45,147 | 1,206 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
bf115ce601a15f27008ac5e83fa0bc6ad62071434ef3a3a87e069c625dcb0152 | C++ | 45,229 | 1,126 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
b1615ab562e1ef84fc8c682ff33919313cebd02ce9e8e1222f3080c29005dbc1 | C++ | 45,575 | 1,437 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
8eeebd7fd269739a7358264a953fbd0c4c72d11777f3b8c2617bb075c6735c1f | C++ | 46,552 | 1,003 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
d9b928fd98f184ec9392fa1eeeff5ade8cf56673e6c66a620f1d222833ca4006 | C++ | 46,634 | 1,532 | /*
* Copyright (C) 2010-2012 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any la... |
1fd661f010090e5fdaffcd6db6e45bc743e211b797cc52fe21a0961dec9bf333 | C++ | 47,512 | 989 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
b2320845bc96ab2894306c277a123cab5331d5f5cf63d514ff44c39afd53ee03 | C++ | 48,173 | 1,380 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <float.h>
#include <math.h>
#include <string.h>
// The block below auto-detects SIMD ISA that can be used on the target platform
#ifndef MESHOPTIMIZER_NO_SIMD
#if defi... |
40a69d3681a06c0f6a9595889af6cedca1d3bdeada8bbbd976c62ba7b65f450f | C++ | 49,296 | 1,318 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
a10aa357b62a516b1ae9be4a21c26a61896c9600ffa5fb455d4c532bd7d7166a | C++ | 49,345 | 1,270 | #include <math.h>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <iomanip>
#include <time.h>
#include <random>
//Equation for gate variables:
inline double x_inf(double v,double V12,double k) { return 1./(1.+exp(-(v-V12)/k)); }
inline double tau_inf(double ta... |
c6ef6270d8605a90d9be6bc84f2b46ac681f718215ee91a7032cca88daf8028e | C++ | 50,524 | 1,402 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
83dcd10434eaa25b082a520def289f3afb912262dae89a2c0ded8d9337f3d373 | C++ | 50,886 | 1,412 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
49f7f5eb9e80a16aa458d6f1772c84a0b4fe0e6944f8b469fbe5614f925df67c | C++ | 50,899 | 1,359 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
24b170555a2b8766a35acce326fbfd631241f50d19c472212d36ca2f5cd633f7 | C++ | 51,169 | 1,766 | /*
Bayesian Functional GWAS --- MCMC (bfGWAS:MCMC)
Copyright (C) 2016 Jingjing Yang
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 3 of the License, or
(at your ... |
9d26d1ddbe96a0ba9d838ff2ea0958c995f56bee871cbeb285054ea377d30f7f | C++ | 52,651 | 1,032 |
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
#include "test_common.hpp"
#include "steps/geom/dist/distmesh.hpp"
#include "steps/util/debug.hpp"
#include "steps/util/finish.hpp"
#include "steps/util/init.hpp"
namespace osh = Omega_h;
namespace steps::dist {
... |
bafef57ea9e3342bfab2472e7074caab1b1c43b83c530b63303a27a5f0ab7926 | C++ | 52,899 | 1,174 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
36a9ef5ac2f354001e432a259ced379f168a39e7ce4d2d62cae4ee55b17e83db | C++ | 53,448 | 1,408 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
9dcd2c09f806e677b63055aa06e164ec13be0b8bee085b0fdf31590ef12bbc02 | C++ | 53,696 | 1,653 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
75185ffe911d64b10974af1c10cd828d850f33380a93de1aae2e86129a6f39c3 | C++ | 53,724 | 1,656 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
25a60bb7001643275ed12c58aac5b8037d975b0fd9d3f652d5a1345892ef1962 | C++ | 54,009 | 1,621 | // ***************************************************************************
// bamtools_resolve.cpp (c) 2011
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 24 July 2013 (DB)
// --------------------------------------... |
da4ecc7f4c19f22660d58315776cf0887bec59fd21fe70c4ec90b17d25967f91 | C++ | 54,185 | 1,862 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <float.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
static const char* componentType(cgltf_component_type type)
{
switch (type)
{
case cgltf_component_type_r_8:
return "5... |
c3858daf7b36b1ada9660e30448ee4fe6781969d6d9900e31b9998590984f00c | C++ | 55,000 | 1,840 | #include "stdafx.h"
#include <sstream>
#include <cmath>
#include <string>
#include <omp.h>
#include <time.h>
#include "Labeling.h"
#else // Release���[�h�̏ꍇ
#pragma comment( lib,"opencv_world411.lib") //
#endif
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/i... |
780e7f95024b577b8adcb8ee2a2e442294ebd62a1b6aaf37627fc1ff3cac4ff3 | C++ | 55,477 | 1,503 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <math.h>
#include <string.h>
// The block below auto-detects SIMD ISA that can be used on the target platform
#ifndef MESHOPTIMIZER_NO_SIMD
// The SIMD implementation requires SSE2, whic... |
70718f509f0e18c15a033a9114c0011bf01488b14609a106f2a778f51f8d321f | C++ | 57,137 | 1,900 | #include "stdafx.h"
#include <sstream>
#include <cmath>
#include <string>
#include <omp.h>
#include <time.h>
#include "Labeling.h"
#else // Release[hÌê
#pragma comment( lib,"opencv_world411.lib") //
#endif
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv... |
88e55d38536eec1e33eb4ce1d066bf74ef6873c85a018b202cdafd748b22a274 | C++ | 57,215 | 1,248 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
5c5fb512cf9cd5229b7366eb57dbf45fc34254244c5871d81e0f28307c0b92fe | C++ | 57,896 | 1,828 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
961f1d66ea0efe84f8191f0eb7524d161daf98719cabcc94081252150707514a | C++ | 58,172 | 1,832 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
ffe189f5c98241ae13cf3729b94fb7306388ef4f57876b157e359d646b733425 | C++ | 58,747 | 1,186 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include "../inst/include/STAAR.h"
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <string>
#include <set>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& ... |
c365f1d657bf5704f2d66907614c126b328066b706c508038b7681804ece6d06 | C++ | 59,432 | 951 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
0033d8b56f3f46a13d1e47db73f6828b2a172fbaa5b761d4ad8a72f16bf989b1 | C++ | 59,966 | 1,574 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
a608d788580971e97096ed472cac6c5f0f9baf68e3ceb44cb51370355adc6ee7 | C++ | 60,435 | 1,926 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <algorithm>
#include <unordered_map>
#include <locale.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#ifdef __wasi__
#include <unistd.h>
#endif
#include "../src/meshoptimize... |
2025e82349c9ab073b035fa036c94c95ffa05d6282763fd4b2408d7f95d0de4f | C++ | 61,618 | 1,897 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <string.h>
// The block below auto-detects SIMD ISA that can be used on the target platform
#ifndef MESHOPTIMIZER_NO_SIMD
// The SIMD implementation requires SSSE3+PO... |
a8b122a1bc9a66c79f6be544f24e9a5cc0567302280b4f07c13b6f1c698319b1 | C++ | 61,640 | 1,498 | #include <gtc/matrix_transform.hpp>
#include <numeric>
#include "Shader/ApplySlopeError.h"
#include "Shader/Approx.h"
#include "Shader/Crystal.h"
#include "Shader/LineDensity.h"
#include "Shader/Rand.h"
#include "Shader/Refrac.h"
#include "Shader/SphericalCoords.h"
#include "Shader/Utils.h"
#include "setupTests.h"
TE... |
f8bf6a9578aa4c5f1797a2e43f5649414062ead5c08c182f170df87d39080c39 | C++ | 62,722 | 1,785 | // survival_analysis.cpp : R\[ AvP[VÌGg |Cgðè`µÜ·B
//
#ifdef _WIN32
#include "stdafx.h"
#endif
#include <iostream>
#include <fstream>
#include <sstream>
#include <cmath>
#include <string>
#include <omp.h>
#include <time.h>
#include "Labeling.h"
#else // Release... |
ddf2cdfd54361ed46400822da4293751daf0c29f5687f4b32a472946cbd335f8 | C++ | 62,888 | 1,543 | #include "simulation.hpp"
#include <limits>
#include <memory>
#include <numeric>
#include <Omega_h_for.hpp>
#include <Omega_h_shape.hpp>
#if USE_PETSC
#include "mpi/dist/tetopsplit/operator/efield_operator.hpp"
#endif // USE_PETSC
#include "geom/dist/distmemb.hpp"
#include "geom/dist/distpatch.hpp"
#include "mpi/d... |
bc73813ade2c5d7c2647ec2f669721afd110269ddae43d7196ddca4a701514fc | C++ | 67,303 | 1,961 | // pff_2ch_tracking.cpp : R\[ AvP[VÌGg |Cgðè`µÜ·B
//
#include "stdafx.h"
#include <iostream>
#include <fstream>
#include <sstream>
#include <cmath>
#include <string>
#include <omp.h>
#include <time.h>
#include <direct.h>
#else // Release[hÌê
#pragma comment(... |
d65b3b718e44d483cacaafb3c1f2daa4b2790182f736c70392d1164dd4d6405e | C++ | 72,538 | 1,818 | #include "distmesh.hpp"
#include <algorithm>
#include <limits>
#include <Omega_h_array_ops.hpp>
#include <Omega_h_file.hpp>
#include <Omega_h_for.hpp>
#include <Omega_h_map.hpp>
#include <Omega_h_mark.hpp>
#include <Omega_h_shape.hpp>
#include <boost/algorithm/string/classification.hpp>
#include <boost/algorithm/stri... |
998f7f0ff3a739c685f03372fc5ec9620d734f084d31b9019c2fabfe630b3cec | C++ | 75,544 | 1,947 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any later v... |
27b205b3221022a37063230ca4c93a400a8d805ac76b41c89c96aa01d0988712 | C++ | 76,850 | 2,253 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
fad28bd7d34d6861ca1516053ea4cc4b1d2b3048cf21129cd4bcdb35edee1f23 | C++ | 76,897 | 1,983 | #ifndef _CRT_SECURE_NO_WARNINGS
#define _CRT_SECURE_NO_WARNINGS
#endif
#include "../src/meshoptimizer.h"
#include <assert.h>
#include <float.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <vector>
#define FAST_OBJ_IMPLEMENTATION
#include "../extern/fast_obj.h"
#define SDEFL_... |
707ff9b6a56ea9663173ef53f16380fcabb022c07a5fb59ed2a2e6fbe7dcf898 | C++ | 78,770 | 2,522 | #include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "auxillary.h"
#include "genotype.h"
#include "genomult.h"
#include "arg... |
861adefdef26bdbac86d0493d2510691627bb4180b03b1efdab0346e518c5f88 | C++ | 89,651 | 2,461 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
42b22617cfac047fbdedcf810fff20d732c23108d85344f05ccdd39723328ab3 | C++ | 93,636 | 2,577 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
1a05df0c7845b9a7bfc02dd44a4bb9e2d9255eb2be168764e46cc38486549b03 | C++ | 94,920 | 2,487 |
#include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "genotype.h"
#include "arguments.h"
#include "storage.h"
#include "mat... |
e25fee524542b8d3c1175ecb718a884d209fc963056962335c8f4136bf9661db | C++ | 101,188 | 3,236 | #include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "auxillary.h"
#include "genotype.h"
#include "genomult.h"
#include "arg... |
1486df00809d506581c7838eb9818c5234103dc0b9312f08c845b54115b6f178 | C++ | 102,209 | 2,529 |
#include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "genotype.h"
#include "arguments.h"
#include "storage.h"
#include "mat... |
a990c250c2c99d196d29ded6abb90b4666e7166f4d7bf57aaa949c97987465c1 | C++ | 105,130 | 3,279 | #include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "auxillary.h"
#include "genotype.h"
#include "genomult.h"
#include "arg... |
719303b6970398631e30724e8eebc6cd2e7e08b67fe8ab7cbf7eecafdaa08616 | C++ | 107,217 | 2,947 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <float.h>
#include <math.h>
#include <string.h>
#ifndef TRACE
#define TRACE 0
#endif
#if TRACE
#include <stdio.h>
#endif
#if TRACE
#define TRACESTATS(i) stats[i]++;
... |
05570153e2421c658c1260672e2d1b057de6b58c21d10011f9f05c72f570d379 | C++ | 108,572 | 3,731 | #include "../src/meshoptimizer.h"
#include <assert.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <vector>
// This file uses assert() to verify algorithm correctness
#undef NDEBUG
#include <assert.h>
struct PV
{
unsigned short px, py, pz;
unsigned char nu, nv; // octahedron encoded normal, ... |
1c43780cc1a695e0636560b0d456850d723fdd13426eb7534e126e68b9dfe251 | C++ | 109,058 | 2,611 |
#include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "genotype.h"
#include "arguments.h"
#include "storage.h"
#include "mat... |
fd1bb0654c59656d3e3b37b2281713996e9a016ee5a9b9cd752e39cc5c7bd417 | C++ | 110,825 | 3,096 | /*
Bayesian Functional GWAS --- MCMC (bfGWAS:MCMC)
Copyright (C) 2016 Jingjing Yang
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 3 of the License, or
(at your ... |
4d2f2acaab17469a6c259f74effabe3ef05551d47cd793d39393adb287282e9e | C++ | 111,849 | 2,664 |
#include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
#include <random>
// #include <bits/stdc++.h>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "genotype.h"
// #include "mailman.h"
#incl... |
c1ef89a060045deb0fa55ebb74c14e51eb6de3dcdc805aa125a5ab1511bcf3bc | C++ | 114,112 | 3,700 | /*
* Copyright (C) 2010-2012 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any la... |
952f62a44912ab5c3b9848eddee46f8e1d9aea98ba562e1517050ae4abdb33b9 | C++ | 120,288 | 3,230 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
646d4d6337f9039db3bef188e5966cfc8c87e03c3a3c08eae002eb1a5ae56eaf | C++ | 120,499 | 3,028 | #include "distmesh.hpp"
#include "util/strong_ids.hpp"
#include "util/vocabulary.hpp"
#include <Omega_h_array.hpp>
#include <Omega_h_defines.hpp>
#include <algorithm>
#include <limits>
#include <Omega_h_array_ops.hpp>
#include <Omega_h_file.hpp>
#include <Omega_h_for.hpp>
#include <Omega_h_map.hpp>
#include <Omega_h_... |
505a84074afeef0aac86050eb4f6210d8fe555c51d803cc44db71d15d3ec3ceb | C++ | 120,611 | 3,243 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
e4375ec5ff1f113569148c103e831202a0d2d6f2442f73b2fbdfa5a307195ef3 | C++ | 120,771 | 2,950 | /*
* Copyright (C) 2011-2013 Regents of the University of Michigan
*
* 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 3 of the License, or
* (at your option) any la... |
887791935e41f143e93a17342c202992508c347b223b22df27f478da032bea87 | C++ | 125,840 | 3,745 | /*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright (C) 2011 Xiang Zhou
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 3 of the License, or
(at your option) any... |
d567b075f875d7bbbaf318bfc1b8dc41b459861ea4ad0479980336d0c28bffa3 | C++ | 138,815 | 3,093 |
#include <fstream>
#include <iostream>
#include <string>
#include <stdlib.h>
#include <vector>
//#include <random>
#include <bits/stdc++.h>
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <Eigen/QR>
#include "time.h"
#include "genotype.h"
// #include "mailman.h"
#inclu... |
0c9198277b7c1c9f528f5970215f04329867d0fd5818b035636e9ee8947f21cd | C++ | 142,960 | 3,540 | #include "simulation.hpp"
#include "model/ohmiccurr.hpp"
#include "mpi/dist/tetopsplit/definition/statedef.hpp"
#include "mpi/dist/tetopsplit/fwd.hpp"
#include "util/common.hpp"
#include "util/vocabulary.hpp"
#include <Omega_h_defines.hpp>
#include <limits>
#include <memory>
#include <numeric>
#include <Omega_h_for.h... |
ec38f339b55112a1ed7064ab9cf0d650a2b8491a1ead4fc646eba3ec4ad49972 | C++ | 149,896 | 3,374 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
610a3c03d9b9b2a8e50d1b6c3f6a0c5b8d0c4bbe81abb71dab8d0199e3f2eeb4 | C++ | 158,165 | 5,386 | /// Json-cpp amalgated source (http://jsoncpp.sourceforge.net/).
/// It is intended to be used with #include "json/json.h"
// //////////////////////////////////////////////////////////////////////
// Beginning of content of file: LICENSE
// //////////////////////////////////////////////////////////////////////
/*
The... |
1af80d56157b461cabb20db88e4627d06729a7bdfba3d6f4611c8faa1a125a6e | C++ | 182,765 | 5,445 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
3ce78178d21f6554057943fbcbb11a629055fc80326d64dfc55324fa904adf67 | C++ | 185,401 | 5,524 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
e2247618221d92de7d67e7ebe83d49a2afc5ece43baddde7d0c41e937fa7d1ce | C++ | 191,931 | 4,919 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
23b420dc928989b7cf166fc41bd3b32d4820b70dcca1cc5546b2b5cdc53ff700 | C++ | 197,254 | 3,927 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
3063fba6a121b35ad407517ed57611961a1f6f11aae9197c621be572c9df18cd | C++ | 200,000 | 47 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
450d3c1df789c678d5bb7ae17188cfb030b585b2c9ff7c7e18c93098b865eb51 | C++ | 200,000 | 3,565 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
54ac47c9df196b9733ed8766388c326e1eba947ae668bbebe3342de231c2f875 | C++ | 200,000 | 4,451 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
739fdd3e546442abf4d0be7d100718e83d52129816f885485ec0dd99a913e9c5 | C++ | 200,000 | 6,084 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
83966490b1544eb818c1d93e23ab949c845c9a5e693f7785fb38ea29138c35bf | C++ | 200,000 | 6,079 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
afb3d6cdcb5fcb883874a37af5f358f9219d92ba87add7c25344d010d78ffb2b | C++ | 200,000 | 5,698 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
b940719662d22094f27eb273d2854ee332983e497ad6c199d82bcd3df5f54e1e | C++ | 200,000 | 5,074 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
dea4a0bfa62085a56c7d9cf004e1a92f77c3b0dc2f0432a898e18d493996c684 | C++ | 200,000 | 5,342 | /*
Bayesian Functional GWAS --- MCMC (BFGWAS:MCMC)
... |
eca2dede09321b034aaed281dc1d751a45cde8a476469419d9f6783cd349431e | C++ | 200,000 | 5,761 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
fa1f0b42e5ee24d92928adb5dee1b13657515c607ad90d3ac83c99c85917c962 | C/C++ | 88 | 5 | #pragma once
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "setupTests.h"
|
6765417a16172a59929f6531e201e061b7c760a4f6b9aadc48afa72a770d1e08 | C/C++ | 124 | 9 | #pragma once
#include "Core.h"
namespace rayx {
RAYX_FN_ACC double RAYX_API dpow(double a, int b);
} // namespace rayx
|
f0d7627f91b1355bca51eabcdc31cd21b640ab2ea9f59931f4c538cf08af79d9 | C/C++ | 141 | 12 | #ifndef PRINTABLE_H
#define PRINTABLE_H
#include "std.h"
class printable {
public:
virtual string to_string () const = 0 ;
};
#endif
|
20c220a709b236dd5e4f231f54a86a0fb06192cad94cce40d6fa5fba1bb0127c | C/C++ | 151 | 12 | #pragma once
#include "LightSource.h"
#include "Rays.h"
namespace rayx {
struct RAYX_API RayListSource {
RaysPtr rays;
};
} // namespace rayx
|
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