sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
17e37397736bf8146a77cd49ed06aa05361ccfaff8fcbecf0d36b369c53b411c | C++ | 20,673 | 483 | /* 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... |
b5dfece7c8523c711b94220edf31f436276c66abf0be779312c6a1ccff61d5b8 | C++ | 20,696 | 616 | #include "xml.h"
#include <cstdio>
#include <cstring>
#include <filesystem>
#include <utility>
#include "Angle.h"
#include "Beamline/Beamline.h"
#include "Beamline/EnergyDistribution.h"
#include "Beamline/StringConversion.h"
#include "Debug/Debug.h"
#include "Element/Element.h"
#include "Shader/Constants.h"
namespac... |
f272a02f6e0f1c517310992481578452b5e7e85a5579aa29633da8672536ed0d | C++ | 20,713 | 617 | /* 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... |
4a573ab5b2a278bacb5bf48350a43b26b2fa0e4074e67da54b34832d61110a07 | C++ | 20,828 | 641 | // ***************************************************************************
// BamReader_p.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 18 November 2012 (DB)
// -------------------------... |
a30b9e529521b3545681280eb58c1dbef15bd6f7e480a7b27aa9ede6f0c5dd75 | C++ | 21,126 | 674 | /*
* Test file for MaCaQuE and serial_communication class
*
* This is a simple command line interface to communicate with MaCaQuE based on the serial_communication class.
* It is necessary to set the correct communication port in the code (see below).
*
* author: Michael Berger
* German Primate Center
* mail: ... |
b1ee0c8871f90e9d0e6cdab011dd6873913605b0cbaa54ae1ff5e06842f85867 | C++ | 21,266 | 685 | /* 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... |
cc5a068101addaf0074330a3d8faa5d185b7f2a73ef6f2ccfee020b6b3bdea2a | C++ | 21,452 | 580 | /* 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... |
d2eb6447afccd87d4cfef9d02b9e8396748df6d02b4f079f7f8a19a35b257e66 | C++ | 21,600 | 708 | // 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:
// Fabian Giesen. Simple lossless index buffer compression & follow-up. 2013
// Conor Stokes. Vertex Cache Optimised Index Buffer ... |
c17b42db5821ed7cef7c9db2435a654a8d222e8d76e9c28fe493bfaa5e3f83dc | C++ | 22,280 | 597 | /*
#################################################################################
#
# 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... |
15847edf7e85af9544a0e45c1d433e8d6b6cab2a921bdc2c911acbe462d7de2f | C++ | 22,296 | 597 | /*
#################################################################################
#
# 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 ... |
82ca22ebcd16e6a2fd84bbe62a026e6d427e74df8fe0acb037a8535f8fe54a7b | C++ | 22,349 | 492 | /* 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... |
9b2ac8c611cfc85bb65db19423c7bfcc465f81dc64751dccfcc6179b59a0dd6d | C++ | 22,683 | 724 | /*
#################################################################################
#
# 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... |
4b188899492bda3aed0c6db6a0d42862b01cec941327254ac8fcd9d623f94d07 | C++ | 22,699 | 724 | /*
#################################################################################
#
# 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 ... |
8e33d937833ba30f97cda116b70936611dfd6a91b73e916504ad64939ec16a48 | C++ | 22,741 | 576 | /* 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... |
f572ec25636487c7879f24dbafbdc1ed36748fe4cda293e0d8800ee2a6e6e88c | C++ | 22,771 | 709 | /*!
* @file Adafruit_BME280.cpp
*
* @mainpage Adafruit BME280 humidity, temperature & pressure sensor
*
* @section intro_sec Introduction
*
* Driver for the BME280 humidity, temperature & pressure sensor
*
* These sensors use I2C or SPI to communicate, 2 or 4 pins are required
* to interface.
*
* Designed ... |
aa47ff9a87a699dc9ba8d442751774902823b00483cc5093ed07f11eda234635 | C++ | 22,906 | 617 | /*
#################################################################################
#
# 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... |
4822bf3128bad48a32a7c65fb454484f12b2890fa1fb55b368fc714abdf4c4e8 | C++ | 22,992 | 510 | #include "BeamlineDesignHandler.h"
#include <imgui_impl_sdl3.h>
#include <imgui_impl_vulkan.h>
#include <imgui_internal.h>
#include <algorithm>
#include <iostream>
#include <string>
#include <unordered_set>
#include "Beamline/Beamline.h"
#include "Beamline/StringConversion.h"
#include "Debug/Instrumentor.h"
#include... |
fb0c38b64ee3593f52e2d5b3e1a100cffe603250ffc415b2543be1b7066b481e | C++ | 23,102 | 619 | /* 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... |
e2eb79026042a3e108a887129cb394cf4a6ef57c7231633e4a207853175109de | C++ | 23,126 | 631 | /*
#################################################################################
#
# 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 ... |
6f014a26971e5020eb4b40187b311bb6df7366acaa38639901019e6f5d7032d7 | C++ | 23,172 | 707 | /*
* 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... |
971d044c85aa5156bb331466997b8278cdcd9d5a573cdbb72a71e34cfd7ccfa7 | C++ | 23,218 | 619 | /*
#################################################################################
#
# 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 ... |
5b53cdd20f5194191384d0d42f27285658a9c3ded32d6c473203f3c7a6de7344 | C++ | 23,219 | 650 | /*
* 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... |
bf30296c26619cb0ad3f4e0caea5c12850a6d1d23221bb9abb8c7a71146eae87 | C++ | 23,243 | 641 | // ***************************************************************************
// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 18 November 2012 (DB)
// -------------------------... |
596126eac038f817c8d85d10a4efb129c3b4ec3411612fceb21713b63dcb40a1 | C++ | 23,289 | 929 | /*
* 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... |
ec9f72eb11f2d816460ac1c10c4449b6bb9aba5bedd55b591bedf1a7bc559ebe | C++ | 23,549 | 674 | /* 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... |
161b8db313b74842df02d0788caced266410e52f5bcbd0a5dd97a0420d93c8ab | C++ | 23,569 | 618 | /* 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... |
c5ec82b45a55fbe5b7b1fec6ce30c40a1ca0ef1531c8642668a9469c6e080ac7 | C++ | 23,572 | 676 | /* 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... |
d18e89cbd5d4978bb20461fa7501a28efd98e741ea5580411fb0204ca0de8550 | C++ | 23,638 | 718 | // ***************************************************************************
// BamToolsIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// -----------------------... |
39534927a797ccfc91803445098219cce1e4c9da225ccf14bd903affbc73c663 | C++ | 23,757 | 730 | /*
#################################################################################
#
# 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... |
0ef6c34386d8242fb15271c0a787b449a2a1d53819171cecb9c8cbaa42918fd1 | C++ | 23,773 | 730 | /*
#################################################################################
#
# 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 ... |
821ea78c5703c53a95ac08aeddb0c67c2a72f076afc6e72af42b76ea010d5dfb | C++ | 23,870 | 716 | // This is an independent project of an individual developer. Dear PVS-Studio, please check it.
// PVS-Studio Static Code Analyzer for C, C++ and C#: http://www.viva64.com
// Copyright 2018 Stephane Cuillerdier @Aiekick
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this softwar... |
0fb2ef73f7418e63eb6cdc71f1a10e476fecfaac77a637213edb350858b2b9c7 | C++ | 23,936 | 552 | /*
#################################################################################
#
# 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... |
809281212b73262820a94901b35ab06f423bfec0de7938661d34db419696346b | C++ | 24,014 | 574 | /*
* 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... |
d4650dd1a14a244e55f6e75cdf788b26d31f1642a2f701bb101f963ab3bacc49 | C++ | 24,129 | 723 | /*
#################################################################################
#
# 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 ... |
f041f5972015d1ef788076e5091a5b3fa29c32fa5277d1c0dbfab4e762fb0885 | C++ | 24,175 | 757 | /*
#################################################################################
#
# 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 ... |
7f66b0a5d7bc19df25661663df1374247f00a7a6b5fc57c1f63bfd3decc30619 | C++ | 24,210 | 758 | /*
#################################################################################
#
# 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... |
e1c6d4f904f79765b7e18d664e0ac5630db0dfe866113366d6f21d541ff8dfcb | C++ | 24,216 | 723 | /*
#################################################################################
#
# 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... |
34b1bb4049e2e7879c7163618dad6079fc046df40f474e2591bf44c3428e9d16 | C++ | 24,544 | 824 | /* 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... |
f362cdcd8af10016333bf699347a9364335987f413f061e5b7e8cafe3b498948 | C++ | 24,600 | 825 | // 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:
// Matthias Teschner, Bruno Heidelberger, Matthias Mueller, Danat Pomeranets, Markus Gross. Optimized Spatial Hashing for Collisio... |
4537fd7b2a8b48b03d0d83cd3c9a6aedfad9c922774527c6132e7b7208f1cbf9 | C++ | 24,916 | 652 | /*
*! @title Axi DMA using proxy driver
*! @file AxiDma.cpp
*! @author Romain Beaubois
*! @date 08 Nov 2022
*! @copyright
*! SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*!
*! @brief
*!
*! @details
*! > **08 Nov 202... |
ca0e2c724767f0eecd22f186cb493dd83eb21defb9c50cfa496089662d2ba930 | C++ | 25,001 | 688 | /*
#################################################################################
#
# 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... |
f10301ece9fb365d563f19d8a23ae95ad930ea444e1e095aae497dac2f19c629 | C++ | 25,239 | 586 | #include "efield_operator.hpp"
#include <Omega_h_adj.hpp>
#include <Omega_h_for.hpp>
#include <Omega_h_map.hpp>
#include <Omega_h_mesh.hpp>
#include <Omega_h_shape.hpp>
#include <petscmat.h>
#include "../mol_state.hpp"
#include "geom/dist/distmesh.hpp"
#include "util/mesh.hpp"
#include "util/petsc.hpp"
#include "util... |
d36aee613a370e2bbe08433feb9fa57dc73c0be5ab2f6b3144ff10700947845e | C++ | 25,386 | 632 | /* 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... |
56bd18409294852deaab380ea09a63a6495e7eda46057ad234ed625bed6ac466 | C++ | 25,452 | 791 | /*
#################################################################################
#
# 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 ... |
bca63c6a6125df4ec0b4eddc4c66bd11c850f3274ea973c12d069b01512c30c2 | C++ | 25,754 | 873 | /**
* 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 "model.h"
#include <boost/archive/binary_iarchive.hpp>
#include <boost/archive/binary_oarchive.hpp>
#include <boost/arch... |
59b1d2437472b4ff550ace2a7f06407ea6f52178f0e79b919a8060ce2e216138 | C++ | 25,815 | 801 | // ***************************************************************************
// bamtools_split.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 24 July 2013 (DB)
// -----------... |
efad072e58b69468c0a2843616e7b1943620dee12809746e1937917124329f52 | C++ | 25,843 | 586 | /*
#################################################################################
#
# 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... |
1616157dec1d25dd273bc1e180f225649a42c94b82a0653c34e3657ebb4db5b0 | C++ | 25,859 | 586 | /*
#################################################################################
#
# 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 ... |
ae8ea6aa19eca61660ed659c1c13fe504075a51e8c7c29516c1079d8aebdef41 | C++ | 25,918 | 761 | /*
#################################################################################
#
# 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... |
b9d9d999c8e621ff77c80a307ea36f5e6f644088631bb485deeb408d63b84061 | C++ | 25,934 | 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 ... |
dc04510adea2556fcabf33c7a5fcfea363e6e267a6d2e4f7ca8c2a498447393c | C++ | 26,133 | 549 | #include "Collision.h"
#include "ApplySlopeError.h"
#include "Cubic.h"
#include "CutoutFns.h"
#include "InvocationState.h"
#include "Throw.h"
#include "Utils.h"
#include "Variant.h"
namespace {
constexpr double COLLISION_EPSILON = 1e-6;
} // unnamed namespace
namespace rayx {
/*************************************... |
4d3efb319b8b6eb44e87d7898bd4639415b0864f3f0ce24da3d7f1a5f6967e09 | C++ | 26,158 | 697 | //------------------------------------------------------------------
// Released under the BDS License
//
// Located at http://sourceforge.net/projects/varflow
//
//------------------------------------------------------------------
#include "VarFlow.h"
#include <iostream>
using namespace std;
/**
Initializes all v... |
d4d0c1edd50416126cc8196f2f49a4571963fd584f225db3d23003e2b38b0831 | C++ | 26,198 | 585 | /* 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... |
e92a3d994ad81a98f26412c05df42be35a680f9d76de601195d5c42203b54cf2 | C++ | 26,417 | 874 |
#include "stdafx.h"
#include <iostream>
#include <fstream>
#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 <o... |
1e155455312c7ed1e9f1c9712bc25dd78cb4f59f3cbe89d58fc04fe2d6189ba8 | C++ | 26,446 | 900 | /*
* 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... |
cc0c5cf331b0e24ab2fe2d7aba5cd2f86d29e0619939cde0140a2f7d13af13b3 | C++ | 26,487 | 786 | /*
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 ... |
c1ccca21d6ae16f0f17d0e06e90277830416c42a1ede19ac692a4d687a760c74 | C++ | 26,613 | 822 | /*
#################################################################################
#
# 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 ... |
927c0e0fc12c8577c99a77bafeeec3563291935ffe976aa340cd4227daf403d8 | C++ | 26,687 | 931 | #include <dirent.h>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <sstream>
#include <vector>
#ifndef SUP_FUINCTIONS_HPP_
#include "../sup_source/sup_functions.hpp"
#endif
#ifndef GDATA_CLASS_HPP_
#include "classes/gdata_class.hpp"
#endif
#ifndef DICTIONARY_HPP_
#include "dictionary.hpp"
#endif
#... |
fff3897123af7660f83342edc44b9b563896bc115cad3e11776cb6d00473ffd8 | C++ | 26,715 | 822 | /*
#################################################################################
#
# 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... |
6e73e674a200249ba9c1661604721305a610b753bffff33b27648abd97be361e | C++ | 26,768 | 898 | /*
#################################################################################
#
# 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 ... |
51a06f9d348709b99e2f750710cc607793c8a08c5486193d8622ca2a06f67fb2 | C++ | 27,168 | 782 | // 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
// Note: this is only exposed for developmen... |
8f8eeb270663452f706fdb57be820d0ef0886d4914e98f710a07831567df8fb4 | C++ | 27,265 | 756 | // 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... |
f41f30235fccdc872c54724d5d03f206e0c6649596c24007dc1832ad91e1829e | C++ | 27,314 | 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... |
09c084279b3d306130cf04a13d4dd6e809a230ba171d960257950a82bee0506e | C++ | 27,417 | 750 | // 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:
// Morten Mikkelsen. Simulation of wrinkled surfaces revisited. 2008
// Matthias Teschner, Bruno Heidelberger, M... |
6ef2f7b1a3cc6de6b81e79cbfd4695c5529d9f2fee3509ae8d0914199bc09872 | C++ | 27,448 | 767 | /*
#################################################################################
#
# 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 ... |
e7ccc3a61c8e553cc26309bc3ce138b1142b5c0e076c52d5427da47827b6ba45 | C++ | 27,479 | 885 | /*
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... |
35490d9c17ceae75ab2b424d681afe5e61ce8def9fd558484ac966ad7e4000c4 | C++ | 27,566 | 914 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <algorithm>
#include <float.h>
#include <limits.h>
#include <math.h>
#include <stdint.h>
#include <string.h>
#include "../src/meshoptimizer.h"
struct Bounds
{
Attr min, max;
Bounds()
{
min.f[0] = min.f[... |
8e7c5a4779945114bd9f489f2f4aa2044f2b4eda1b5e094a917e7d92a7064738 | C++ | 28,159 | 584 | #include "tetopsplit.hpp"
#include <iostream>
#ifdef USE_PETSC
#include <petscksp.h>
#endif // USE_PETSC
#include "definition/compdef.hpp"
#include "definition/diffdef.hpp"
#include "definition/patchdef.hpp"
#include "definition/reacdef.hpp"
#include "definition/sreacdef.hpp"
#include "util/mpitools.hpp"
namespace... |
05eb6a467cd086d85ccbd1ec7715f9fa228423aa716d10da9b50ff55cd50fafd | C++ | 28,257 | 580 | /* 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... |
f5ae346f08fb4145de54c437d8f715010cc15f4e73fbbfa0eb21757f77e44850 | C++ | 28,379 | 600 | #include "surface_reactions.hpp"
#include <cassert>
#include <functional>
#include <Omega_h_map.hpp>
#include <Omega_h_mark.hpp>
#include <Omega_h_shape.hpp>
#include "geom/dist/distmesh.hpp"
#include "math/constants.hpp"
#include "mpi/dist/tetopsplit/definition/sreacdef.hpp"
#include "util/vocabulary.hpp"
namespac... |
fe9754a4131c6cf6e101d1d134383c2f922e0cf2c8593900984f027e8a8131c8 | C++ | 28,493 | 648 | #include "efield_operator.hpp"
#include <Omega_h_adj.hpp>
#include <Omega_h_for.hpp>
#include <Omega_h_map.hpp>
#include <Omega_h_mesh.hpp>
#include <Omega_h_shape.hpp>
#include <algorithm>
#include <petscmat.h>
#include "../mol_state.hpp"
#include "geom/dist/distmesh.hpp"
#include "util/mesh.hpp"
#include "util/pets... |
7f4f49099873d65bf81c7ae5941512b9fcde2b4ac8ad33e786ec64e19a67a32c | C++ | 28,878 | 621 | #include "UIHandler.h"
#undef APIENTRY
#include <imgui_impl_sdl3.h>
#include <imgui_impl_vulkan.h>
#include <imgui_internal.h>
#include <portable-file-dialogs.h>
#include <fstream>
#include <rapidxml.hpp>
#include "Colors.h"
#include "Debug/Instrumentor.h"
#include "RayProcessing.h"
#include "Rml/Locate.h"
void che... |
a8310d64006249a3d80f8315105c2c0f9cdf2014b9d7a6705754d9427e3252b4 | C++ | 29,446 | 751 | /* 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... |
911fe9e0f2a033e100e77b588f7575a89dbd39f23c7a8166d073ef432deef419 | C++ | 29,616 | 808 | /*
*
* Old compiling notes:
* --------------------
* mex sdk_mex.cpp ADIDatIOWin.lib
* mex -v sdk_mex.cpp LoadADIDatDll.cpp ADIDatIOWin64.lib
*
* Compiling should be done via:
* adi.sdk.makeMex()
*
* http://www.mathworks.com/help/matlab/matlab_external/passing-arguments-to-s... |
2df0c942b87a1fd41956e808d2ecec728a959f10497f8dceb77d33784ba99c94 | C++ | 30,103 | 923 | /*
#################################################################################
#
# 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... |
5940867ce2b1a4187f27b41d448c295ed68171ef9b2e7351f4664277648e1e3f | C++ | 30,114 | 941 | /*
* 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... |
107b1726e79dc674c2127c2276ffe89ae429416fb241739f50210888eee52850 | C++ | 30,123 | 998 | /*
#################################################################################
#
# 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... |
59991e58a893ffd4bfc70e7efd4241d00743a96f3be581ad6c32ebf92e466998 | C++ | 30,267 | 632 |
#include "kproc_state.hpp"
#include <cstddef>
#include <stdexcept>
#include <Omega_h_for.hpp>
#include <boost/graph/connected_components.hpp>
#include <boost/graph/copy.hpp>
#include <boost/graph/graphviz.hpp>
#include "diffusions.hpp"
#include "mpi/dist/tetopsplit/definition/compdef.hpp"
#include "mpi/dist/tetopsp... |
51c8b95837aeeb2ecd47894ef967bcca487d9905abac0aea6f5257916067c5ff | C++ | 30,314 | 703 | /* 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... |
ee4c56f9c9817b6fc1e35c3b2ade8b41e5016a38a25e6045f121f4a4f9d9d959 | C++ | 30,883 | 909 | /* 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... |
3401b2a29f95ed702af82b837dab905a131ef411e24f67320178fad058a9978f | C++ | 31,318 | 882 | /*
#################################################################################
#
# 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... |
9d2e150a63a3dc4437d44f5e83e2200cea22c7ad66ae887c2bde24e9287a9d71 | C++ | 31,440 | 951 | /* 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... |
44b069cbcd6f5d49c0ae7f974fd2b57fb84e9a4537d68101e5eacb469424d724 | C++ | 31,516 | 986 | /*
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 ... |
95328704fec8687d11e56c9de2f006c6cf99ed31fbd0d5cf14ed8cfe41fc41ca | C++ | 31,713 | 971 | // ***************************************************************************
// BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 24 July 2013 (DB)
// ---------... |
e3762046235ece83455195efc73321d0215b760ba24825dde92128944f481029 | C++ | 32,222 | 566 | #include "DesignElement.h"
#include <iostream>
#include <memory>
#include "Debug/Debug.h"
#include "Debug/Instrumentor.h"
namespace rayx {
namespace {
std::string getUniqueUnnamedElementName() {
static size_t counter = 0;
return std::format("<unnamed_element_{}>", counter++);
}
} // unnamed namespace
Desi... |
10b7e3e19e73bd2dcfb0052b86c7779f9e156788e713f9dc7a59be13a89668a6 | C++ | 32,428 | 973 | /*
#################################################################################
#
# 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 ... |
944d691e0856dbff56fb676defdc013f6b2544d9af259b9d91bf34030906fc88 | C++ | 32,685 | 1,616 | /*
* 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... |
80255c28cb196b6a1f645d4757ee4fb194186bf74cb42156043cb6d0758aa73a | C++ | 32,742 | 825 | /*
* 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... |
edfb8e0a0f7709bfa414e4f06eac6bef1ad647be16fe773d5b65df03e14167f5 | C++ | 32,764 | 776 | #include "statedef.hpp"
#include <algorithm>
#include <sstream>
#include "compdef.hpp"
#include "diffdef.hpp"
#include "patchdef.hpp"
#include "reacdef.hpp"
#include "geom/dist/distcomp.hpp"
#include "geom/dist/distmemb.hpp"
#include "geom/dist/distmesh.hpp"
#include "geom/dist/distpatch.hpp"
#include "math/constant... |
f07fc7832534e9d1e6f513786874662dfb655dd6cf734d54aff6b3b1bcee0c92 | C++ | 32,982 | 852 | /* 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... |
d854ec5e37c2c83ecd32a8b6bb3e582dddb6c71d42f6c56d61bbf3eed5d22ba0 | C++ | 33,167 | 1,209 | /*
* 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... |
bd3ba09f4926bf458ecdeb6e5e93b164fd5e8e7ca1e3750168633b74818c6ac2 | C++ | 33,191 | 955 | /*
* 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... |
17edbdb1c16f60edae0630d8850071fe544bd34ba765e66319f19b2add7bf68e | C++ | 33,492 | 968 | /*
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 ... |
f7bad517cb77a646ba0beef916ac42715c2fe18002f29e12c6cd4ccd5835e678 | C++ | 33,807 | 1,051 | // 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 SSE4.1, ... |
0bc908b69137be0f3a7dd71fcb4cc4bb232972bc4f4d5106c9bbd24fe5382c28 | C++ | 33,863 | 878 | /* 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... |
e2047ba7a861f0552966e297af08d2f0a706982be74ea9aa25c0bba808f566fd | C++ | 33,865 | 863 | /* 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... |
552b580153805661121330aff6f6566a2f67c055477ecc188f62adc40c290380 | C++ | 34,245 | 844 | /* 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... |
fda94710533f65f88f087d35af9d307e42764805b0c14de77125039123179543 | C++ | 34,599 | 943 | /* 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... |
dbb677568e32cb1d5d0d236d5c5216f929004222ec8614965649c9cbfb41a53f | C++ | 35,144 | 945 | /* 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... |
2d0e33a9e9b08607994aacab8f39ee6c0f2a835d3d666570bb664b4ac5197657 | C++ | 35,386 | 1,017 | /*
#################################################################################
#
# 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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