sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b6d5389f26d3d5a3bb283afb384679a450d90a30db289191f3b518c5ec14cd60 | C++ | 1,666 | 63 | #include <cassert>
#include <cstddef>
#include <limits>
#include "lapack_common.hpp"
// estimate condition number of general nxn matrix A in row-major
// order, using LAPACK.
extern "C" {
double dlange_(const char* norm, int* m, int* n, double* a, int* lda, double* work);
void dgetrf_(int* m, int* n, double* a, int*... |
4b76aebe9eb7ed182056cbf57958c54c684605492c33879128068f681f42c2c0 | C++ | 1,685 | 92 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <float.h>
#include <math.h>
#include <stdio.h>
void comma(std::string& s)
{
char ch = s.empty() ? 0 : s[s.size() - 1];
if (ch != 0 && ch != '[' && ch != '{')
s += ",";
}
void append(std::string& s, size_t... |
f55c3a68b5c89c0282aa9dc03f2ea32817e33cf03358a490c0c4f3533a232b29 | C++ | 1,706 | 48 | /*
#################################################################################
#
# 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... |
6d1ddae4f5c60762850a36f03770da76f4510fde4cd247f8f775c75151d33ef4 | C++ | 1,707 | 91 | // [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
static double sparse_col_dot(const arma::sp_mat& A, const arma::sp_mat& B, arma::uword col)
{
arma::sp_mat::const_col_iterator a_it = A.begin_col(col);
arma::sp_mat::const_col_iterator a... |
40aaf2e457c840cf2f5deca4b7dc3b1e30703c85c730bad5b4b7753f55c2cf82 | C++ | 1,708 | 55 | /*
#################################################################################
#
# 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... |
d855f1600bb8378a87802805dcf228dfab8e05a0893e85bcbf6da96ce10b3fe6 | C++ | 1,711 | 67 | /* 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... |
9236937b9651cf2052d1f1d5bd5dff9e7763991c5075e92352cd7955a61e95b4 | C++ | 1,724 | 55 | /*
#################################################################################
#
# 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 ... |
eb6f4d5b0f1e3853a86dcb5cf86a209a9f70827b7674a3687f955690f36b5f0e | C++ | 1,726 | 50 | #include <cassert>
#include "Chromosome.h"
Chromosome::Chromosome(GenomeSequence* gs, unsigned int chromosomeIndex)
{
assert(gs);
assert(chromosomeIndex < (unsigned int)gs->getChromosomeCount());
this->gs = gs;
this->chromosomeIndex = chromosomeIndex;
this->offset = gs->getChromosomeStart((int)chr... |
8ad5fcaaa2a234dbba83f74c17b5fa2cf88bf52461e3bb09cc632838a1c5b2d4 | C++ | 1,729 | 61 | /*
* 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... |
9faf11393c955de3f6ea538e3d5afe432ddd0b74894fdff0728d87a4a4eebe7d | C++ | 1,733 | 72 | /* 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... |
24a09b3883f2adb6e2303a1226f007047217c8e658c85aa74dd202924d097a0b | C++ | 1,734 | 66 | #include <Rcpp.h>
#include <algorithm>
using namespace std;
using namespace Rcpp;
// [[Rcpp::export]]
IntegerVector matcher(NumericVector obs, NumericVector mis, int k) {
// fast predictive mean matching algorithm
// for each of the n0 elements in mis
// 1) calculate the difference with obs
// 2) add small noi... |
44eb9db49c76cd609a626c87ce48c312beb99c3c7c96bddd9d9d3870f558a56a | C++ | 1,739 | 66 | /* 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... |
c2e5c38dee0025310683cc40c09d1c6d94e3b90510b34df1145183d72d82d4da | C++ | 1,740 | 69 | /* 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... |
21e4dbd84a7073e7c5ef9b58bfbc445a25c295c96e231c9d19b00509f56459dd | C++ | 1,755 | 47 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
cad2adf406536c1e011a36bd4b792ab4dfa4377b9ccfae0b8c614b935bee81e9 | C++ | 1,758 | 80 | // [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::interfaces(r, cpp)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <math.h>
using namespace Rcpp;
// declare K1_Binary_SPA (first derivative)
double K1_Binary_SPA(double x, arma::vec muhat, arma::vec G, double q);
// declare K1_Binary_S... |
65f5694a27fb4dd53bccb91e6b857b218d2f98a69c313c906e92bb56014ee851 | C++ | 1,759 | 66 | /* 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... |
53663a9e7f7b8fb54f5cd2c3c8d764d37f4c0659ca984defa55fe7c9f5fabe7b | C++ | 1,762 | 57 | #include <cmath>
#include <iostream>
#include "util/tracker/memory_tracker.hpp"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
using steps::util::MemoryTracker;
TEST_CASE("MemoryTracker_zero") {
MemoryTracker tracker{};
tracker.start();
tracker.stop(... |
b4330df0951e13119e4f5b22f20b9974fea88ce4bb1022e6ecdfc7c8cd467c06 | C++ | 1,763 | 57 | #include <cmath>
#include <iostream>
#include "util/tracker/memory_tracker.hpp"
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
using steps::util::MemoryTracker;
TEST_CASE("MemoryTracker_zero") {
MemoryTracker tracker{};
tracker.start();
tracker.stop(... |
435ffcd0bb7b8019ef8ecede97c1d092b9647b91acf27f22be780e2881bf6c0d | C++ | 1,772 | 57 | /*
#################################################################################
#
# 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... |
f146f5c35ca769fc40c2bd47d9a04956a16f4afc30d7d5f2d4f7faf0b47dbbc2 | C++ | 1,775 | 75 | #include "debug.hpp"
#include <climits>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <unistd.h>
#ifndef HOST_NAME_MAX
#if defined(_POSIX_HOST_NAME_MAX)
#define HOST_NAME_MAX _POSIX_HOST_NAME_MAX
#elif defined(MAXHOSTNAMELEN)
#define HOST_NAME_MAX MAXHOSTNAMELEN
#endif
#endif /* HOST_NAME_MAX */
... |
3317407f184db78548cf2c5fd407a738ff8163c4f58e32ecfc22789209ca72aa | C++ | 1,785 | 56 | /*
#################################################################################
#
# 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 ... |
f3fd079ca14a17a88dc1515078a807af3dd1701feccaeb400efc9ee946a0c017 | C++ | 1,787 | 63 | /* 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... |
a76fae7a33c79fc2a1d6cd61b0dfcf3b074470f5c13ef3fef0a19a046fe3738d | C++ | 1,788 | 57 | /*
#################################################################################
#
# 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 ... |
a0bcb4906f6c048b5890b5a6021e86c6fa1cc44f869a01d9cfbd141b9211a979 | C++ | 1,797 | 59 | /*
* Copyright (c) 2009 Regents of the University of Michigan
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
... |
eb856394380c21dfc4060c2309aef8b2aaf5d8710cc734af5ce6f8efd09b70e0 | C++ | 1,800 | 57 | /*
#################################################################################
#
# 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... |
8df326965d8f7d8b85ca9d53a45396b567028f010efbe5be22b705ec195f2c82 | C++ | 1,802 | 32 | #include "RayRenderSystem.h"
#include "RenderObject.h"
#include "Rml/Locate.h"
#include "Vertex.h"
RayRenderSystem::RayRenderSystem(Device& device, VkRenderPass renderPass, const std::vector<VkDescriptorSetLayout>& setLayouts)
: RenderSystem(device, fillInput(renderPass), setLayouts) {}
void RayRenderSystem::ren... |
9469ff8e0ebccc2d03f2e5e2504d47bcd933810a8040a2acd3c44b9db055b5dd | C++ | 1,804 | 67 | /* 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... |
e55cbedb035a691a5c34571709e483ca75cfae10474547ea545529f40795f6cb | C++ | 1,815 | 62 | /* 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... |
ba060596092b3ec06d6ee059915b2c8a4f130f991b0971474299e3cc3645ccfb | C++ | 1,816 | 62 | /*
* 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... |
bf2f17de6203880af7b4f98e3a0f8ff63d7e7d36d2c736541039c33fac4b96b5 | C++ | 1,830 | 54 | /*
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... |
3f709c8e9983dcbc26d1743f72a3d293ded0b2c177dcff98b6e609b44543b2ab | C++ | 1,848 | 53 | #include "measure.hpp"
#include "mpi/mpi_init.hpp"
namespace steps::dist {
Measure::Measure(MPI_Comm comm,
osh::Int num_compartments,
const element_measure_func& t_element_measure_func)
: comm_(comm)
, rank_(mpi::getRank(comm_))
, num_measures_per_rank_(1 + num_compartme... |
74bc81fc450faba51d1300a1759828bf55ba5bd660b688b27ff00a125a544dbc | C++ | 1,848 | 47 | #include "diffusions.hpp"
#include "../simulation_data.hpp"
#include "geom/dist/distmesh.hpp"
namespace steps::dist::kproc {
DiffusionDiscretizedRates::DiffusionDiscretizedRates(const osh::LOs& neighbors_per_elements,
const osh::LOs& species_per_elements)
: su... |
f886122b21a54acb5d0a9bdf3bf10c5c26cef8140c27cb173914bf908ce0ed28 | C++ | 1,861 | 60 | /*
#################################################################################
#
# 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... |
2930280939f51a122f9c9d3e6d1974dcd7ed3fe913948519b7572c047d16d44d | C++ | 1,877 | 64 | #include <stdio.h>
#include <string.h>
#include <fstream>
#include <iostream>
#include <cstdlib>
using namespace std;
#include "resampler.h"
// Function to print help message
void printHelp() {
std::cout << "Usage: resampler_test [options]" << std::endl;
std::cout << "Options:" << std::endl;
std::cout <<... |
102c6328749225aad57287f3d5788c636ee792400b7dfcbfe0ccc2cf88062a1a | C++ | 1,892 | 67 | /* 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... |
25c9212df3a44166b83c75a2da0235eb2ebbf4960f666d42d0dfb852e617fbb4 | C++ | 1,892 | 50 | // resampler_mex.cpp: MATLAB mexFunction interface for the Resampler class
#include <iostream>
#include "mex.h"
#include "resampler.h"
// Function to perform resampling using the Resampler class
void resampleSignal(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) {
// Check input and output arguments
... |
3ca3f9297d9960241000475409b0b80390f1e0a4b79fa964406dfbb039e14956 | C++ | 1,898 | 58 | /*
#################################################################################
#
# 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... |
c919812e6bf3bc8aa83bd7243f1dca4b172610dc6382f9f22c6a180a6191b5cf | C++ | 1,907 | 60 | /*
#################################################################################
#
# 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... |
b70b4152b901059093c54b3df3fc550163ac832e308fe897b65ec63a39f6f5b2 | C++ | 1,914 | 58 | /*
#################################################################################
#
# 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 ... |
1fb47c40c69b323546691047271b893404c9efdb4e97ce53fdf60447eb74dc78 | C++ | 1,915 | 63 | // ***************************************************************************
// ILocalIODevice_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 27 July 2012 (DB)
// ------------------------... |
aa534bb8150ca27ae229c58a0dc51f85f9acccbc5d4214f4c82edd91fc08e478 | C++ | 1,915 | 71 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <string.h>
size_t meshopt_optimizeVertexFetchRemap(unsigned int* destination, const unsigned int* indices, size_t index_count, size_t vertex_count)
{
memset(destinati... |
62160e2ea1af04df0c172549555b9f4e96cf8c7025fb7430b92339d5f7cdb41c | C++ | 1,923 | 60 | /*
#################################################################################
#
# 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 ... |
70d0bc34c035612c3d718c830b1e6a744c26f565f06679a72446f5fee765ab7f | C++ | 1,923 | 67 | #ifndef GDATA_CLASS_HPP_
#include "gdata_class.hpp"
#endif
// class Position
bool Position::operator==(const Position& position) const {
bool x_check = (this->x == position.x);
bool y_check = (this->y == position.y);
bool z_check = (this->z == position.z);
bool set_check = (this->set == position.set);
... |
45a458fb35e9867cb10f1fc3edbdc965c12cda9efa4f3f31425178215557ebb9 | C++ | 1,925 | 62 | /*
#################################################################################
#
# 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... |
eb6890711d7215f69abca11d1f4c98db7bda65372bd36d572d168ee9a5e768ba | C++ | 1,926 | 65 | /* 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... |
de4da36b32b1410b6a62d820835593a31a66ec1d2d328ed042fc5c412c275cdd | C++ | 1,935 | 70 | // [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::interfaces(r, cpp)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <math.h>
using namespace Rcpp;
// declare K_Binary_SPA
double K_Binary_SPA(double x, arma::vec muhat, arma::vec G);
// declare K_Binary_SPA_alt (alternative way if not c... |
8d5188981e336b24be7ec7ee8b8d65f6d6a02b96a890d14804c10664dfae33c7 | C++ | 1,940 | 63 | /*
#################################################################################
#
# 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... |
a39a49db3fbb508396859b3b5cf5bb4dd084aa368e9879c85e0d4d47d243c905 | C++ | 1,941 | 62 | /*
#################################################################################
#
# 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 ... |
869267dd786236345f4a4037e9d9f32358e09d5e3aa1679ed130d990842d201c | C++ | 1,944 | 60 | /* 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... |
4391ec73aa97f40a15e981c3bbb61efe222a300256e6d9c88c3cf7b9ad9beb67 | C++ | 1,945 | 64 | /*
* 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... |
4589f0f3b13f068a36f5b3382c0789dc14ad51d82cc7cc416e727d466af68bf8 | C++ | 1,956 | 63 | /*
#################################################################################
#
# 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 ... |
7665b8114bb94202742b5f0b5eb3c0a398e6d3de4989cb5047b9e112511aa2bc | C++ | 1,961 | 73 | /*
* 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... |
206291d353c947135ef72473a7ac4ec4635b9bed93092930868d88f1cf0721f3 | C++ | 1,964 | 65 | /*
* 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... |
221f86547fb1bcfb3ededa1ab15073a61a902e1c1ed9145dce5f8db0983a5627 | C++ | 1,973 | 69 | /* 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... |
ac6bfec8e2e068fa4d8217babf5ab6eab062acb9aa0cf37bd3c265256c91907f | C++ | 1,980 | 53 | /*
* 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... |
6384f7d48ee1273d35a4cd8576333671c30fbedb29e74cf62c1879fe0a4f7181 | C++ | 1,999 | 62 | /*
#################################################################################
#
# 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... |
bec34fe6f59a4bdc025b3400cc995efd935beebe38aba34ef27c10fd2822795f | C++ | 2,013 | 59 | #include "Window.h"
#include <SDL3/SDL_vulkan.h>
#include <stdexcept>
#include "Debug/Debug.h"
/**
* This constructor performs several key tasks:
* - Initializes GLFW using glfwInit().
* - Sets GLFW to not create an OpenGL context with glfwWindowHint().
* - Creates a new GLFW window and stores its pointer.
* -... |
ab7def0ceab85c0abe96c15ba6089dab3035c2857aa35e806068c051e10b8cb8 | C++ | 2,015 | 62 | /*
#################################################################################
#
# 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 ... |
9b463948122aa84a387ae0a884bdf5c2f48b366f72b5183085b0464c1d69b1e6 | C++ | 2,024 | 61 | /* 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... |
1a50d3493a0457a610afe9230b6e5d498956382b31d10390fde415116d8c6646 | C++ | 2,028 | 64 | /*
#################################################################################
#
# 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... |
920345cbd77e536516613097bd64a58a164851f1de5fa032fddc042d41fb785a | C++ | 2,029 | 82 | /*
* Copyright (C) 2010-2011 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... |
d83b193f396383f38996fc5d73998bb2c282a7904c32536dcaec7bf6b0c22db1 | C++ | 2,031 | 69 | /*
#################################################################################
#
# 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... |
e8f63bf6547bffb101fd9cfaaaccb07a24e4a008ede16b8e8be8223ecf6a53aa | C++ | 2,031 | 72 | /* 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... |
56d8edad022d9115149dd7545e91e4cb8a750bf9ffd9f94df4a25aac688e8387 | C++ | 2,035 | 32 | #include "GridRenderSystem.h"
#include "Rml/Locate.h"
GridRenderSystem::GridRenderSystem(Device& device, VkRenderPass renderPass, const std::vector<VkDescriptorSetLayout>& setLayouts)
: RenderSystem(device, fillInput(renderPass), setLayouts) {}
void GridRenderSystem::render(FrameInfo& frameInfo, [[maybe_unused]]... |
7f04d5fe6f34dae65b865fec529f5fd1baa5fadbd0a40e7075593a02a68067c8 | C++ | 2,035 | 94 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/RoadTest.cpp#2 $$Change: 2062 $
** $Date: 2016/01/17 $$Author: bbarber $
**
**************************************************************... |
a0e52af404e310ceeea38a63e713adf1b243cc33b5dbb8709ce9c6bb44dec288 | C++ | 2,042 | 116 | #ifndef __wasi__
#error This file contains libc stubs for WASI SDK and should only be used in non-Emscripten WebAssembly builds
#endif
#include <assert.h>
#include <stddef.h>
#include <stdint.h>
extern unsigned char __heap_base;
static intptr_t sbrkp = intptr_t(&__heap_base);
static const int WASM_PAGE_SIZE = 64 * 1... |
0987f51c16bcf10c6f501d83e92ae1bbdf00fa609ac27bd559fab8e79c52651c | C++ | 2,044 | 64 | /*
#################################################################################
#
# 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 ... |
2647cedd0e9d0ebd8d9ac45095efa714733a29f3aabec01e017b48eec3c8038c | C++ | 2,047 | 63 | /* 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... |
47062f554bdf8c4c772c99ac0cf966ec9448d87ff604f1557e4205fddad8981e | C++ | 2,047 | 69 | /*
#################################################################################
#
# 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 ... |
cef4f74dd2eed497559e04cb40c719eef4d46cfc254eac117e7db04ddf391afc | C++ | 2,048 | 65 | /* 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... |
637366168b496361b142f259a14e9f3d5d48183dbc4768d20d3de4a0a4032e6e | C++ | 2,049 | 61 | #include <iostream>
#include <time.h>
#include "GenomeSequence.h"
#include "InputFile.h"
void readDbsnp(mmapArrayBool_t& dbSNP, const char* fileName, GenomeSequence& ref);
int main(int argc, char ** argv)
{
// time_t startTime;
// time_t endTime;
// startTime = time(NULL);
GenomeSequence* ref... |
5b579a8a0babfe1b662146a7ba24ecff78a95fe57b36dd0a6fd2893d842d26b4 | C++ | 2,053 | 59 | #include "measure.hpp"
#include "distcomp.hpp"
#include "distmesh.hpp"
#include "mpi/mpi_init.hpp"
#include "util/strong_ra.hpp"
#include "util/vocabulary.hpp"
namespace steps::dist {
Measure::Measure(MPI_Comm comm,
osh::Int num_compartments,
const element_measure_func& t_element_me... |
9874e1eaf21a959d8f39be9f7505cce8a2d1fa3b0adb5daf63ee25caf33ebb35 | C++ | 2,055 | 66 | #include "DatFile.h"
#include <fstream>
#include <iostream>
#include <sstream>
#include "Debug/Debug.h"
#include "Random.h"
namespace rayx {
bool DatFile::load(const std::filesystem::path& filename, DatFile* out) {
try {
std::ifstream s(filename);
RAYX_VERB << filename;
std::string line;
... |
42329f62dd3cfa6664e84d896ebb1d7a73390e6d04c8bdc7efa35527633d1c5f | C++ | 2,064 | 73 | #include <fstream>
#include "CanonicalizePath.h"
#include "Debug/Debug.h"
namespace rayx {
std::optional<std::vector<uint8_t>> readFile(const std::string& filename, const uint32_t count) {
std::vector<uint8_t> data;
std::ifstream file;
file.open(filename, std::ios::in | std::ios::binary);
if (!fil... |
6d4414f1153ab1d199b3291652b6692b53d50728531e747cb1409711d227dcce | C++ | 2,072 | 65 | /* 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... |
b9103a7255ad932023cbc7ff8661ddbdc643d88107cf63f3d88b4b68b82db0c0 | C++ | 2,073 | 64 | /* 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... |
0c0be956b542abe0e8bcf5daef3495c4f4e3ce8c163cedb84d1d2472cfb4a2b8 | C++ | 2,080 | 71 | /* 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... |
14e1a87d7ea1248d6fbf54b97a25b30d28d5e445ff4ce5a543a20a9b3d72622d | C++ | 2,083 | 84 | /*
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 ... |
ea690894a22702503548838924f38e7dc57ee731adc90468871c034621195143 | C++ | 2,106 | 63 | /*
*! @title Application argument parser
*! @file ArgParse.cpp
*! @author Romain Beaubois
*! @date 08 Mar 2023
*! @copyright
*! SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*!
*! @brief
*!
*! @details
*! > **08 Mar ... |
83e96f2c4279e3131666fa29e0a071b76b244d36e257328e438a3abf82ff8598 | C++ | 2,112 | 66 | /*
#################################################################################
#
# 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... |
9c494c1c04fd4f53a1dad4f03aefcb59c3cf605f9dd23e3fcae7a25f4023689a | C++ | 2,112 | 54 | #include "CommandParser.h"
#include <cstring>
#include "Debug/Debug.h"
#include "Debug/Instrumentor.h"
CommandParser::CommandParser(int _argc, char* const* _argv) : m_cli11{std::make_shared<CLI::App>("for rayx-ui CLI")} {
for (const std::pair<char, Options> option : m_ParserCommands) {
// Full name strin... |
8b0474bb36dde3aed1ca2dda0a56ffdcb3e33a30a68f0bbb4b1a675313e17088 | C++ | 2,125 | 95 | /*
* 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... |
b75492a478a47c484a0a806ed1d88532ba4559c79bd76835b945a368e7fa32ae | C++ | 2,128 | 66 | /*
#################################################################################
#
# 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 ... |
f8f8d83c5e1dee366d9b3e7100c4b501d48b78c1a34971913f277562546fb569 | C++ | 2,129 | 71 | // ***************************************************************************
// BamFile_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// ---------------------------... |
d0da20720daee572bc19454320f6d1b79e9679dfd7007b7461c2b11c763d5715 | C++ | 2,136 | 84 | /* 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... |
24085ed31278253d38e73b42c1888450a0c9e2db858de7543a4d4f6e6711274e | C++ | 2,138 | 88 | // [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::interfaces(r, cpp)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <math.h>
using namespace Rcpp;
// declare K1_Binary_SPA (first derivative)
double K1_Binary_SPA(double x, arma::vec muhat, arma::vec G, double q);
// declare K1_Binary_SP... |
995c0831c488ffd7cb26562f4d250ecb2f5b84d9338c522eff41b90ae221d218 | C++ | 2,149 | 81 | /* 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... |
71e342fac47f10e414ceb4f7c51519fda5f8e2e9bcfbd36a19ab428745d12ac3 | C++ | 2,171 | 69 | /*
#################################################################################
#
# 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... |
f57d3dd0dfb4b99bbe67b1fca296b90b9da5e3226acc05d211be559fee4eda53 | C++ | 2,171 | 91 | /*
* 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... |
a3daeb329bb901036f81470ce3313a8e013a2e980586b13289c5a5acdac391d8 | C++ | 2,174 | 43 | #include "ObjectRenderSystem.h"
#include <filesystem>
#include "Rml/Locate.h"
#include "Vertex.h"
ObjectRenderSystem::ObjectRenderSystem(Device& device, VkRenderPass renderPass, const std::vector<VkDescriptorSetLayout>& setLayouts)
: RenderSystem(device, fillInput(renderPass), setLayouts) {}
void ObjectRenderSy... |
0a0068a1bd9a4435f6fa22664fe797b581b4a5461d1fe489151012850f1b2d1d | C++ | 2,187 | 69 | /*
#################################################################################
#
# 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 ... |
c793ee916b120d4e71dcf1259378c052525671b0b9ff88edf6f9666203a29ddd | C++ | 2,188 | 58 | /* 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... |
4411f30a7aa51acf01c9b4be5d1e5ddb68638d5fbc8c490b87e7b94ee4f16e37 | C++ | 2,192 | 62 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(... |
87c2ecce0f25c7903768421300d80bf6d3bce7dea67d90eac47392f506ee1ea1 | C++ | 2,205 | 73 | // ***************************************************************************
// BamPipe_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 18 October 2012 (DB)
// ----------------------------... |
9f18d6d89755ee80273f582c04c359e8e6b944bb5033aae4de46ec855dbce805 | C++ | 2,215 | 66 | /* 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... |
a6b46b6cfc238f049ed333ffe279423323e05b1c73f9be0674fcd3846c6c9fb7 | C++ | 2,225 | 65 | #include "reacdef.hpp"
#include <set>
#include "model/complexreac.hpp"
#include "model/reac.hpp"
#include "model/spec.hpp"
#include "solver/fwd.hpp"
#include "statedef.hpp"
#include "util/vocabulary.hpp"
namespace steps::dist {
void report_molecule(std::stringstream& s,
const model::species_na... |
fac624d8ad9aafc9fc752f3e174322fc682c6f4542c75c81f7476785433abb0b | C++ | 2,242 | 78 | /* 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... |
47f026262ea84c3ea29961ab7a9f75ab96fd6e51b2b58daae55a23c5ef62e755 | C++ | 2,243 | 70 | /*
#################################################################################
#
# 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... |
833c5e2c48d26a3143fea59fd654e3ea20839e8bb8cf60f3454929ef44f698cc | C++ | 2,243 | 75 | /* 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... |
b3477c7cd0f5e0dc93383f57badda68bcaec2c57c4e49b0e0fbc7433849e3b22 | C++ | 2,243 | 97 | #ifndef GRAPH_HPP_
#include "graph.hpp"
#endif
void Graph::error (int error_num) const {
switch (error_num) {
case 1: throw runtime_error("Error GR1: input graph is not square!\n"); break;
default: throw invalid_argument("Error GR0: invalid error argument received!\n"); break;
}
}
void G... |
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