sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b37e045416405d83514dc6bd91ec5d24f54d03175d377705bcc9d1b5fcc2a7cc | C++ | 10,544 | 268 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include "NcbiTaxonomy.h"
#include "FastSort.h"
#include "MemoryMapped.h"
#include "GzReader.h"
#ifdef OPENMP
#include <omp.h>
#endif
static bool compareToFirstString(const std::pair<std::string, TaxID>& lhs, cons... |
2267ef34aa0b260abb8edc48317e889735a50384bf8dec250bd5742b43dcc6b0 | C++ | 10,593 | 263 | //
// Written by Martin Steinegger
//
// Wrapper for KSW2 aligner.
// Local banded nucleotide aligner
//
#include "Parameters.h"
#include "DistanceCalculator.h"
#include "ksw2.h"
#include "BandedNucleotideAligner.h"
#include "Util.h"
#include "SubstitutionMatrix.h"
#include "Debug.h"
#include "StripedSmithWaterman.h"
... |
1b5099f51a5daba3abef1cb1c224c9c108e93d707e94b641a3745a1af00a4510 | C++ | 10,607 | 463 | #include "NumPyHelper.h"
#ifdef BOOSTPYTHON
np::ndarray toNumPyArray(const std::vector<float>& val)
{
int n = val.size();
p::tuple shape = p::make_tuple(n);
np::dtype dtype = np::dtype::get_builtin<float>();
np::ndarray array = np::empty(shape,dtype);
float* dest = reinterpret_cast<float*>(array.get_data());
fo... |
f63886e4457eb08f50e93495ff552a25d0cf71aefcf915c9363fcef377228cd7 | C++ | 10,642 | 343 | // 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... |
1c8c663dd5d187e6fd591e8bad1fc6349cc214abf59646b44d87a39a80a1552b | C++ | 10,672 | 253 | #include "MultipleAlignment.h"
#include "Debug.h"
#include "simd.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#include "Util.h"
#include "Orf.h"
MultipleAlignment::MultipleAlignment(size_t maxSeqLen, SubstitutionMatrix *subMat)
: subMat(subMat), maxSeqLen(maxSeqLen), maxMsaSeqLen(maxSeqLen * 2) {
... |
1012579a0f788c6e73572da8a7f33522541d47e4a9da24347321a95129f55741 | C++ | 10,685 | 325 | #include <boost/thread.hpp>
#include <glog/logging.h>
#include <cmath>
#include <cstdio>
#include <ctime>
#include "caffe/common.hpp"
#include "caffe/util/rng.hpp"
namespace caffe {
// Make sure each thread can have different values.
static boost::thread_specific_ptr<Caffe> thread_instance_;
Caffe& Caffe::Get() {
... |
710e82aa1ee6cda499854930f537d19fe1346c0f3b4123fc0a0d811c88bdf850 | C++ | 10,688 | 216 | // 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.)
// (GL3W is a helper ... |
b85f6d87f512dd694078d7d369405d3693d6416fdda5902baf6e3f2ad3a6b204 | C++ | 10,694 | 386 | /*
* Symmetric Dustmasker mostly based on a similarly named implementation
* by Heng Li as part of the minimap project.
*/
#include <algorithm>
#include <deque>
#include <functional>
#include <future>
#include <iostream>
#include <string>
#include <vector>
#include <queue>
#include <ctype.h>
#include <getopt.h>
#i... |
137acea597c91475ab04ef01ee7617c7628efd3bc3a337183cebbb94b5bc4896 | C++ | 10,704 | 347 | #include "computation_discrete.h"
#include <algorithm> // std::min
#define _USE_MATH_DEFINES
#include <cmath>
#include <numeric> // std::iota
#include "linear_allocator.h"
#include "mutual_information.h"
#include "structure.h"
constexpr int BIC = 0;
namespace miic {
namespace computation {
using std::log;
using s... |
5577a587f78ce0ede8e82666b47d4bb58b8c3ab81a488e264279d1b015b00ccf | C++ | 10,741 | 383 | /*
* extractA3M adapted from HH-suite 3.0: a3m_compress.h
* Original Author: meiermark
* Relicensed with permission from jsoeding to MIT
*/
#include "CompressedA3M.h"
#include "DBConcat.h"
#include <sstream>
void readU16(const char **ptr, uint16_t &result) {
unsigned char array[2];
array[0] = (unsigned c... |
2d19a46ecb8617b63c8e9b156bda7ffe8aa23203c856e024875038f3bf7afb60 | C++ | 10,935 | 459 | /*
* 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
* ... |
f12ae7b883f56556893bd7cf99bd3957db7ed8e7e57f88f561f3d5c74a6632fb | C++ | 11,009 | 386 | /*
* 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
* ... |
b920707f098d20571f72e14a1d3693728be2e5374fb253fdd1ba4cc6d47c3e87 | C++ | 11,026 | 371 | #ifdef USE_NCCL
#include <cuda_runtime.h>
#include <glog/logging.h>
#include <stdio.h>
#include <sstream>
#include <string>
#include <vector>
#include "caffe/caffe.hpp"
#include "caffe/parallel.hpp"
#include "caffe/sgd_solvers.hpp"
namespace caffe {
enum Op {
copy,
replace_cpu,
replace_gpu,
replace_cpu_diff... |
79820b326a8c3524d6e276e699d0ecf5c3837988749ec2b4d16c958ef6ab3dfd | C++ | 11,078 | 205 | #include <iostream>
#include <list>
#include <algorithm>
#include <cmath>
#include "SequenceLookup.h"
#include "SubstitutionMatrix.h"
#include "UngappedAlignment.h"
#include "ExtendedSubstitutionMatrix.h"
#include "Clustering.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Parameters.h"
const char* binary_n... |
9ff613f2733d71e2c8f6f2d5f355949de6ff5334aa5473e5dc163ef775e71fcb | C++ | 11,143 | 354 | // Created by: Yang Zhang
// Description: Python bindings for all actions in the library
// Functionality:
// 1. frame_voxelize: Voxelization of a single frame
// 2. frame_observation: Compute the observable for a single frame
// 3. marching_observer: Marching observer algorithm for a slice of frames/trajectory
// 4.... |
a32110966712ddd5b30d7e759b3318a18d0279a15af6e1765259f30d98f42050 | C++ | 11,300 | 486 | //
// Copyright (c) 2009-2010 Mikko Mononen memon@inside.org
//
// 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 software for any purpose... |
b2e00ef6d66aee521ba6d648250c03050f86c34b34b5d9cee82837196933f82a | C++ | 11,381 | 326 | /*
* 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
* ... |
5fe136c5bb154f6b29a00f6114021b4de5876fb5bfddc8493253307f6bebfa93 | C++ | 11,402 | 411 | /**
* Copyright 2017-2024 by XGBoost contributors
*/
#ifdef XGBOOST_USE_SYCL
// implementation of HostDeviceVector with sycl support
#include <memory>
#include <utility>
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-W#pragma-messages"
#pragma GCC diagnostic ignored "-Wtautological-constant-compare"
... |
eb581076cba70a16d810920d7b6bf16b4b806686b6211f576435b0b31e1e1590 | C++ | 11,404 | 268 | #include "Clustering.h"
#include "ClusteringAlgorithms.h"
#include "AlignmentSymmetry.h"
#include "Debug.h"
#include "Util.h"
#include "itoa.h"
#include "Timer.h"
#include "SequenceWeights.h"
#include <fstream>
Clustering::Clustering(const std::string &seqDB, const std::string &seqDBIndex,
const... |
2d47f2a3bb834d308d87d007496517ae96c3a3262fa5dd2aed75159e0700b203 | C++ | 11,426 | 437 | #include <sstream>
#include "exp.h"
#include "regex_yaml.h"
#include "regeximpl.h"
#include "scanner.h"
#include "scanscalar.h"
#include "scantag.h" // IWYU pragma: keep
#include "tag.h" // IWYU pragma: keep
#include "token.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep
#include "yaml-cpp/mark.h"
nam... |
908e81dbcb7a4306dfddfb025a704b7a779ef2e6d37249cf5fd13fa33ded4d5a | C++ | 11,441 | 414 | #include <algorithm>
#include <cstdio>
#include <sstream>
#include "collectionstack.h" // IWYU pragma: keep
#include "scanner.h"
#include "singledocparser.h"
#include "tag.h"
#include "token.h"
#include "yaml-cpp/emitterstyle.h"
#include "yaml-cpp/eventhandler.h"
#include "yaml-cpp/exceptions.h" // IWYU pragma: keep... |
0e5fa2ba94955963731efcd2786247e224e24d29dc6ca7e80756adef72d94267 | C++ | 11,589 | 296 | #include <string>
#include <vector>
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layer.hpp"
#include "caffe/layers/recurrent_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void RecurrentLayer<Dtype>::LayerSetUp(cons... |
88b46ba21c1347667193e82797317fba50a2726d7d6c55a04666398d8e677a35 | C++ | 11,611 | 557 | #include "BVH.h"
#include <iostream>
#include <Eigen/Geometry>
#include "dart/dart.hpp"
using namespace dart::dynamics;
namespace MASS
{
Eigen::Matrix3d
R_x(double x)
{
double cosa = cos(x * 3.141592 / 180.0);
double sina = sin(x * 3.141592 / 180.0);
Eigen::Matrix3d R;
R << 1, 0, 0,
0, cosa, -sina,
0, ... |
9986dd01648fc05128fae24e402a3c726442dff9f2ab5e37dc2b56e0945396c6 | C++ | 11,685 | 426 | /*
* 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
* ... |
b568017e203e5edbaa7acb25ee673f8ea0e437bc25b907a97722f7c921bc8341 | C++ | 11,776 | 448 | #include <iostream>
#include "stream.h"
#ifndef YAML_PREFETCH_SIZE
#define YAML_PREFETCH_SIZE 2048
#endif
#define S_ARRAY_SIZE(A) (sizeof(A) / sizeof(*(A)))
#define S_ARRAY_END(A) ((A) + S_ARRAY_SIZE(A))
#define CP_REPLACEMENT_CHARACTER (0xFFFD)
namespace YAML {
enum UtfIntroState {
uis_start,
uis_utfbe_b1,
... |
d16e10dc207b012860683628d3e8f263486559ef9bc0465c3fe2857624d6a76e | C++ | 11,848 | 293 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "FastSort.h"
#include "MappingReader.h"
#include <unordered_map>
#include "krona_prelude.html.h"
#ifdef OPENMP
#include <omp.h>
#endif
unsigned int cladeCountVal(const std::uno... |
79e448324b04f242a9376ee6c5a5d3205b99e9ac10ecf5663a3f795aca071f29 | C++ | 11,982 | 271 | #include "IndexBuilder.h"
#include "tantan.h"
#include "ExtendedSubstitutionMatrix.h"
#include "Masker.h"
#include <vector>
#ifdef OPENMP
#include <omp.h>
#endif
char* getScoreLookup(BaseMatrix &matrix) {
char *idScoreLookup = NULL;
idScoreLookup = new char[matrix.alphabetSize];
for (int aa = 0; aa < matr... |
e8d5648509a54eb714dc9714fa97929acca1c386b81ca8f3ac4452aefe25c88a | C++ | 12,017 | 329 | #include <algorithm>
#include <cfloat>
#include <vector>
#include "caffe/layers/pooling_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
using std::min;
using std::max;
template <typename Dtype>
void PoolingLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dty... |
32e274d6209328407ddf92e4f71b1eef176dee28f76af51b7ec2dda7f19563ac | C++ | 12,028 | 289 | #include "FileUtil.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "PatternCompiler.h"
#include "microtar.h"
#ifdef OPENMP
#include <omp.h>
#endif
#ifdef HAVE_ZLIB
#include <zlib.h>
static int file_gzread(mtar_t *tar, void *data, size_t size) {
size_t res = gzread((gzFile)tar->stream, data... |
693d06c8ef595944c6fc5631d7e339eea5d66e96e9ae5006f2998cab90bade06 | C++ | 12,064 | 327 | #ifdef USE_CUDNN
#include <algorithm>
#include <vector>
#include "caffe/layers/cudnn_deconv_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
#d... |
2524d54079039ce6bfa1ba840f71514201539d4a896fc84326c7835727da4ca4 | C++ | 12,084 | 275 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "SubstitutionMatrix.h"
#include "Matcher.h"
#include "MultipleAlignment.h"
#include "PSSMCalculator.h"
#include "EvalueComputation.h"
#include "Sequence.h"
#include <climits>
#include <cfloat>
#include <cm... |
6fce095843e17feff830f685848da5e41af25a87140e7e04fa7e1587f2b12a9b | C++ | 12,138 | 316 | // dear imgui: Renderer + Platform Binding for Marmalade + IwGx
// Marmalade code: Copyright (C) 2015 by Giovanni Zito (this file is part of Dear ImGui)
// Implemented features:
// [X] Renderer: User texture binding. Use 'CIwTexture*' as ImTextureID. Read the FAQ about ImTextureID!
// Missing features:
// [ ] Render... |
756d12a3f66014b0f9c2e6bd8a24f09a7304abf9be26f8d5ab477cdad751bfca | C++ | 12,140 | 402 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#if defined(__CYGWIN__) || defined(__EMSCRIPTEN__)
int apply(int, const char **, const Command&) {
Debug(Debug::ERROR) << "\"apply\" is not supported on this platform\n";
EXIT(EXIT_FAILURE);
}
#else
#includ... |
7f57989d78765d2cbba809d3e497d92de0085074ed4399cbc918d9e0279f360a | C++ | 12,204 | 353 | /**
* Copyright 2019-2025, by XGBoost Contributors
*/
#if defined(__unix__) || defined(__APPLE__)
#include <fcntl.h> // for open, O_RDONLY, posix_fadvise
#include <sys/mman.h> // for mmap, munmap, madvise
#include <unistd.h> // for close, getpagesize
#else
#include <xgboost/windefs.h>
#if defined(xgboost_... |
c9473001fd2f04358a68043c7837aa7fdfcfa7ce60d9ad5311da42153cb58a28 | C++ | 12,228 | 285 | /*
The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
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, includin... |
da1960418723829437787f4f730df03e5a97796e0c18ccf31d0f94b3f920a64c | C++ | 12,243 | 369 | /*
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... |
d93b5238b62d1c52cef1cc4bcacaeb9d89ad0f1bbc64961d036082dcf40db4bc | C++ | 12,246 | 400 | /*++
Module Name:
FASTA.cpp
Abstract:
FASTA reader
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#include "stdafx.h"
#include "Compat.h"
#include "FASTA.h"
#include "Error.h"
#include "exit.h"... |
1f984de880fb17cc2f1c6d49c1b35b9a1e1861bf3953b74c07306cc49487b0a4 | C++ | 12,251 | 248 | // dear imgui: Renderer for OpenGL2 (legacy OpenGL, fixed pipeline)
// This needs to be used along with a Platform Binding (e.g. GLFW, SDL, Win32, custom..)
// Implemented features:
// [X] Renderer: User texture binding. Use 'GLuint' OpenGL texture identifier as void*/ImTextureID. Read the FAQ about ImTextureID!
// ... |
f8724c9414c407c7e44ca0ad4fd2bb5b963675ec88f32a645bf0d4e3ac56e80c | C++ | 12,275 | 367 | // 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... |
592df7586a3b9db004ab38a9fe85d2ca78090bf0a32726e1798d909f37afa197 | C++ | 12,293 | 393 | /*
* Copyright (C) 2019-2024 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Founda... |
49e7299512d0b23be019ce66eabdfec6e97b6fe200fc1b5c451358d0fad6d105 | C++ | 12,327 | 428 | // 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 ... |
107573f5e7f8ba32d9d6d4987ce70055472e8bc5ed4b3e4acd621cbdccb52a0d | C++ | 12,331 | 484 | //usage: a.out prefix_of_allele_information alignment.bam [-b backbone_id]
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <vector>
#include <map>
#include <algorithm>
#include "alignments.hpp"
struct _compatible
{
int weight ;
double value ;
} ;
struct _snpInfo
{
char type ; // d, s, i
int po... |
918677a05eab650696d14dcfcc68979da1ef8bab3b3526e55c4aefa2d9475309 | C++ | 12,335 | 380 | // 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 a... |
6b1c3839d7a6d3df466a58595bf6ca7f1451376d9176219cc4babba93c311fde | C++ | 12,365 | 454 | /*
* 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... |
5c8573c3b16bda70f95e2cc331a9931a96d6f13a4b103b078bab44204e6e0467 | C++ | 12,368 | 483 | #include <iomanip>
#include <sstream>
#include "emitterutils.h"
#include "exp.h"
#include "indentation.h"
#include "regex_yaml.h"
#include "regeximpl.h"
#include "stringsource.h"
#include "yaml-cpp/binary.h" // IWYU pragma: keep
#include "yaml-cpp/ostream_wrapper.h"
#include "yaml-cpp/null.h"
namespace YAML {
namesp... |
d268f62867d471f42d2125b8fd6d010e74fa1bfa782601ff0b619612356b3c57 | C++ | 12,402 | 326 | /*
This file is part of the Firmware project to interface with small Async or Neuromorphic chips
Copyright (C) 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
the Fre... |
5efb75a359d399818af875e241f02bbe98a7783a762f4f811884c61f460636d3 | C++ | 12,465 | 517 | #include "yaml-cpp/emitter.h"
#include "yaml-cpp/node/emit.h"
#include "yaml-cpp/node/node.h"
#include "yaml-cpp/node/impl.h"
#include "yaml-cpp/node/convert.h"
#include "yaml-cpp/node/iterator.h"
#include "yaml-cpp/node/detail/impl.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
using ::testing::AnyOf;
using ::... |
d1f86fafc6249dac85ffba3e73c5414b95ad38ab8d244214c0ae2c0c185c9798 | C++ | 12,491 | 393 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* qr.cpp
*
* Code generation for function 'qr'
*
*/
/* Include files */
#include "qr.h"
#include "eml_int_fo... |
9e74847990ffe8c73ea7c9b985b7e0b1360fe193fd761bbddcc491a06f755008 | C++ | 12,558 | 312 | /*
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... |
4e2b004e78578ea1f0bf2d396de07ca93b9162e17487c7adc34f66b2564bc0dd | C++ | 12,625 | 373 | // 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 ... |
125a7126c55f70388d86495fc8bd21277f139216f54b9c0ec0ce067d22c7bd92 | C++ | 12,646 | 501 | /*
* 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... |
56955f8f44b587aaed9e85e366ccd24d61aebed13877ff2f1b87d996c47ac2d3 | C++ | 12,669 | 292 | //
// Created by Martin Steinegger on 2019-01-04.
//
#include "FileUtil.h"
#include "LinsearchIndexReader.h"
#include "PrefilteringIndexReader.h"
#include "Debug.h"
#include "Timer.h"
#include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "KmerIndex.h"
#include "kmersearch.h"
... |
92cd8061cb8415c0cd564cc56f7d35656a32d7b446973bf13dc247161a6190a5 | C++ | 12,823 | 314 | //*****************************************************************************
// Filename : tmiic.cpp Creation date: 07 may 2020
//
// Description: Store functions for temporal mode of miic (tmiic)
//
// Author : Franck SIMON
//**********************************************************... |
355e79dd61fd664826f4d13da6edfe1bd0e5fca18ccd9a5807412275a13c9f36 | C++ | 12,848 | 370 | #include <cfloat>
#include <vector>
#include "gtest/gtest.h"
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/filler.hpp"
#include "caffe/layers/accuracy_layer.hpp"
#include "caffe/util/rng.hpp"
#include "caffe/test/test_caffe_main.hpp"
namespace caffe {
template <typename TypeParam>
class Acc... |
33f56edc00c96ff93ca519f7df12fe2ce9c5f09fb3a1c9ec382ddd54cd2b66e1 | C++ | 13,052 | 424 | // 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 ... |
5fe826d7ffa461da40c1b330c924cfe01b8ca5512ff6e8419c0fad9594ca18e4 | C++ | 13,195 | 341 | // 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... |
4cad95be5852ba772a78de1e02f94a67a88ad48f70284819300f630907343d07 | C++ | 13,208 | 432 | #include "result2stats.h"
#include "AminoAcidLookupTables.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "itoa.h"
#include "Parameters.h"
#include <sstream>
#ifdef OPENMP
#include <omp.h>
#endif
enum {
STAT_LINECOUNT,
STAT_MEAN,
STAT_MAX,
STAT_MIN,
STAT_SUM,
STAT_DOOL... |
b195ce97f370b11de40aea35d7bcd03af750074940a63209e38925afb85a23a7 | C++ | 13,218 | 355 | /**
* Copyright 2014-2025, XGBoost Contributors
* \file gblinear.cc
* \brief Implementation of Linear booster, with L1/L2 regularization: Elastic Net
* the update rule is parallel coordinate descent (shotgun)
* \author Tianqi Chen
*/
#include <dmlc/omp.h>
#include <dmlc/parameter.h>
#include <algorithm>
#... |
acb80496ab21ca74dc04179347159e9623d1be6b94f521d9a07941d8aea373c3 | C++ | 13,241 | 484 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* multitaper_spectrogram_coder_emxutil.cpp
*
* Code generation for function 'multitaper_spectrogram_coder_emxut... |
fffdd87e3958b8c4ec9241f440b617fc027620211ce00e44e1a9f3638aaee6f9 | C++ | 13,275 | 458 | /*
*
* Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* 1. Redistributions of source code must retain the above ... |
3fd84790a94526dc5fb6f94772156b75e64939404854b892bdeb5c5e1f6d9724 | C++ | 13,334 | 384 | // dear imgui
// (binary_to_compressed_c.cpp)
// Helper tool to turn a file into a C array, if you want to embed font data in your source code.
// The data is first compressed with stb_compress() to reduce source code size,
// then encoded in Base85 to fit in a string so we can fit roughly 4 bytes of compressed data i... |
df07fe7b35a9b07370f995857053f4b77d6202c9cc7bbf7885d3c7e38cdc2a3a | C++ | 13,370 | 359 | /*
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... |
f533c5ede8c8d3f04412cc12506c884db96a9822e12b1b41fbdd3eaacc2c95a2 | C++ | 13,394 | 284 | // dear imgui: Renderer for DirectX9
// This needs to be used along with a Platform Binding (e.g. Win32)
// Implemented features:
// [X] Renderer: User texture binding. Use 'LPDIRECT3DTEXTURE9' as ImTextureID. Read the FAQ about ImTextureID!
// [X] Renderer: Support for large meshes (64k+ vertices) with 16-bit indic... |
ba3fc76a266c7b51a4544114f432ef4b8f419018988e1aba1a6e695f4d7d3bb6 | C++ | 13,402 | 364 | /**
* Copyright 2021-2024, XGBoost Contributors
*/
#include "../test_evaluate_splits.h"
#include <gtest/gtest.h>
#include <xgboost/base.h> // for GradientPairPrecise, Args, Gradie...
#include <xgboost/context.h> // for Context
#include <xgboost/data.h> // for FeatureType, DMatrix, MetaInfo
#include... |
38e84be67dca6c08625a9ae94acb456788cafe95da66d2a18f8871c038bf2a4c | C++ | 13,428 | 362 | /**
* Copyright 2023-2025, XGBoost Contributors
*/
#include "test_lambdarank_obj.h"
#include <gtest/gtest.h> // for Test, Message, TestPartResult, CmpHel...
#include <algorithm> // for sort
#include <cstddef> // for size_t
#include <initializer_list> // for initializer_list
#include <memory> ... |
700d4484ce869fb872cb7a78f197bf1f71a1f31162bbe0a394ed063ae10071d9 | C++ | 13,573 | 394 | /**
* Copyright 2020-2024, XGBoost Contributors
*/
#include "test_quantile.h"
#include <gtest/gtest.h>
#include <cstdint> // for int64_t
#include "../../../src/collective/allreduce.h"
#include "../../../src/common/hist_util.h"
#include "../../../src/data/adapter.h"
#include "../collective/test_worker.h" // for T... |
6762cb4a3c14358d9d52be09ee22ad0dab61f0d8923b8080b8dbedeabb933576 | C++ | 13,594 | 375 | #include <string>
#include <vector>
#include "caffe/sgd_solvers.hpp"
#include "caffe/util/hdf5.hpp"
#include "caffe/util/io.hpp"
#include "caffe/util/upgrade_proto.hpp"
namespace caffe {
// Return the current learning rate. The currently implemented learning rate
// policies are as follows:
// - fixed: always ret... |
af6515284b5ed484c390498294049ed057517c6b5f53782b2d4158b997147be8 | C++ | 13,636 | 545 | #include "Muscle.h"
using namespace MASS;
using namespace dart::dynamics;
std::vector<int> sort_indices(const std::vector<double> &val)
{
std::vector<int> idx(val.size());
std::iota(idx.begin(), idx.end(), 0);
std::sort(idx.begin(), idx.end(), [&val](int i1, int i2)
{ return val[i1] < val[i2]; });
return id... |
999ea909914031a2f2230327c2a054571d623f6c943932ce9bc3e32fabf0f019 | C++ | 13,640 | 330 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
*
* multitaper_spectrogram_coder_data.cpp
*
* Code generation for function 'multitaper_spectrogram_coder_data'
*... |
e16e381ff1b037466f27a53533a2aa037c3667aa923bbb4ca6adc250b643e28a | C++ | 13,683 | 272 | #include "options.hpp"
#include "types.hpp"
#include "hpc_helpers/all_helpers.cuh"
#include <string>
#include <iostream>
void printOptions(const ProgramOptions& options){
std::cout << "Selected options:\n";
std::cout << "verbose: " << options.verbose << "\n";
std::cout << "interactive: " << options.inte... |
67a5d9a0dbdb1f26c4c94628b589304010e9d293eb560f006187408ef5e76eca | C++ | 13,701 | 335 | /**
* Copyright 2021-2024, XGBoost contributors
*
* \brief Implementation for the approx tree method.
*/
#include <algorithm> // for max, transform, fill_n
#include <cstddef> // for size_t
#include <map> // for map
#include <memory> // for allocator, unique_ptr, make_shared, make_unique
#include <uti... |
0f64b994f69d67167f058774883d903f2a8c048702acd49e0b58871bfa0655b4 | C++ | 13,723 | 345 | #include <Rcpp.h>
#include "orientation.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#include <algorithm> // std::minmax, std::remove, std::transform
#define _USE_MATH_DEFINES
#include <cmath>
#include <map>
#include "get_information.h"
#include "linear_allocator.h"
#include "proba_orientation.h"
#include "tmiic.h"
n... |
a2b7d107a6040ca602a3e944478fdbe36c7f77b4fbb96381493ad30a7e8adfe3 | C++ | 13,730 | 400 | /**
* Copyright 2016-2025, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/data.h>
#include <future>
#include <thread>
#include "../../../src/common/io.h"
#include "../../../src/data/adapter.h"
#include "../../../src/data/batch_utils.h" // for MatchingPageBytes
#include "../../../src/data/file_i... |
2df5af50bc4ac9dc7ad2c3be4ab8edb3c008156f0648dce72bc279fe60222502 | C++ | 13,736 | 380 | /*!
* Copyright by Contributors 2017-2023
*/
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wtautological-constant-compare"
#pragma GCC diagnostic ignored "-W#pragma-messages"
#pragma GCC diagnostic pop
#include <cstddef>
#include <limits>
#include <mutex>
#include <sycl/sycl.hpp>
#include "../data.h... |
e092929f079b9140633de0c68eeb38d5e49d9381f8b6191797ecd8dd550d57a4 | C++ | 13,761 | 409 | /**
* Copyright 2019-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <vector>
#include <string>
#include "../../../src/common/hist_util.h"
#include "../../../src/data/gradient_index.h"
#include "../helpers.h"
#include "test_hist_util.h"
namespace xgboost {
namespace common {
void ParallelGHistBuild... |
97f96cab412a7a6224fddc0efbee186630b3c59e36e330e081c73211a57aed3b | C++ | 13,777 | 441 | /*
* Copyright (C) 2016-2025 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Founda... |
0d1653a4a8a88548b10e30c8832459a459d5a459b6289dd677cdcc745119e575 | C++ | 13,825 | 335 | #include "proba_orientation.h"
#include <algorithm> // std::sort
#define _USE_MATH_DEFINES
#include <cmath>
#include <limits> // std::numeric_limits
#include <numeric> // std::iota
#include <tuple> // std::tie
namespace miic {
namespace reconstruction {
using std::vector;
namespace {
constexpr int kRemovalM... |
5b77964c8c4add2dae2bb7b00648a5e73d2bf0e94971c91445bb6f3d1912c86a | C++ | 13,862 | 353 | #include "get_information.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#include <algorithm> // std::remove_if
#define _USE_MATH_DEFINES
#include <cmath>
#include <limits>
#include <tuple> // std::tie
#include "computation_continuous.h"
#include "computation_discrete.h"
#include "structure.h"
#include "utilities.h"
n... |
f046aabae136e3591d89da46724623e01707bc753f8f992230365530be4d0e0a | C++ | 13,871 | 428 | /*
* Copyright (c) 2016-present, 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 tree).
*/
#include "Opti... |
c7921cb95a9685cb0b29064a3c1740da0366300330b998e82c0c79c4ce901a1d | C++ | 13,886 | 438 | /*
* Copyright (C) 2020-2024 Matthias Klumpp <matthias@tenstral.net>
*
* Licensed under the GNU Lesser General Public License Version 3
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Founda... |
c39fc37a9a95e279f969b80155b6b7d9b78c7e63493fc0e9f0d569160a8a3f92 | C++ | 13,934 | 427 | #include "DARTHelper.h"
#include <tinyxml2.h>
using namespace dart::dynamics;
typedef tinyxml2::XMLElement TiXmlElement;
typedef tinyxml2::XMLDocument TiXmlDocument;
ShapePtr
MASS::
MakeSphereShape(double radius)
{
return std::shared_ptr<SphereShape>(new SphereShape(radius));
}
ShapePtr
MASS::
MakeBoxShape(const E... |
0799a5f1b13eccc3afb30fdace7d3ab7af24bee9d3b19d4469cf519b2d61bc6a | C++ | 14,190 | 506 | /*
* 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
* ... |
5fe91726a7c39115571eb9508dc97ee54359e6b3e4cca2e6c32b1baa046c6174 | C++ | 14,245 | 433 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include "comm.h"
#include <algorithm> // for copy
#include <chrono> // for seconds
#include <cstdint> // for int32_t
#include <cstdlib> // for exit
#include <memory> // for shared_ptr
#include <string> // for string
#include <thread> // for t... |
ac77981e5f7faeb2e0eae013880cc391e29f12e5f8cd9b6ddbb6f00762f5779f | C++ | 14,280 | 425 | /*++
Module Name:
SingleAligner.cpp
Abstract:
Functions for running the single end aligner sub-program.
Authors:
Matei Zaharia, February, 2012
Environment:
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
#include "stdafx.h"... |
91e2ebba079de7daea8d3a42b7fd4b967e2cbd9b9e9f5c271bfc07daad2dca96 | C++ | 14,337 | 355 | /*
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... |
3501e58dd516b1402d620f3373fae9fd8c8a7acb19cafbf17e4800ef25968913 | C++ | 14,353 | 375 | #include "Parameters.h"
#include "Util.h"
#include "Debug.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "SubstitutionMatrix.h"
#include "CompressedA3M.h"
#include "MathUtil.h"
#include "Domain.h"
#include <fstream>
#include <iomanip>
#ifdef OPENMP
#include <omp.h>
#endif
#include "kseq.h"
#include "KSeqBuf... |
6e2efc6bbf6edd355fa050347005014b12ecad88a75d1b3b57503832c0e0d32d | C++ | 14,495 | 396 | /*
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... |
b5f852fe14e754d9f44cfdf4a4d5ce126db55eee432900008661f58db1382b08 | C++ | 14,508 | 540 | /*
* 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
* ... |
78e6ce441734a2b13cc7fcccb86a6bbfc124913a0ee8172151400d22a1435a5f | C++ | 14,526 | 561 | #include <climits>
#include <vector>
#include "caffe/blob.hpp"
#include "caffe/common.hpp"
#include "caffe/syncedmem.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void Blob<Dtype>::Reshape(const int num, const int channels, const int height,
const int width) {
vector... |
fa19cf65ed1674354d41cf96ea0dd595627c29f8f55a830e55baf93463016ab6 | C++ | 14,541 | 373 | /**
* Copyright 2017-2023 by XGBoost Contributors
* \file hist_util.cc
*/
#include "hist_util.h"
#include <dmlc/timer.h>
#include <vector>
#include "../data/adapter.h" // for SparsePageAdapterBatch
#include "../data/gradient_index.h" // for GHistIndexMatrix
#include "quantile.h"
#include "xgboost/base.h"... |
d39a22e46a112d69733f3681e63e1898e9019de239b1cb4f4c61ad7ac2e8b580 | C++ | 14,553 | 387 | // 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 ... |
f8f5cafce68377f1216e1956e80d904d45ad849fb263bc6773642f3cf9732733 | C++ | 14,560 | 449 | #ifdef WITH_PYTHON_LAYER
#include "boost/python.hpp"
namespace bp = boost::python;
#endif
#include <gflags/gflags.h>
#include <glog/logging.h>
#include <cstring>
#include <map>
#include <string>
#include <vector>
#include "boost/algorithm/string.hpp"
#include "caffe/caffe.hpp"
#include "caffe/util/signal_handler.h"
... |
111a7211e513f9db5c2872c69f787413308d9315bdfe24eed6625d2ea41d063c | C++ | 14,686 | 353 | #include "dbdata.hpp"
#include "length_partitions.hpp"
#include "hpc_helpers/all_helpers.cuh"
#include <type_traits>
#include <string>
#include <fstream>
#include <algorithm>
#include <numeric>
namespace cudasw4{
//write vector to file, overwrites existing file
template<class T>
void writeTrivialVectorT... |
910b08af72891bf467ead74027fe89bfaf03f0bef20605dc173e14115088063c | C++ | 14,808 | 360 | #include "Matcher.h"
#include "SubstitutionMatrix.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "QueryMatcher.h"
#include "Parameters.h"
#include "AlignmentSymmetry.h"
#include "PrefilteringIndexReader.h"
#include "IndexReader.h"
#include "FastSort.h"
#ifdef OPENMP
#inclu... |
51f683656ca9f4a6432dcdce5d5daf4ea76befef607f3692094aa2758051b770 | C++ | 15,017 | 522 | /*++
Module Name:
GzipDataWriter.cpp
Abstract:
File writer that compresses data into zip format.
Environment:
User mode service.
Not thread safe.
--*/
#include "stdafx.h"
#include "GzipDataWriter.h"
#include "BigAlloc.h"
#include "VariableSizeVector.h"
#include "ParallelTask.h"
#include "RangeS... |
cba528d87476c718980e4d4205bbdd0431f118b37f24f8214a0f344c2ecae03d | C++ | 15,023 | 469 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#if defined(__unix__) || defined(__APPLE__)
#include <netdb.h> // gethostbyname
#include <sys/socket.h> // socket, AF_INET6, AF_INET, connect, getsockname
#endif // defined(__unix__) || defined(__APPLE__)
#if defined(_WIN32)
// Guard the in... |
4eb07bcc9dae93ab50b29944bccc35b175aaa4ecee6e4a02ac59a1713ae25f0e | C++ | 15,025 | 450 |
#include "ProfileStates.h"
#include "Util.h"
#include "MathUtil.h"
#include <sstream>
#include <simd.h>
//#include <LibraryPure.lib.h>
//#include <LibraryPureMMorder.lib.h>
//#include <Library_Training2_run17.lib.h>
//#include <LibraryExpOpt.lib.h>
//#include <LibraryExpOpt7_10_polished.lib.h>
//#include <LibraryMix.l... |
3e5ce23e365d4ec4f55e842f9087a6e9895142e50d6c7539ca3ec5aba5e036b6 | C++ | 15,115 | 389 |
#define THRUST_DEVICE_SYSTEM THRUST_DEVICE_SYSTEM_OMP
#include <algorithm>
#include <iterator>
#include <iostream>
#include <chrono>
#include <unistd.h>
#include <sys/resource.h>
#include <sys/time.h>
#include <sys/resource.h>
#include "config.hpp"
#include "hpc_helpers/all_helpers.cuh"
#include "sequence_io.h"
#i... |
378ccd922175008c392a24cbbcf69dc4337c0709af7bdcc74eb2d35c79d2376e | C++ | 15,232 | 386 | #include "DBConcat.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "itoa.h"
#include "Util.h"
#include "Debug.h"
#include "FileUtil.h"
#include "Parameters.h"
#include <algorithm>
#ifdef OPENMP
#include <omp.h>
#endif
DBConcat::DBConcat(const std::string &dataFileNameA, const std::string &indexFileNameA,
... |
d3da08adb5d9a457e5640b2a8d2daf04dce6ae0225bcf032f313c1c1e1921579 | C++ | 15,306 | 102 | // main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include <iostream>
#include "Parameters.h"
#include "StripedSmithWaterman.h"
#include "MsaFilter.h"
#include "PSSMCalculator.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#includ... |
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