sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9c9abfdc06f7982bef11fd7adaf9c691f61e81583e6bbcc6554180befd92f2f6 | C++ | 7,353 | 159 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "CommandCaller.h"
#include "PrefilteringIndexReader.h"
#include "taxpercontig.sh.h"
#include "taxonomy.sh.h"
extern int computeSearchMode(int queryDbType, int targetDbType, int targetSrcDbType, int searchType);
void setTaxono... |
f5c606c37608f7b909ceca7bb0f2ebfc9af0ebdcca6ad2973bfe0ec0b4353fca | C++ | 7,396 | 238 | #include <fcntl.h>
#include <google/protobuf/io/coded_stream.h>
#include <google/protobuf/io/zero_copy_stream_impl.h>
#include <google/protobuf/text_format.h>
#ifdef USE_OPENCV
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/highgui/highgui_c.h>
#include <opencv2/imgproc/imgpro... |
100efa08eb0b544d9bfb77a0e35ff673e4f6151539c90973272fdbe70814f5b6 | C++ | 7,424 | 252 | #include "HeaderSummarizer.h"
#include "Util.h"
#include "Debug.h"
#include "PatternCompiler.h"
#include <set>
#include <algorithm>
#include <sstream>
struct UniprotHeader {
std::string dbType;
std::string identifier;
std::string proteinName;
std::string organismName;
unsigned int existence;
u... |
a606e419cca918a962d164888e1ad367aec2155744bdc6d29193de9331f01508 | C++ | 7,463 | 196 | #include <algorithm>
#include <cstring>
#include <vector>
#include "pybind11/numpy.h"
#include "pybind11/pybind11.h"
namespace py = pybind11;
namespace {
using FloatInput = py::array_t<float, py::array::c_style | py::array::forcecast>;
// Coordinates arrive as float64 (pytraj's native dtype); keeping this distinct f... |
be932aff2bb5793c49e610dd83352278a958f919b0947546dbf9b8494a75a5b3 | C++ | 7,475 | 241 | #include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include "gtest/gtest.h"
namespace YAML {
namespace {
TEST(LoadNodeTest, Reassign) {
Node node = Load("foo");
node = Node();
}
TEST(LoadNodeTest, FallbackValues) {
Node node = Load("foo: bar\nx: 2");
EXPECT_EQ("bar", node["foo"].as<std::string>());
EXPECT_EQ... |
6688aa4fb76403915a32e5c69493b44ee497a7ec8b0cb6fb2a0b8036419d8156 | C++ | 7,508 | 216 | // dear imgui: Platform Binding for GLUT/FreeGLUT
// This needs to be used along with a Renderer (e.g. OpenGL2)
// !!! GLUT/FreeGLUT IS OBSOLETE SOFTWARE. Using GLUT is not recommended unless you really miss the 90's. !!!
// !!! If someone or something is teaching you GLUT in 2020, you are being abused. Please show so... |
d5ab4977a78aed70ce74f77173f07682dbe232329ec2de0903773c8d11c85198 | C++ | 7,581 | 224 | /*
* Copyright (c) 2016-present, Przemyslaw Skibinski, Facebook, Inc.
* All rights reserved.
*
* This source code is licensed under both the BSD-style license (found in the
* LICENSE file in the root directory of this source tree) and the GPLv2 (found
* in the COPYING file in the root directory of this source tre... |
fddc1e22973c930e4361e1d6a3681dbe08daf673fdcc470f45bc109d83ed25be | C++ | 7,613 | 158 | // dear imgui: standalone example application for GLFW + OpenGL2, using legacy fixed pipeline
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// (GLFW is a cross-platform general purpose library for handling windows, inputs, OpenGL/Vulkan/Metal graphics context creati... |
cfe6bc507d8ea0ca839e4546fbe6085dab3047789334d75e0f86b045b17a44ab | C++ | 7,661 | 243 | #include "biconnected_component.h"
#include <algorithm> // std::copy_if, std::count
#include <queue>
#include <iterator> // std::inserter, std::back_inserter
#include "linear_allocator.h"
namespace miic {
namespace reconstruction {
namespace detail {
using std::copy_if;
using std::make_pair;
using std::min;
set<... |
a7a254b9aaf15b6bb8a638b0152eaf094c257d130b61c37c393d030a3de74ac8 | C++ | 7,663 | 156 | // dear imgui: standalone example application for SDL2 + OpenGL
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// (SDL is a cross-platform general purpose library for handling windows, inputs, OpenGL/Vulkan/Metal graphics context creation, etc.)
// **DO NOT USE THIS... |
796dc49227747f6229341348e61547713559c77e098b58bf189ce8b61d083de8 | C++ | 7,770 | 192 | #include "DBWriter.h"
#include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "Debug.h"
#include "DBReader.h"
#include "ReducedMatrix.h"
#include "DistanceCalculator.h"
#include "Orf.h"
#include "FastSort.h"
#ifdef OPENMP
#include <omp.h>
#endif
int clusthash(int argc, const char **argv, const Command... |
2119beaffbe72f93d031f6ca58d36af5395b903b7b7793a505e2766ca0a98943 | C++ | 7,835 | 196 | /**
* Copyright 2014-2025, XGBoost Contributors
* \file sparse_page_dmatrix.cc
*
* \brief The external memory version of Page Iterator.
* \author Tianqi Chen
*/
#include "sparse_page_dmatrix.h"
#include <algorithm> // for max
#include <memory> // for make_shared
#include <string> // for string
#include ... |
273f8d5f624286adc0f53ce9046c9aff0547fc63218ce91580d47855a4b6a123 | C++ | 7,853 | 197 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "KmerGenerator.h"
#... |
7f6ab622583b51c848840f8ce94fddb7447e4eac92336d27bb1b43e6b971d7c3 | C++ | 7,869 | 181 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <cmath>
#include "StripedSmithWaterman.h"
#include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionMatrix.h"
#inc... |
fe90e6cbc1dd04b4802b7171a6882d25c9f556e825537f9a3a41f8488547fa71 | C++ | 7,870 | 243 | #include "Debug.h"
#include "Util.h"
#include "Command.h"
#include "DistanceCalculator.h"
#include "FileUtil.h"
#include "Timer.h"
#include <iomanip>
extern const char *binary_name;
extern const char *tool_name;
extern const char *tool_introduction;
extern const char *main_author;
extern const char *version;
extern c... |
89cc0e62d9f1a883ca506b87c6d3e6f758deae45cb3654a58bf74719baf2f3cf | C++ | 7,877 | 340 | /* Adapted from MemoryMapped.h (http://create.stephan-brumme.com/portable-memory-mapping/)
* Copyright (c) 2013 Stephan Brumme. All rights reserved.
* License
* All source code published on http://create.stephan-brumme.com and its sub-pages is licensed similar to the zlib license:
*
* This software is provided 'a... |
9acc850822995a7885dbce17ca0e6ddf32808a771918a86f199ae3f4612453a7 | C++ | 7,908 | 191 | #include "Parameters.h"
#include "FileUtil.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FastSort.h"
#include <climits>
static bool compareToFirst(const std::pair<DBKeyType, DBKeyType>& lhs, const std::pair<DBKeyType, DBKeyType>& rhs){
return (lhs.first <= rhs.first... |
9655f84737be5800b5c10720e023eaf88530f75473b3a71abf81abe4b58f9456 | C++ | 7,938 | 215 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
97577b48540f48c66b563a1d06e478213ba1b0b4df68a930d2d9195cf1c7f74e | C++ | 7,939 | 190 | #include "Parameters.h"
#include "Util.h"
#include "DBReader.h"
#include "CommandCaller.h"
#include "Debug.h"
#include "FileUtil.h"
#include "Sequence.h"
#include "createindex.sh.h"
#include <string>
#include <cassert>
#include <climits>
#ifdef RIBOSEEK
extern void setRnaSearchDefaults(Parameters *par);
#endif
int ... |
cbc37107d7b27c7891cfb68b6bbfcc5c2f8b097d16f9d1c14368a432ac9cb451 | C++ | 8,002 | 253 | //----------------------------------------------------------------------------------
// File: common/egl_setup/source/egl_setup.cpp
// SDK Version: v1.0
// Site: http://developer.nvidia.com/
//
// Copyright (C) 2013 NVIDIA CORPORATION. All Rights Reserved.
//
// NVIDIA CORPORATION and its licensors ret... |
81ead6e99037aa2d9b67bee8a30405e0948084b926916be27b59f2243c452b3d | C++ | 8,007 | 278 | /**
* Copyright 2022-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/linalg.h> // Tensor,Vector
#include <algorithm> // for min
#include <thread> // for thread
#include "../../../src/common/linalg_op.h" // for begin, end
#include "../../../src/common/stat... |
6f548223737802cb031992d6b49e70f8e99d7b0e8eedfaadd6297182741e6b49 | C++ | 8,057 | 200 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "Matcher.h"
#include <map>
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
int aggregate(const bool useAln, int argc, const char **argv, const Command& command) {
... |
76c8d56aaf7852bcb8cf39066028bdccedccbfd3c99005a8b9e7ee4b629c8dce | C++ | 8,059 | 129 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2022-2023 Ole Richter - University of Groningen
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
th... |
70da58dd543f4222591c32f7daa3b2175d6e56f0cbee89c8821797b10a6f73b7 | C++ | 8,066 | 223 | #include <algorithm>
#include <cmath>
#include <vector>
#include "caffe/layers/infogain_loss_layer.hpp"
#include "caffe/util/io.hpp" // for bolb reading of matrix H
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void InfogainLossLayer<Dtype>::LayerSetUp(
const vector<Blob<D... |
bbc8b9d00b1e76703277b6d5693c91f57eede5067c2ab63d41e72fa0a498f03a | C++ | 8,085 | 212 | #include "DBReader.h"
#include "FastSort.h"
#include "Debug.h"
#include "Util.h"
#include <algorithm>
#include <cstddef>
#include <random>
#include <utility>
template<>
void DBReader<std::string>::sortIndex(bool isSortedById) {
if (accessType == SORT_BY_ID){
if (isSortedById) {
return;
... |
d6d53cb3f235917f439afa9d31daa2fc9a24f66bcc84b78d30202eb27cea23a5 | C++ | 8,099 | 359 | #include "stdafx.h" // pre-compiled headers
#include "defines.h"
#include "globaldata.h"
#include "script.h"
#include "script_object.h"
#include "script_func_impl.h"
//
// Object()
//
BIF_DECL(Op_Object)
{
IObject *obj = Object::Create(aParam, aParamCount, &aResultToken);
if (obj)
{
// DO NOT ADDREF: the calle... |
f4d27b2944e3793e053b52ab6c4ad00b092bcace703c3121beac736e1a7f5ca0 | C++ | 8,157 | 213 | /**
* Copyright 2022-2025, XGBoost contributors
*/
#include "iterative_dmatrix.h"
#include <algorithm> // for copy
#include <cstddef> // for size_t
#include <memory> // for shared_ptr
#include <utility> // for move
#include <vector> // for vector
#include "../common/categorical.h" // common::IsCat
#... |
9611c9d7c9a4bfff50bc9c6482dcb3acca3f864571e8b79f797ea41dbe70924a | C++ | 8,171 | 271 | /**
* Copyright 2020-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h> // for Context
#include <xgboost/task.h> // for ObjInfo
#include <xgboost/tree_model.h> // for RegTree
#include <xgboost/tree_updater.h> // for TreeUpdater
#include <memory> // for unique_ptr
... |
94f9c98d46e0aa9a8c6945d2d1ede86b295ed6345000757b6d75271d1ebfdfb1 | C++ | 8,186 | 291 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
9ac9f3aab931883907efb2ed9db55500aa2ad84e18978e405850d65aa249a791 | C++ | 8,188 | 212 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
3cbdb4747dd9887710eae3f358166e5dc0c5a9ffa96f0068c1ed6b9853ea7edc | C++ | 8,193 | 253 | // Copyright 2008, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
dbfa31cfc328a1cb0eb6a3fc64fdd2631594d4287401090155c18d28ed0dbba8 | C++ | 8,265 | 217 | /*++
Module Name:
AlignmentAdjuster.cpp
Abstract:
Code to adjust alignments to avoid indels at ends, or overhanging contig boundaries
Authors:
Bill Bolosky, May, 2016
Environment:
User mode service.
Revision History:
Pulled out of other places in SNAP
--*/
#include "stdafx.h"
#include "A... |
95b5bb0e4950de624195646abfac93d8809fb98a2ceec974e7a84e3b5078deb5 | C++ | 8,293 | 261 | #include <Rcpp.h>
#include <algorithm>
#include <cfloat>
#define _USE_MATH_DEFINES
#include <cmath>
#include <vector>
using namespace Rcpp;
namespace {
double ramanujan(int n) {
// Returns log(fac(n)) with Ramanujan's approximation.
if (n == 0) {
return (0);
}
double N = n * log(1.0 * n) - n +
... |
ce3f7c44f54d0efb78edcba7e2b17f6bb3986c9a33090ea1ee92cd363cf9ddc3 | C++ | 8,324 | 187 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
b785ca30fa01aad0381f6a6f73c6b318824484b98e021dfd217591516052af6a | C++ | 8,333 | 209 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "IndexReader.h"
#include "FileUtil.h"
#ifdef OPENMP
#include <omp.h>
#endif
#ifndef SIZE_T_MAX
#define SIZE_T_MAX ((size_t) -1)
#endif
int createtsv(int argc, const char **argv, const Command &command) ... |
89db94acd164e47a7d2d45277aca26ecb99eedc8a448a8f45c374fdd3765f84a | C++ | 8,336 | 210 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "Matcher.h"
#include "MappingReader.h"
#ifdef OPENMP
#include <omp.h>
#endif
int dolca(int argc, const char **argv, const Command& command, bool majority) {
Parameters& par =... |
6e72e57f27ed4adc326943cac7f5557a3d5b5e3b3610db94794c6bd39957bf85 | C++ | 8,370 | 244 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2022-2023 Ole Richter - University of Groningen
Copyright (C) 2022 Benjamin Hucko
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General... |
47318d2cee437d0368330e6014638ef7482f385439f1865991398bbc302b3e0b | C++ | 8,382 | 382 | /*++
Module Name:
GenericFile_HDFS.cpp
Abstract:
Generic IO class for SNAP that can read from HDFS.
Authors:
Jeremy Elson, February 2014
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#ifdef SNAP_HDFS
#include "Compat.h"
#include "Error.h"
#include "GenericFile.... |
834c439991cf204d11935617c878c4d727364c6a3ccb5909b576ce552cbc66ad | C++ | 8,384 | 360 | // This code contains NVIDIA Confidential Information and is disclosed to you
// under a form of NVIDIA software license agreement provided separately to you.
//
// Notice
// NVIDIA Corporation and its licensors retain all intellectual property and
// proprietary rights in and to this software and related documentation... |
d9c1e1fdba26990936efbfb0711c7356efd6061d2c1022fb48b2489aa578d1af | C++ | 8,426 | 304 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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 opt... |
9065f31ccf746cf8b390121f958f9e959033af864aed779597066625ed56bc36 | C++ | 8,534 | 288 | #include "win32_window.h"
#include <dwmapi.h>
#include <flutter_windows.h>
#include "resource.h"
namespace {
/// Window attribute that enables dark mode window decorations.
///
/// Redefined in case the developer's machine has a Windows SDK older than
/// version 10.0.22000.0.
/// See: https://docs.microsoft.com/wi... |
11da6ab2ae8c00d35c5cbf54eaeb7fc096fb99993d72ecf474c6cf24a874b004 | C++ | 8,586 | 232 | #include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "CompressedA3M.h"
#include "MathUtil.h"
#include "Domain.h"
#include <fstream>
#include <iomanip>
#include <map>
#ifdef OPENMP
#include <omp.h>
#endif
static inline float getOverlap(const std::vector<boo... |
fb0ecf2966bc15b16fe338facb82a929e19b974a964387174096710d044abdb7 | C++ | 8,591 | 236 | #include <string>
#include <vector>
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layer.hpp"
#include "caffe/layers/rnn_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void RNNLayer<Dtype>::RecurrentInputBlobNames(vec... |
699dddea05976d5f5efa69a753168c0f51dada312864c56839737fd981f0cd35 | C++ | 8,629 | 316 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
0e8bdd5431f5062c8a9ab7691ce819a0e422e2dc9478d78b21098af942b19ad2 | C++ | 8,646 | 246 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2022 Matteo Cartiglia - University of Zurich
Copyright (C) 2022-2023 Ole Richter - University of Groningen
This program is free software: you can redistribute it and/or modify
it under the... |
55650bbf848480476832c52b24d9b4e988e9f1c3a23045eec993bf9d02d7ac95 | C++ | 8,651 | 234 | /**
* Copyright 2021-2024, XGBoost contributors.
*/
#include <gtest/gtest.h>
#include <xgboost/tree_updater.h> // for TreeUpdater
#include <algorithm> // for transform
#include <memory> // for unique_ptr
#include <vector> // for vector
#include "../../../src/tree/common_row_partitioner.h"
#include "../../... |
90becc411754d3fd5766b30b7ea6f7cc7315bbf7b21324751d720695cbd166a7 | C++ | 8,652 | 260 | /*++
Module Name:
RangeSplitter.cpp
Abstract:
Code to split a range into pieces for multiple cores to process. It's designed
to handle cores that proceed at varying rates.
Authors:
Bill Bolosky, 2011
Environment:
User mode service.
Revision History:
Pulled out of cSNAP.cpp to make it ... |
e5ffa6acf532cdb4f2e5dbaf6904e7c8370f9b375c702afd3623ff44082ffea0 | C++ | 8,653 | 280 | /*
AutoHotkey
Copyright 2003-2009 Chris Mallett (support@autohotkey.com)
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 2
of the License, or (at your option) any later version.
This... |
9719484a797c186c2b266ca1996a78fcd7f2ad2a3d5f25fccb61e2aaa74c160e | C++ | 8,661 | 265 | #include <caffe/caffe.hpp>
#ifdef USE_OPENCV
#include <opencv2/core/core.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <opencv2/imgproc/imgproc.hpp>
#endif // USE_OPENCV
#include <algorithm>
#include <iosfwd>
#include <memory>
#include <string>
#include <utility>
#include <vector>
#ifdef USE_OPENCV
using names... |
24cd226b7ff1a38857e7809b76d211c68d74d9a91e974719217d9b1bbbae9748 | C++ | 8,773 | 211 | #include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "MemoryMapped.h"
#include "Orf.h"
#include "Parameters.h"
#ifdef OPENMP
#include <omp.h>
#endif
int gff2db(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parsePara... |
b9b941b95a743da254472f190ce814030ad5dba11e449a2a75d0f192e3e307bb | C++ | 8,849 | 259 | /**
* Copyright 2025, XGBoost Contributors
*/
#include "cat_container.h"
#include <algorithm> // for copy
#include <cstddef> // for size_t
#include <memory> // for make_unique
#include <utility> // for move
#include <vector> // for vector
#include "../common/error_msg.h" // for NoFloatCat
#include "... |
70da9f56240227e8639f747bc4948fd384191a8b5d16eec97b91c3458878a819 | C++ | 8,870 | 173 | // dear imgui: standalone example application for Emscripten, using SDL2 + OpenGL3
// This is mostly the same code as the SDL2 + OpenGL3 example, simply with the modifications needed to run on Emscripten.
// It is possible to combine both code into a single source file that will compile properly on Desktop and using Em... |
e3bbe4ff0c1876279da0d5c31ed2cfd4ca2672e1baf484ce4c9d32e844db5af0 | C++ | 8,877 | 386 | #include <cassert>
#include <memory>
#include "exp.h"
#include "scanner.h"
#include "token.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
namespace YAML {
Scanner::Scanner(std::istream& in)
: INPUT(in),
m_startedStream(false),
m_endedStream(false),
m_simpleKeyAllowed(false),
m_c... |
e12134fee2e41016a9c7ddb1a0b763f62420cf318284206c2c74cb6511f2ac7d | C++ | 8,901 | 221 | #include "Debug.h"
#include "Parameters.h"
#include "FastSort.h"
#include "Aggregation.h"
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
struct compareByStart {
bool operator()(const std::pair<long, long> &lhs,
const std::pair<long, long> &rhs) const {
return (lhs.first < ... |
5d5f1306362fcc7a564559f7a3ad124dc8f8b3fe01dcda65a3dbe27468c927d6 | C++ | 8,904 | 309 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
89969599b60a5f396053d03f2ba4d3299621399318567367e4af412b87cedce3 | C++ | 8,919 | 311 | // Copyright 2010, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
45db6b65dcc48edefb983b051f0e5b4cd58e489b6502991b989fc27093b65727 | C++ | 8,952 | 269 | #include "skeleton.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#include <Rcpp.h>
#include <algorithm> // std::sort, std::max_element
#include <vector>
#include "get_information.h"
#include "structure.h"
#include "utilities.h"
namespace miic {
namespace reconstruction {
using Rcpp::Rcerr;
using Rcpp::Rcout;
using na... |
c7bc04f9b67abf0ec7f80e750ae7196d5f561056e778432a61e14301593e282d | C++ | 9,108 | 374 | /*++
Module Name:
Util.cpp
Abstract:
Generic support routines that don't seem to belong elsewhere.
Authors:
Bill Bolosky, March, 2013
Environment:
User mode service.
Revision History:
Factored from other places
--*/
#include "stdafx.h"
#include "Util.h"
#include "Error.h"
#include "Gener... |
a4349281cf83c81aa625cdff6725182dd77c38ce0e53a31d6655c018c7200891 | C++ | 9,127 | 233 | /**
* Copyright 2018-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/host_device_vector.h>
#include <xgboost/tree_updater.h>
#include <cstddef> // for size_t
#include <string>
#include <vector>
#include "../../../src/tree/common_row_partitioner.h"
#include "../../../src/tree/hist/expand_en... |
a818948b7329f6db6db83bd733952640f1b4d612b1be8b9f6b82b995dc98a4ac | C++ | 9,158 | 320 | /* -*- mode: c++; tab-width: 2; indent-tabs-mode: nil; -*-
Copyright (c) 2010-2012 Marcus Geelnard
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
Permission is granted to anyone to use this ... |
0e4580f07ec3ad1449797ef432de620bc9826b5beb80310a523b469070f21bc6 | C++ | 9,177 | 218 | #include "KmerGenerator.h"
#include "simd.h"
#include <algorithm> // std::reverse
KmerGenerator::KmerGenerator(size_t kmerSize, size_t alphabetSize, short threshold ){
this->threshold = threshold;
this->kmerSize = kmerSize;
this->indexer = new Indexer((int) alphabetSize, (int)kmerSize);
// calcDivide... |
7b1956dde6c0d9f6f79ced22e786613787b51b8d69a70cd35480d3d7a1ec1bb8 | C++ | 9,194 | 291 | /**
* Copyright 2014-2025, XGBoost Contributors
*
* \brief Context object used for controlling runtime parameters.
*/
#include "xgboost/context.h"
#include <algorithm> // for find_if
#include <charconv> // for from_chars
#include <iterator> // for distance
#include <optional> // for optional
#include <regex... |
8fbfc6ce45cf175aa93573e75039be55384a9f8a63964c16cc8e5f7eb203777b | C++ | 9,207 | 229 | #include "Debug.h"
#include "Parameters.h"
#include "Aggregation.h"
#include "itoa.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
double LBinCoeff(double* lookup, int M, int k) {
return lookup[M + 1] - lookup[M - k + 1] - lookup[k + 1];
}
// Precompute coefficients logB[i] = log(B[i])
void precomput... |
ca99a9dec9bb0cb5261c7d671599bb843bb3963eff2aa5f2f91e674f83682299 | C++ | 9,212 | 268 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include <chrono> // for seconds
#include <future> // for future
#include <memory> // for unique_ptr
#include <string> // for string
#include <thread> // for sleep_for
#include <type_traits> // for is_same_v, remove_pointer_t
#include <... |
77657e51ee689b38cb4f363303edc4f914c3aecca8788116ed82f7eeee36b437 | C++ | 9,215 | 237 | /**
* Copyright 2021-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/data.h> // for BatchIterator, BatchSet, DMatrix, BatchParam
#include <algorithm> // for sort, unique
#include <cmath> // for isnan
#include <cs... |
aaacc0619ec825be750e37c38747b8a196314fc02f605c6e05574553d212da2c | C++ | 9,215 | 365 | #include <limits>
#include "emitterstate.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
namespace YAML {
EmitterState::EmitterState()
: m_isGood(true),
m_curIndent(0),
m_hasAnchor(false),
m_hasTag(false),
m_hasNonContent(false),
m_docCount(0) {
// set default global mani... |
d0461932e7ae1a4111fbf8433707458f950b2d321dbce737140fbf72db33c345 | C++ | 9,225 | 214 | #include "Util.h"
#include "Parameters.h"
#include "Matcher.h"
#include "itoa.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#ifdef OPENMP
#include <omp.h>
#endif
int proteinaln2nucl(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.pars... |
dca828ddf5f225de648dee771a7e2ee387803508afba87beaaa90041aa8fdad8 | C++ | 9,239 | 203 | /**
* Copyright by XGBoost Contributors 2017-2022
*/
#include "cpu_treeshap.h"
#include <algorithm> // copy
#include <cinttypes> // std::uint32_t
#include "predict_fn.h" // GetNextNode
#include "xgboost/base.h" // bst_node_t
#include "xgboost/logging.h"
#include "xgboost/tree... |
1febce770de49c6bca617573ca63a3dc393ba299e6fdef820b34ef18c251e473 | C++ | 9,327 | 322 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
3be7f115c60934e984e57bc5b24f27efc7f4bf60effab1604554dde75284a24a | C++ | 9,331 | 296 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "taxonomy.h"
using std::string;
using std::map;
using std::set;
using std::ifstream;
using std::istringstream;
using std::queue;
using std::ofstream;
namespace kra... |
33ada7d1b327b166487a298896a69a4c3d439d80fb8ab87de2157c2f1aa53f23 | C++ | 9,447 | 227 | #include <algorithm>
#include <vector>
#include "caffe/filler.hpp"
#include "caffe/layer_factory.hpp"
#include "caffe/layers/scale_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void ScaleLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<... |
1b7cdf6a4a1ea883e3c75566bf7649dc2710d666e96e9cdc4c6adb02e9eb98b3 | C++ | 9,468 | 248 | /**
* Copyright 2023-2025, XGBoost Contributors
*/
#include "xgboost/multi_target_tree_model.h"
#include <algorithm> // for copy_n
#include <cstddef> // for size_t
#include <cstdint> // for int32_t, uint8_t
#include <limits> // for numeric_limits
#include <string_view> // for string_view
#include... |
dd70d06ad2f54f19e340454b514230725187ed86f139aa2f442251cb6f590ac4 | C++ | 9,495 | 286 | /*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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 opt... |
f388d01a67bb66ff1f504f5b33cf13623c86d9990ef8d68f05bb3dd30bd7ffbb | C++ | 9,563 | 244 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "mmscanner.h"
#include <cassert>
using std::string;
using std::vector;
namespace kraken2 {
void MinimizerScanner::set_lookup_table_character(char c, uint8_t val) ... |
4fb365a71a0e892d23fd3711a421a13207c17579f114f3271e23a7915210df20 | C++ | 9,587 | 239 | // dear imgui: standalone example application for DirectX 10
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
#include "imgui.h"
#include "imgui_impl_win32.h"
#include "imgui_impl_dx10.h"
#include <d3d10_1.h>
#include <d3d10.h>
#define DIRECTINPUT_VERSION 0x0800
#incl... |
6d730ea705a76684dec466261638f891121a282d33a24a98ef9fac4974738c8b | C++ | 9,623 | 208 | #include "Parameters.h"
#include "Util.h"
#include "DBWriter.h"
#include "CommandCaller.h"
#include "Debug.h"
#include "FileUtil.h"
#include "linclust.sh.h"
#include <cassert>
void setLinclustWorkflowDefaults(Parameters *p) {
p->spacedKmer = false;
p->covThr = 0.8;
p->maskMode = 0;
p->evalThr = 0.001... |
22db7a4e98f79209ef6b5c1e28ba6fc51df8ed2d325eb86dd0e73f236eade780 | C++ | 9,641 | 256 | // Copyright 2007, Google Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions ... |
ba79ed780de06c8c9b50b849b12a02690e070c1ca99e8c0b6f912b944026791d | C++ | 9,648 | 290 | /**
* Copyright 2022-2023, XGBoost contributors
*/
#include "in_memory_handler.h"
#include <algorithm>
#include <functional>
#include "comm.h"
namespace xgboost::collective {
/**
* @brief Functor for allgather.
*/
class AllgatherFunctor {
public:
std::string const name{"Allgather"};
AllgatherFunctor(std::in... |
b1f1cb9745880a0bc5369572b0333868f4d6099b3578d3d2a608a10746927628 | C++ | 9,671 | 234 | // dear imgui: standalone example application for DirectX 9
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
#include "imgui.h"
#include "imgui_impl_dx9.h"
#include "imgui_impl_win32.h"
#include <d3d9.h>
#define DIRECTINPUT_VERSION 0x0800
#include <dinput.h>
#include ... |
0ff1c14ab467998d53c2bf7c28506ca0c9243da6e60c9c5324011cee7c6edff5 | C++ | 9,679 | 304 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "reports.h"
#include "kraken2_data.h"
#include "omp_hack.h"
using std::vector;
using std::string;
using std::ofstream;
namespace kraken2 {
void dumpTaxonCounters... |
55f75efe6449ebb295dcffe8d2a104c7832eb4a3120061d5606e837cb0fe764f | C++ | 9,812 | 246 | #include "r_cpp_interface.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#include <string>
#include <vector>
namespace miic {
namespace utility {
constexpr double kMagnitudeTies = 0.00005;
using namespace structure;
using Rcpp::as;
using std::vector;
void setEnvironmentFromR(const Rcpp::List& input_data,
const Rcp... |
19b352c8d2275be1aedd8f382473050a12db0490cf4cd696b2652a502932d7e0 | C++ | 9,832 | 311 | // Copyright 2009 Google Inc. All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and ... |
06b60c42c8316409ebffbc3e9aaa1c01d3a847fb40fa1a2234a5e29a62204767 | C++ | 9,876 | 301 | //
// Created by lasagnaphil on 20. 9. 22..
//
#include "ShapeRenderer.h"
#include <glad/glad.h>
#include "GLfunctions.h"
std::vector<Eigen::Vector3f> buildCircle(float radius, int steps)
{
std::vector<Eigen::Vector3f> points(steps + 1);
if (steps < 2)
return points;
const float PI2 = acos(-1) *... |
bbd3274a0ddd0afcb452d173612d15422f512da05f2e030ff984daffa447d44f | C++ | 9,928 | 228 | // dear imgui: standalone example application for SDL2 + DirectX 11
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// (SDL is a cross-platform general purpose library for handling windows, inputs, OpenGL/Vulkan/Metal graphics context creation, etc.)
#include "imgui.... |
b362cf403bc97a5a5492ea92849c61afa9e510d657dc0320f7ed6eaed1025520 | C++ | 9,967 | 243 | // dear imgui - standalone example application for DirectX 11
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
#include "imgui.h"
#include "imgui_impl_win32.h"
#include "imgui_impl_dx11.h"
#include <d3d11.h>
#define DIRECTINPUT_VERSION 0x0800
#include <dinput.h>
#incl... |
748c97b173dd902388fc88389286c697d138cfa3ea3e6a4e2ccee4b99cafb72b | C++ | 10,014 | 251 | #include <algorithm>
#include <vector>
#include "caffe/layers/batch_norm_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void BatchNormLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
BatchNormParameter param = thi... |
8cdd90bdf454f224ce2e6157bd0329e6e4b48a3ad795c60ec468725a55002190 | C++ | 10,042 | 284 | #include <cmath>
#include "ReducedMatrix.h"
#include "Util.h"
ReducedMatrix::ReducedMatrix(double **probMatrix, float ** rMatrix,
unsigned char* aa2num, char* num2aa,
size_t orgAlphabetSize,
size_t reducedAlphabetSize, float bitFact... |
01352d102ec1a5009e41421b32fb43aa14d6dd1a5a8bb38a83572b84d766ad29 | C++ | 10,061 | 298 | /*++
Module Name:
MultiInputReadSupplier.cpp
Abstract:
A read supplier that combines other read suppliers. It's used when there are muliple input files to process.
Authors:
Bill Bolosky, November, 2012
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Read... |
a82071c3151058a923cce1315ff9216b1a384d4e7b7b64b3fb3fcdfffd7b8ae9 | C++ | 10,138 | 269 | #ifdef USE_CUDNN
#include <algorithm>
#include <vector>
#include "caffe/layers/cudnn_conv_layer.hpp"
namespace caffe {
// Set to three for the benefit of the backward pass, which
// can use separate streams for calculating the gradient w.r.t.
// bias, filter weights, and bottom data for each group independently
#def... |
9a6c572e41ca97222286fed4fee9c86e1f0d389d3f6029a37a023dcb08c8e8df | C++ | 10,179 | 224 | #include "DBReader.h"
#include "Util.h"
#include "FileUtil.h"
#include "PrefilteringIndexReader.h"
#include "Prefiltering.h"
#include "Parameters.h"
#include "Sequence.h"
#ifdef OPENMP
#include <omp.h>
#endif
void setIndexDbDefaults(Parameters *p) {
p->sensitivity = 5.7;
}
std::string findIncompatibleParameter(D... |
c917f9db9873ca876d0aaac993fe39ed8887412398a5b63d3c145f741e23dde6 | C++ | 10,181 | 278 | // main.cpp
// TestBestAlphabet
//
// Created by Johannes Soeding on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include <cmath>
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "BaseMatrix.h"
#include "Parameters.h"
#include <cfloat>
#include "DBReader.h"
#inc... |
11d83c29131712ad62c02524d2687afbce5bb7df1a8d00e1d710ada000d6e8ee | C++ | 10,262 | 214 | // dear imgui: standalone example application for GLFW + OpenGL 3, using programmable pipeline
// If you are new to dear imgui, see examples/README.txt and documentation at the top of imgui.cpp.
// (GLFW is a cross-platform general purpose library for handling windows, inputs, OpenGL/Vulkan/Metal graphics context creat... |
cf0a4a2093ae703bddff8ad101cee3013fc308c652e000247c5c3aa256c5b0d7 | C++ | 10,311 | 252 | /**
* Copyright 2017-2025, XGBoost Contributors
* \brief Data type for fast histogram aggregation.
*/
#include "gradient_index.h"
#include <limits>
#include <memory>
#include <utility> // for forward
#include "../common/column_matrix.h"
#include "../common/hist_util.h"
#include "../common/numeric.h"
#include "../... |
18507afacdbafdd69ae49cc50f096b47704f8c76505a7b0e7fa4c518f3f7435e | C++ | 10,314 | 327 | /*
* Bshouty Lung Model - Pulmonary Circulation Simulation
* Copyright (c) 1989-2014 Zoheir Bshouty, MD, PhD, FRCPC
* Copyright (c) 2011-2014 Adam Majer
*
* 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
* ... |
4e8f17c95c85f58d667e9404f68710ce678c91c19abc0686eb9946fbaed94f27 | C++ | 10,366 | 385 | #include <boost/math/special_functions/next.hpp>
#include <boost/random.hpp>
#include <limits>
#include "caffe/common.hpp"
#include "caffe/util/math_functions.hpp"
#include "caffe/util/rng.hpp"
namespace caffe {
template<>
void caffe_cpu_gemm<float>(const CBLAS_TRANSPOSE TransA,
const CBLAS_TRANSPOSE TransB, co... |
3691c6a999952e55cff700ef80af79cc815fc6310e5a1d0cc82de611752f1704 | C++ | 10,444 | 343 | /*++
Module Name:
HashTable.cpp
Abstract:
Large closed hash table, specialized for SNAP
Authors:
Bill Bolosky, March, 2011
Environment:
--*/
#include "stdafx.h"
#include "HashTable.h"
#include "BigAlloc.h"
#include "exit.h"
#include "Genome.h"
#include "Error.h"
#include "GenericFile_Blob.h"
SNAPHash... |
fcd05b235fcd239581c1c7cdce61d6ae646bd871930dcb871406b78d1ab0a60c | C++ | 10,461 | 309 | // Make sure we include Python.h before any system header
// to avoid _POSIX_C_SOURCE redefinition
#ifdef WITH_PYTHON_LAYER
#include <boost/python.hpp>
#endif
#include <string>
#include "caffe/layer.hpp"
#include "caffe/layer_factory.hpp"
#include "caffe/layers/clip_layer.hpp"
#include "caffe/layers/conv_layer.hpp"
#i... |
462884a0e6066c3527b5f5569435f9650d3761f6e0dadf9b84ea20c525d6ee1e | C++ | 10,473 | 375 | /**
* Copyright 2021-2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/context.h>
#include <xgboost/host_device_vector.h> // for HostDeviceVector
#include <xgboost/linalg.h>
#include <cstddef> // size_t
#include <numeric> // iota
#include <vector>
#include "../../../src/common/linalg_op.... |
3381a62d16558ee499b203a271bed8ef3641d3053f5e5c1762c500ef266ed300 | C++ | 10,484 | 245 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 2022-2023 Ole Richter - University of Groningen
Copyright (C) 2022 Benjamin Hucko
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General... |
ae659378d240677311d691e30a1f49bce1618866ac60046f95f39522b252aae6 | C++ | 10,506 | 329 | /*
* Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
*
* This file is part of the Kraken 2 taxonomic sequence classification system.
*/
#include "build_db.h"
#include "kraken2_headers.h"
#include "taxonomy.h"
#include "mmscanner.h"
#include "compact_hash.h"
#include "kraken2_data.h"
#include "utilities.h"
us... |
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