sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9eb81c72a5e7bf268c71be8c79677f9ef5491524de765ac1a50fb4ea10a420f9 | C++ | 1,831 | 75 | #include <algorithm>
#include "yaml-cpp/node/convert.h"
namespace {
// we're not gonna mess with the mess that is all the isupper/etc. functions
bool IsLower(char ch) { return 'a' <= ch && ch <= 'z'; }
bool IsUpper(char ch) { return 'A' <= ch && ch <= 'Z'; }
char ToLower(char ch) { return IsUpper(ch) ? ch + 'a' - 'A'... |
d44cb69e69246af90fc6c91c4b8c011a3729e6cc392b57fa2aecd2a10d6a7350 | C++ | 1,831 | 65 | /*
* 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
* ... |
a0520097bffb32e4b6e8b0b1f8562849e3b76b7a828f0ee4655888cfa282d21f | C++ | 1,835 | 61 | #include <vector>
#include "caffe/sgd_solvers.hpp"
namespace caffe {
#ifndef CPU_ONLY
template <typename Dtype>
void nesterov_update_gpu(int N, Dtype* g, Dtype* h, Dtype momentum,
Dtype local_rate);
#endif
template <typename Dtype>
void NesterovSolver<Dtype>::ComputeUpdateValue(int param_id, Dtype rate) {
con... |
e80e96d329320d96c54b306e78259cb7ad6a72d19e56734f5ee365fd115d5db5 | C++ | 1,848 | 57 | /**
* Copyright 2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <cstddef> // std::size_t
#include <string> // std::to_string
#include "../../../../src/tree/hist/sampler.h" // SampleGradient
#include "../../../../src/tree/param.h" // TrainParam
#include "xgboost/base.h" ... |
58da400611462019b1ac42c5fb41bce8adb17529a3373973487291d2c6f73b66 | C++ | 1,865 | 48 | #include <CommandCaller.h>
#include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBWriter.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "createtaxdb.sh.h"
int createtaxdb(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parse... |
b920e8b331827b1cff5523c778ad322a44faaab819081b771c368277191a5d57 | C++ | 1,885 | 56 | /******************************************************************
* *
* Copyright by Joachim Saul <saul@gfz-potsdam.de> *
* *
***********************************************... |
a37b54a6348d90515c1cd90695d04459b78888bf1ddea4d8cbbf238b1860773a | C++ | 1,915 | 56 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#ifdef OPENMP
#include <omp.h>
#endif
int doCompression(int argc, const char **argv, const Command& command, bool shouldCompress) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true,... |
ee56d548232e21b65efd7cffbf7ae405ffbf3089d30eae959e0f9c5c493960ac | C++ | 1,918 | 81 | /**
* Copyright 2024, XGBoost Contributors
*/
#include "xgboost/collective/result.h"
#include <filesystem> // for path
#include <sstream> // for stringstream
#include <stack> // for stack
#include "xgboost/logging.h"
namespace xgboost::collective {
namespace detail {
[[nodiscard]] std::string ResultImp... |
1c02928c297e3a1ac838213556d85ade6b672a1039f5e7d8a9c8b5c23cdec20f | C++ | 1,930 | 59 | /**
* Copyright 2018-2023 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/host_device_vector.h>
#include <xgboost/task.h> // for ObjInfo
#include <xgboost/tree_updater.h>
#include <memory>
#include <string>
#include <vector>
#include "../../../src/tree/param.h" // for TrainParam
#include "..... |
207da019fbc81a5d7629686392f7945351641bc34d814306fe3cb7464ca4d6a7 | C++ | 1,942 | 72 | /**
* Copyright 2015-2023 by XGBoost Contributors
* \file metric_registry.cc
* \brief Registry of objective functions.
*/
#include <dmlc/registry.h>
#include <xgboost/context.h>
#include <xgboost/metric.h>
#include "metric_common.h"
namespace xgboost {
template <typename MetricRegistry>
Metric* CreateMetricImpl(c... |
d98a59dd5cb5d64e504802494278a0019e12403e9537f0d5a905b4a8467fd068 | C++ | 1,948 | 56 | /**
* Copyright 2018-2023, XGBoost Contributors
*/
#include <xgboost/objective.h>
#include <xgboost/context.h>
#include <limits>
#include "../helpers.h"
#include "test_hinge.h"
#include "../../../src/common/linalg_op.h"
namespace xgboost {
void TestHingeObj(const Context* ctx) {
std::unique_ptr<ObjFunction> obj{O... |
948e11dc10584976dc7a65e1fb06ea4dd8deebf2e5f6660bd5242f144873d593 | C++ | 1,950 | 89 | /*
* 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 "util... |
6bed9996beb8c18e8b94f92494d0cd9f9afb79cc87ca44ae1101ea075a0144a2 | C++ | 1,951 | 40 | // 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 ... |
aa8cc8ac5267ce48cf05dd8484e472f20b8e8b5fb0c31c3811a99b68018e323b | C++ | 1,951 | 40 | // 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 ... |
4898458c80ed420882085983deff39b10cc60263bafc5eac63989b7a403e710f | C++ | 1,970 | 62 | #include "NcbiTaxonomy.h"
#include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "TaxonomyExpression.h"
#ifdef OPENMP
#include <omp.h>
#endif
int filtertaxdb(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance(... |
bb8c4a182344bbab7fedaf9227a2e866dba02f3d8f6374959d2b41b7ff5aed3e | C++ | 1,979 | 68 | /*
* 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.
*
* FFTWApi.cpp
*
* Code generation for function 'FFTWApi'
*
*/
/* Include files */
#include "FFTWApi.h"
#incl... |
d530da208dcd8026e89b0581234b303457e6448ba4fea89dc16e8e4332d900fb | C++ | 1,983 | 51 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
int splitdb(int argc, const char **argv, const Command& command) {
Parameters &par = Parameters::getInstance();
par.overrideParameterDescription(par.PARAM_SPLIT, "Split input into N equally distributed chun... |
8af4575a82806cac7c60f8bd637752fc2b9c288e89f6dc73db338c5e58d53da8 | C++ | 1,987 | 57 | /**
* Copyright 2020-2023, XGBoost Contributors
*/
#include "random.h"
#include <algorithm> // for sort, max, copy
#include <memory> // for shared_ptr
#include "xgboost/host_device_vector.h" // for HostDeviceVector
namespace xgboost::common {
std::shared_ptr<HostDeviceVector<bst_feature_t>> ColumnSampler::Co... |
6c39721e2bdfb87838fb6fbd9cbe8a9755b90d91325b14b21518a9e12df2244b | C++ | 1,988 | 80 | /*
* 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... |
bf5041792f130d8a3799e9d30d8cb693ad9f9e300a86416b2c5f802f727463a3 | C++ | 2,019 | 55 | #include "Parameters.h"
#include "IndexReader.h"
#include "Debug.h"
#include "Util.h"
int view(int argc, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argc, argv, command, false, 0, 0);
std::vector<std::string> ids = Util::split(par.idList, ",... |
00e05250f3a9be7b5723e8ae41ae55831e287de5717e202c1a0771c74dcc0330 | C++ | 2,020 | 43 | // 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 ... |
eb4413051c527ab53f1179389fffdb0104f485b6e6c554a55eaa36cf21e4b78e | C++ | 2,026 | 69 | /*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 option... |
f95395a35dc6eca991403fd68abf543dd77b5ab9466de00c5cc4abd0400f671b | C++ | 2,033 | 82 | /*
* 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 "util... |
617a7680902ce53b0d5c9ea08fa806b1065b93e5598eb27d5b65e7d76660fa5d | C++ | 2,039 | 54 | #include "Parameters.h"
#include "Matcher.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Orf.h"
#include "Debug.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
int orftocontig(int argn, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parsePara... |
0fbb7d56f6d6a31df88f4864de29a9c4f8c6ca11311318f62f6b023dcd388a0f | C++ | 2,045 | 64 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "Matcher.h"
#include "CompressedA3M.h"
#ifdef OPENMP
#include <omp.h>
#endif
int convertca3m(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par... |
a590e2e470067fa8ec59eba30ea51b677e846d31e49157a58dce26afe9bf77db | C++ | 2,045 | 103 | /*++
Module Name:
Histogram.cpp
Abstract:
Cheezy histogram class
Authors:
Bill Bolosky, September, 2011
Environment:
User mode service.
This class is NOT thread safe. It's the caller's responsibility to ensure that
at most one thread uses an instance at any time.
Revision History:
--... |
022caa44f5c35edfac95fbfd2c80654e566e30ada262150f69333b6ad5e34422 | C++ | 2,055 | 64 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "CommandCaller.h"
#include "map.sh.h"
#include <cassert>
void setMapWorkflowDefaults(Parameters *p) {
p->compBiasCorrection = 0;
p->maskMode = 0;
p->covThr = 0.95;
p->covMode = 2;
p->seqIdThr = 0.9;
p-... |
df7e231fa2342e332f70007e77ad3c718cb9b903783abfc37ab58c9a1bd84150 | C++ | 2,059 | 84 | /*
* 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.
*
* mean.cpp
*
* Code generation for function 'mean'
*
*/
/* Include files */
#include "mean.h"
#include "eml_... |
48a1d05fa41e16ba60fc7285476af4c2e528621b5ca156696bed3e34c59d66ba | C++ | 2,076 | 71 | /*!
* Copyright 2018-2019 by Contributors
*/
#include <xgboost/linear_updater.h>
#include <xgboost/gbm.h>
#include "../helpers.h"
#include "test_json_io.h"
#include "../../../src/gbm/gblinear_model.h"
#include "xgboost/base.h"
namespace xgboost {
TEST(Linear, Shotgun) {
size_t constexpr kRows = 10;
size_t cons... |
b9dd23de63ced5c43d2794a9e5e918d64570676a5419f982b0536141707148c1 | C++ | 2,084 | 70 | /*
* 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... |
c132af0870af7d4660f16d3a17620159532aaf2730e9c2010fe89235985abfe8 | C++ | 2,087 | 70 | /*
* 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... |
0c552aacfe8ad0d356df48b7c4ec904461e7c050b09f31236e749bac361a9c42 | C++ | 2,089 | 105 | /*++
Module Name:
SNAPCommand.cpp
Abstract:
Send a command to SNAP running daemon mode
Authors:
Matei Zaharia & Bill Bolosky, February, 2012
Environment:
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
#include "stdafx.h"
#include "Compat.h"
#... |
a44a8b77a43dcc9a29ceeb57ec5b3eba2c5c7bdd5b541b606ad0536369b25a4c | C++ | 2,091 | 69 | /**
* Copyright 2017-2024, XGBoost contributors
*/
#include "../../../src/common/compressed_iterator.h"
#include "gtest/gtest.h"
#include <algorithm>
namespace xgboost::common {
TEST(CompressedIterator, Size) {
bst_idx_t n = 2048;
{
bst_idx_t n_symbols = 256;
auto n_bytes = CompressedBufferWriter::Calcul... |
2e07f815752a334f652ed95942cb5896aedd6b2f9bf9e515fb0d71724cc672ea | C++ | 2,100 | 75 | /**
* Copyright 2015-2024, XGBoost Contributors
*/
#include "common.h"
#include <dmlc/thread_local.h> // for ThreadLocalStore
#include <cmath> // for pow
#include <cstdint> // for uint8_t
#include <cstdio> // for snprintf, size_t
#include <string> // for string
#include <utility> // for pair
#include "./... |
dd185884c0b5301d400b58f12ebb36b1c8b326531597e531b40e44a6eeb0e943 | C++ | 2,122 | 71 | #include "flutter_window.h"
#include <optional>
#include "flutter/generated_plugin_registrant.h"
FlutterWindow::FlutterWindow(const flutter::DartProject& project)
: project_(project) {}
FlutterWindow::~FlutterWindow() {}
bool FlutterWindow::OnCreate() {
if (!Win32Window::OnCreate()) {
return false;
}
... |
6cda309b0155d2e0e9931cf7733472441c22c760659b5aa9d2561b1e5247b7d7 | C++ | 2,142 | 60 | #include "computation_cache.h"
namespace miic {
namespace computation {
namespace detail {
double CtermCache::getLogC(int n, int level) {
if (n == 0 || level == 0) return 0;
if (level <= kLevelLimit) {
double res = log_c_(n - 1, level - 1);
if (res != -1) return res;
}
if (level == 1) {
log_c_(n -... |
daee40c767bc8a51a4b945eed5da1006bcb660d3f63b030270261cddbf68dd8a | C++ | 2,145 | 69 | #include <vector>
#include "caffe/sgd_solvers.hpp"
namespace caffe {
#ifndef CPU_ONLY
template <typename Dtype>
void adagrad_update_gpu(int N, Dtype* g, Dtype* h, Dtype delta,
Dtype local_rate);
#endif
template <typename Dtype>
void AdaGradSolver<Dtype>::ComputeUpdateValue(int param_id, Dtype rate) {
const ve... |
c9f5f6c6e08815a2d7b279bd43a5207f7b2abf0bff072523669ca4710bccc081 | C++ | 2,150 | 47 | // 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 ... |
08c31eb060cb424f0a90a035ea91cd3333011222120e92e8a1deaff7e183558a | C++ | 2,177 | 58 | /**
* Copyright 2023-2024, XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/json.h> // for Json
#include <xgboost/tree_model.h> // for RegTree
#include "../../../../src/common/categorical.h" // for CatBitField
#include "../../../../src/tree/hist/expand_entry.h"
namespace xgboost::tree {
T... |
ecc11563b693bd2b46c6c5d916cabcc1cbdc1d57448c8920b8d3671f2f91097d | C++ | 2,178 | 64 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#ifdef OPENMP
#include <omp.h>
#endif
int reverseseq(int argn, const char **argv, const Command& command) {
Parameters& par = Parameters::getInstance();
par.parseParameters(argn, argv... |
b6e34fd3a67000f6318fd8b1390d441845c06fa9baa01efd611b780e96241ff3 | C++ | 2,185 | 65 | /**
* Copyright 2024, XGBoost Contributors
*/
#include "test_column_split.h"
#include <gtest/gtest.h>
#include <xgboost/tree_model.h> // for RegTree
#include <xgboost/tree_updater.h> // for TreeUpdater
#include <vector> // for vector
#include "../../../src/tree/param.h" // for TrainParam
#include "../colle... |
6da4cdd2ac322616bc29ccb24bf4e67fd2ae46715af91c98b4a842fff21c626a | C++ | 2,202 | 57 | /**
* Copyright 2022-2023 by XGBoost contributors
*/
#include "init_estimation.h"
#include <memory> // unique_ptr
#include "../common/stats.h" // Mean
#include "../tree/fit_stump.h" // FitStump
#include "xgboost/base.h" // GradientPair
#include "xgboost/da... |
2fa58f990956c5603cdf696e7b20053e60b7d85c53f118740ab0277284bcb56a | C++ | 2,208 | 62 | /**
* Copyright 2021-2024, XGBoost contributors
*/
#include <gtest/gtest.h>
#include <xgboost/data.h> // for CSCPage, SortedCSCPage, SparsePage
#include <memory> // for allocator, unique_ptr, __shared_ptr_ac...
#include <string> // for char_traits, operator+, basic_string
#include "../../../src/common/io.h" // ... |
fa2e07cd2ee6bc25b4e9d23ba40bf1c34dfe6bdad3b713ec2a2af0ae844bcac9 | C++ | 2,212 | 76 | /*
* 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.
*
* power.cpp
*
* Code generation for function 'power'
*
*/
/* Include files */
#include "power.h"
#include "e... |
34acba4b90d7ab80ebcad8fbe8b45db7bd961d5670ee22eb4d8ffebe4d1b96f0 | C++ | 2,227 | 77 | //
// 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"
const char* binary_name ... |
cd5e38b8cfa8121c1661c236e2b53b8096ca07a40b8cdcd4a33d79bda90b7722 | C++ | 2,228 | 67 | //
// main.cpp
// forautocompl
//
// Created by Martin Steinegger on 26.11.12.
// Copyright (c) 2012 -. All rights reserved.
//
#include "BaseMatrix.h"
#include "ReducedMatrix.h"
#include "SubstitutionMatrix.h"
#include "Parameters.h"
#include <iostream>
const char* binary_name = "test_reducematrix";
DEFAULT_PARA... |
7faed508dfd5eba33b6c9a1caf7c7608bbcdb5f1f39fcc9006f03101302f15da | C++ | 2,233 | 61 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#ifdef OPENMP
#include <omp.h>
#endif
int result2repseq(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0,... |
33a89320e4105b127fb2f5a62fc908881a6ca51c372e430d913627ded216071c | C++ | 2,254 | 65 | #include <mex.h>
#include <math.h>
const double PI = 3.14159265358979323846;
/*
This function will replace imrotate(image,angle,'crop') for any 3 dims image, UINT8 class.
Work ten times faster, tested on matlab 7, VC6.
Compile it using the mex tools -
mex fast_rotate.cpp.
*/
void mexFunction(int nlhs, mxArray *... |
9138b125e5a4dbf8485998b13bfa39e788c1f3c214a132a74a7324747bde28bc | C++ | 2,268 | 68 | //
// Created by mad on 10/26/15.
//
#include <iostream>
#include "SubstitutionMatrix.h"
#include "Sequence.h"
#include "Parameters.h"
const char* binary_name = "test_compositionbias";
DEFAULT_PARAMETER_SINGLETON_INIT
void calcLocalAaBiasCorrection(Sequence* seq, SubstitutionMatrix * m){
const int windowSize = ... |
11f46e025d3cf671f363f1ab6a0b8bfc4f1baeca3721a193e3f0c967c840b2eb | C++ | 2,273 | 62 | /*
* 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
* ... |
13471fc9dcf65696e371e892b54461e48d98d1f2434cd2d23abdda238a9dc7c2 | C++ | 2,280 | 62 | #include "Parameters.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Util.h"
#include "Debug.h"
#include "Sequence.h"
#include "SubstitutionMatrix.h"
#ifdef OPENMP
#include <omp.h>
#endif
int profile2seq(int argc, const char **argv, const Command &command, bool consensus) {
Parameters &par = Parameters::... |
2221af389082635997b51fa7a9f5e8d747751f0509a4e7f105999a332e6e2bfe | C++ | 2,282 | 125 | /*++
Module Name:
GenericFile_Blob.cpp
Abstract:
Generic IO class for SNAP that can read from an in-memory blob.
Authors:
Bill Bolosky, March, 2014
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "GenericFile_Blob.h"
GenericFile_Blob::GenericFile_Blob(voi... |
699cdbcd512ea131fdcce56894e51cd8577f46a6f0f0baf23779f0706cc1fd67 | C++ | 2,283 | 81 | /*
* 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
* ... |
17bfa3962c5922c6e68c4e42c24262bdbce5f053b61f2b420c3b03dad50d407a | C++ | 2,304 | 80 | /*
* Copyright 2012, 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... |
f18bc8d5317f95e36fd5d5d78919773d16378fdb778f57b55bd7933fa7136e05 | C++ | 2,304 | 68 | // 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... |
3201b6ccdd0b313180ab2cfd8d7996d2f423c71924e6bca9d0da612080914f2e | C++ | 2,308 | 77 | // Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
// ED1
arma::mat ED1(const arma::mat& x);
RcppExport SEXP _SC3_ED1(SEXP xSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_... |
d0987c22781fd28fb7b6f9631f7eb8bf35b8002aa58b274d5618b1ae15e4c671 | C++ | 2,309 | 103 | #include <RcppArmadillo.h>
using namespace arma;
//' Compute Euclidean distance matrix by rows
//'
//' Used in consmx function
//'
//' @param x A numeric matrix.
// [[Rcpp::export]]
arma::mat ED1(const arma::mat & x) {
unsigned int outrows = x.n_rows, i = 0, j = 0;
double d;
mat out = zeros<mat>(outrows, outrows... |
9a0d53880ad3a6f673f0979dccbe83757a9af897f76adb57625c35d5256dfae2 | C++ | 2,321 | 77 | #include <sstream>
#include <fstream>
#include "Parameters.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
int tsv2db(int argc, const char **argv, const Command& command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, true, 0, 0);
Debug(Debug::INFO) ... |
1c7f4ca8821b6d6765c2f38af057f6102159182988cc0de8e86d4f05debd36ac | C++ | 2,322 | 79 | /*
* 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
* ... |
1dba0d18fcfa59b71bed86e74cd9f5dac1a0d1c8f6b834f7c9433ab262e25bd2 | C++ | 2,325 | 75 | //
// Created by mad on 12/14/15.
//
#include <new>
#include <cstring>
#include <sys/mman.h>
#include "Debug.h"
#include "Util.h"
#include "SequenceLookup.h"
SequenceLookup::SequenceLookup(size_t sequenceCount, size_t dataSize)
: sequenceCount(sequenceCount), dataSize(dataSize), currentIndex(0), currentOffset(... |
d56011e9f00e1a1d3b77dbe45f67bcba982d6a5a23719e50d94c5e0fc71aaed7 | C++ | 2,328 | 72 | /*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 option... |
8cfc476f92feb9f77b0b34c93b16d2e0525aa7bc88950a04bb4d2d086115b4d0 | C++ | 2,339 | 73 | /**
* Copyright 2017-2024 by XGBoost contributors
*/
#include <xgboost/base.h> // Args
#include <xgboost/context.h> // Context
#include <xgboost/objective.h> // ObjFunction
#include <xgboost/span.h> // Span
#include <memory> // std::unique_ptr
#include <vector> // std::vec... |
b3fd3573b0e9fddf5b02a85de236174132787cd81cf0275c652d69e53c54aac9 | C++ | 2,343 | 61 | /**
* Copyright 2024, XGBoost Contributors
*/
#include "test_extmem_quantile_dmatrix.h" // for TestExtMemQdmBasic
#include <gtest/gtest.h>
#include <xgboost/data.h> // for BatchParam
#include <algorithm> // for equal
#include "../../../src/common/column_matrix.h" // for ColumnMatrix
#include "../../../src/data... |
baf9f0f2b9686b6fd4e2b6ee6c59f3d2aad6f3d8eda0eea6e5238959d679be77 | C++ | 2,347 | 67 | #include "NucleotideMatrix.h"
#include <cctype>
#include <climits>
NucleotideMatrix::NucleotideMatrix(const char* scoringMatrixFileName, float bitFactor, float scoreBias)
: SubstitutionMatrix(scoringMatrixFileName, bitFactor, scoreBias) {
setupLetterMapping();
reverseLookup = new int[alphabetSize];
... |
7d1825db715e7e31ef92f1a4dce5ff3901f38298b1e98c7cf44494ba1ed00c23 | C++ | 2,348 | 68 | #include <cmath>
#include <vector>
#include "caffe/layers/swish_layer.hpp"
#include "caffe/util/math_functions.hpp"
namespace caffe {
template <typename Dtype>
void SwishLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
NeuronLayer<Dtype>::LayerSetUp(bottom, top)... |
e7eb3671cb9346142ee116f6d7a49f5527d2ff7719d5003f1cf8c4bc55d6f6b0 | C++ | 2,354 | 88 | /*
* Copyright (C) 2019-2026 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... |
cc12c89ad2cd806acabb535fe7aa94d764a7d703a78a856d0c42c32f219ef578 | C++ | 2,357 | 70 | #include "stdafx.h"
#include "Compat.h"
#include "TestLib.h"
#include "ProbabilityDistance.h"
// Test fixture for all the ProbabilityDistance tests
struct ProbabilityDistanceTest {
ProbabilityDistance dist;
double prob;
ProbabilityDistanceTest(): dist(0.1, 0.01, 0.2) {}
};
TEST_F(ProbabilityDistance... |
ceeba6e12046bfefc035a401d0444798db8665876c862412d36f3823b860c15d | C++ | 2,358 | 98 | /*++
Module Name:
Error.cpp
Abstract:
SNAP error-message writer
Authors:
Bill Bolosky, Feburary, 2014
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "Compat.h"
#include "Error.h"
#include "AlignerOptions.h"
#include "CommandProcessor.h"
void
WriteMessag... |
dc0de54c0a2d835e2fa75d594b240bc57121a9c256250c344bb3571443567e74 | C++ | 2,376 | 63 | /**
* Copyright 2023 by XGBoost Contributors
*/
#include "histogram.h"
#include <cstddef> // for size_t
#include <numeric> // for accumulate
#include <utility> // for swap
#include <vector> // for vector
#include "../../common/transform_iterator.h" // for MakeIndexTransformIter
#include "expand_entry.h" ... |
651a5b2ce6bd410828fa4f6f2e561116589c0514d71d8da0f60da62c0b75d91d | C++ | 2,379 | 80 | /*
* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 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 versio... |
c917a4f68abe64812d6195225bb5cab337b4108dd608a1704a9ff939afe9a4cd | C++ | 2,393 | 62 | #include "NucleotideMatrix.h"
#include "SubstitutionMatrix.h"
#include "tantan.h"
#include "DBReader.h"
#include "DBWriter.h"
#include "Debug.h"
#include "Util.h"
#include "FileUtil.h"
#include "Masker.h"
#ifdef OPENMP
#include <omp.h>
#endif
int masksequence(int argc, const char **argv, const Command& command) {
... |
2acc28331538ba227d98235a876a099a9b6dab920b53719f718f3c80376362e4 | C++ | 2,426 | 61 | #include <cassert>
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "easyproteomesearch.sh.h"
void setEasyproteomesearchDefaults(Parameters *p) {
p->removeTmpFiles = true;
p->alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_COV_SEQID;
... |
44462af2fa9dadb0623aec728e3b1ef82ed57c06f3dbf2459d632c7081324c50 | C++ | 2,447 | 56 | // Copyright 2006, 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 ... |
94ce7ed61153b73cd1ee3a25075b6047170213d880b7bcee1f3da20a73acabc2 | C++ | 2,462 | 63 | #include "MultiParam.h"
template<typename T>
MultiParam<T>::MultiParam(const char *parametercstring) {
values.first = T::max;
values.second = T::max;
if (strchr(parametercstring, ',') == NULL) {
if (assign(parametercstring, values.second) == false) {
values.first = values.second = T::ma... |
4c4ec53fdfe56b403246a97056358c7e86a25ef071191f30f580eb183dc3f772 | C++ | 2,468 | 91 | #include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include <strings.h>
#include <cstdlib>
#include <unistd.h>
#include <sstream>
#include <iostream>
#ifdef OPENMP
#include <omp.h>
#endif
CommandCaller::CommandCaller() {
#ifdef OPENMP
#if _OPENMP >= 201307
if(omp_get_proc_bind() != omp_proc_bind_fa... |
083ef7c98d7d413ea2cb2befabad7e4540595dd8d34f9234edf56d454d6fa5b5 | C++ | 2,488 | 72 | /*
* 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
* ... |
9464b46059dd6a0161c599c825dfb74c98e8f8fab3566a5f0bec5d79d870c206 | C++ | 2,501 | 61 | #include "ExpressionParser.h"
#include <set>
#include <cstddef>
ExpressionParser::ExpressionParser(const char* expression) : ExpressionParser(expression, {}) {
}
ExpressionParser::ExpressionParser(const char* expression, const std::vector<te_variable>& lookup) {
#define str2(s) #s
#define str(s) str2(s)
#define V(x) ... |
4510e50aae816bfb323e2308d93551d3d99a87d3294713a6d288680ef0b0fb42 | C++ | 2,502 | 79 | /*!
* Copyright 2018-2023 XGBoost contributors
*/
#include <xgboost/objective.h>
#include <xgboost/context.h>
#include "../../src/common/common.h"
#include "../helpers.h"
#include "test_multiclass_obj.h"
namespace xgboost {
void TestSoftmaxMultiClassObjGPair(const Context* ctx) {
std::vector<std::pair<std::string... |
d285d422b530d2e2c7ed5e526070ca4dbdd10c497066ad3a461173978e91e0b3 | C++ | 2,514 | 74 | // RayTrace_ScreenPos_X_MEX.c
//
// [x_pixels_left,x_pixels_right] = RayTrace_ScreenPos_X(zdist_fromScreen, ipd, viewdist, pix_per_cm, xpos_world)
//
// Calculate the horizontal screen position (in pixels) of a point distance xpos_world from the visual midline
// and zdist_fromScreen in infront (-ve) or behind (+... |
6e8af2c7b0a1aa51022de27421e5fe805d3189d6ac5c65ff8c8f6fc695d98c5d | C++ | 2,532 | 103 | #include "yaml-cpp/emitterstyle.h"
#include "yaml-cpp/eventhandler.h"
#include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include <cstdlib>
#include <fstream>
#include <iostream>
class NullEventHandler : public YAML::EventHandler {
public:
typedef YAML::Mark Mark;
typedef YAML::anchor_t anchor_t;
NullEventHandl... |
f499018acf4ce3787b11204d7bee64530aaa6a61f7d6a6ba270f97d16c065f77 | C++ | 2,556 | 77 | #include "Sequence.h"
#include "Indexer.h"
#include "NucleotideMatrix.h"
#include "BaseMatrix.h"
#include "Parameters.h"
#include "Orf.h"
const char* binary_name = "test_kmernucl";
DEFAULT_PARAMETER_SINGLETON_INIT
std::string kmerToSting(size_t idx, int size) {
char output[32];
char nuclCode[4] = {'A','C','T'... |
3913a60e5f6fd5aa1c25ece630e71af908505fb7cffa0e87b729dae74db4f1d8 | C++ | 2,587 | 68 | #include "Parameters.h"
#include "FileUtil.h"
#include "Debug.h"
#include "Util.h"
#include "DBReader.h"
#include "CommandCaller.h"
#include "multihitdb.sh.h"
void setMultiHitDbWorkflowDefaults(Parameters *p) {
p->orfMinLength = 30;
}
int multihitdb(int argc, const char **argv, const Command &command) {
Para... |
b947890a3d92b3a41fe86b972f782dc07934d11d3d8d0f5d1b7025e8345c4826 | C++ | 2,587 | 51 | // 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 ... |
219c3c2ce28cf79e7fd09f3e8cf08b77b4ea2cf60a4f795e20f8249c8444017e | C++ | 2,593 | 54 | // 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 ... |
806222170a2ed32bfcb02ac0f6fafbb6148562ef7039b880d660d27be0545ab1 | C++ | 2,595 | 86 | /*
* 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).
*/
extern "C" {
#... |
db6d9fad7afa63ad8137b21043d60077624bdbfbfa0bb03245ac5eb5c748d254 | C++ | 2,601 | 67 | #include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "rbh.sh.h"
#include <cassert>
void setRbhDefaults(Parameters *p) {
p->compBiasCorrection = 0;
p->alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_COV_SEQID;
p->maskMode = 0;
p->orfSta... |
417ec1687a4466b5acd76cda1550c8ead1a02bdd1d2f89835a932cb2b6145ea7 | C++ | 2,603 | 76 | #ifdef USE_HDF5
#include <vector>
#include "hdf5.h"
#include "hdf5_hl.h"
#include "caffe/layers/hdf5_output_layer.hpp"
#include "caffe/util/hdf5.hpp"
namespace caffe {
template <typename Dtype>
void HDF5OutputLayer<Dtype>::LayerSetUp(const vector<Blob<Dtype>*>& bottom,
const vector<Blob<Dtype>*>& top) {
file_... |
fcda041dcdb04069448ba46c8069250fcbecf5d92b30c7d773d4bf9504e80c6d | C++ | 2,603 | 93 | /*!
* Copyright 2021-2022 by XGBoost Contributors
*/
#include <gtest/gtest.h>
#include <xgboost/json.h>
#include <xgboost/learner.h>
#include <limits>
#include "../../../src/common/categorical.h"
#include "../helpers.h"
namespace xgboost {
namespace common {
TEST(Categorical, Decision) {
// inf
float a = std::... |
68f87f6e3108a1cd8694a92e04b510e272d6b51f324f39a51ce1c44ca18ec36c | C++ | 2,622 | 63 | //
// Created by mad on 10/26/15.
//
#include <iostream>
#include <cstring>
#include <math.h>
#include "tantan.h"
#include "SubstitutionMatrix.h"
#include "Sequence.h"
#include "Parameters.h"
const char* binary_name = "test_tantan";
DEFAULT_PARAMETER_SINGLETON_INIT
int main (int, const char**) {
const size_t kme... |
b2d7acaedfbc6a301090a86de5663a1e0c9b0b1f5e86a0b57d20f866e68bfce3 | C++ | 2,654 | 105 | /*!
* Copyright (c) by Contributors 2019
*/
#include <gtest/gtest.h>
#include <xgboost/base.h>
#include <xgboost/parameter.h>
enum class Foo : int {
kBar = 0, kFrog = 1, kCat = 2, kDog = 3
};
DECLARE_FIELD_ENUM_CLASS(Foo);
struct MyEnumParam : xgboost::XGBoostParameter<MyEnumParam> {
Foo foo;
int bar;
DML... |
4b3d196a33cbcfff65c32190a80dfabf51c4a2ed54c973e15eb9fb30b0d03790 | C++ | 2,668 | 88 | /*
* 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... |
d078291af05244cbac622e0dc65c683715aabcc555cbd72e369c80f096986455 | C++ | 2,688 | 105 | // Copyright by Contributors
#include "../../../src/tree/param.h"
#include "../helpers.h"
#include <gtest/gtest.h>
TEST(Param, VectorIOStream) {
std::vector<int> vals = {3, 2, 1};
std::stringstream ss;
std::vector<int> vals_in;
ss << vals;
EXPECT_EQ(ss.str(), "(3,2,1)");
ss >> vals_in;
EXPECT_EQ(vals_i... |
d51293e908450536e81a8d1eb31572144a2850cc4a1e8f43fa651aaa7273cfc8 | C++ | 2,696 | 66 | #include <cassert>
#include "FileUtil.h"
#include "CommandCaller.h"
#include "Util.h"
#include "Debug.h"
#include "Parameters.h"
#include "easyproteomecluster.sh.h"
void setEasyproteomeclusterDefaults(Parameters *p) {
p->alignmentMode = Parameters::ALIGNMENT_MODE_SCORE_COV_SEQID;
p->weightClusterCount = 1.0;... |
aa035d083c7eacb4c07c98b2d7eba5d7672c7269778b23db01ff8d3c08c4ddfc | C++ | 2,702 | 70 | /* coding=utf-8
* Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*... |
240c22c54c2db25f830441d6ab97d5538720b6fb2e5bc76d63a2c18c62a5a867 | C++ | 2,706 | 76 | #include "handler_test.h"
#include "specexamples.h" // IWYU pragma: keep
#include "yaml-cpp/yaml.h" // IWYU pragma: keep
#include "gmock/gmock.h"
#include "gtest/gtest.h"
using ::testing::_;
#define EXPECT_THROW_PARSER_EXCEPTION(statement, message) \
ASSERT_THROW(statement, ParserException); \
t... |
ed1f38aae93d51cfabc8094caee775b5111e481fe19a10e1af23d213a8ae4033 | C++ | 2,712 | 87 | /*
* 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... |
a1b515bbd236f0401530c5069a25aebff534c5ffced4008668cbd5a83f7fb984 | C++ | 2,741 | 58 | #include <iostream>
#include <list>
#include <algorithm>
#include <cmath>
#include "Clustering.h"
#include "DBReader.h"
#include "DBWriter.h"
const char* binary_name = "test_dbreader";
int main (int, const char**) {
// DBReader test
DBReader<DBKeyType> reader("dataLinear", "dataLinear.index", 1, 0);
read... |
d2b139adf2a30c853c9a71fadd6d477c9669a999f5c29d7c342aac129d050520 | C++ | 2,744 | 94 | #include "graphbuilderadapter.h"
#include "yaml-cpp/contrib/graphbuilder.h"
namespace YAML {
struct Mark;
int GraphBuilderAdapter::ContainerFrame::sequenceMarker;
void GraphBuilderAdapter::OnNull(const Mark &mark, anchor_t anchor) {
void *pParent = GetCurrentParent();
void *pNode = m_builder.NewNull(mark, pParen... |
9bd6e0195e81a0f86deac77f7fb01487d9baf5368660b6425bf229e1fe9eeda3 | C++ | 2,755 | 84 | #include "Sequence.h"
#include "Indexer.h"
#include "ExtendedSubstitutionMatrix.h"
#include "SubstitutionMatrix.h"
#include "ReducedMatrix.h"
#include "KmerGenerator.h"
#include "BaseMatrix.h"
#include "Timer.h"
#include <iostream>
#include <unistd.h>
#include <string>
const char* binary_name = "test_kmergeneratorper... |
c8feb7957f017373059376ae258070edfaa50a3fa5c513b344313bd74401e246 | C++ | 2,759 | 62 | #include "Prefiltering.h"
#include "Util.h"
#include "Parameters.h"
#include "MMseqsMPI.h"
#include "DBReader.h"
#include "Timer.h"
#include "FileUtil.h"
#ifdef OPENMP
#include <omp.h>
#endif
int prefilter(int argc, const char **argv, const Command& command) {
MMseqsMPI::init(argc, argv);
Parameters& par = P... |
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