sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
34c0f08627bcf87e818040462be2f67f3bb487251b6e56c213bbe45be624fc4b | C/C++ | 2,765 | 109 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// STCommon.h - Base classes and data structures
//
#ifndef STCOMMON_H
#define STCOMMON_H
#in... |
7112acba61ae7cd4e02a281bf90056b55ac8112ba3febb14d04151de66a07feb | C/C++ | 2,765 | 70 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#pragma once
#include <vector>
#include <map>
#include ... |
cef0a0280815d0b8e4e8efc91654a9494315673e2ffdf41bffa4cccf1e948d0f | C/C++ | 2,765 | 74 | #pragma once
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include <random>
namespace OpenViBE {
namespace AcquisitionServer {
/**
* \class CDriverSimulatedDeviator
* \brief Simulates a drifting acquisition device by changing the sample rate by a random process.
* \author Jussi T. Lindgren (Inria)
*
* T... |
8d55b3f9c5146c12c713ef8fe7a84452b827aaea76b05e2e17d7fa2200fc7671 | C/C++ | 2,769 | 102 |
/********************
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... |
71e8025e9709c3095fe3413decc70c8f7ffe2529f63c7039afe1e72496908760 | C/C++ | 2,772 | 78 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// SGAlgorithms - Algorithms for manipulating
// the string graph
//
#ifndef SGALGORITHMS_H
#... |
ab20bf3fe3e7172c56e79cbb6b7245905e9a57242360c208520aa54795bba2f5 | C/C++ | 2,774 | 101 |
/********************
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... |
216c6b149494dff23fbbe0db65bce455f39fded1e3b86ff3cd53bd8b04092847 | C/C++ | 2,775 | 82 | #pragma once
/**
* @file CClient.h
* @brief Header file for the CClient class.
* @details This file contains the declaration of the CClient class, which provides methods to connect to a server,
* send and receive messages, and manage the connection state.
* The class is designed to be used in a networked environment w... |
a0536744e1b5035456adb4677b873f087afd359a24bbb9b313441ff9e38d800f | C/C++ | 2,776 | 109 | #pragma once
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include "../ovasCSettingsHelper.h"
#include "../ovasCSettingsHelperOperators.h"
#include <openvibe/ov_all.h>
#include <socket/IConnectionClient.h>
#define NB_CHAN_RECORDED_MAX 410
#define NB_SAMP_ACQ_Packet 28160
namespace OpenViBE {
namespace A... |
c3a8fc12c7df86e9a1ee0450a50fb3c2e4e32cc4361f42be8cabf7d2015c8e8c | C/C++ | 2,781 | 81 | #pragma once
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include "../ovasCSettingsHelper.h"
#include <random>
namespace OpenViBE {
namespace AcquisitionServer {
/**
* \class CDriverSimulatedDeviator
* \brief Simulates a drifting acquisition device by changing the sample rate by a random process.
* \aut... |
48a19f0b4384a059c689ee70f9a263491868b7b8b7fb772b6c2ea398d59cb201 | C/C++ | 2,783 | 101 | // threadpool.h
#pragma once
#include <deque>
#include <memory>
#include <mutex>
#include <condition_variable>
#include <thread>
#include <vector>
#include <atomic>
#include "SvabaSharedConfig.h"
#include "SvabaOutputWriter.h"
#include "SvabaOptions.h"
#include "SvabaThreadUnit.h"
// A simple thread safe queue for u... |
0e475f6a45b4270a87a5b87415143616ef63c49d814d31a041238a11c13ecf33 | C/C++ | 2,790 | 72 | #pragma once
// @author Gipsa-lab
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
/**
Use this class to receive send and stimulations channels
*/
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CInputChannel
{
typedef enum
{
SIGNAL_CHANNEL,
STIMULAT... |
43db2cf9b3d39fdbce385c04ac49fc70a57e5c5ab4b682d5c71ae9654b784e82 | C/C++ | 2,801 | 59 | // dear imgui test engine
// (coroutine interface + optional implementation)
// Read https://github.com/ocornut/imgui_test_engine/wiki/Setting-Up
// This file is governed by the "Dear ImGui Test Engine License".
// Details of the license are provided in the LICENSE.txt file in the same directory.
#pragma once
#ifnde... |
5ee16512d138435c542c37d0fbb9bca8fd20c8f14b2ceb16ef6a2ef04485329e | C/C++ | 2,802 | 82 | #pragma once
/**
* \brief Acquisition Server plugin adding the capability to receive stimulations from external sources
*
* \author Anton Andreev
* \author Jozef Legeny
*
* \note This plugin is deprecated. The users are recommended to use the TCP Tagging plugin instead. (11.05.2016)
*
*/
#include <thr... |
6b77d319443c33fcf8fae9f7be2adf6d6cb5c4a2c1ec2f8bef513c5108b0ce9e | C/C++ | 2,803 | 119 |
/********************
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... |
ee694684e84eed490d6acc88a0adf5d8563053b530b4442728cb967e205cdb8d | C/C++ | 2,808 | 91 | #pragma once
#include "ovas_base.h"
#include "ovasIDriver.h"
#include "ovasIHeader.h"
#include "ovasCHeader.h"
#include <thread>
#include <gtk/gtk.h>
namespace OpenViBE {
namespace AcquisitionServer {
class CAcquisitionServer;
class CAcquisitionServerThread;
class IAcquisitionServerPlugin;
struct PluginSetting;
cla... |
61b30b659af54de071bcb01b3a7d77fb39fa27fc857669167179b1d19e30f231 | C/C++ | 2,812 | 86 | #pragma once
#include <openvibe/ov_all.h>
#include <fs/Files.h>
namespace OpenViBE {
namespace Tracker {
/**
* \class WorkspaceNotes
* \brief An overly complicated wrapper for a text string.
* \author J. T. Lindgren
*
* This class is needed in order to use CCommentEditorDialog from Designer. The
* implementa... |
b04a821737f887a09ae7206a4c74eeedda3c8202a6f911b71dd6c64794c7a880 | C/C++ | 2,832 | 90 | /*******************************************************************************
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:... |
069386ca821a305f005c2dda333d63383ae92397e1b3a1da58216e8f742aa511 | C/C++ | 2,836 | 97 | #pragma once
#include <openvibe/ov_all.h>
#include "Contexted.h"
#include "StreamBundle.h"
#include "BoxAdapterHelper.h"
#include "Encoder.h"
#include "Decoder.h"
namespace OpenViBE {
namespace Tracker {
/**
* \class BoxAdapter
* \brief A partially abstract class allowing processing data with OpenViBE boxes u... |
e3057c6172670b8bb8f5f54b3f41ad8631c4bfcba5d73a41ef0783798c4c61cb | C/C++ | 2,847 | 115 |
/********************
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... |
990bb9de22e8417c115597ce030079dbc4cfed45a9f5c698787c883bc75e0820 | C/C++ | 2,850 | 93 | /*******************************************************************************
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:... |
1198c65c5825d85069edb3c68d205f6039ad115202290b0c9da7e1abe22c73ff | C/C++ | 2,853 | 74 | // ***************************************************************************
// SamHeader.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ------------------------------... |
21f6b20cb6989b617e2b9f35221c162a1233200acf8da8120313163d8c74ed4a | C/C++ | 2,856 | 104 | ///----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// HaplotypeBuilder - Construct candidate
// haplotypes from a pair of k-mer seeds.
//
#ifnde... |
48d88c3d510beacb53acf70a3814ce9b50bb07b9921f56951f553066b350260f | C/C++ | 2,862 | 67 | #pragma once
#include "../../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <xml/IReader.h>
#include <stack>
#include <string>
namespace OpenViBE {
namespace Plugins {
namespace FileIO {
class CAlgorithmXMLScenarioImporter final : public Toolkit::CAlgorithmScenarioImporter, public ... |
42304fa0cbbd107f8d4dbfa107aa6780bb6aa93dfa3c7dd4d38d908178e9d425 | C/C++ | 2,885 | 93 | /* This driver uses the FieldTrip buffer open source library.
* See http://www.ru.nl/fcdonders/fieldtrip for details.
*/
#pragma once
#if defined(TARGET_HAS_PThread)
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include <openvibe/ov_all.h>
#include "fieldtrip/message.h"
#include "../ovasCSettingsHelper.h... |
6021412dbd38d9f64442037c9154d2add50d61defe48496d58c447e60864d5be | C/C++ | 2,889 | 54 | #include "Python.h"
#include <gsl/gsl_rng.h>
// p4_tree.c
p4_tree *p4_newTree(int nNodes, int nLeaves, int *preOrder, int *postOrder, double *partLikes, data *aData, p4_model *aModel, int *newtAndBrentPowellOptPassLimit);
void p4_freeTree(p4_tree *aTree);
void p4_dumpTree(p4_tree *aTree);
void p4_setPrams(p4_tree *aT... |
776be44b0d60e6c02fedae4c9042cc40dcb62315ee006b777189a224b2ff1977 | C/C++ | 2,889 | 96 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// FMMarkers - Marker classes used in the FM-index
// implementation
//
#ifndef FMMARKERS_H
... |
6dc8e59c5754ac70529a4fdab1bc6780a27a2f8db6f8c70da109c5c0119a862b | C/C++ | 2,891 | 102 |
/********************
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... |
b1026fc9ebf9b8aa07267a279d4bd16ae02c409aecaf8e179f5fbdc862dee4b8 | C/C++ | 2,891 | 97 | #pragma once
#include "ovIPluginObjectDesc.h"
namespace OpenViBE {
namespace Kernel {
class IBoxProto;
class IBoxAlgorithmContext;
} //namespace Kernel
namespace Plugins {
class IBoxListener;
/**
* \class IBoxAlgorithmDesc
* \author Yann Renard (INRIA/IRISA)
* \date 2006-06-19
* \brief Box algorithm plugin des... |
8d4fbde89c40f2ee1d127c4f49a5ae99433052947fcc8c44ed1096b545e0b338 | C/C++ | 2,896 | 109 | /**
* @file PackedVector.h
* @author Mattia Tomasoni
* @section DESCRIPTION
* The class PackedVector augments the class Vector with algebraic operations
* on packed Vectors.
*/
#ifndef _PackedVector_H
#define _PackedVector_H
#define PACK
#define ALLOW_ZERO
#include "Vector.h"
class PackedVector : public Vector... |
1b5b17409b3ccbe019f6ba856b41350bae151c16d31800b57566cff7981d77bd | C/C++ | 2,901 | 131 |
/********************
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... |
cf6c95f03ef8eb31f2e8a7ddfbe5bb42d2dc297c09f4db2cc8956272809f6d2c | C/C++ | 2,908 | 89 | #pragma once
#ifdef TARGET_HAS_ThirdPartyOpenViBEPluginsGlobalDefines
#include "../../ovtk_base.h"
#include "ovtkTStreamedMatrixEncoder.h"
namespace OpenViBE {
namespace Toolkit {
template <class T>
class TSignalEncoderLocal : public T
{
protected:
//The signal stream is a streamed matrix plus a sampling rate
... |
0854fa44d4ccd4a9d9195a93f08df67adf97014e5b69816db4a3f65adfd32fa5 | C/C++ | 2,926 | 86 | #pragma once
#include "../ovIKernelObject.h"
namespace OpenViBE {
namespace Kernel {
class IBox;
class IBoxIO;
class IPlayerContext;
/**
* \class IBoxAlgorithmContext
* \author Yann Renard (INRIA/IRISA)
* \date 2006-07-07
* \brief Specific context to use for box algorithm plugins
* \ingroup Group_Player
* \ing... |
40597042340e2429c09b84e88bd78740e2fef54795390fe14ee03e6a17fa77bd | C/C++ | 2,930 | 124 |
/********************
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... |
969cd72742b03843a7bce370291d22ba45d0f25891c6d61a4aa37b6dc169da6c | C/C++ | 2,931 | 109 | // SPDX-FileCopyrightText: Inria <tristan.cabel@inria.fr>
// SPDX-License-Identifier: AGPL-3.0-only
#pragma once
#include <openvibe/ov_all.h>
#include <QtCore>
#include <QQmlEngine>
#include <QtQml>
#include <QJSValue>
#include <QQuickItem>
namespace OpenViBE {
namespace Plugins {
namespace SimpleVisualization {
cl... |
db51f964f37fdeb7e32d6f2f42b14478bbbde0741e74177fb26bb0dae1e87f1c | C/C++ | 2,944 | 96 | #pragma once
#if defined(TARGET_HAS_ThirdPartyEnobioAPI)
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include <openvibe/ov_all.h>
#include "../ovasCSettingsHelper.h"
#include "../ovasCSettingsHelperOperators.h"
// Including Enobio headers gave 4275 on 11.07.2014 w/ VS2010
#pragma warning(disable:4275)
#in... |
5020e3b2327f68d6bf928b61ecca1ee86d6e606f8a8a0316f2362ca79b0b9578 | C/C++ | 2,947 | 101 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// NoCodec - Testing codec for EncodedString
// that does not encode anything - it just retur... |
8defc640f264147b05518e266110e4af562ec2c98f20eff407d850d5cca33724 | C/C++ | 2,950 | 87 | #pragma once
#include "../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include "edf/edflib.h"
#include <queue>
#include <deque>
#include <vector>
namespace OpenViBE {
namespace Plugins {
namespace FileIO {
typedef struct SChannel
{
double min;
double max;
} channel_info_t;
cla... |
9909314518f206a7e9168dc795f274a36d973732e3efff50ebc7bef2d402bb77 | C/C++ | 2,950 | 89 | /*******************************************************************************
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:... |
5befbd083e7776b3f7020171ebcd3194eb784d3514cfb9627fab370457d13684 | C/C++ | 2,954 | 77 | #pragma once
#if defined TARGET_HAS_ThirdPartyITPP
#include "../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <itpp/itstat.h>
#include <itpp/itsignal.h>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CApplyTemporalFilter final : virtual public Tool... |
169c6230bccfb97d8e68c121e12ca1530657ea4622527b91224ec935492026a2 | C/C++ | 2,961 | 58 | #ifndef LEPTON_EXCEPTION_H_
#define LEPTON_EXCEPTION_H_
/* -------------------------------------------------------------------------- *
* Lepton *
* -------------------------------------------------------------------------- *
* This is part of the ... |
8aca047795ef8d45d57049b9acf2f6c9f9346002c46417f8b5f4c08c6549af1e | C/C++ | 2,962 | 75 | /****************************************************************************
* Copyright (C) 2014 by Taylor Arnold, Ryan Tibshirani, Veerun Sadhanala *
* *
* This file is part of the glmgen library / package. *
* ... |
d43c37dca3e3304c4377fa3d4b71c833aa4f72af8dfd2e1c0ee7ca89372eb456 | C/C++ | 2,963 | 74 | //
//
#pragma once
#include <string>
#include <vector>
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <system/ovCTime.h>
#include "Contexted.h"
namespace OpenViBE {
namespace Kernel {
/**
* \class IBoxIOProxy
* \brief This proxy is intended for reusing codecs from the toolkit.
* @fixme it... |
492a634509790a51dbfdfaf00c92e3d47666c4459b41edcaa014f9f38a7d2fef | C/C++ | 2,964 | 67 | #pragma once
#include "../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CDetectingMinMax final : virtual public Toolkit::TAlgorithm<IAlgorithm>
{
public:
void release() override { delete this; }
bool ini... |
9d32b56962af22190dc57ab1529f18cebb828e69604dccbc81b6b5e2d861d41b | C/C++ | 2,967 | 64 | #pragma once
#include "../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CDownsampling final : virtual public Toolkit::TAlgorithm<IAlgorithm>
{
public:
void release() override { delete this; }
bool initializ... |
e64c5455d8f423044b9806dd052f14609954abfc9a8e80d13c14d9a41d2e1168 | C/C++ | 2,974 | 100 | #pragma once
#include <map>
#include <list>
#include <deque>
#include <vector>
#include <functional>
#include <mutex>
#include <condition_variable>
#include <thread>
/*
* Class allowing creating a set of worker threads that then pull jobs from a job list.
*
* Before this class can be used safely, various componen... |
26a4b4b4b2d4aaaa390e22b57fc9589f68e7c81aff3f1aa9e93a7f306d93798f | C/C++ | 2,979 | 84 | #pragma once
#ifdef TARGET_HAS_ThirdPartyOpenViBEPluginsGlobalDefines
#include "../../ovtk_base.h"
#include "ovtkTStreamedMatrixDecoder.h"
namespace OpenViBE {
namespace Toolkit {
template <class T>
class TSpectrumDecoderLocal : public T
{
protected:
Kernel::TParameterHandler<CMatrix*> m_frequencyAbscissa;
... |
d1a0a2919f1a78a9adeb57fc053f6bdba2aaf3c7e388d0b5b449a203428bd0e6 | C/C++ | 2,980 | 98 | #pragma once
#if defined(TARGET_HAS_ThirdPartyGNEEDaccessAPI)
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include <openvibe/ov_all.h>
#include "../ovasCSettingsHelper.h"
#include "../ovasCSettingsHelperOperators.h"
#include <GDSClientAPI.h>
#include <GDSClientAPI_gNautilus.h>
#include <vector>
#include <s... |
3a501edb99cba2e59a988da459b60fc3f89f38e96afca28798f8cd43cec2bd37 | C/C++ | 2,987 | 75 | //-----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL license
//-----------------------------------------------
//
// BWTCABauerCoxRosone - In-memory version of Illumina's
// BWT construction algorith... |
d5697d313735966bd0b6c1a725784dca8c356e637332f388bf963bf9b9333295 | C/C++ | 2,992 | 103 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// DNACodec - Encoder/decoder for a DNA alphabet
// of A,C,G,T using 2 bits per symbol
//
#if... |
1d53a40b4bbd23645a3ee5f473e3ddb56be441232de84a62d2132bd21903d46c | C/C++ | 3,012 | 87 | #pragma once
#ifdef TARGET_HAS_ThirdPartyOpenViBEPluginsGlobalDefines
#include "../../ovtk_base.h"
#include "ovtkTStreamedMatrixEncoder.h"
namespace OpenViBE {
namespace Toolkit {
template <class T>
class TSpectrumEncoderLocal : public T
{
protected:
Kernel::TParameterHandler<CMatrix*> m_iFrequencyAbscissa;
... |
f5764b831fc6a5c66522f3f1d90b6a21ba9acacbb49b1f85c6165c5f04155da7 | C/C++ | 3,013 | 109 | #ifndef COLOR_H
#define COLOR_H
/*
Szymon Rusinkiewicz
Princeton University
Color.h
Random class for encapsulating colors...
*/
#include "Vec.h"
#include <cmath>
#include <algorithm>
#ifndef M_PI
# define M_PI 3.14159265358979323846
#endif
class Color : public Vec<3,double> {
public:
Color()
... |
4d493f3eeb6a396e660c23a0d2d0c3c9b23f77810d4a7b8e288e5b627c683d2d | C/C++ | 3,025 | 79 | ///-------------------------------------------------------------------------------------------------
///
/// \file ovasCConfigurationBrainmasterDiscovery.h
/// \copyright Copyright (C) 2012, Yann Renard. All rights reserved.
///
/// This library is free software; you can redistribute it and/or
/// modify it under the... |
7476445959ff72ca9cf7b720d1aa9591d8cf557cf1bf54e7ed7791acf402aebb | C/C++ | 3,042 | 97 | /**
* SPDX-FileCopyrightText: Inria <tristan.cabel@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
#pragma once
#include <QtCore>
#include <QtQml>
class OVLogControllerItem;
class OVLogController : public QObject
{
Q_OBJECT
QML_ELEMENT
QML_SINGLETON
Q_PROPERTY(QQmlListProperty<OVLogControll... |
81c833eeacd34262b0d247be0cf50dfa8194507cb817c4ff7b935ae861f7ea72 | C/C++ | 3,046 | 101 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// SQG - Common definitions and functions for parsing
// assembly and sequence graph files
/... |
373736b7173966b2d152be48f843296cc709098ca2e0435430c5e2b12f3deb9c | C/C++ | 3,049 | 96 | #pragma once
#include "../ovIKernelObject.h"
namespace OpenViBE {
namespace Kernel {
/**
* \class IBoxListenerContext
* \author Yann Renard (INRIA/IRISA)
* \date 2007-11-06
* \brief Exectution context for box algorithm descriptors
* \ingroup Group_Kernel
* \ingroup Group_Extend
* \sa Plugins::IBoxAlgorithmDesc... |
cc455aa0c8caf613b8759f3ddc58660576e1def22880df6e7c957dab3702029f | C/C++ | 3,049 | 93 | #pragma once
#include "IReader.h"
namespace EBML {
/**
* \class IReaderHelper
* \author Yann Renard (INRIA/IRISA)
* \date 2006-08-07
* \brief Helper to read basic EBML types
*
* This class may be used by a IReaderCallback instance
* in order to correctly parse simple types defined in the
* EBML description su... |
eb4defdf3f3a5132a937d886eb70e4852d59eacb1cbdebcb5c2c7265b4371c6a | C/C++ | 3,059 | 76 | # pragma once
#include "defines.hpp"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <Eigen/Dense>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CAlgorithmARBurgMethod final : public Toolkit::TAlgorithm<IAlgorithm>
{
public:
void release() override { delete this;... |
3c652f6d01c18a4bdd7e00cf5f96b2f681e2999062c63942a3a0b46a75948025 | C/C++ | 3,064 | 75 | #pragma once
#include "ovas_base.h"
#include "boost/variant.hpp"
#include <deque>
/**
* \brief Interface for acquisition server plugins
*
* Contains an interface to the acquisition server plugins. Any plugin must inherit from this class in order to be able to register with the acquisition server.
*/
namespa... |
509c697290c7fbec9d67ab71a7813d1e2f1c71c2e7ccfabf24cd26d140041a6d | C/C++ | 3,066 | 100 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// SBWT - Uncompressed burrows Wheeler transform
// of a set of sequence reads
// ... |
2969b9e61fa48fff7d3a508dd001d32213b4cd40bba9eb853f3f89cd2e6a04d4 | C/C++ | 3,067 | 100 | #pragma once
#include <set>
//#include <atomic>
#include "SeqLib/BWAIndex.h"
#include "SeqLib/BamHeader.h"
#include "SeqLib/GenomicRegionCollection.h"
#include "SeqLib/ReadFilter.h"
#include "LearnBamParams.h"
#include <ctime>
class SvabaOutputWriter;
class SvabaLogger;
class SvabaOptions;
class SvabaOutputWriter;
c... |
a4280499437835fda23301e373b0ac167f2b22bbb9c1ee3db6c771ddcf93b4e8 | C/C++ | 3,068 | 110 | #pragma once
#include "defines.h"
#include <string>
#include <cstdlib> // fix Unix compatibility
namespace XML {
/**
* @class IXMLNode
* @author Guillaume Serrière (INRIA/Loria)
* @brief Symbolize a node in a XML tree structure.
* @sa XML
*/
class XML_API IXMLNode
{
public:
virtual void release() = 0;
... |
99a94d15ac64165c9c10a62c12b9922c5acc8d576cd2f4a3d828c565ca3ab9d2 | C/C++ | 3,072 | 105 |
/********************
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... |
34ff1cc4a5769fb2a0226ca032d99c49311dc58a9ce67deb5fca542ddd532b35 | C/C++ | 3,076 | 118 | /*****************************************************************************
* SV_SplitRead.h
* (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 Healt... |
ab3dfc5ed001591462234e5f464135f9508e798b59e1a9cab263d16185741140 | C/C++ | 3,087 | 71 | // @copyright notice: Possibly due to dependencies, this box used to be GPL before upgrade to AGPL3
#pragma once
#include "../ovp_defines.h"
#include <toolkit/ovtk_all.h>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CTemporalFilterBoxAlgorithm final : virtual public Toolkit::TBoxAlgor... |
59a271c25eb743dbbce89e3ac7969a3e4df7ed52f40687d0eee918088fd7a9c3 | C/C++ | 3,091 | 144 |
/********************
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... |
c5abf75c0cc227dc5410693c016dc0ded04a84bb4f41a20c4255ce70178ac5d6 | C/C++ | 3,094 | 113 | /* -*- mode: C++; indent-tabs-mode: nil; -*-
*
* This file is a part of LEMON, a generic C++ optimization library.
*
* Copyright (C) 2003-2009
* Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
* (Egervary Research Group on Combinatorial Optimization, EGRES).
*
* Permission to use, modify and distribut... |
a4164fe6e1a7029a8ee6437ab5ccc9137d1a8d7e274a167692a66197ee29b2f1 | C/C++ | 3,096 | 85 | ///-------------------------------------------------------------------------------------------------
///
/// \file ovasCDriverEncephalan.h
/// \brief The CDriverEncephalan allows the acquisition server to acquire data from a Encephalan device.
/// \author Alexey Minin (UrFU)
/// \version 1.0.
/// \date 02/01/2019.
///... |
a54d042cbf4bc2ad31bced040a6fa8ffd518933f5b75bd217008067299301a96 | C/C++ | 3,097 | 122 |
/********************
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... |
a7a66d658ea942855793b21e3aeeb718295c23b2eaf988ddbc9e866e4d47a369 | C/C++ | 3,099 | 87 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
cb20a46fef667b3bf602f7c8563cac415c7f3d3569893e75229c6c27605021af | C/C++ | 3,100 | 95 | // @copyright notice: Possibly due to dependencies, this box used to be GPL before upgrade to AGPL3
#pragma once
#if defined TARGET_HAS_ThirdPartyITPP
#include "../ovp_defines.h"
#include <toolkit/ovtk_all.h>
#include <map>
#include <string>
#ifndef CString2Boolean
#define CString2Boolean(string) (strcmp(string,... |
680e622db98d9f85e0ed1c7719204b92037fd112a3848c8f965af514e085942f | C/C++ | 3,115 | 89 | #pragma once
#include "defines.hpp"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
namespace OpenViBE {
namespace Plugins {
namespace SignalProcessing {
class CBoxAlgorithmERSPAverage final : virtual public Toolkit::TBoxAlgorithm<IBoxAlgorithm>
{
public:
void release() override { delete this; }
b... |
7ecb760f618816c39b673fc813cf6c460be2555d7de5d3eac7fcf86b5cd67ecf | C/C++ | 3,115 | 112 |
/********************
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... |
f5b5dbf84c83eead0f7b59c5763796d94a53013e573e2769b36078750db0b098 | C/C++ | 3,121 | 113 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL license
//-----------------------------------------------
//
// BWTInterval - Data structures for holding and manipulating
// the coordinates in a... |
d6b0dbfc60c2ef91f5c55058c2fc07465caa1a775c8d3016ba23a98bbb2d0a39 | C/C++ | 3,144 | 63 | #pragma once
// Extract every read pair from a BAM where either mate's SEQ matches any of
// a small set of query sequences (or their reverse complements). Drop-in
// replacement for scripts/extract_pairs_by_seq.sh, but BAM-native end-to-end
// — no SAM text round-trip, no gratuitous final sort.
//
// Algorithm (two p... |
5e6942efe35e16ad2422fbf9a07de1750d8f28f564aa98da23aec36d877a9dad | C/C++ | 3,151 | 97 | //===--- DemangleConfig.h ---------------------------------------*- C++ -*-===//
//
// 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
//
//===---------------------------... |
62966a894ad2fcd594238086bb8be8abbdcdc5de811843f415b02dd4ca815990 | C/C++ | 3,160 | 91 | /**-------------------------------------------------------------------------------------------------
* \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... |
dc0881b71ee2fe14cb76a2d961518eed85953bb8bef02062ff54f422037da11d | C/C++ | 3,177 | 107 | /*****************************************************************************
* SV_PairReader.h
* (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 Heal... |
7dc3e3a5efbfa98b239a77062e7f4ca7ce401dd28ce628727d9471a8ef4c7b5c | C/C++ | 3,191 | 58 | #pragma once
#include "ovkTKernelObject.h"
#include <map>
#include <set>
#include <vector>
#include <mutex>
namespace OpenViBE {
namespace Kernel {
class CTypeManager final : public TKernelObject<ITypeManager>
{
public:
explicit CTypeManager(const IKernelContext& ctx);
CIdentifier getNextTypeIdentifier(cons... |
819ce800355b67b9dfede14749e4d3bea0f6679d04e0eace8c1f695397c2a1ac | C/C++ | 3,193 | 138 | ///----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// GapFillProcess - Fill in gaps in a scaffold
//
#ifndef GAPFILL_PROCESS_H
#define GAPFILL_P... |
1959b53ced7e5d6b147df10fef038d36cfa9ea16128178745432acff9bcdb8bd | C/C++ | 3,197 | 85 | /*
* The only purpose of this class is to hide the gtec API
* data types from the ov driver header. An approach resembling
* this is sometimes called a 'd-pointer'.
*
* Previous situation:
*
* gUsbamp ov driver header depends on gtec gUSBAmp API types
* gMobilab ov driver header depends on gtec gMobilab API ty... |
31adb9ea7e7ee04d4b99fd50983600186f834cb0861c8de3467545992187d244 | C/C++ | 3,198 | 116 |
/********************
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... |
a7e6a5086e2683d6476177083a5eb40c2119197dc6042997cb715876f7b827b7 | C/C++ | 3,205 | 75 | #pragma once
#include "../ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <socket/IConnectionClient.h>
namespace OpenViBE {
namespace Plugins {
namespace Acquisition {
class CBoxAlgorithmAcquisitionClientLegacy final : public Toolkit::TBoxAlgorithm<IBoxAlgorithm>
{
public:
void... |
6356649233e7383ffb1c95a6e18b2aabbe313eb38525a70d6bb933c92b070cff | C/C++ | 3,213 | 131 | /* -*- mode: C++; indent-tabs-mode: nil; -*-
*
* This file is a part of LEMON, a generic C++ optimization library.
*
* Copyright (C) 2003-2009
* Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
* (Egervary Research Group on Combinatorial Optimization, EGRES).
*
* Permission to use, modify and distribut... |
5a5048e65f0c9e1ff98bd74f0b5e5a9a556353310dd34fb8faeabca0b3b9f597 | C/C++ | 3,214 | 105 | // ***************************************************************************
// SamHeaderValidator.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 6 October 2011 (DB)
// ----------------------... |
e5a2f3e0fd0761c596e29916915b15a00ad0f06eaf030620dda9c9a9ec247a8b | C/C++ | 3,215 | 99 | // Copyright [1999-2017] EMBL-European Bioinformatics Institute
//
// 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
//
// Unless required b... |
88f903093eb528b20477be23718ed9ed7a856deeda2a077e971e5c46e696a643 | C/C++ | 3,216 | 128 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// SeqCoord - A data structure holding the coordinate
// of a substring of a sequence which c... |
bf05e5e3ace7e22999f52e0d558b917f570dc61297163439d8573b301d01d6cc | C/C++ | 3,218 | 67 | #pragma once
#include "../../ovp_defines.h"
#include "ovpCEBMLBaseEncoder.h"
namespace OpenViBE {
namespace Plugins {
namespace StreamCodecs {
class CAcquisitionEncoder final : public CEBMLBaseEncoder
{
public:
void release() override { delete this; }
bool initialize() override;
bool uninitialize() overri... |
27cf2a8ed7dd0933b414dcc66d37d546a250134d52cdbaf72f438d1b225b63d9 | C/C++ | 3,230 | 103 | // ***************************************************************************
// TcpSocketEngine_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 December 2011 (DB)
// ----------------------... |
0ed043382eae7d139f4069ebf1aa5b8871143a4a61721f213a8933316137da98 | C/C++ | 3,237 | 74 | #pragma once
#if defined TARGET_HAS_ThirdPartyMatlab
#include "ovp_defines.h"
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <engine.h>
namespace OpenViBE {
namespace Plugins {
namespace Matlab {
class CMatlabHelper
{
public:
CMatlabHelper(Kernel::ILogManager& /*logManager*/, Kernel::CError... |
052524a33154c710d4b8b595ad6a8e4665600ccd32002618f2c7a1de8e6a2a3b | C/C++ | 3,243 | 90 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// CompleteOverlapSet - A collection of all
// valid overlaps for a given vertex. This is
// ... |
001c42037c602b24dc6a7e7fc53a373e757a14aa3348cacce070b4bcc477d953 | C/C++ | 3,244 | 115 | /*****************************************************************************
* SV_Pair.h
* (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 Gen... |
7db3265d3f16c2de7a67aabc9909d8430a2361d0d643ded3c8ffe7811e0d007d | C/C++ | 3,244 | 75 | #pragma once
/**
* SPDX-FileCopyrightText: Inria <florent.leray@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
/**
* @file DriftCalculator.h
* @brief Header file for the DriftCalculator class.
*
* This file declares the `DriftCalculator` class, which is responsible for
* calculating various latency and ... |
d07c99da1cf842bb46f1b9f3c9f9619aa911295eedd8036ee605a721d02fb386 | C/C++ | 3,251 | 87 | #pragma once
#include <openvibe/ov_all.h>
#include <toolkit/ovtk_all.h>
#include <vector>
#include <map>
#define OVP_ClassId_BoxAlgorithm_OutlierRemovalDesc OpenViBE::CIdentifier(0x11DA1C24, 0x4C7A74C0)
#define OVP_ClassId_BoxAlgorithm_OutlierRemoval OpenViBE::CIdentifier(0x09E41B92, 0x4291B612)
namespa... |
4fd420d23fa850d11d85ae2f859b144214e59ca910349d5d50ed88248acd5547 | C/C++ | 3,258 | 110 | #pragma once
#if defined TARGET_HAS_ThirdPartyEmotivAPI
#include "ovasIDriver.h"
#include "../ovasCHeader.h"
#include "../ovasCSettingsHelper.h"
#include "../ovasCSettingsHelperOperators.h"
#include <openvibe/ov_all.h>
#if defined(TARGET_HAS_ThirdPartyEmotivResearchAPI3x)
#include "IEmoStateDLL.h"
#include "Iedk.h... |
8bd41a0b2ec4c38bb3d1530cb9a3f63512b0e3e5b191b9ebae5c0dacebcfb2f7 | C/C++ | 3,270 | 113 | #pragma once
#include <ctime>
#include <sstream>
#include <unordered_map>
#include <map>
#include <chrono>
#include <tuple>
#include "SvabaLogger.h"
#include "SeqLib/BamReader.h"
#include "SeqLib/BamWriter.h"
#include "SeqLib/RefGenome.h"
#include "SeqLib/GenomicRegion.h"
typedef std::pair<size_t, size_t> CountPair... |
9bd2ffaf6cba086b77ba58fef88d2b88076e2664caab13390e62f57712976791 | C/C++ | 3,270 | 83 | ///-------------------------------------------------------------------------------------------------
///
/// \file CBoxAlgorithmLevelMeasure.hpp
/// \brief Classes for the Box Level measure.
/// \author Yann Renard (INRIA/IRISA).
/// \version 1.0.
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free so... |
71124dc0d849c633a6697aeea1575bb588d524ef21996e71e445a6d4e3cdee65 | C/C++ | 3,274 | 89 | #pragma once
#include "../ovIKernelObject.h"
namespace OpenViBE {
namespace Plugins {
class IPluginObjectDesc;
} // namespace Plugins
namespace Kernel {
/**
* \class IPluginModule
* \brief Plugin module
* \author Yann Renard (INRIA/IRISA)
* \date 2006-09-26
* \ingroup Group_Plugins
* \ingroup Group_Kernel
*
... |
17eb4db64a84a6e9170f43b5cce06fc24c4571da06a1db1c5edcfcfd564c2095 | C/C++ | 3,282 | 107 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// BWT4Codec - Encoder/decoder for a BWT
// string over the alphabet $ACGT using 4
// bits pe... |
81051f493845dd2e17d249a5dfd7507167e1dc4ac52c495d91f894d4ba4111f6 | C/C++ | 3,287 | 89 | ///-------------------------------------------------------------------------------------------------
///
/// \file Processor.h
/// \author J. T. Lindgren / Inria.
/// \copyright Copyright (C) 2022 Inria
///
/// This program is free software: you can redistribute it and/or modify
/// it under the terms of the GNU Affer... |
7973afc3363ca61ba9aae216dc72d01c32bb0910fba174d1a8a4b18a2baa4eee | C/C++ | 3,292 | 90 | //-----------------------------------------------
// 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 ... |
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