sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d1841d15936db6a01a307dfa9a22b0676be059cd9df82a7a93c9d4ed1741e32f | C++ | 15,126 | 431 | // SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
// SPDX-License-Identifier: AGPL-3.0-only
#include "CBridgeBioSemiActiveThree.h"
#include <cstdlib>
#include <cstring>
#include <iostream>
#ifndef WIN32_LEAN_AND_MEAN
#define WIN32_LEAN_AND_MEAN
#endif
#include <windows.h>
#include <bsif.h>
#include <labvi... |
11941bcc43b28401e951bb96024e70bcf69a91ee3c1d6d35a153fb9a11edbf2e | C++ | 15,232 | 443 | #include <hex/api/plugin_manager.hpp>
#include <hex/api/imhex_api/system.hpp>
#include <hex/helpers/logger.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/helpers/auto_reset.hpp>
#include <hex/helpers/utils.hpp>
#include <hex/helpers/default_paths.hpp>
#include <wolv/utils/string.hpp>
#include <filesystem>
#if de... |
fb3e9238b7a7092ec2933f93325d8b4d627faaa40787f808646723d913e8555a | C++ | 15,263 | 522 | //-----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// MultiAlignment - Class constructing a multiple
// alignment between a root sequence and a ... |
b8793057091bb9b8113a4cba9e02beea8bd38bed806aefc35ad6f2b55e0c695e | C++ | 15,351 | 413 | #include "R2CDatabase.h"
#include <stdexcept>
#include <string>
// SQLite3 is an OPTIONAL dependency (see R2CDatabase.h and CMakeLists.txt).
// When -DSVABA_HAS_SQLITE3 is defined we pull in sqlite3.h and provide
// the real implementation. Otherwise this translation unit compiles
// without sqlite3 — the class still ... |
3395c2580f454b8c1368bce7f480e638bfd938bd8b78a135804c6ee7b747f74e | C++ | 15,375 | 603 | /* -*- mode: C++; indent-tabs-mode: nil; -*-
*
* This file is a part of LEMON, a generic C++ optimization library.
*
* Copyright (C) 2003-2013
* Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
* (Egervary Research Group on Combinatorial Optimization, EGRES).
*
* Permission to use, modify and distribut... |
21b19c6d24898e4d8d2a7b5433898cea439ef8fbbf123a40ab9d2602326ea8c1 | C++ | 15,426 | 366 | /**-------------------------------------------------------------------------------------------------
* \copyright Copyright (C) 2012, Mensia Technologies SA. All rights reserved.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License... |
19e81aad3bfe0d14f80c2fffaf880827f4abc61ff8d52e51a98ec20b56a1fe42 | C++ | 15,501 | 480 | /**********************************************************
*** adapted from crux/src/c/ProteinPeptideIterator.cpp ***
**********************************************************/
/**
* \file ProteinPeptideIterator.cpp
* $Revision: 0.0 $
*/
#include "ProteinPeptideIterator.h"
using namespace std;
using namespace... |
993215e2150197a4fee3386b579c740891063415d1cf686d3f0ad0f802141259 | C++ | 15,503 | 531 | /**
Optimizers for problems dealing with TV-L2 norm regularization.
@author Álvaro Barbero Jiménez
@author Suvrit Sra
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <float.h>
#include <limits.h>
#include <wchar.h>
#include <time.h>
#include "TVopt.h"
#include "... |
88734e6fbda7ec4e44507ee3b24d70a65bc19cb25df87429dc947a77ddce4cf5 | C++ | 15,523 | 414 | /**
* SPDX-FileCopyrightText: Inria / Gipsa-lab
* SPDX-License-Identifier: AGPL-3.0-only
*
* Ported from the Gipsa-lab g.tec Unicorn Hybrid Black driver (originally by Anton Andreev,
* VIBS team).
*/
#include "CDriverGTecUnicorn.h"
#include <algorithm>
#include <iostream>
#include <memory>
// ─────────────────... |
c6ff553430858769e1dd54e7bb65ec9b336af6631fdd3a0951c15d02e5b3f640 | C++ | 15,526 | 400 | // refilter.cpp — re-apply LOD / PASS filtering to an existing bps.txt.gz
//
// The goal here is to avoid re-running assembly when the user only wants to
// tweak filtering thresholds. We read bps.txt.gz line-by-line, reconstruct
// BreakPoint objects via BreakPoint(line, sc*), rescore, redump, and
// regenerate the VC... |
ce99a0126feb030b3f67cc0fa37c0ee720aa8a15a31e9ae8054e0d7cfc8ae7c2 | C++ | 15,549 | 220 | ///-------------------------------------------------------------------------------------------------
///
/// \file main.cpp
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free software: you can redistribute it and/or modify
/// it under the terms of the GNU Affero General Public License as published
/... |
0574e8944e6b2387ed8d8db83854634dd6ef818f1179e932231efdb2741f7a3a | C++ | 15,590 | 432 | /**
* The gMobilab Linux driver was contributed by Lucie Daubigney from Supelec Metz
*
* Windows compatibility + gusbamp coexistence added by Jussi T. Lindgren / Inria
*
*/
#include "ovasCDriverGTecGMobiLabPlus.h"
#include "ovasCConfigurationGTecGMobiLabPlus.h"
#if defined TARGET_HAS_ThirdPartyGMobiLabPlusAPI
#... |
dd1391247fe35cd815e3ab5f7c36de49dd104bc685f1931fe1f1e95b6f5c56b0 | C++ | 15,623 | 422 | #if defined TARGET_HAS_ThirdPartyEmotivAPI
#include "ovasCDriverEmotivEPOC.h"
#include "ovasCConfigurationEmotivEPOC.h"
#include <system/ovCTime.h>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <vector>
#if defined(TARGET_OS_Windows)
#include <delayimp.h>
#endif
namespace OpenViBE {
namespace... |
ae03961f0f748475758e4f7bc161dc446c8401b35c1ab91d44ba5f213c068e85 | C++ | 15,627 | 422 | #if defined TARGET_HAS_ThirdPartyEmotivAPI
#include "ovasCDriverEmotivEPOC.h"
#include "ovasCConfigurationEmotivEPOC.h"
#include <system/ovCTime.h>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <vector>
#if defined(TARGET_OS_Windows)
#include <delayimp.h>
#endif
namespace OpenViBE {
namespace... |
539dd476c882be96a0d3528fd5f9d6548c7769bbc78af45c28533c06a968027a | C++ | 15,629 | 344 | //
// @todo the code logic in process() should be simplified and made more clear, perhaps by adding more states to the machine
//
#include "CBoxAlgorithmP300SpellerStimulator.hpp"
#include <cstdlib>
namespace OpenViBE {
namespace Plugins {
namespace Stimulation {
/*
CString toString(const EStates state)
{
switch... |
e00f43e1263f3eeaf6c1ef20365958faf32fe1515b77d959df016efe82bc96d8 | C++ | 15,677 | 357 | #include "ovkCPlayer.h"
#include "ovkCSimulatedBox.h"
#include "ovkCScheduler.h"
#include "../configuration/ovkCConfigurationManager.h"
#include "../scenario/ovkCScenarioManager.h"
#include "../scenario/ovkCScenarioSettingKeywordParserCallback.h"
#include <system/ovCTime.h>
#include <xml/IReader.h>
#include <string... |
4992839d456bc9b147c429b65a9e3fe9c8e237d1a927123cf2bb85c227b740c6 | C++ | 15,729 | 409 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// overlap - compute pairwise overlaps between reads
//
#include <iostream>
#include <fstream... |
836af21f76d0be85fced3cae38439d9ca9004bef43a390cf51f060392522ebd2 | C++ | 15,808 | 615 |
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it wil... |
654cff4a2f713c08cfd78f503b71a078f4a6f114ee41585e5dd0676f0d01fe37 | C++ | 15,918 | 455 | // SPDX-License-Identifier: AGPL-3.0-only
// SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
#include "SessionManager.h"
#include <algorithm>
#include <iostream>
#include <list>
#include <openvibe/Services/IService.h>
#include "AbstractWriter.h"
#include "Acquisition.h"
#include "AcquisitionManager.h"
#inc... |
6121ccc7fede994c99be83f093d3191082a603365d6282f8c55c30db82cf5d86 | C++ | 15,943 | 476 | #include "ProcExternalProcessing.h"
#include <iostream>
#include <thread>
#include <deque>
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <system/ovCTime.h>
#include <algorithm> // std::max
#include "CodecFactory.h"
// thread::
// wait for connection;
// while(connected ||!quit)
// {
// wa... |
5015cf1b38322fe93ed1d60504e850123888229d97dd9f34433238986b0afdfa | C++ | 16,041 | 496 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================
*/
#include <cstdio>
#include <map>
#include <set>
#include ... |
3fea28bcfbd99015d0ee0f7bd465679d2f1224eda7871ad526b2ae2fa1c39572 | C++ | 16,070 | 331 | #include "internal.hpp"
#include <content/project.hpp>
#include <algorithm>
#include <cctype>
#include <limits>
#include <hex/api/imhex_api/provider.hpp>
#include <hex/api/project_manager.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/helpers/logger.hpp>
#include <hex/helpers/file_attached_data.hpp>
#include <hex... |
8f39966000962a590ac740cfebef5b4137d42aff5d1c7ca240c91b6d63be630b | C++ | 16,087 | 364 | #include "internal.hpp"
#include <content/project.hpp>
#include <hex/api/achievement_manager.hpp>
#include <hex/api/events/events_lifecycle.hpp>
#include <hex/api/events/requests_gui.hpp>
#include <hex/api/imhex_api/provider.hpp>
#include <hex/api/project_manager.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/help... |
bdea0ff6fc7f35aa04008f121256aa0e1e48332b30f4c6043c921821e16b64b1 | C++ | 16,105 | 325 | ///-------------------------------------------------------------------------------------------------
///
/// \file CBoxAlgorithmOVCSVFileReader.cpp
/// \brief Classes of the box CSV File Reader.
/// \author Victor Herlin (Mensia), Thomas Prampart (Inria).
/// \version 1.2.0
/// \date 07/05/2021
/// \copyright Copyrigh... |
a4c5b3345d531a466d6a2c468f1c2cd3b3abf7d7e0afa63bc0befdf1440a604e | C++ | 16,107 | 423 | #include "ovkCLogListenerConsole.h"
#include <iostream>
#include <sstream>
#if defined TARGET_OS_Windows
#include <Windows.h>
#endif
namespace OpenViBE {
namespace Kernel {
CLogListenerConsole::CLogListenerConsole(const IKernelContext& ctx, const CString& sApplicationName)
: TKernelObject<ILogListener>(ctx), m_... |
866b5d4a1845b2ea3cf87ce8915bd98f870d1fe5ddccd4b85a0fdcb83c8f72d8 | C++ | 16,118 | 388 | /* -------------------------------------------------------------------------- *
* Lepton *
* -------------------------------------------------------------------------- *
* This is part of the Lepton expression parser originating from *
... |
34d09a4dccf42326db13ae2e6c73d13ce992a87b847c3230c89c0c895cfc6fe2 | C++ | 16,138 | 436 | #include <hex/helpers/crypto.hpp>
#include <hex/test/tests.hpp>
#include <array>
#include <cstdlib>
#include <string_view>
#include <vector>
namespace {
struct AesDecryptVector {
hex::crypt::AESMode mode;
hex::crypt::KeyLength keyLength;
std::vector<u8> key;
std::vector<u8> nonce;... |
f139584f8375f3a8080e4a5a092f47492ef68b448aeb1eabc6e3408a4b5bb325 | C++ | 16,140 | 447 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================
*/
/*
Below, the sense of permutation, is reversed. Though c... |
8077ff8f2ca69bde80f78f7fcb1c213b5c7fa1c606877dcfe0521ac1fc3a6396 | C++ | 16,142 | 418 | //
// OpenViBE Tracker
//
// @todo catch way more errors, currently most return values are ignored by callers
// @todo Change error handling to use the macros introduced in certivibe
// @todo clean the code to be more conforming to coding rules
// @todo Implement vertical slider / scale
// @todo Fix time units
// @tod... |
d461548f2c112c76bd5550b0aa5b92fadaa5fddf1463e5910f41fe406c96a5ab | C++ | 16,165 | 372 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================
*/
#include "report_handler.hpp"
#include "coreneuron/io/nrn... |
3e945fe68c6ac02fba1acd61ff600b89852ff00b08eb68dde94c2af7debb6b2b | C++ | 16,168 | 680 |
/********************
PhyloBayes MPI. Copyright 2010-2013 Nicolas Lartillot, Nicolas Rodrigue, Daniel Stubbs, Jacques Richer.
PhyloBayes 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 L... |
41d102321495b933b0158334f96e7c49f666217c44c599c43ff3406e691e5efb | C++ | 16,262 | 530 | ///----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
//
// ExtensionDP - Class implementing an iterative
// dynamic programming alignment. The ali... |
51ad01f40dc7c22b2855621e907c1f8b346e8f541372ac23c382ca057f351ff6 | C++ | 16,285 | 433 | ///-------------------------------------------------------------------------------------------------
///
/// \file CAbstractTree.cpp
/// \brief Classes implementation for the Abstract Tree.
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free software: you can redistribute it and/or modify
/// it under... |
f665a55ced29a8459f9f61e53d42f360873ff62abc186c79407c6505570dc663 | C++ | 16,342 | 555 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#include <cstdio>
#include <cstdlib>
#include <cstring>
... |
a5cfe2319b627325797255b15528c0af7975bc838fc54546bca509d3a02874fa | C++ | 16,369 | 423 | /*
* NeuroServo driver for OpenViBE
*
* \author (NeuroServo)
* \date Wed Nov 23 00:24:00 2016
*
* \note This driver will not compile with VS2010 due to missing HID library. Use VS2013.
*
*/
#if defined TARGET_OS_Windows
#if defined TARGET_HAS_ThirdPartyNeuroServo
#include "ovasCDriverNeuroServoHid.h"
#include "ovasCC... |
50e0d1697e1d0addbe10f9989213ae8a306d912ac66ce827959378adf02439ee | C++ | 16,385 | 425 | /*
* NeuroServo driver for OpenViBE
*
* \author (NeuroServo)
* \date Wed Nov 23 00:24:00 2016
*
* \note This driver will not compile with VS2010 due to missing HID library. Use VS2013.
*
*/
#if defined TARGET_OS_Windows
#if defined TARGET_HAS_ThirdPartyNeuroServo
#include "ovasCDriverNeuroServoHid.h"
#include "ovasCC... |
c78aa5566f9f81b51eb087b5b56cdd327671d1da8bd27c20587562fc96c6d99d | C++ | 16,485 | 494 | #include <vector>
#include <array>
#include <string>
#include <cstdint>
#include <thread>
#include <mutex>
#include <memory>
#include <map>
#include "ovCMessaging.h"
#include "ovCMessagingImpl.hpp"
namespace Communication {
static const std::map<CMessaging::ELibraryError, std::string> ERRORS_STRING =
{
{ CMessag... |
8c8faaa729ebe5ac0b7c911f22756723f6d66d591a621b59b04a6be3d10f71c4 | C++ | 16,490 | 371 | #include "content/views/view_highlight_rules.hpp"
#include <hex/api/content_registry/user_interface.hpp>
#include <hex/api/content_registry/views.hpp>
#include <hex/api/events/events_provider.hpp>
#include <hex/api/events/events_interaction.hpp>
#include <fonts/vscode_icons.hpp>
#include <imgui_internal.h>
#include <... |
d2d7e6072b30552984f02183075bbb47e43b3cca0759847aacb0f4857b5c2d64 | C++ | 16,506 | 430 | #include "ovtkMatrix.h"
#include <fs/Files.h>
#include <cstring>
#include <cmath>
#include <cstdlib>
#include <cerrno>
// for save/load
#include <fstream>
#include <iostream>
#include <vector>
#include <locale> // std::isspace
#include <sstream>
namespace OpenViBE {
namespace Toolkit {
namespace Matrix {
enum clas... |
b6ac64c6e020948153c25bf27a42415bf2d9bdf4bd743a648d503adfa55d0751 | C++ | 16,548 | 371 | #include "content/views/view_store.hpp"
#include <hex/api/theme_manager.hpp>
#include <hex/api/achievement_manager.hpp>
#include <hex/api/content_registry/user_interface.hpp>
#include <hex/api/content_registry/settings.hpp>
#include <hex/api/events/events_interaction.hpp>
#include <popups/popup_notification.hpp>
#inc... |
b446fc8cc79d4e875998df56eadf593021c5d43f75620f6f3ff6ef65a6ace876 | C++ | 16,575 | 231 | #include "ovpCMasterAcquisitionEncoder.h"
#include "../../algorithms/encoders/ovpCAcquisitionEncoder.h"
#include "../../algorithms/encoders/ovpCExperimentInfoEncoder.h"
#include "../../algorithms/encoders/ovpCSignalEncoder.h"
#include "../../algorithms/encoders/ovpCStimulationEncoder.h"
#include "../../algorithms/encod... |
8b1a37657ed329501465ed1943c90be1ca540166603e12bc233c3a710d5e720e | C++ | 16,637 | 411 | #include "ovkCPluginManager.h"
#include "ovkCPluginModule.h"
#include <fs/IEntryEnumerator.h>
#include <fs/Files.h>
#include <cinttypes>
#include <cstdio>
#include <iostream>
#include <map>
#include <algorithm>
#include "../../tools/ovkSBoxProto.h"
namespace OpenViBE {
namespace Kernel {
class CPluginManagerEntryEn... |
5a7e7d68195a43d4a47c61c9f024440305b8fac819dcb989a6d415739b659715 | C++ | 16,710 | 445 | //----------------------------------------------------------------------
// File: kd_dump.cc
// Programmer: David Mount
// Description: Dump and Load for kd- and bd-trees
// Last modified: 01/04/05 (Version 1.0)
//----------------------------------------------------------------------
// Copyright (c) 1997-2005 Univ... |
9f5a6dc555947210763f4fe287dd69e9dae1ca7334fb9598ae39736d9fcc4a19 | C++ | 16,753 | 508 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// bwt_algorithms.cpp - Algorithms for aligning to a bwt structure
//
#include "BWTAlgorithms... |
89ddab6886e8781109f9a212261e5e73ce1a9284a7b74ddeb13cc3cc30066df3 | C++ | 16,799 | 460 | /*******************************************************************************
Copyright 2006-2012 Lukas Käll <lukas.kall@scilifelab.se>
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:... |
513d84e33280c1fc77521f1c0f19d9fe0a82855531e0518d606b1e2c585e7fbb | C++ | 16,813 | 502 | /**
* @file CClient.cpp
* @brief Implementation of the CClient class for managing client-side network operations.
* @details This file contains the implementation of the CClient class, which handles
* connecting to a server, data transmission, and callback management for a network client.
* It utilizes sockets for comm... |
ecc65d03ec26bfe2f504fee268ae4436af50517d24ef4f8640305451c190fb8d | C++ | 16,935 | 489 | #include "ovp_gdf_helpers.h"
#include <system/ovCMemory.h>
#include <iostream>
#include <cstring>
namespace OpenViBE {
namespace Plugins {
namespace FileIO {
GDF::CFixedGDF1Header::CFixedGDF1Header()
{
memset(m_PatientID, ' ', sizeof(m_PatientID));
memset(m_RecordingID, ' ', sizeof(m_RecordingID));
memse... |
4ccb715f8f8c66f05dc9522f698da6d3b36cb8ac25c4e75fd0a47002576c82f8 | C++ | 16,973 | 392 | /*
# =============================================================================
# Copyright (c) 2022 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#include "coreneuron/apps/corenrn_parameters.hpp"
#include "core... |
f6c2ea91c6edf7899aa4d0183e55b1b05b67869977f016b60cb23cde6d027fe1 | C++ | 17,038 | 443 | #include <RcppArmadillo.h>
#include "sampling_functions.h"
using namespace Rcpp;
using namespace arma;
// FUNCTION DEFINITIONS
// ---------------------
//' Perform guided sparse factor analysis (GSFA) given a normalized expression
//' matrix and a perturbation matrix using Gibbs sampling.
//'
//' @param Y sample by ... |
1259d5dbb2771f22aa1d5e0cc3dc66e46411f3065214ccdcc75c3698bab1ccc5 | C++ | 17,066 | 416 | #include "content/views/view_hashes.hpp"
#include <hex/api/achievement_manager.hpp>
#include <hex/api/events/events_interaction.hpp>
#include <hex/api/content_registry/hashes.hpp>
#include <hex/helpers/crypto.hpp>
#include <hex/ui/popup.hpp>
#include <fonts/vscode_icons.hpp>
#include <imgui_internal.h>
#include <nl... |
a2a5bad5775ec211eb14199e4c935a06f44f5715496e6526513f710de0a7df80 | C++ | 17,082 | 594 | //===--- DLangDemangle.cpp ------------------------------------------------===//
//
// Part of the LLVM Project, under the Apache License v2.0 with LLVM Exceptions.
// See https://llvm.org/LICENSE.txt for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//===---------------------------... |
8b4474ab12a7cd0df6134a9a5e2d0edce47874ad9d56c958e5755b856b550155 | C++ | 17,187 | 474 | #include "ovkCTypeManager.h"
#include "lepton/Lepton.h"
#include <string>
#include <algorithm>
#include <functional>
#include <cctype>
#include <algorithm>
#define OV_TRACE_K(message) this->getLogManager() << OpenViBE::Kernel::LogLevel_Trace << message << "\n";
#define OV_DEBUG_K(message) this->getLogManager() << Op... |
d370004e7e7b4524c0e929019111e5bc86c777f2cee14e81d5bfe93497dc1c84 | C++ | 17,238 | 597 | //===------------------------- ItaniumDemangle.cpp ------------------------===//
//
// Part of the LLVM Project, under the Apache License v2.0 with LLVM Exceptions.
// See https://llvm.org/LICENSE.txt for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//===---------------------------... |
ec03fa6d574b505608d3f88e96d6475b12e46e832d84b77027c365013c45fa05 | C++ | 17,242 | 411 | #include "CMatrix.hpp"
#include <algorithm>
#include <sstream>
#include <string>
#include <cmath>
#include <fstream>
#include <iostream>
namespace OpenViBE {
//--------------------------------------------------------------------------------
static std::string trim(const std::string& in, const bool space = true, cons... |
b2a4f8d3da9e1d81e1fac99241be4f472c783eb7cf25a5395a6d5ea5cff0c330 | C++ | 17,281 | 549 | #include "SvabaUtils.h"
#include <iomanip>
#include <filesystem> // C++17
namespace fs = std::filesystem;
namespace svabaUtils {
static std::string POLYA = "AAAAAAAAAAAAAAAAAAA";
static std::string POLYT = "TTTTTTTTTTTTTTTTTTT";
static std::string POLYC = "CCCCCCCCCCCCCCCCCCC";
static std::string POLYG = "GGGGGGGGG... |
a785f6b61a2de6db3df8a491c1cbf05df86a8808ef93ace343c163a40fab81bd | C++ | 17,362 | 548 | /* -*- mode: C++; indent-tabs-mode: nil; -*-
*
* This file is a part of LEMON, a generic C++ optimization library.
*
* Copyright (C) 2003-2013
* Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
* (Egervary Research Group on Combinatorial Optimization, EGRES).
*
* Permission to use, modify and distribut... |
7034b2b6434a221cace8619a92347611e0e7c36743f1b6250e68dbd2c1c0d9ee | C++ | 17,452 | 623 | // ***************************************************************************
// bamtools_fasta.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 9 March 2012 (DB)
// -----------... |
2f0894e17c614db0ff12fe11a09ce5faa73ad8999ec0728f4b6dcf6e93c05df6 | C++ | 17,575 | 371 | // @note in this code, conversion in time or in second are sometimes used simply to convert between floating and fixed point even if the units are not seconds.
#include "ovasCDriftCorrection.h"
#include <toolkit/ovtk_all.h>
#include <ovp_global_defines.h>
#include <system/ovCTime.h>
#include <cmath> // std::abs
#inc... |
ebc9d1d6f7920c7a700a4c2c0642b3f368a168e46ee9bd6beb830cd91c90d477 | C++ | 17,581 | 428 | #include "ovkCSimulatedBox.h"
#include "ovkCPlayer.h"
#include "ovkCBoxAlgorithmContext.h"
#include <cstdlib>
#include <algorithm>
#include <cassert>
namespace OpenViBE {
namespace Kernel {
#define OV_IncorrectTime 0xffffffffffffffffULL
CSimulatedBox::CSimulatedBox(const IKernelContext& ctx, CScheduler& scheduler)
... |
f0b4a1b059082c084256207308e7c4509faa518b4b1a3e93284162c81a8bad32 | C++ | 17,623 | 610 | /*****************************************************************************
* SV_Pair.cpp
* (c) 2012 - Ryan M. Layer
* Hall Laboratory
* Quinlan Laboratory
* Department of Computer Science
* Department of Biochemistry and Molecular Genetics
* Department of Public Health Sciences and Center for Public Health G... |
f2939aa1f984a6a701e4f56c85f12a47f6ed3da6451e24bb2b3551df345cfc3f | C++ | 17,624 | 402 | ///-------------------------------------------------------------------------------------------------
///
/// \file CEquationParser.cpp
/// \brief Classes implementation for the Equation Parser.
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free software: you can redistribute it and/or modify
/// it u... |
9f9be571ca5731f8c3a29a7da2482729c1fe24a36d59e8c1f8b2e8d1a7d91faa | C++ | 17,657 | 417 | ///-------------------------------------------------------------------------------------------------
///
/// \file CAlgorithmClassifierLDA.cpp
/// \brief Classes implementation for the Algorithm LDA.
/// \author Jussi T. Lindgren (Inria) / Guillaume Serriere (Loria).
/// \version 2.0.
/// \copyright Copyright (C) 2022... |
7651c61f96b1774851c25d39682e1c564aa3b07757a3ac3fe551320fff8ad156 | C++ | 17,704 | 515 | #include "content/providers/file_provider.hpp"
#include "content/providers/memory_file_provider.hpp"
#include <hex/api/content_registry/settings.hpp>
#include <hex/api/localization_manager.hpp>
#include <hex/api/project_manager.hpp>
#include <hex/api/events/requests_gui.hpp>
#include <hex/api/events/events_interaction... |
1b20da17f9bdbdfab8c5cfc503a70f335c2a9a222d4e9faf5c553cb798318431 | C++ | 17,718 | 465 | ///-----------------------------------------------
// Copyright 2012 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// KmerOverlaps - Overlap computation functions
// seeded by exact kmer matches
//
#include ... |
6236479fd8148ab03b39a4b75ba2ed9b69b9c633d7174c9d2726eb154ebaab0f | C++ | 17,740 | 383 | // @note in this code, conversion in time or in second are sometimes used simply to convert between floating and fixed point even if the units are not seconds.
#include "ovasCDriftCorrection.h"
#include <toolkit/ovtk_all.h>
#include <ovp_global_defines.h>
#include <system/ovCTime.h>
#include <cmath> // std::abs
#inc... |
894b6d9d12dac8e42dcc4afd8262aa54f4ee67edb5c9a86d8b18293ad463bcbf | C++ | 17,864 | 405 | ///-------------------------------------------------------------------------------------------------
///
/// \file CGrazMultiVisualization.cpp
/// \brief Classes implementation for the Generalized Graz Visualization box.
/// \author Thibaut Monseigne (Inria).
/// \version 1.0.
/// \date 28/05/2019.
/// \copyright Copy... |
c1068466fd0b54c5dc41c009bd62d869736fe50c5dbd58a12dcc42ce5757d2b7 | C++ | 17,872 | 420 | #include <hex.hpp>
#include <hex/plugin.hpp>
#include <hex/api/content_registry/pattern_language.hpp>
#include <hex/helpers/literals.hpp>
#include <pl/core/evaluator.hpp>
#include <pl/patterns/pattern.hpp>
#include <wolv/utils/guards.hpp>
#include <vector>
#include <optional>
#include <cstring>
#include <algorithm>
... |
ac9105397d621896c44c3424d6da8e2633ad91fee30b82cf9cdd5991bfae0a1d | C++ | 17,915 | 510 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// OverlapBlock - Data structures holding
// the result of the alignment of a sequence read
/... |
52e078507723fa9089e820d60d27bf447bb73f273ba3a8b0394d72d209d40193 | C++ | 17,930 | 496 | // SPDX - License - Identifier: AGPL - 3.0 - only
// SPDX-FileCopyrightText: Inria <florent.leray@inria.fr>
#include <CInitApp.h>
// Standard Library
#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
// Project Headers
#include <openvibe/Services/IService.h>
#include <ISettingsProvider.h>
... |
6e42519a553b560842d9e18321e06ae9f9f3eefdba0a6df73ce39c7dce282bc5 | C++ | 17,981 | 520 | #if !defined(OS_WEB)
#include "content/providers/disk_provider.hpp"
#include <hex/api/localization_manager.hpp>
#include <hex/helpers/logger.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/helpers/utils.hpp>
#include <hex/helpers/scaling.hpp>
#include <hex/ui/imgui_imhex_extensions.h>
#include <wolv/utils/string... |
e057eb627d629eed682922f152cf4d388b4bb38a143ed73d5125fd9088d62c14 | C++ | 18,028 | 565 | #include <array>
#include <string>
#include <algorithm>
#include <cstring>
#include "ovCMessaging.h"
namespace Communication {
/**
* \brief Copy a string to buffer
*
* \param [out] dest The buffer destination
* \param [out] bufferIndex The index of the buffer where the beginning of the string must be copi... |
88d4f5162ba5536b160ffad0fca3865091ca4ee5bf71575a0695f32e1ddcfbe7 | C++ | 18,063 | 390 | #include <content/legacy_project_importer.hpp>
#include <hex/api/content_registry/user_interface.hpp>
#include <hex/api/imhex_api/provider.hpp>
#include <hex/api/localization_manager.hpp>
#include <hex/api/project_manager.hpp>
#include <hex/api/task_manager.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/helpers/fs.... |
a6fad2e44562bfed7812c7daeb4e70afc49dcef7c6953c7cf08e4c0af94c2813 | C++ | 18,088 | 572 | /*******************************************************************************
Copyright 2006-2012 Lukas Käll <lukas.kall@scilifelab.se>
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:... |
16b73e980d5824ee9daf5933f06602a9334a3e597b26b9454b463ad62b317968 | C++ | 18,100 | 419 | #include <ui/markdown.hpp>
#include <imgui.h>
#include <fonts/fonts.hpp>
#include <hex/api/task_manager.hpp>
#include <hex/helpers/fmt.hpp>
#include <hex/helpers/logger.hpp>
#include <hex/ui/imgui_imhex_extensions.h>
#include <romfs/romfs.hpp>
#include <chrono>
#include <fonts/vscode_icons.hpp>
#include <hex/helpers/... |
bb316904a3aae308e5f95e56086a44d58229bb3874cea35ce4f83c563cdddac2 | C++ | 18,165 | 462 | #if defined(TARGET_HAS_ThirdPartyGNEEDaccessAPI)
#include "ovasCDrivergNautilusInterface.h"
#include "ovasCConfigurationgNautilusInterface.h"
#include <toolkit/ovtk_all.h>
namespace OpenViBE {
namespace AcquisitionServer {
// global functions, event handles and variables
void OnDataReadyEventHandler(GDS_HANDLE hand... |
0cc3c668349b367bf4803094540b7d63ea95e3707a53168e29fee1dc1bfe235d | C++ | 18,342 | 451 | // test_svaba.cpp
//
// `svaba test` — a "secret" subcommand (not listed in the top-level help)
// that runs a minimal microbenchmark of svaba's five main hot paths:
//
// 1. walk — read N reads from a BAM
// 2. correct — BFC error-correct those reads
// 3. realign — BWA-MEM align each *corrected* read back... |
f8a3fb2d301a61739201a3209caed22fd8d2e07250c096bdb3636e1112603ef4 | C++ | 18,344 | 511 | // SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
// SPDX-License-Identifier: AGPL-3.0-only
#include "CVisualizationTree.hpp"
#include "CVisualizationWidget.hpp"
#include "json/json.h"
namespace OpenViBE {
namespace Designer {
CVisualizationTree::~CVisualizationTree() {
}
bool CVisualizationTree::in... |
b9dec0885aefc0e397eaa0f2329e0ab14757a27da0facea01b03639482e7219a | C++ | 18,438 | 404 | #include "SvabaModels.h"
#include <iostream>
#include <cmath>
#include <algorithm>
#include <cstring>
namespace SvabaModels {
double LogLikelihood(double ref,
double alt,
double f,
double e_fwd,
double e_back) {
// less negative log-likelihoods means more likely
//... |
b6fb682059dc9452a29090d26613bfdcc7826dbb1bb27c222bcfae025227722e | C++ | 18,693 | 578 | /* -*- mode: C++; indent-tabs-mode: nil; -*-
*
* This file is a part of LEMON, a generic C++ optimization library.
*
* Copyright (C) 2003-2013
* Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
* (Egervary Research Group on Combinatorial Optimization, EGRES).
*
* Permission to use, modify and distribut... |
710e3575b38abddbfb39c10c2f44e7a28b8b91d7c9f3e8a21aeea3c46880e025 | C++ | 18,763 | 425 | ///-------------------------------------------------------------------------------------------------
///
/// \file ovasCDriverBrainProductsLiveAmp.cpp
/// \brief Brain Products LiveAmp driver for OpenViBE
/// \author Ratko Petrovic
/// \copyright Copyright (C) 2017 Brain Products
///
/// This library is free software... |
245fbdd30aa87b76ce8c4ad997c7b0eedcb763334c5c8b097d1a7b803302a549 | C++ | 18,784 | 403 | ///-------------------------------------------------------------------------------------------------
///
/// \file CBoxAlgorithmRegularizedCSPTrainer.cpp
/// \brief Classes implementation for the Box Regularized CSP Trainer.
/// \author Jussi T. Lindgren (Inria).
/// \version 1.0.
/// \copyright Copyright (C) 2022 Inr... |
5f5fce21d2b6173a75b2c0dd44fb7e8c62a733e4fa51c7e7c94d0c277e44deab | C++ | 18,852 | 463 | #include "CTopographicMap2DView.hpp"
#include <QQmlContext>
#include <QQuickItem>
#include <QQmlEngine>
#include <QQmlComponent>
#include <QColor>
#include <QVector>
#include <cmath>
#include <array>
namespace OpenViBE {
namespace Plugins {
namespace SimpleVisualization {
//static double Deg2Rad(const double x) { r... |
b5540f412f9760e78f7ab8450d78c2b0ff5fd6ad171bf3fa0d5dd1aa0d3e4e53 | C++ | 18,860 | 447 | /*
# =============================================================================
# Copyright (c) 2016 - 2022 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#include <sstream>
#include "coreneuron/nrnconf.h"
#incl... |
d97757787ba673e0a2c761e955b14701ca0eab8a07828f014b80b41c9982fe27 | C++ | 18,996 | 436 | /*******************************************************************************
Copyright 2006-2012 Lukas Käll <lukas.kall@scilifelab.se>
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:... |
0096a36dd97ab11572f5e67aa644825c598b6d65db5eeac8636cfdd9522d9939 | C++ | 19,057 | 402 | #include <content/views/view_pattern_data.hpp>
#include <hex/api/content_registry/settings.hpp>
#include <hex/providers/memory_provider.hpp>
#include <hex/api/events/requests_interaction.hpp>
#include <hex/api/events/events_interaction.hpp>
#include <fonts/vscode_icons.hpp>
#include <fonts/tabler_icons.hpp>
#include... |
b2554c40a569d13c30d8b88bc2fbf8b1a2f6d8901e0471b7a3b6490ca3a989ba | C++ | 19,073 | 444 | #if defined TARGET_HAS_ThirdPartyThinkGearAPI
#include "ovasCDriverNeuroskyMindset.h"
#include "ovasCConfigurationNeuroskyMindset.h"
#include <sstream>
#include <system/ovCTime.h>
#include <thinkgear.h>
namespace OpenViBE {
namespace AcquisitionServer {
CDriverNeuroskyMindset::CDriverNeuroskyMindset(IDriverContext... |
9dbef50878ea238be298e3166433a3c435d6f0d883b153e7c0248490b95fbe79 | C++ | 19,077 | 445 | #if defined TARGET_HAS_ThirdPartyThinkGearAPI
#include "ovasCDriverNeuroskyMindset.h"
#include "ovasCConfigurationNeuroskyMindset.h"
#include <sstream>
#include <system/ovCTime.h>
#include <thinkgear.h>
namespace OpenViBE {
namespace AcquisitionServer {
CDriverNeuroskyMindset::CDriverNeuroskyMindset(IDriverContext... |
2bd6b43b8a3088d42bc5c3ca76f798d5a2edb42cfb2ba4e2dbdaae78491b6fa2 | C++ | 19,107 | 475 | // SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
// SPDX-License-Identifier: AGPL-3.0-only
#include "CSignalDisplayController.h"
#include "CSignalTraceItem.h"
#include <QQmlComponent>
#include <QQmlContext>
#include <QQmlEngine>
#include <QQuickItem>
#include <QVariantMap>
#include <algorithm>
namespace... |
e5f1b4a1d8fb704774c334dd4f8ef83248937d4f32801041b0f5dea97cdfe37a | C++ | 19,213 | 544 | #include <hex/api/tutorial_manager.hpp>
#include <hex/api/imhex_api/system.hpp>
#include <hex/api/localization_manager.hpp>
#include <hex/api/task_manager.hpp>
#include <hex/api/events/events_gui.hpp>
#include <hex/helpers/auto_reset.hpp>
#include <imgui_internal.h>
#include <hex/helpers/utils.hpp>
#include <hex/help... |
414cb7572b01982c947f051a8fc3ed055f884014cdcb493cf306f8b7de378800 | C++ | 19,218 | 825 |
/********************
PhyloBayes MPI. Copyright 2010-2013 Nicolas Lartillot, Nicolas Rodrigue, Daniel Stubbs, Jacques Richer.
PhyloBayes 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 L... |
d7375388cd0f82c368478ab54ba80bbd09f0d65a4dff406934ce6a0a18929978 | C++ | 19,350 | 536 | /*******************************************************************************
Copyright 2006-2012 Lukas Käll <lukas.kall@scilifelab.se>
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:... |
a79a4611d11195c2f1de4d6993243d63d2f997d41d057ef5c9ac96bf59a88591 | C++ | 19,409 | 784 | /*******************************************
*** adapted from crux/src/c/Protein.cpp ***
*******************************************/
/*************************************************************************//**
* \file protein.cpp
* \brief Object for representing a single protein.
******************************... |
c3a763f3c5d029c0af8cc3fb399dbacc5ecc8f0a8eebf11fef1dc2da70cd35e2 | C++ | 19,415 | 603 | ///-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// ErrorCorrectProcess - Wrapper to perform error correction
// for a sequence work item
//
... |
8aaefbfb9cdd02881aeda8aa983c41aa5c103abf7da7d5575cf11da0599f6058 | C++ | 19,443 | 411 | #include "SvabaOptions.h"
#include <sstream> // for std::ostringstream
#include <iomanip> // for std::setw and std::setfill
#include <getopt.h>
#include <iostream>
#include <stdexcept>
#include "SvabaLogger.h"
#include "SvabaAssemblerConfig.h" // SVABA_ASSEMBLER_FERMI for SGA guards
#include "R2C... |
16ae94df0d451712abf30153e04481fce5b4c735adc5cb1bee46008714141b3f | C++ | 19,446 | 612 | #include <hex/api/task_manager.hpp>
#include <hex/api/localization_manager.hpp>
#include <hex/helpers/logger.hpp>
#include <algorithm>
#include <ranges>
#include <jthread.hpp>
#include <hex/helpers/debugging.hpp>
#include <hex/trace/exceptions.hpp>
#include <wolv/utils/string.hpp>
#include <utility>
#if defined(OS_... |
9f25eb62e51d51e22aabfcf0ec8f8e9bcf3ffd297b2fdd56b2f78f4ad435ecc0 | C++ | 19,595 | 467 | #include "views/view_tty_console.hpp"
#include <imgui_internal.h>
#include <implot.h>
#include <hex/api/task_manager.hpp>
#include <hex/helpers/utils.hpp>
#include <toasts/toast_notification.hpp>
#include <wolv/utils/guards.hpp>
namespace hex::plugin::windows {
ViewTTYConsole::ViewTTYConsole() : View::Window(... |
e8b8c061e2f59cef9e4457f740749a33ccdf6904328679fe2c2e1039c83f4efb | C++ | 19,643 | 462 | ///-------------------------------------------------------------------------------------------------
///
/// \file CLogListenerDesigner.cpp
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free software: you can redistribute it and/or modify
/// it under the terms of the GNU Affero General Public Licens... |
b0c63894c6572884929e463b8bc2031914f4cf1e8f7f5d90f5477ca4f762767e | C++ | 19,724 | 453 | #include "ovpCAlgorithmClassifierMLP.h"
#include "../ovp_defines.h"
#include <map>
#include <sstream>
#include <iostream>
#include <algorithm>
#include <cmath>
#include <Eigen/Dense>
#include <Eigen/Core>
namespace OpenViBE {
namespace Plugins {
namespace Classification {
static const char* const MLP_EVALUATION_FUN... |
ea7e02a5b5d6d02b563cfae413ab4dab20ca10b303cb8de65a2cb62bc09b07f8 | C++ | 19,732 | 533 | /* This driver uses the FieldTrip buffer open source library.
* See http://www.ru.nl/fcdonders/fieldtrip for details.
*/
#if defined(TARGET_HAS_PThread)
#include "ovasCDriverFieldtrip.h"
#include "ovasCConfigurationFieldtrip.h"
#include <toolkit/ovtk_all.h>
#include <pthread.h>
#include "fieldtrip/buffer.h"
#incl... |
cc8d46a8ba818bbdb00a0e63d20790edaf17f8dcee8da81e654005fa22fb37b5 | C++ | 19,783 | 530 | //
// bedFilePE.cpp
// BEDTools
//
// Created by Aaron Quinlan Spring 2009.
// Copyright 2009 Aaron Quinlan. All rights reserved.
//
// Summary: Contains common functions for finding BED overlaps.
//
// Acknowledgments: Much of the code herein is taken from Jim Kent's
// BED processing code. I... |
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