sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
41f704129715d2ecffc27596f6a4aaf036220f051963d33cb31d19d0f395c772 | C++ | 11,811 | 372 | // ***************************************************************************
// bamtools_pileup_engine.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 9 March 2012 (DB)
// ---... |
0a953b16fdd146b986afae89623d1fc3d97f4442096ac52a1475ec7e50a5adf9 | C++ | 11,884 | 310 | /* 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... |
5a2f8b19ed11d51aa5a396d705ad5f361d3f81e6f65bc5517f80af070918b6d2 | C++ | 11,952 | 262 | #if defined(WIN32) || defined(_WIN32) || defined(WIN64) || defined(_WIN64)
#define WINDOWS_LEAN_AND_MEAN // Please, not too much windows shenanigans
#endif
// Standard libs
#include <string>
#include <cstdio>
// Trimesh for model importing
#include "TriMesh.h"
// Util
#include "util.h"
#include "util_io.h... |
06c6bfc6f2d6ff3174f90707a6af2143c77fedd3904042a453cc85e4460e4464 | C++ | 11,985 | 437 | /*
* 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... |
70a92e5b88872b2bb457b049fe6e5b78240f13ef5cf790f3f96cc906b7e9e74f | C++ | 11,997 | 429 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullHyperplane_test.cpp#4 $$Change: 2064 $
** $DateTime: 2016/01/18 12:36:08 $$Author: bbarber $
**
*************************************... |
e4d07846a95ef706941ca1324f7623b2f55256c3f6cb6d9fdfbfb86d9f092bfa | C++ | 12,043 | 352 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/Qhull.cpp#4 $$Change: 2078 $
** $DateTime: 2016/02/07 16:53:56 $$Author: bbarber $
**
**************************************************... |
26c5b137f1175cea32c51aa347a4e1551898815bdca3e7aae3f3a4b3b538bd72 | C++ | 12,077 | 380 | #ifdef _OPENMP
#include <omp.h>
#endif
#include <time.h>
#include "labeling.h"
#define _USE_MATH_DEFINES
#include <math.h>
#else // Release[hÌê
#pragma comment( lib,"opencv_world411.lib") //
#endif
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/imgp... |
9048b00f311ae47976f8533c0ea321719ef842cda742764182b7e6a22443b7ea | C++ | 12,092 | 425 | /* 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... |
13c29318925ee00646c91dc77efa1a9c9e4ae3f7d4b328cbd0d6f0b7a9dbb695 | C++ | 12,099 | 254 | #include "RefractiveIndex.h"
#include "Throw.h"
namespace rayx {
// The materialTable table consists of all the entries from the Palik & Nff tables for all materials that were loaded into the shader.
// Thus, when you want to get some concrete palik entry for a particular element, you need the materialIndices table ... |
ef61cfe2c5e15f12613331e0ba98952ad8e8c8a381119b9ea90455aac8ef6dad | C++ | 12,100 | 280 | #include "RayProcessing.h"
#include <imgui_impl_sdl3.h>
#include <imgui_impl_vulkan.h>
#include <algorithm>
#include <cmath> // for std::pow and std::log
#include <numeric>
#include <unordered_set>
#include "Application.h"
#include "Beamline/Beamline.h"
#include "Colors.h"
#include "Debug/Instrumentor.h"
void disp... |
af1ca70ccd903b599539e62ccba821eefb4f01cffe96e0b8c55d034d8c42a1cf | C++ | 12,101 | 318 | /*
* 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... |
8138e16e4066b8b798c7c830ff654818d38700d329a363f29de920ab27e3a932 | C++ | 12,119 | 386 | /* 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... |
bc455a70793da6fcad525c0a9b60b896edd693bad7bb52b16dac7ab186b75e3f | C++ | 12,131 | 434 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullSet_test.cpp#3 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
********************************************... |
2473680f9bb3fb0990b74b2038680dcaf41348f3aeb7df9a78dc44e74900cad7 | C++ | 12,144 | 260 | #include "Behave.h"
#include "Crystal.h"
#include "CutoutFns.h"
#include "Diffraction.h"
#include "Efficiency.h"
#include "EventType.h"
#include "LineDensity.h"
#include "Rand.h"
#include "Ray.h"
#include "Refrac.h"
#include "RefractiveIndex.h"
#include "SphericalCoords.h"
#include "Throw.h"
#include "Transmission.h"
... |
9a8b544462bde5a6ba185fa2418350f8cc5fe5dff7270c36935b80d8077a75ab | C++ | 12,157 | 378 | /* 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... |
faa27e3fae4beef771c75a2090779a2c105c559e13530268a27a33d805ef22a3 | C++ | 12,198 | 391 | // ***************************************************************************
// bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 27 March 2012 (DB)
// -----------... |
a7770112fd3b7f4f525376dad5d740e3eecf9b400068f79e195f58f44eb76587 | C++ | 12,221 | 291 | #include <fstream>
#include "Shader/LightSources/DipoleSource.h"
#include "setupTests.h"
void checkEnergyDistribution(const Rays& rays, double photonEnergy, double energySpread) {
CHECK(rays.energy.size() > 0);
for (const auto energy : rays.energy) { CHECK_IN(energy, photonEnergy - energySpread, photonEnergy ... |
caa842f0456ec3e22372ad9151d7a83e5dd300becd70484bdfce2fdb26bca18d | C++ | 12,269 | 336 | /*
#################################################################################
#
# 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... |
bf1eeb986eca6375c2e3cde9ceeaa01267de4e9b3becd037009bae7c71f5d87d | C++ | 12,414 | 425 | /*
#################################################################################
#
# 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... |
66f5f405ba1f942179d359bf6d3ab27095a68b0d8e2f40a20d423389f98ef61b | C++ | 12,430 | 425 | /*
#################################################################################
#
# 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 ... |
b0cd5e10363ebfd5128f4cfeb28a2044c0dfa0b866490d9a6bc336d1665aa64c | C++ | 12,451 | 280 | /* 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... |
5fec8a02e748ebeb0e8928d003bae91376cd0c491275c62b59c48e2b7703d0df | C++ | 12,472 | 447 | // ***************************************************************************
// HttpHeader_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 13 January 2012 (DB)
// -------------------------... |
ef5f9a91601f9cff832c45bb41dcca983e60c74676935811697e83985c4f6cad | C++ | 12,505 | 418 | /*
#################################################################################
#
# 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... |
834f4991ac956f4beaa47c0a3d6b667b539a0fd2af669045c3925d8c68bca58b | C++ | 12,521 | 418 | /*
#################################################################################
#
# 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 ... |
e585c43074308416907546fbfb233194246d4f7885a6418ea5ab78575813554e | C++ | 12,541 | 436 | /*
#################################################################################
#
# 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 ... |
1c64e238cdb1ce8a4bfb60162b770f985f6ff546e5d001a5d8fee6bbef9173a2 | C++ | 12,568 | 436 | /*
#################################################################################
#
# 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... |
2e836bf5a7fc6ce978b422bfe5049720f53a7e3af8dbba96a91311d4bd11f70b | C++ | 12,591 | 315 | /*
#################################################################################
#
# 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... |
9efe8a9ac16dae01bd643bcf5c0087305d2e85c69caa3510e6c54857be68b24e | C++ | 12,597 | 413 | /*
#################################################################################
#
# 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 ... |
b81f66ab0a85b506ba3088b491816725642e28d9cb5e685026aeb61cfdeefd2b | C++ | 12,641 | 416 | /*
* 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... |
c565ff68185c18b578dcb60fd603e6c0597e4550c8f46f328709fbaa1d92947e | C++ | 12,816 | 423 | /*
#################################################################################
#
# 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 ... |
e5d9e72b8d3d3e6c4f687cbb1b5613a02e1d9c9e76afdfdd0ff0663577a52e64 | C++ | 12,816 | 312 | // ***************************************************************************
// bamtools_options.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011
// -----------... |
ae8e261dde319390597fb34ad98fcf89f9a2e58a0f33a6253cca36cd2c5272f8 | C++ | 12,857 | 291 | /*
* 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... |
44d9fc58e1cae9522cae2b6eb356e550668dd9a97140852a7fb10532c03f86ac | C++ | 12,883 | 305 | /* 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... |
686feab099019829721c215fd4c056fbf458f859033bb85a65260e3086f23417 | C++ | 12,944 | 315 | #include "cpu_voxelizer.h"
#define float_error 0.000001
namespace cpu_voxelizer {
// Set specific bit in voxel table
void setBit(unsigned int* voxel_table, size_t index) {
size_t int_location = index / size_t(32);
uint32_t bit_pos = size_t(31) - (index % size_t(32)); // we count bit positions RtL, but array ind... |
9730df1116c0376f023bb2a35afd1adef8086721030ba90d81ce7d50ac161f50 | C++ | 13,029 | 433 | /*
#################################################################################
#
# 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... |
ea8f3de8cf3c9fc3bfa295d613d783ef499289e7bf25a5a3034ca3a300b9ade7 | C++ | 13,058 | 373 | /* 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... |
d5e2dd537dcac9b2ed56a74cf7bc2b784862d1c54af3bf5f0b876970bf9a5501 | C++ | 13,081 | 423 | /*
#################################################################################
#
# 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... |
485a45a669b6fb8e2fb999901e2dda9a683c90f3d9dbd948af1d5ebb0672a8d4 | C++ | 13,086 | 348 | /* 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... |
c5a92736922e98f13a277549a75660e4f5e5ab4c50cc8a8d0669ab44a1508230 | C++ | 13,089 | 413 | #include "matmult.h"
#include "mailman.h"
#include "helper.h"
#include <iostream>
#include <thread>
#include <vector>
#include <Eigen/Dense>
#include <Eigen/Core>
#if defined(SSE_SUPPORT) && SSE_SUPPORT == 1
#define fastmultiply fastmultiply_sse
#define fastmultiply_pre fastmultiply_pre_sse
#else
#define fastmult... |
d4badaeb32c4a7b8579982df5c26874caf5f44a13d1d9c337dc81a421d35c83b | C++ | 13,128 | 435 | /*
#################################################################################
#
# 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 ... |
0c24bcbd2effe0e97ebb2445d84f6f781672b52672a583f4b79495a0f122f2f5 | C++ | 13,166 | 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... |
5127198bac773b33910e2dff3f250dd1dee28237e62322f406df7d4cdbe4baa2 | C++ | 13,233 | 465 | // ***************************************************************************
// TcpSocket_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 5 January 2012 (DB)
// ---------------------------... |
bdf2dac5326905aaf141a35e93b28d12f7b4118f4864906a0a3b4036384449e7 | C++ | 13,270 | 437 | /*
#################################################################################
#
# 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... |
1296b197320f419177930b8aead9d20ce03332017dd194011f21e580b19783d7 | C++ | 13,286 | 437 | /*
#################################################################################
#
# 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 ... |
46b6a224dc4ee8bd688efb97650a582a1ae30ff2ad048ae89460707946216a8f | C++ | 13,312 | 330 | /* 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... |
4a74be8d442e7bf18d9cb63b310611a482769f134480fea77214a3a6873c4cf6 | C++ | 13,314 | 421 | /*
#################################################################################
#
# 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... |
2a332d396b683dcda2c023c2908c5659932be50bc2a3fd21e8254a4f48ce1b08 | C++ | 13,350 | 375 | /*
#################################################################################
#
# 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 ... |
f1b0e427aa9678b25eb2e2efc875ca90ac82d8b9a713dc3a86c1d8ba2bc706e2 | C++ | 13,359 | 537 | /*
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 ... |
914d77da7fd7dd72903c96a68065d1eb2c5dc60edabf3b316a837451a24e121f | C++ | 13,403 | 423 | /*
#################################################################################
#
# 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 ... |
893b77185b1e16c255c7b91935e2e536b81504f70a897d25561f8c65506f97d3 | C++ | 13,414 | 401 | /* 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... |
b04e38d297ba7457677d98840aa64069e0fbe5d51594b60e89e20c0406394cd6 | C++ | 13,414 | 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... |
65949b1877de8a9f8de560bbb4b7081ccc71e740b4035bdd62a573262d7191ac | C++ | 13,493 | 519 | #ifndef _CRT_SECURE_NO_WARNINGS
#define _CRT_SECURE_NO_WARNINGS
#endif
#ifdef _WIN32
#include <assert.h>
#include <d3d11.h>
#include <d3dcompiler.h>
#include <stdio.h>
#include <cassert>
#include <cmath>
#include <algorithm>
#include <vector>
#define FAST_OBJ_IMPLEMENTATION
#include "../extern/fast_obj.h"
#include... |
7345ab8d0d4c7b12f8df5c16ce6369c945e862385eb3840849301a0368eaf11d | C++ | 13,547 | 407 | // ***************************************************************************
// BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 29 July 2013 (DB)
// ------------... |
26cd0326152488a6f10eac3f52e430f41bd645ea35a54e126556877c5ec720f1 | C++ | 13,578 | 294 | /* 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... |
98654756a7a3e1872a08ad5a86316392397ffedbf2461db6de4950bc74599517 | C++ | 13,597 | 444 | /*
#################################################################################
#
# 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... |
cbbd62514bb8f766c0e00ee07b9ed20af5c3dbf9119c7fb64829cca99a441a49 | C++ | 13,626 | 381 | /* 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... |
bcaba1475cfb91ecd68cc6a142aa6c758b45282448e1ad157ffa668abbd271b6 | C++ | 13,627 | 394 | /* 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... |
9227d4caec27cd56dcac9665fc0519765b1c3765c856029fe88c64f036f1cd62 | C++ | 13,704 | 478 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/PointCoordinates_test.cpp#2 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
************************************... |
26e888fde9cb3b99a1ae035201c27a2816909139df40d0468e6baa9e54031cac | C++ | 13,768 | 539 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/Coordinates_test.cpp#2 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
*****************************************... |
0c7bd211b47e86a8aca498ab0d743e89ee4b65675e07055309a7d01157fc730d | C++ | 13,778 | 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... |
ef60de24364ba51a03d2888a5cad490e75ec2db320957e077eeb501cffe21f14 | C++ | 13,843 | 685 | /*
* 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... |
ff6cd138159c79bd72916a6d2d8f46fafa69cadb5487d1d3669f90843ed71fce | C++ | 13,927 | 447 | /*
#################################################################################
#
# 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 ... |
58558e352efbbb099972d644f090ed694f2a0a33b0272826c90f79578473aa3d | C++ | 13,931 | 453 | #include "../src/meshoptimizer.h"
#include <algorithm>
#include <vector>
#include <stdint.h>
#include <stdio.h>
#include <string.h>
#include <time.h>
#ifdef __EMSCRIPTEN__
#include <emscripten.h>
double timestamp()
{
return emscripten_get_now() * 1e-3;
}
#elif defined(_WIN32)
struct LARGE_INTEGER
{
__int64 QuadPa... |
687e4abf185b53ea0231b0f675ee4f1bdf866b5b445805747a90c1a9da3d7c16 | C++ | 14,054 | 519 | // ***************************************************************************
// BamFtp_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 December 2011 (DB)
// -----------------------------... |
1f7e3267bdc895868d534b5bb7de856176ea96f0c8eda00fdec42db55889f966 | C++ | 14,128 | 377 | #include "TerminalApp.h"
#ifndef NO_H5
#include <highfive/H5DataSet.hpp>
#include <highfive/H5File.hpp>
#endif
#include <algorithm>
#include <filesystem>
#include <memory>
#include <stdexcept>
#include <vector>
#include "Beamline/StringConversion.h"
#include "Debug/Debug.h"
#include "Random.h"
#include "Rml/Importer... |
618429ef4db8ab9b16fde4e73dcf425d89452acbf103085478bc8b1761fa6689 | C++ | 14,171 | 467 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <string.h>
// This work is based on:
// Tom Forsyth. Linear-Speed Vertex Cache Optimisation. 2006
// Pedro Sander, Diego Nehab and Joshua Barczak. Fast Triangle Reorde... |
205a0b39694816ee6b134afd1e211ed5b7eda76dbce0bb3b92e4bc5db08d14b1 | C++ | 14,188 | 380 | /* 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... |
75afec6c4433c799a345e27aa4a8f4e4c9fce317224eb7e158a60cfbbbed2883 | C++ | 14,207 | 293 | /* 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... |
6773c1ed553799742a6ccf7015118a0401923ca858ceba5ba318c19468b025bd | C++ | 14,209 | 447 | /*
#################################################################################
#
# 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... |
37e7c33287a6187e8814d90ad2d90cdcd26ef0d2628734fac0b8ed586780833c | C++ | 14,279 | 327 | #include "Texture.h"
#include "Debug/Debug.h"
#define STB_IMAGE_IMPLEMENTATION
#include <stb_image.h>
#include <utility>
#include "Buffer.h"
#include "Debug/Instrumentor.h"
#include "Rml/Locate.h"
Texture::Texture(const Device& device)
: m_Device{device},
m_extent{0, 0},
m_format{VK_FORMAT_R8G8B8A8... |
7ebaae085cc349c0d8d724a4c41f4fc3ab86919f00c687fdc76a7b5a16786c6c | C++ | 14,380 | 463 | /*
#################################################################################
#
# 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 ... |
ff5540bbdf3ce664951d9798fd211ea866c16fe60be3cb01031183df3b49f24e | C++ | 14,394 | 464 | /*
#################################################################################
#
# 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... |
d1130ba988e2f3fb85c140ed5b7df8715b6a8b204176feb2eecaf773b98c4f28 | C++ | 14,415 | 444 | /*
##############################################################################
#
# Optimize MARA model parameters (find maximum likelihood estimates)
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREATED: ... |
bc56996c99706daab44e468c9f4a51550c036d9aa89e4aeea0e448cac5e3284c | C++ | 14,418 | 415 | #include "geom/tetmesh.hpp"
#include <cmath>
#include <iostream>
#include <limits>
#include <memory>
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
#define COORDS v_coords
#define TETINDICES t_indices
#include "sample_meshdata.h"
#undef COORDS
#undef TETINDI... |
5b758d9c768154735a988f06512fb8223d5a41b61c2e56c0f54827d700f6763b | C++ | 14,431 | 381 | /* 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... |
93c3f473055767144f3a20f21d2df924aff540f775d13a7f02f78c98c5237073 | C++ | 14,457 | 384 | /* 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... |
c45388d5c9481b758de2685bb33fcd3778414e8eb9c430b7f5e6cbd33269801c | C++ | 14,467 | 470 | /*
#################################################################################
#
# 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... |
26b582fc6e9d7c2f7aaf992cc997a7a6d61fa35cd4a0058e30c62d84446b69ee | C++ | 14,483 | 470 | /*
#################################################################################
#
# 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 ... |
4770c96f10d2cbcccaa60ab283c6e89012fa115c73712feded90e3b001125881 | C++ | 14,498 | 433 | #include <stdlib.h>
#include <iostream>
#include <vector>
#ifndef GDATA_HPP_
#include "gdata.hpp"
#endif
#ifndef TUI_HPP_
#include "tui.hpp"
#endif
#ifndef SUP_FUNCTIONS_HPP_
#include "../sup_source/sup_functions.hpp"
#endif
string cppgd_version = "1.2";
using namespace std;
void show_help() {
string help_info... |
7941e00d68e7a7067b85441db9cea8ef6df259e360108b90459fcd28b48ae0f0 | C++ | 14,501 | 515 | /**
* Copyright (c) Facebook, Inc. and its affiliates.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
#include "starspace.h"
#include <iostream>
#include <queue>
#include <unordered_set>
#include <boost/algorithm/string.hpp>
usin... |
ac006f0040c823262e221d6fbef0b055f7f89a4addb0b845e282d19e9bc80daa | C++ | 14,524 | 364 | #include "propensities.hpp"
#include "kproc_state.hpp"
#include "mpi/dist/tetopsplit/kproc/kproc_id.hpp"
#include "mpi/dist/tetopsplit/mol_state.hpp"
#include "util/debug.hpp"
#include "util/vocabulary.hpp"
#include <algorithm>
#include <limits>
#include <variant>
namespace steps::dist::kproc {
//------------------... |
fa4da7c759210d1ddbe2c8d5a300c11c8e908122f98dc763653378d1011b1261 | C++ | 14,532 | 505 | /*
* Copyright (C) 2010-2011 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 la... |
fca5641b5b3e845801ce162344cca9a1a697117c45da69a590c6a8ef5a0df53d | C++ | 14,571 | 528 | /*
#################################################################################
#
# 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... |
4179e88d73d65803aa0b1d3c22b384573621e43fbdead694523e2cf61287a736 | C++ | 14,579 | 458 | /*
#################################################################################
#
# 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 ... |
6ba56c8df4dbbdc4bc7f6107eb528d5cf1242414c671487be1e38f3764fca466 | C++ | 14,587 | 528 | /*
#################################################################################
#
# 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 ... |
d38eeda86452a592b1b15b951bc3e759c06f475990c55fdb3d58c45e36523037 | C++ | 14,614 | 440 | /*
* LiquidCrystalFast.cpp, version 1.1
*
Copyright (c) 2010 John Raines
Minor changes by Paul Stoffregen <paul@pjrc.com>, Copyright 2011
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundat... |
0606216b67d0e81d255d43e5f5b81a141cc7a2fdfeffcba236197e337f9827de | C++ | 14,621 | 421 | /* 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... |
418f93d362a9cefc73e51b354d018acf6666182d8e1dbfc4501c9570c8069121 | C++ | 14,694 | 313 | #include "DesignSource.h"
#include <filesystem>
#include <memory>
#include "Debug/Debug.h"
namespace rayx {
namespace {
std::string getUniqueUnnamedSourceName() {
static size_t counter = 0;
return std::format("<unnamed_source_{}>", counter++);
}
} // unnamed namespace
DesignSource::DesignSource() : m_elem... |
e24a2063dfaf32fcffc14e0beebb76ceb9191a9ac145f59d3b2ec2a14006790e | C++ | 14,788 | 470 | /*
#################################################################################
#
# 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 ... |
f406e2b566f3bc9dc5ff586df49cb1439b3d76572f7cc3a3d873b57d9f097163 | C++ | 14,875 | 368 | /* 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... |
01f383e9eb4eb24302756d0034d781ca7f7e653f1364b2f587c8d7c8bac342fb | C++ | 14,914 | 359 | #include "sreacdef.hpp"
#include "model/chanstate.hpp"
#include "model/complexevents.hpp"
#include "model/complexsreac.hpp"
#include "model/ghkcurr.hpp"
#include "model/model.hpp"
#include "model/surfsys.hpp"
#include "patchdef.hpp"
#include "statedef.hpp"
#include "util/vocabulary.hpp"
#include <type_traits>
namespa... |
22901cbcf824771595681cfd3fbaf1e2bc82a5dcfded3cd4faf645be1f7eb811 | C++ | 14,916 | 576 | /*!
* @file Adafruit_TCS34725.cpp
*
* @mainpage Driver for the TCS34725 digital color sensors.
*
* @section intro_sec Introduction
*
* Adafruit invests time and resources providing this open source code,
* please support Adafruit and open-source hardware by purchasing
* products from Adafruit!
*
* @se... |
b7fd362131039f003c4821d78205c39c76afc1c3be0242fe58872281ce5cc701 | C++ | 14,918 | 508 | /*
#################################################################################
#
# 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 ... |
b4cd8b05a6977c84a6ad16ee88d60407ed91167b30b12628707129deaa62287c | C++ | 14,931 | 322 | #include "Renderer.h"
#include <array>
#include "Buffer.h"
#include "Debug/Debug.h"
#include "Texture.h"
Renderer::Renderer(Window& window, Device& device) : m_Window(window), m_Device(device) {
recreateSwapChain();
createCommandBuffers();
initializeOffscreenRendering();
}
Renderer::~Renderer() {
vk... |
5313d54b61d166c972639179965eccb7cb3b16aace2244386e7a6d5ab14f9e44 | C++ | 14,945 | 508 | /*
#################################################################################
#
# 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... |
fbe3dc79e9331fd43f82f291dea252cf9c56225f2862baba4defed7901bcfcbd | C++ | 15,039 | 484 | /* 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... |
49c108e997ba02740168d4ee43a2af9f5d36c6f40a78e60f77105876b4b79923 | C++ | 15,048 | 467 | /*
#################################################################################
#
# 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... |
939a445fee503403a95faf1b8127f2fdfccbb2e3757771577697ce2c28afd1b1 | C++ | 15,064 | 393 | /* 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... |
8738d4533492139caaeafd1fc5fbda6502e6dc0ac1b4914a13b14bc081ca975b | C++ | 15,066 | 377 | /*
#################################################################################
#
# 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... |
168fefc81f229d4a2bd320881ccc81505f02d1fe1aaba25c028daa4dbf162dcf | C++ | 15,082 | 377 | /*
#################################################################################
#
# 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 ... |
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