sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a079d6bad604466593ffedfc3ebd56a89f03f9fe15fdcbdfe7bb3c2fee304366 | C++ | 9,278 | 399 | /*
* 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... |
fd28dd8756a8e438f120d0bbac0d55a31327e9cd1f87fe663ed32a275dafdb3c | C++ | 9,285 | 372 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <stdlib.h>
#include <string.h>
static const char* kMimeTypes[][2] = {
{"image/jpeg", ".jpg"},
{"image/jpeg", ".jpeg"},
{"image/png", ".png"},
{"image/ktx2", ".ktx2"},
{"image/webp", ".webp"}... |
444ac12faef0c09265f7f1b0e56c695e242c4771b708fa160838f69b6b46f7d4 | C++ | 9,307 | 208 | #include "rssa_operator.hpp"
#include <functional>
#include <vector>
#include "mpi/dist/tetopsplit/definition/reacdef.hpp"
#include "mpi/dist/tetopsplit/kproc/diffusions.hpp"
#include "mpi/dist/tetopsplit/kproc/fwd.hpp"
#include "mpi/dist/tetopsplit/kproc/kproc_state.hpp"
#include "mpi/dist/tetopsplit/kproc/reactions... |
c313777c8679112475992ae2c363273077d60e590ab9d2dccb680ab17c17ef1a | C++ | 9,335 | 374 | /*
* 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... |
7c9eb712c010bd7fb3e0e25d8b3c75ca4055c00ec358f0e48f2841a175d710ea | C++ | 9,346 | 304 | /* 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... |
d0105466265c21691539e4f10a12dfa4b84d1473f223a50e67716cbb6990cc2d | C++ | 9,363 | 316 | /* 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... |
986d7bbdddd229933b218472b99d71cc4193171dd27e7bfa3f05681e89f642b3 | C++ | 9,382 | 262 | /*
#################################################################################
#
# 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... |
0418e2b91d6595204dc7aceb11d06f7cceeef5be3657edbe26f23f2f3ec30312 | C++ | 9,397 | 316 | #include <cmath>
#include <limits>
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
#include "math/point.hpp"
#include "math/tetrahedron.hpp"
#include "math/triangle.hpp"
using namespace steps::math;
TEST_CASE("Point3d_constructors") {
point3d p1;
REQUIR... |
d4bacf5285326c1faf9e13107fff3865cf5033737b928e3bb83dead5cffeb7f1 | C++ | 9,398 | 262 | /*
#################################################################################
#
# 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 ... |
1c0d5bade0033180c21c877e0c0f7fd14c07c313b1ab5b155f549e0518ac8634 | C++ | 9,416 | 245 | /* 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... |
7c272dce9dbc50af6bf7b971f9fbd92d5b7e0f1f65505bcfeaef880ee0017c07 | C++ | 9,432 | 256 | /*
#################################################################################
#
# 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... |
0cb42c96c76c96eb5c277a9c1d9aa2c379f0c4084077073be880d5a780ed2767 | C++ | 9,492 | 273 | // ***************************************************************************
// SamFormatParser.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 December 2011 (DB)
// ----------------------... |
c2f99a3d252c27c8e4f7f7335d5a836eb5d987b8a19909fa7e0427fcdc3d348d | C++ | 9,510 | 356 | /*
* Copyright (C) 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 later v... |
08b85a1a39bfd9d517df8f779fcacd940b5282d389c8156d73c30a5ba52ccf9d | C++ | 9,560 | 336 | /*
#################################################################################
#
# 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 ... |
24560e486357ad802ecb6f3abbce72bcbcdf7260cf938b33cdfd7f088b99faab | C++ | 9,569 | 299 | /*
#################################################################################
#
# 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... |
99f24a69f5ab0bca1ccf42e50bd737f32a47b83920e325afeeb96271ae411aca | C++ | 9,569 | 278 | /*
#################################################################################
#
# 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 ... |
e71c1502b5e2615e1b0bf0c6a89174f634e17507eb6d57e966ff5146d9167c5b | C++ | 9,577 | 348 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/PointCoordinates.cpp#3 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
***************************************... |
9551fe9aed6e5b995f6fd1685a93198f31b0ab122b2e92718852d594a61d9193 | C++ | 9,609 | 337 | /*
#################################################################################
#
# 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... |
d0d4c3b30419f276e29444760a74529dcfd3fe63fe0c956442cbabcc81743ad8 | C++ | 9,610 | 232 | /* 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... |
69930c91ee7c97bc5cd62f4755446d796e514f5c1bc16836310cb659d414ebfd | C++ | 9,621 | 283 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullFacet_test.cpp#4 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
******************************************... |
466e5adb85594f2c0aa4fd3bd707f6e7d7035351856094741b853f9473717608 | C++ | 9,719 | 261 | #include "distcomp.hpp"
#include <Omega_h_array.hpp>
#include <Omega_h_for.hpp>
#include <sstream>
#include "util/error.hpp"
#include "util/mpitools.hpp"
#include "util/vocabulary.hpp"
namespace steps::dist {
DistComp::DistComp(const mesh::compartment_name& compartment, DistMesh& mesh, double cond)
: DistComp(c... |
8aceaedb0381142aa5cc675f1b76055e6449de8e9c3064cc206ee24e1a493cd1 | C++ | 9,731 | 303 | /*
#################################################################################
#
# 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 ... |
76a64477bcf94c5984a853660322684c90788ea3a356e87a31681e13ae4f0673 | C++ | 9,740 | 311 | // ***************************************************************************
// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011 (DB)
// ---------------... |
0444f87f896ac7185d233c6974431d30a4f4b794cdf53a5e4520dc69926db992 | C++ | 9,757 | 388 | /* 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... |
c6ab2a5bc01608d99e748df1e0f3e9fe9ce11a037d5395ddad000012c777685a | C++ | 9,826 | 326 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include "../extern/fast_obj.h"
#include "../src/meshoptimizer.h"
#include <stdlib.h>
#include <string.h>
static void defaultFree(void*, void* p)
{
free(p);
}
static int textureIndex(const std::vector<unsigned int>& ... |
2c107a8ad19b6ab9d323d9602ec177b83b26316f89b3d8f3fc32088e09fe9b79 | C++ | 9,853 | 324 | /* 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... |
e83789290a8e74cdc3da40c6dbc002d4fcc58bdd383212cd5573de2471424458 | C++ | 9,874 | 314 | // ***************************************************************************
// SamSequenceDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011 (DB)
// ----------------... |
691c91b33f14edcb098c8a0463f52b989244d253390d7493458023722a7bac89 | C++ | 9,881 | 309 | /*
#################################################################################
#
# 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... |
e5009282c42a9fd99bfb90c02adbea9f870d896c3d996f079052845013bbb1aa | C++ | 9,895 | 356 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <algorithm>
#include <float.h>
#include <math.h>
#include <string.h>
static float getScaleDelta(float l, float r)
{
float d = fabsf(l - r);
float m = std::max(fabsf(l), fabsf(r));
return m == 0.f ? 0.f : d ... |
f90466bd088da6200289eea61efc5bb56074bd335ebb7ce76301866f68a28046 | C++ | 9,897 | 309 | /*
#################################################################################
#
# 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 ... |
fbdb11c894071c67681ecb2a36804c3d9bd0c44a9e53620c75500ea5c3d7dd8a | C++ | 9,931 | 281 | /* 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... |
fb1dfd16e0c8c1de5a458603a5eaec1614b10b352503f3027dab9a747f53e320 | C++ | 10,008 | 309 | #include "statedef.hpp"
#include <algorithm>
#include <sstream>
#include "compdef.hpp"
#include "complexdef.hpp"
#include "diffdef.hpp"
#include "efield.hpp"
#include "fwd.hpp"
#include "patchdef.hpp"
#include "reacdef.hpp"
#include "geom/dist/distcomp.hpp"
#include "geom/dist/distmemb.hpp"
#include "geom/dist/distm... |
141585b64e721829b281d0e89d82524d2dbbd4b821675199b891624e563040af | C++ | 10,054 | 224 | /* 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... |
93b25cac13e6c466abe140be56e682e8d06c31c01421a1f4c0f76d42aa85aeb9 | C++ | 10,085 | 305 | /*
#################################################################################
#
# 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 ... |
e3955fef3fcc4884371169d5cab79b52c5601d815dd35824edf98fe0471a4c2b | C++ | 10,085 | 281 | /*
#################################################################################
#
# 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... |
28e778ef3512cb4d28dd854388cc76e416e7d708d37f53f9ed037126630277c9 | C++ | 10,088 | 345 | /*
* 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... |
409f80672c31bbf0f0a8a7f8961365045b2ac10e9a73deca3876923bda94cf4e | C++ | 10,129 | 289 | /*
#################################################################################
#
# 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 ... |
4abe5793d0841420669fe5c0c2638bcdfcb1f031d63fca0647075ca16c19c295 | C++ | 10,163 | 353 | //------------------------------------------------------------------
// Released under the BDS License
//
// Located at http://sourceforge.net/projects/varflow
//
//------------------------------------------------------------------
//-------------------------------------------------------------------------------------... |
2acd51b8d04683175d42f4f62947435a541cf57bee7e2e84ec5b8953bbfd4aca | C++ | 10,181 | 305 | /*
#################################################################################
#
# 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... |
af4b3f144916a98197d15265e5253ff125ce4d8ce571cfa46a5f331102f2ea8a | C++ | 10,198 | 347 | /*
#################################################################################
#
# 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 ... |
18f290f242f40a0c221a2021ecc5d0955f86608bcd4136d6914b5a05803963ad | C++ | 10,226 | 245 | /* 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... |
9c497dca76edc709deb2754c9ea248fa2ae74f8eb7ba2d1abd226d733dbd46be | C++ | 10,268 | 348 | /*
#################################################################################
#
# 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... |
2666b0926ef4bcb36df361e8ba162f036dee40ea8649ea2d6ec1ee9978c750a4 | C++ | 10,329 | 312 | /*
#################################################################################
#
# 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 ... |
af94707783cbc73ffe0affe77a1f1bbb804e92a3278d25dad7782dc35f818038 | C++ | 10,343 | 454 | /*
* 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... |
e47f92f59c3024f28d10fdf1de2aefab17cabde4f9ae6cd96a6cbc584d5e77e9 | C++ | 10,406 | 323 | // ***************************************************************************
// BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 25 October 2011(DB)
// -----------... |
44bcb53c4d901c96f203a8757b259cbbdb3249d0ea625d64098764ecf3ffdddd | C++ | 10,441 | 317 | /*
#################################################################################
#
# 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 ... |
73ab99a3555c28da499dcd35890b77d6f2742674434782073ad4ad1ed830de79 | C++ | 10,449 | 275 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 l... |
533653e30eceb337b3d9aa41649262bfc42724ec404e410199c4a8f62ef8ab34 | C++ | 10,450 | 378 | /****************************************************************************
**
** Copyright (p) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullPointSet_test.cpp#3 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
***************************************... |
58856f55f96801ead5cb2547401c07557399bc3a94eec2f15508b9a5bb83831e | C++ | 10,526 | 436 | /*
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 ... |
9a03ff08fd33e7229c7ce9efb0e17e8a101b5239bbe6876147dc6cf66d13f8a3 | C++ | 10,532 | 317 | /*
#################################################################################
#
# 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... |
e539dc173c96e7428e296e298eae5f0bfb143e8c51c74bfeff91ff7ee1f0dca6 | C++ | 10,537 | 317 | /*
#################################################################################
#
# 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... |
ceb4b2676a6e80ad8c66b44b1f8d88ea60f65dfea7fb39608e5fbcd6019d6787 | C++ | 10,543 | 328 | /* 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... |
ece070666b5190dad8559b0a5227ed0155cea5f115c4aec37c7af023e26d7eea | C++ | 10,581 | 293 | /*
#################################################################################
#
# 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... |
2617ca9744635ecf4fbf16925afab6426e02883d11df19b2537ae93cc4ad88d1 | C++ | 10,605 | 245 | /* 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... |
fef2eca589954976cb429686c5c381ae46bc6e1371d5a660362ed79fccdda23a | C++ | 10,610 | 347 | /*
* 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... |
1edb51a7a778d9cc8632e09dc32236c92fb81edaded1b9676551e08f956a5cac | C++ | 10,655 | 295 | /* 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... |
1f51bb08acab690cb3413c117d64ec46517c3f326efd63920a3fe71da72f25d8 | C++ | 10,666 | 285 | #include "util_io.h"
using namespace std;
// helper function to get file length (in number of ASCII characters)
size_t get_file_length(const std::string base_filename){
// open file at the end
std::ifstream input(base_filename.c_str(), ios_base::ate | ios_base::binary);
assert(input);
size_t length = inp... |
980a73ebae14016d0d8dc3b0c7199781aa3f05fc73fea400e3a5f085a929e8fa | C++ | 10,672 | 344 | #include "matmult.h"
#include "mailman.h"
#include "helper.h"
#include <iostream>
#include <thread>
#include <Eigen/Dense>
#include <Eigen/Core>
#if SSE_SUPPORT==1
#define fastmultiply fastmultiply_sse
#define fastmultiply_pre fastmultiply_pre_sse
#else
#define fastmultiply fastmultiply_normal
#define fastmultip... |
a6ed5ec5ede5b210be99b6682ceef7925ce3de54087059e515c1c2fa9672a295 | C++ | 10,674 | 391 | /*
* 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... |
3e3661ec498308defac890f8cdcc642b698281667c7ed8574829b6dff5277246 | C++ | 10,684 | 352 | // ***************************************************************************
// bamtools_cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 December 2012
// ------------------... |
286ca398d27801d563e52bbc92f7d340772ac88a487e6ac0fdc9a8af9df68e9a | C++ | 10,711 | 453 | #include "auxillary.h"
#include <iostream>
#include <fstream>
#include <vector>
using namespace std;
// Read environmental variable file
// Inputs: Number of individuals, filename
// Return number of environments
int read_env (int Nind, std::string filename){
ifstream ifs(filename.c_str(), ios::in);
if (!ifs.is_op... |
9a9c5ad8fdd56f835b0478270d090db2a4b794966bcdb2b3c42af690d4cc750f | C++ | 10,751 | 284 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
0b1116b7e51a14c6295c1d50d442891f91258b5017719385796a315ec8d5bcab | C++ | 10,761 | 320 | // ***************************************************************************
// bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 24 July 2013 (DB)
// ----------... |
99d0852ff538d10bbbfe46164d2bf2ddff3cf9921cd4896c0b196d2c394c0f2c | C++ | 10,763 | 409 | /*
* 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... |
c4a7b85c5eca84db098652267de5b6c1ec1c82570816302cc81b271acf4b7eee | C++ | 10,807 | 308 | /* 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... |
61061bf0de744a25f07bbc9c9c31c50d3dd0642c1942186a4401338bcb13c146 | C++ | 10,813 | 275 | /* 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... |
676f7923c82fc92a521c0491ac454e87baf4d6b2f2a1b5d9e42b6614aeaca222 | C++ | 10,851 | 339 | /* 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... |
ebf8ca3b49d167bcdbd772dc52505b63dac9f4df14497652845bbfc7e0984a9a | C++ | 10,851 | 190 | #include "GraphicsPipeline.h"
#include <fstream>
#include "Vertex.h"
VkShaderModule createShaderModule(VkDevice device, const std::vector<char>& code) {
VkShaderModuleCreateInfo createInfo{};
createInfo.sType = VK_STRUCTURE_TYPE_SHADER_MODULE_CREATE_INFO;
createInfo.codeSize = code.size();
createI... |
34c3d5ed12ab0e7ac0edc7bf750d1a6727f2329b94fd0113d2e940cf8baa8845 | C++ | 10,855 | 334 | /* 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... |
203b84ad6043f2167ff534d8fdb7fdfe7b1b32fca1cb3c0f149deac2a65b9805 | C++ | 10,859 | 280 | /*
#################################################################################
#
# 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 ... |
2801769e850f5af12f545bdf5a0c73b90ce92fadbe48268a293f22d6f9787907 | C++ | 10,915 | 292 | // Copyright 2026 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
423dbb3cad9afd0b5105ea941f35825193008663d8eb7cfd3c137123ad2403bf | C++ | 10,939 | 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... |
e575e881b2b0492e254208dd3c9dc5f06948fda45a2011de55c776714b9461ea | C++ | 10,958 | 327 | /*
#################################################################################
#
# 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 ... |
216283c009a3078d8168dfb8b4f28593ab0c4c62a69f355fb6ac3c680204727c | C++ | 11,091 | 360 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/Qhull_test.cpp#4 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
***********************************************... |
9005ee0069ed8c56797606de80c0cd951ab55ffb608bc3af83c4e5b2517371b1 | C++ | 11,093 | 341 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <float.h>
#include <string.h>
// This work is based on:
// Fabian Giesen. Decoding Morton codes. 2009
namespace meshopt
{
// "Insert" two 0 bits after each of the 20 ... |
ea9dafb968c02e28845b74e0bb45c4e5542badf5dc1706b14bc54a1d1233d5db | C++ | 11,108 | 272 | /* 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... |
742817c463121e51705495bde4edf1ce73da93ead50e84702329f67afebc0997 | C++ | 11,202 | 321 | /* 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... |
2aeecf597e75b422bddad97e7cddd34993f500cbd54ce801e754efac305e392b | C++ | 11,236 | 333 | /* 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... |
9999237824a2fdc01929a05b2f805c304d91731f750dd2adf74899a47a938619 | C++ | 11,258 | 409 | #ifndef GDATA_CLASS_HPP_
#include "gdata_class.hpp"
#endif
void Molecule::error(int error_num) const {
switch (error_num) {
case 1:
throw runtime_error(
"Error M1: this molecule has no bonding data!\n");
break;
case 2:
throw runtime_error(
... |
fced664c3f5c652a3bda907f6fa91647f2f478b58b9473dc9367d6a3e6731f2d | C++ | 11,280 | 447 | #include "sample_matching.h"
#include "auxillary.h"
#include <iostream>
#include <fstream>
#include <sstream>
using namespace std;
//=============================================================================
// read_fam_ids: Read FAM file and build sample index
//==================================================... |
119ab4848225deaac5f69fed4f90ac4738f9a561ef74e6d89c9c2402ee15767f | C++ | 11,342 | 418 | // ***************************************************************************
// HostAddress_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 December 2011 (DB)
// ------------------------... |
335fb3adf8c96727b6e9f65bf12d9ab692dbfb4081b58a5175b09a55dcfe8592 | C++ | 11,359 | 286 | /* 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... |
950ab6662995b23cf482f512cd144c5c2fc9f72cf6cac4d9cf3e676ba8f363a9 | C++ | 11,413 | 361 | /* 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... |
6e2f60096835feae6964bb01e073c65460a4fae58f56b0769c91c3ff410b27e1 | C++ | 11,416 | 437 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullPoint_test.cpp#3 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
******************************************... |
299926eba9459eef06ff43bf3b65f4b22ed245c329bedaeb34c8f2a08db566b5 | C++ | 11,426 | 572 | /*
* 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... |
f1b2fd3e67a1b2f8f24d25a221b9106dcef6198273d1d27ff226ac6c17953586 | C++ | 11,445 | 323 | /* 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... |
bc4c5e2c3a1fa8c3226fbb34ceeeecb89e973431d069af224673f32c4bc7fceb | C++ | 11,507 | 441 | /*
* Copyright (C) 2010-2012 Regents of the University of Michigan,
* Hyun Min Kang, Matthew Flickenger, Matthew Snyder,
* and Goncalo Abecasis
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General... |
fb528f37a940429474279a823fd3c6c9ec8fd9d4e01b017be28c4529089010c8 | C++ | 11,511 | 337 | /* 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... |
cc5d547c362ffe4f6f0cbdce03893e935ff130bd7b812d13b28b7ea3fac2c7d8 | C++ | 11,556 | 365 | // ***************************************************************************
// SamProgramChain.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ----------------------... |
8a68766aa1bac245f8052bfa6db331614efe93e805d57b052a2f471fafad6aa9 | C++ | 11,580 | 508 | #ifndef _CRT_SECURE_NO_WARNINGS
#define _CRT_SECURE_NO_WARNINGS
#endif
#define FAST_OBJ_IMPLEMENTATION
#include "../extern/fast_obj.h"
#include "../src/meshoptimizer.h"
#define SDEFL_IMPLEMENTATION
#include "../extern/sdefl.h"
#include <algorithm>
#include <functional>
#include <vector>
#include <cmath>
#include <... |
7dcc0e132a76916fc05f1ffcf2e451e162cbd37ae82514aaa3c81d69683cc1a0 | C++ | 11,623 | 369 | // ***************************************************************************
// bamtools_utilities.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 October 2011
// ----------... |
9625bd9e074346b0fe1a274ee00174a55a1a9ab2f62a717e62c14d51b1117523 | C++ | 11,635 | 321 | /*
#################################################################################
#
# 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 ... |
7a6cda67cd5dc1b4de2a762f50ee7ac2304e7b09d202360481e44c3c1eef46d8 | C++ | 11,646 | 321 | /*
#################################################################################
#
# 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... |
2681ddfff45af582f96fb4884af3d3778af4a9deb5196760311dcf376ef91c2c | C++ | 11,661 | 283 | /*
* 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... |
a70412562f991133ce52b2833adee9de0a9029dc45312ada1eb5c2452dc4f3ee | C++ | 11,671 | 333 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <math.h>
#include <string.h>
// This work is based on:
// Pedro Sander, Diego Nehab and Joshua Barczak. Fast Triangle Reordering for Vertex Locality and Reduced Overdr... |
bf950c6f56632b76f949f18191741d32bb5a87e02c269d5528cfb578c504874b | C++ | 11,671 | 240 | #include "diffusion_operator.hpp"
#include <random>
#include <Omega_h_for.hpp>
#include "geom/dist/distmesh.hpp"
#include "math/distributions.hpp"
#include "rng/rng.hpp"
#include "util/profile/profiler_interface.hpp"
namespace steps::dist {
DiffusionOperator::DiffusionOperator(DistMesh& t_mesh,
... |
13789680b95ef74fe515238eb499c2236abc31d45dac964d693b335771602227 | C++ | 11,692 | 246 | #include "mex.h"
#include <math.h>
#include <vector>
#include <queue>
using namespace std;
inline double compR(double DI,double *p, double t, double *a) { return (1+a[0] * sin( a[1] * 2 * M_PI * t / 1000)/2)*(p[0]+p[1]*(1.0-exp(-DI/p[2]))); }
inline double compD(double DI,double *p, double t, double *a) { return (1... |
0f79f1daf572010752056d7ee8f46f6794a299e5fce98dd5982dadcc63646cf9 | C++ | 11,740 | 414 | /*
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 yo... |
66d873139efdd969d583fd9d56969d76a8b7c64071f44dca0f4e7895cff97731 | C++ | 11,779 | 353 | /*
Bayesian Functional GWAS with Summary Statistics --- MCMC (BFGWAS_SS: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 th... |
4480cea9a4bbc778009de0bc79566ef4d87efab4953cf66feb14961e580748ce | C++ | 11,806 | 325 | /*
* 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... |
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