sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4c319814af973c2f6bc52b44308f4bbb9a443e514c659a7353ad294a3186a7fb | C/C++ | 197 | 5 | #pragma once
#include "./include/k2c_tensor_include.h"
void emmodel_rnadna(k2c_tensor* input1_input, k2c_tensor* l7_output);
void emmodel_rnadna_initialize();
void emmodel_rnadna_terminate();
|
bb627f728156afddc5df1410c84efb9bcb04a26e74e06bf65289a2503bd7bef1 | C/C++ | 203 | 5 | #pragma once
#include "./include/k2c_tensor_include.h"
void xraymodel_rnadna(k2c_tensor* input1_input, k2c_tensor* l7_output);
void xraymodel_rnadna_initialize();
void xraymodel_rnadna_terminate();
|
988ebd67463f07fd2c2b50b5460eea2040b7d8b8a8dbb38e361c4438047d420d | C/C++ | 204 | 11 | #ifndef __ERR_H__
#define __ERR_H__
#include <stdio.h>
#include <stdarg.h>
void my_err(const char *format, ...);
void my_warn(const char *format, ...);
void my_verbose(const char *format, ...);
#endif
|
426476ed91e7048cb01b97957c28b11f48e5ba32481ca75644d132719a6e20c8 | C/C++ | 216 | 8 | #ifndef SNOWMAN_SPLITCOUNTER_H__
#define SNOWMAN_SPLITCOUNTER_H__
void runSplitCounter(int argc,char** argv);
void parseSplitCounterOptions(int argc, char** argv);
void runSplitFasta(int argc, char** argv);
#endif
|
ee2b798a9c8d651c2cee29d73fb54006891c74209ed050dcc106f8d7a985173e | C/C++ | 225 | 13 | #pragma once
#if defined(OS_WINDOWS)
#include <Windows.h>
#include <GL/GL.h>
#endif
#if defined(OS_WEB)
#define GLFW_INCLUDE_ES3
#include <GLES3/gl3.h>
#else
#include <imgui_impl_opengl3_loader.h>
#endif |
f57be9e04be82bff27c48dd697e0818d9873e06a3ac34fc0bab7d7adcbce45c3 | C/C++ | 232 | 10 | #include <stdlib.h>
using namespace std;
extern "C" {
// Dynamic programming algorithm for the 1d fused lasso problem
// (Ryan's implementation of Nick Johnson's algorithm)
void dp(int n, double *y, double lam, double *beta);
}
|
a5e0931fc4c78eeef45247b1ee491554949ba661d4efa88412371e25cf231dba | C/C++ | 247 | 7 | #include <gsl/gsl_rng.h>
data *newData(int nTax, int nParts);
void freeData(data *theData);
void dumpData(data *theData);
//PyObject *rell(int nBoots, rellStuff *rStuff);
void bootstrapData(data *reference, data *toFill, const gsl_rng *gsl_rng);
|
41435a903922c348e09773e096a63f0ebe642fdea7f4178b1337a48612957f5a | C/C++ | 260 | 12 | #include <string>
#include <iostream>
#include <map>
#include <fstream>
#include "DataSet.h"
#include "TmpDir.h"
class ValidateTabFile {
public:
std::string concatenateMultiplePINs(std::vector<std::basic_string<char>> fileNames);
}; |
3566387731655777a2814fcbf8cbd9f2d21d042530432b857d591144cc0a8784 | C/C++ | 264 | 12 | #ifndef __gettimeofday_h
#define __gettimeofday_h
#include <time.h>
struct timezone {
int tz_minuteswest; /* minutes W of Greenwich */
int tz_dsttime; /* type of dst correction */
};
int gettimeofday(struct timeval *tv, struct timezone *tz);
#endif
|
69f62b503517c403321c2b492daf9b690370baedc60fcfda58c071459f2aba2c | C/C++ | 270 | 1 | void logDetFillFxy(int *nUnambig, int *nAmbig, int *nDoubleGap, char *seq, int sNum1, int sNum2, int *refUnambigCountMatrix, int *refAmbigCountMatrix, int *allSymbolNums, int nTax, int nChar, int dim, int bigDim, double *normUnambig, double *bigFxy, int *equatesArray);
|
611e6b9bdd6e5a4dfc60b46e462afc7c2dc43769f59190b35058b5b67d8901af | C/C++ | 275 | 13 | #ifndef TREFIDE_H
#define TREFIDE_H
#include "../src/utils.h"
#include "../src/ipm.h"
#include "../src/wpdas.h"
#include "../src/line_search.h"
#include "../src/admm.h"
#include "../src/welch.h"
#include "../src/pmd.h"
#include "../src/decimation.h"
#endif /* TREFIDE_H */
|
afb4dec1c7c781a54ba85aa221124f42ed5d2c08e1ab29b16a17e1a02e942b1d | C/C++ | 288 | 6 | #pragma once
// Re-run LOD / PASS filtering against an existing bps.txt.gz. See refilter.cpp
// for option parsing and the supported input layouts (41-col legacy and
// 51-col SvABA2.0). Invoked from svaba.cpp as `svaba refilter ...`.
void runRefilterBreakpoints(int argc, char** argv);
|
174704fed7e9409c8ceccc9b62e703498d2f91270aa212dc2745e89c79f133e7 | C/C++ | 300 | 17 | #pragma once
#include <openvibe/ov_all.h>
namespace OpenViBE {
namespace Kernel {
class CBuffer final : public CMemoryBuffer
{
public:
CBuffer() { }
explicit CBuffer(const CBuffer& buffer);
CBuffer& operator=(const CBuffer& buffer);
};
} // namespace Kernel
} // namespace OpenViBE
|
e07c9120643b4e7ee24d560ef117c5134abf5764a5a65e057a0471a8051b2057 | C/C++ | 306 | 19 | /* prevent double include */
#pragma once
#if defined (__BORLANDC__)
#define COMPILER_BORLAND
#elif defined (_MSC_VER)
#define COMPILER_MSVC
#elif defined (__CYGWIN32__)
#define COMPILER_CYGWIN
#elif defined (__MINGW32__)
#define COMPILER_MINGW
#elif defined (__LCC__)
#define COMPILER_LCC
#endif
|
180b80126f5cde743496d74e49fe536f89b41f361bda787c7267f650c96a54a9 | C/C++ | 328 | 24 | #ifndef SNOWMAN_SIMTRAINER_WALKER_H__
#define SNOWMAN_SIMTRAINER_WALKER_H__
#include "SeqLib/BamReader.h"
#include "BamStats.h"
class SimTrainerWalker : public SeqLib::BamReader {
public:
SimTrainerWalker() {}
void train();
std::string printBamStats() const;
private:
BamStats m_bam_stats;
};
... |
3c1d2d1afcb622dba8e1019d0a3fa77d2b457d87777151dad275949364e77bac | C/C++ | 330 | 14 | #pragma once
#include "IConnection.h"
namespace Socket {
class Socket_API IConnectionClient : public IConnection
{
public:
virtual bool connect(const char* serverName, const size_t serverPort, const size_t timeOut = 0xffffffff) = 0;
};
extern Socket_API IConnectionClient* createConnectionClient();
} // namespa... |
98e2f585037d0a683ffb1df4b0e205b6894388547f79cb96d905c4eb651cf7b6 | C/C++ | 330 | 8 | /* src/nrnoc/nrnconfigargs.h. Generated from nrnconfigargs.h.in by configure. */
#ifndef nrnconfigargs_h
#define nrnconfigargs_h
/* define to the args passed to configure */
#define NRN_CONFIG_ARGS " '--prefix' '/raid/zyc/code_for_dhs_paper/install' '--without-iv' '--with-paranrn' '--with-nrnpython=/usr/bin/python3'... |
207ece75bdb7c1b3a929a7a8e178388c4c2fdd3ce8d31ce183be25f5a7dbf216 | C/C++ | 337 | 6 | #pragma once
// Boxes
//---------------------------------------------------------------------------------------------------
#define OVP_ClassId_BoxAlgorithm_Python3 OpenViBE::CIdentifier(0x5DC4F669, 0xD3FD4D63)
#define OVP_ClassId_BoxAlgorithm_Python3Desc OpenViBE::CIdentifier(0x404B6... |
dfe4f20297b8025c5b359c5dd36c7cf684d6748c2d1747dc500bb3140cb9145c | C/C++ | 337 | 6 | #pragma once
// Boxes
//---------------------------------------------------------------------------------------------------
#define OVP_ClassId_BoxAlgorithm_Python2 OpenViBE::CIdentifier(0x5DC4F669, 0xD3FD4D64)
#define OVP_ClassId_BoxAlgorithm_Python2Desc OpenViBE::CIdentifier(0x404B6... |
62112d846c9366fea6d4c15ed52d7fe4e1c7c6ff30f86771e2fecf8194be4cf0 | C/C++ | 346 | 17 | #pragma once
#include "ovtkIVector.h"
namespace OpenViBE {
namespace Toolkit {
class OVTK_API IFeatureVector : public IVector
{
public:
virtual double getLabel() const = 0;
virtual bool setLabel(const double label) = 0;
_IsDerivedFromClass_(IVector, OVTK_ClassId_FeatureVector)
};
} // namespace Toolkit... |
954d0a233089bd425d4670070af26585e8415e565348ee9b58cf977685f3c79b | C/C++ | 349 | 14 |
#ifndef PROXTV_H
#define PROXTV_H
/* Comparison tolerance */
#define EPSILON 1e-10
#define IS_ZERO(x) (x < EPSILON & x > -EPSILON)
#define IS_POSITIVE(x) (x > EPSILON)
#define IS_NEGATIVE(x) (x < -EPSILON)
int tautString_TV1(double *y,double lambda,double *x,int n);
int tautString_TV1_Weighted(double *y,double *lamb... |
80be38e15479d44955548fc39810a1172abe6380e6d1d1dff5c435332660b8f8 | C/C++ | 352 | 10 | #include "parameterBoolObject.h"
#include "parameterDoubleObject.h"
#include "parameterIntObject.h"
#include "parameterListIntObject.h"
#include "parameterListStringObject.h"
#include "parameterMultiSelectObject.h"
#include "parameterObject.h"
#include "parameterStringObject.h"
#include "parameterStringVectorObject.h"
... |
1ee2c407bc17ff99da88b32c16e1afb110888b7ac954950daad000a2c5aa54c7 | C/C++ | 358 | 19 | #pragma once
#include "wtmath.h"
#include "hsfft.h"
#ifdef __cplusplus
extern "C" {
#endif
void nsfft_exec(fft_object obj, fft_data* inp, fft_data* oup, double lb, double ub,
double* w);// lb -lower bound, ub - upper bound, w - time or frequency grid (Size N)
double cwt_gamma(double x);
int nint(do... |
2859e5f88f83f8c2035ac565be26c0923db8847e9c34db6a161a08637a82d701 | C/C++ | 359 | 22 | #pragma once
#include <openvibe/ov_all.h>
namespace OpenViBE {
namespace Tracker {
/**
* \class TestClass
* \brief Class to try out stuff in the Tracker
* \author J. T. Lindgren
*
*/
class TestClass
{
public:
explicit TestClass(Kernel::IKernelContext& ctx);
Kernel::IKernelContext& m_Ctx;
};
} // name... |
f9d0d0e37a82d9df7b77640a8763490cc985264438e9587dac1e506b2c316242 | C/C++ | 359 | 25 | #pragma once
#include <ov_common_defines.h>
#include <openvibe/parameters/parameterTraits.h>
#include <list>
namespace OpenViBE {
namespace Services {
class IService
{
public:
virtual ~IService() = default;
virtual std::list<Parameters::ParameterTraits*> parameters() = 0;
};
extern "C"
{
OV_API_Export... |
6cef4cbd908bb856180a9aa4416f174d3e93d3a8c0f2f3e71fb4d93f27d38834 | C/C++ | 364 | 16 | #pragma once
/**
* @file drift.h
* @author Florent LERAY
*
*/
#include <cstdint> // for uint64_t
struct drift_st
{
int64_t startLatency; ///< Start latency in nanoseconds.
int64_t globalDrift; ///< Global drift in nanoseconds.
int64_t instantDrift; ///< Instant drift in nanoseconds.
int64_t endL... |
5151d0fed4fda93d414f77daa555f5aaff4d8472f84098c723acf0ce01eb11ea | C/C++ | 370 | 17 | /**
* SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
#pragma once
#include <QObject>
#include <QUrl>
class UpdateHandler : public QObject {
Q_OBJECT
public:
explicit UpdateHandler(QObject *parent = nullptr): QObject(parent) {};
Q_INVOKABLE void pr... |
0ce76b82c793b18ff31cff0403849ba99c1f17ed8564935421948a4152d670cd | C/C++ | 386 | 15 | #pragma once
#include "../plugins/ovIBoxAlgorithmDesc.h"
namespace OpenViBE {
namespace Metabox {
class OV_API IMetaboxObjectDesc : virtual public Plugins::IBoxAlgorithmDesc
{
public:
virtual CString getMetaboxDescriptor() const = 0;
_IsDerivedFromClass_(Plugins::IBoxAlgorithmDesc, OV_ClassId_Metaboxes_Metab... |
8a642990b139a9c868a080eb0683bd6c557e9f6ceaf174852ef9b1289ff11415 | C/C++ | 387 | 7 | // PGF got these from JohnH, who got them from Yang. Not GPL'd, but pretty promiscuous nonetheless.
int DiscreteGamma (double freqK[], double rK[], double alfa, double beta, int K, int median);
double PointChi2 (double prob, double v);
double IncompleteGamma (double x, double alpha, double LnGamma_alpha);
do... |
f4d84913f8312e36903f8cdf86567d7f903c5c25bfc49b311bdc7efc829e08ac | C/C++ | 388 | 21 | /*
* HID driver for OpenViBE
*
* \authors (NeuroServo, NeuroTechX)
* \developer (Innocent Aguié)
* \date Wed Nov 23 00:24:00 2016
*
*/
#pragma once
#if defined TARGET_OS_Windows
#if defined TARGET_HAS_ThirdPartyNeuroServo
#include "HidDeviceNotifier.h"
// Register Device Notification method
int registerNotification... |
3be970bcca3f49d71d990f042df31e4da2b912a375687771544c7dfaf89ef33f | C/C++ | 392 | 21 | #ifndef EXTERN_H
#define EXTERN_H
#include "buffer.h"
extern pthread_mutex_t mutexstatus;
extern int tcpserverStatus;
extern pthread_mutex_t mutexthreadcount;
extern int threadcount;
extern pthread_mutex_t mutexsocketcount;
extern int socketcount;
extern pthread_mutex_t mutexthreadcount;
extern int threadcount;
e... |
50d15bcb23e344b0b7457e142a700a82670083e20deda4d806794bd181b253a3 | C/C++ | 409 | 16 | #pragma once
#include "cwtmath.h"
#ifdef __cplusplus
extern "C" {
#endif
void meyer(const int N, const double lb, const double ub, double* phi, double* psi, double* tgrid);
void gauss(int N, int p, double lb, double ub, double* psi, double* t);
void mexhat(int N, double lb, double ub, double* psi, double* t);
void m... |
6a7285f0bd2f76f36bd233c1524f8c1e3d9d394334535cae4309fe18c760a12b | C/C++ | 409 | 16 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================
*/
#pragma once
#include <string>
namespace coreneuron {
/... |
0accf3f4d33f71562fa60a66cfed119ea85f062d7944a98ddf95c9907bfb19cd | C/C++ | 436 | 24 | #pragma once
#include <vector>
namespace SvabaModels {
double LogLikelihood(double ref,
double alt,
double f,
double e_fwd,
double e_back);
double SomaticLOD(double aN,
double dN,
double aT,
double dT,
double e_fwd,
double e_rev);
double... |
f68ca758c98fabf04dd1e1877947e57b887bff8637eb592215f12bc79cd47841 | C/C++ | 450 | 28 | #ifndef IMAGEWIDGET_H
#define IMAGEWIDGET_H
#include <QWidget>
#include <QPainter>
#include <QPaintEvent>
#include <QPixmap>
class ImageWidget : public QWidget
{
Q_OBJECT
public:
explicit ImageWidget(QWidget *parent = 0);
void paintEvent(QPaintEvent *event);
void showTemplateImage(QPixmap pixmap);
... |
48925a47c63afd6b233abf26d2f1a0c543e5baac9fea1a93fc8ed9515018e39a | C/C++ | 458 | 13 | #pragma once
#include "ovviz_base.h"
namespace OpenViBE {
namespace VisualizationToolkit {
namespace ColorGradient {
OVVIZ_API bool parse(CMatrix& colorGradient, const CString& string);
OVVIZ_API bool format(CString& string, const CMatrix& colorGradient);
OVVIZ_API bool interpolate(CMatrix& interpolatedColorGradient,... |
14ef22699496a817c0e989faf8a3450b20d5c02534e150876854fb683fabb55b | C/C++ | 460 | 18 | #ifndef STRINGUTILITIES_H
#define STRINGUTILITIES_H
#include <cctype>
#include <string>
/****************************************************
// isInteger(s): Tests if string s is a valid integer
*****************************************************/
inline bool isInteger(const std::string& s) {
int len = s.lengt... |
86d4d144422f44cf9f2f6dbff2536ac249a7a347d95357f77d5e016712355a56 | C/C++ | 470 | 25 | #ifndef __SNP_H__
#define __SNP_H__
/* maximum sequence length of alleles (longer are truncated in snp_tab) */
#define SNP_MAX_ALLELE 100
/* maximum length of chromosome name */
/* #define SNP_MAX_CHROM 32 */
/* maximum length of SNP identifier */
#define SNP_MAX_NAME 255
#define SNP_MAX_CHROM 255
typedef struct {... |
3b57ac225ca5f11c0ed4d30d7736ce5b399753395e877c868313559d5fba3f78 | C/C++ | 479 | 25 | #pragma once
#include "IWriter.h"
namespace EBML {
class EBML_API CWriter final : public IWriter
{
public:
explicit CWriter(IWriterCallback& callback);
~CWriter() override;
bool openChild(const CIdentifier& identifier) override;
bool setChildData(const void* buffer, const size_t size) override;
b... |
6ff7499705476b2d3108f4467c955644df38b6c5c4ba23a8ce4dfc89ed2063fb | C/C++ | 485 | 25 | #pragma once
#include "IReader.h"
namespace EBML {
class EBML_API CReader final : public IReader
{
public:
explicit CReader(IReaderCallback& callback);
~CReader() override;
bool processData(const void* buffer, const size_t size) override;
CIdentifier getCurrentNodeID() const override;
size_t getC... |
4a54a81d69c16adc1c71de8d3abfc16730a2ccb8491d5eea7b101ee41908b7a0 | C/C++ | 487 | 23 | #pragma once
#include <QtWidgets/QMainWindow>
#include "ui_QtGuiApplication4.h"
#include <QtWidgets>
#include <QtCharts/QChartView>
#include <QtCharts/QLineSeries>
#include <QtCharts/QVXYModelMapper>
class QtGuiApplication4 : public QMainWindow
{
Q_OBJECT
public:
QtGuiApplication4(QWidget *parent = Q_NULLPTR);
QPu... |
432ec77f9046f72a9d43b24f84225d0e2624750b9bbd8ab0674d6b9ee3ac345a | C/C++ | 488 | 19 | #pragma once
#include "ovkTKernelObject.h"
#include "ovkTConfigurable.h"
namespace OpenViBE {
namespace Kernel {
typedef TBaseConfigurable<TKernelObject<IConfigurable>> configurable;
class CConfigurable final : public configurable
{
public:
explicit CConfigurable(const IKernelContext& ctx) : TBaseConfigurable<T... |
08cf284ccccc3ba8247d5df8dd2d4195d418ad8a0ac6439cf2d0b5b820ec790d | C/C++ | 491 | 8 | #pragma once
void Cal_fi_Integ_SOR(double a, double E, double se, double si, double Cm, double Vm[Nthe + 1], double Vm_pr[Nthe + 1], double g1, double Vrest,
double dr, double dte, double dt, double Ip[Nthe + 1], double fi_o[Nr_o + 1][Nthe + 1], double fi_i[Nr_i + 1][Nthe + 1]);
void Cal_dA_new(double a, double d... |
ca556393ad4320d3c7c1abfefcf5fdb4430c7534f5b40434d66d7b1b3bf61a65 | C/C++ | 500 | 13 | //-----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL license
//-----------------------------------------------
//
// QuickBWT - Construct a simple BWT for a short input string
//
#include "BWT.h"
//... |
5fafb965cdc9446fa25825f6a394b58f2cb2e2bb97ac51eddc98497ac9fb2505 | C/C++ | 503 | 22 | #define LEMON_VERSION "1.3.1"
#define LEMON_HAVE_LONG_LONG 1
/* #undef LEMON_HAVE_LP */
/* #undef LEMON_HAVE_MIP */
/* #undef LEMON_HAVE_GLPK */
/* #undef LEMON_HAVE_CPLEX */
/* #undef LEMON_HAVE_SOPLEX */
/* #undef LEMON_HAVE_CLP */
/* #undef LEMON_HAVE_CBC */
#define _LEMON_CPLEX 1
#define _LEMON_CLP 2
#define _LEM... |
442d7db17ce8c0d9a9b8fd9ad72cd5db9432fabe4b67be5171d5adc3b599da3c | C/C++ | 505 | 24 | #pragma once
#include "defines.h"
#include <cmath>
#include <cstdlib> // fix Unix compatibility
namespace System {
class System_API Math
{
public:
static bool initializeRandomMachine(size_t randomSeed);
static size_t randomI();
// returns a value in [0,upperLimit( -- i.e. upperLimit not included in ra... |
e4f9df1267e64a73be411039a9454a4e9bcf7ecd5d15bbe7e69872fb16fb6ae7 | C/C++ | 506 | 23 | #pragma once
#include <AbstractWriterBuilder.h>
#include <memory>
class NetWriterPrivate;
class NetWriter : public AbstractWriter
{
public:
NetWriter(const std::string& writerName);
virtual ~NetWriter();
std::pair<size_t, void*> sendCallback(void* data, uint64_t clientId);
protected:
virtual size_t... |
0494866061429c06e112d634948d2c9e7d3d3b1be2100f125332578065346fb9 | C/C++ | 512 | 33 | #ifndef __IMPUTE_H__
#define __IMPUTE_H__
#include <zlib.h>
#include "snp.h"
#define IMPUTE_FIX_HEADER 5
typedef struct {
int n_sample;
/* used for reading lines */
size_t buf_size;
char *buf;
/* could store lots of header info here */
} ImputeInfo;
ImputeInfo *impute_info_new();
void impute_inf... |
656be0374d36f6fc95ccf51277235e8eb1f43d602392931281cf21c414a4fc26 | C/C++ | 517 | 24 | #include "Util.h"
#include "api/BamReader.h"
#include "api/BamWriter.h"
#include <vector>
class AlignedContig {
public:
AlignedContig(const BamTools::BamAlignment align) { m_align.push_back(align); }
~AlignedContig() {}
void addAlignement(const BamTools::BamAlignment align) {
m_align.push_back(alig... |
3d2209c609eea22dad365f14cfe17e65de31f8fd3554af49e1cefe02ea350ca0 | C/C++ | 527 | 18 | /**
* SPDX-FileCopyrightText: Inria <tristan.cabel@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
#include "parameterBool.h"
#include "parameterColor.h"
#include "parameterColorGradient.h"
#include "parameterDouble.h"
#include "parameterFactory.h"
#include "parameterInt.h"
#include "parameterListInt.h"
#includ... |
0eef3048aedd7c0570281a8cfb2c5babd6393c4d802f0ebbe7510eedd5751da1 | C/C++ | 528 | 15 |
#pragma once
//___________________________________________________________________//
// //
// Global defines //
//___________________________________________________________________//
// ... |
2ff670ebfd16e8572ea0c7ea7a6fdc9ca0fdc3ff7cb85e4453ab25fdee3d61f1 | C/C++ | 529 | 26 | #ifndef __CHR_H__
#define __CHR_H__
typedef struct {
int id;
char *name;
long len;
char *assembly;
} Chromosome;
Chromosome *chrom_guess_from_string(char *str,
Chromosome *chroms,
int n_chrom);
Chromosome *chrom_guess_from_file(char *filename,
Chromosome *chroms,
int n_chrom);
void... |
a9c40a048e57a5d43f99e49ab4b5852486c9990947769b5fb994ad87e0df4475 | C/C++ | 532 | 23 |
#ifndef __MEMUTIL_H__
#define __MEMUTIL_H__
#include <stdlib.h>
#include "err.h"
void *my_malloc(size_t n_bytes);
void *my_malloc0(size_t n_bytes);
void *my_realloc(void *ptr, size_t n_bytes);
void __MY_FREE(void *ptr, const char *filename, const int line_num);
#define my_new(struct_type, n) \
((struct_type *)m... |
48f42aebbfd84916533ac4cc57f684d367e3686db693e1bacbb7a3ad76417e61 | C/C++ | 535 | 34 | /*
* real.h
*
* Created on: Apr 20, 2013
* Author: Rafat Hussain
*/
#pragma once
#include "hsfft.h"
#ifdef __cplusplus
extern "C" {
#endif
typedef struct fft_real_set* fft_real_object;
fft_real_object fft_real_init(int N, int sgn);
struct fft_real_set
{
fft_object cobj;
fft_data twiddle2[1];
};... |
9c0b1ae9bcb19232950b141e7657697201e5c49b012322caeef626438d45c7fd | C/C++ | 545 | 20 | #pragma once
#include <openvibe/ov_all.h>
namespace OpenViBE {
namespace Kernel {
class CScenarioSettingKeywordParserCallback final : public IConfigurationKeywordExpandCallback
{
public:
explicit CScenarioSettingKeywordParserCallback(const IScenario& scenario)
: m_rScenario(scenario) {}
~CScenarioSet... |
c3507c185f5ccb7c9fae6f4ed1fe0ad63b655f125e6e3f30c9e4999c035467d2 | C/C++ | 553 | 28 | #ifndef SNOWMAN_READ_TO_CONTIG_ALIGNER_H__
#define SNOWMAN_READ_TO_CONTIG_ALIGNER_H__
#include "SnowTools/AlignedContig.h"
#include "SnowTools/BamRead.h"
#include "SnowTools/BWAWrapper.h"
class ReadToContigAligner {
public:
ReadToContigAligner() {}
ReadToContigAligner(const SnowTools::USeqVector& usv, BamRea... |
6459f9d411780225a59137d4e7212a517f83cc03a411c30672f558c33780bd83 | C/C++ | 554 | 18 | void cpREVRMatrix(double **r);
void d78RMatrix(double **r);
void jttRMatrix(double **r);
void mtREV24RMatrix(double **r);
void mtmamRMatrix(double **r);
void wagRMatrix(double **r);
void rtRevRMatrix(double **r);
void tmjtt94RMatrix(double **r);
void tmlg99RMatrix(double **r);
void lgRMatrix(double **r);
void blosum62R... |
8108ef229950bbda94bd205f3c736c7dd2154034ac05ba549ce886279c38c9a3 | C/C++ | 558 | 23 | #pragma once
#include "wavefunc.h"
#ifdef __cplusplus
extern "C" {
#endif
int cwavelet(double* y, int N, double dt, int mother, double param, double s0, double dj, int jtot, int npad, double* wave, double* scale, double* period,
double* coi);
void psi0(int mother, double param, double* val, int* real);... |
6d8ea2fc811cc3a722083c8ab07a0374db78c40221a8c078a0bd3804497f387b | C/C++ | 560 | 18 | #ifndef SNOWMAN_BENCHMARK_H__
#define SNOWMAN_BENCHMARK_H__
#include <string>
#include <vector>
void parseBenchmarkOptions(int argc, char** argv);
void runBenchmark(int argc, char** argv);
void assemblyTest();
void sampleReads(const std::string& seq, std::vector<std::string>& reads, int cov, double error_rate);
void ... |
51bc99ad5a7e89b57fab7bd85fa8cfe8151e32120aabf411c8dc45411ba7b21d | C/C++ | 561 | 28 |
#ifndef TIMER_H_
#define TIMER_H_
#include <string>
#include <ctime>
/* Timer is for measuring wall clock time and CPU time of different code sections. Stop is used to make a checkpoint in time and reset for restarting the timer. */
class Timer
{
public:
Timer();
void reset();
void stop();
std::str... |
b279b512ef3984b3490da899e146d383fc02190e4b18901df164d11981d3a975 | C/C++ | 563 | 22 | #pragma once
#include "IReaderHelper.h"
namespace EBML {
class EBML_API CReaderHelper final : public IReaderHelper
{
public:
CReaderHelper();
~CReaderHelper() override;
uint64_t getUInt(const void* buffer, const size_t size) override;
int64_t getInt(const void* buffer, const size_t size) override;
... |
e965d40430faea09d0ca42224c1a29151f24f0c03c05e057c61bf9e6aa704f0d | C/C++ | 567 | 24 | #pragma once
#include "../ovasCConfigurationBuilder.h"
#include "ovasIDriver.h"
namespace OpenViBE {
namespace AcquisitionServer {
/**
* \class CConfigurationGenericTimeSignal
* \sa CDriverGenericTimeSignal
*/
class CConfigurationGenericTimeSignal final : public CConfigurationBuilder
{
public:
CConfigurationGe... |
b43d22e9fefd006a460c4d7d5d3510b49d057fdc130396a47406ca6fa4497b97 | C/C++ | 569 | 21 | //-----------------------------------------------
// Copyright 2012 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// BWTCARopebwt - Construct the BWT for a set of reads
// using Heng Li's ropebwt implementat... |
a41bce8e16876e520feacdbd7271b17d6f9fc31082be7a78e45f74441afba686 | C/C++ | 573 | 26 | /*
Copyright (c) 2014, Rafat Hussain
Copyright (c) 2016, Holger Nahrstaedt
*/
#pragma once
#include <stdio.h>
#include "conv.h"
#include "math.h"
#ifdef __cplusplus
extern "C" {
#endif
int filtlength(const char* name);
int filtcoef(const char* name, double* lp1, double* hp1, double* lp2, double* hp2);
void copy_r... |
7c1cca186e874e6d08f443239131a1891fc9efcf16171f467c6bab6d7c503f30 | C/C++ | 578 | 34 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
#pragma once
#undef v
#undef area
#undef thisnode
#unde... |
684757ae6ab20dd8da14ac0d7d27707f0ed3e67d3cf1b0b7e297e743dc699402 | C/C++ | 579 | 25 | #pragma once
#include <ov_common_defines.h>
namespace OpenViBE {
class CString;
namespace Kernel {
/**
* \class IConfigurationKeywordExpandCallback
* \author Jozef Legeny (Mensia Technologies)
* \date 2014-05-06
* \brief Callback used for overriding a keyword in IConfigurationManager
* \ingroup Group_Config
* ... |
48f8be914cb1f6983355e91a8d23306e500e16566132162c92a340a51cabd86c | C/C++ | 581 | 14 | #pragma once
#define OVP_Classification_BoxTrainerFormatVersion 4
#define OVP_Classification_BoxTrainerFormatVersionRequired 4
#ifdef TARGET_HAS_ThirdPartyOpenViBEPluginsGlobalDefines
#include "ovp_global_defines.h"
#endif // TARGET_HAS_ThirdPartyOpenViBEPluginsGlobalDefines
#define OVP_Ty... |
31a8c40c0445d1da25b1e22bb396feb135351e3fb1e57134c3b527643eacbec7 | C/C++ | 584 | 21 | #pragma once
#include <openvibe/ov_all.h>
#include <map>
template <class T>
OpenViBE::CIdentifier getNextIdentifier(const std::map<OpenViBE::CIdentifier, T>& map, const OpenViBE::CIdentifier& previousID)
{
typename std::map<OpenViBE::CIdentifier, T>::const_iterator it;
if (previousID == OpenViBE::CIdentifie... |
a9072bd1a375cb908bbbff5ff9ab24d012e407208eb294754f6d7ff9df4669d5 | C/C++ | 586 | 20 | //
// OpenViBE Tracker
//
//
// n.b. having this as a separate file so EBML/Demuxer dependencies do not get pulled into StreamBundle
//
#pragma once
#include <openvibe/ov_all.h>
#include "StreamBundle.h"
namespace OpenViBE {
namespace Tracker {
// These functions import/export stream bundles from .ov files
StreamBu... |
338246e0d423dc56a3a6dd9ffa1734a6511f7c929fbacc0dff8e215f84bba947 | C/C++ | 590 | 33 | #ifndef SNOWMAN_SIMGENOME_H__
#define SNOWMAN_SIMGENOME_H__
#include "SeqFrag.h"
#include "ReadSim.h"
class SimGenome {
public:
SimGenome(const SeqLib::GenomicRegion& gr, int nbreaks, int nindels, faidx_t * findex, bool scramble, int viral_count);
void addBreak(int b);
friend std::ostream& operator<<(std... |
7e5b6a284f2813fd96ea7e5f44aef7b2cb8a6bcff03c0ab28340979db0eed5f7 | C/C++ | 592 | 24 | /*
Copyright (c) 2014, Rafat Hussain
*/
#pragma once
#include "wavefilt.h"
#ifdef __cplusplus
extern "C" {
#endif
int upsamp(double* x, int lenx, int M, double* y);
int upsamp2(double* x, int lenx, int M, double* y);
int downsamp(double* x, int lenx, int M, double* y);
int per_ext(double* sig, int len, int a, double... |
4411e424ed54016811c2cf0de40bc066dc0e34a1fa5c4391b9263653f0ab9bb3 | C/C++ | 597 | 29 | /**
* SPDX-FileCopyrightText: Inria <tristan.cabel@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
#pragma once
#include <QtCore>
namespace OpenViBE {
namespace Designer {
class BoxTreeModelFilter: public QSortFilterProxyModel {
Q_OBJECT
public:
BoxTreeModelFilter(QObject *parent = nullptr) : QSor... |
88a4fec3f55c3f99c9d0824e9cceb802f8ab45cb3ba9498534ba3c4d3f75893f | C/C++ | 599 | 27 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// overlap - Overlap reads using a bwt
//
#ifndef OVERLAP_H
#define OVERLAP_H
#include <getop... |
eca7cd6f859dfcb97a083ef08b199c54dd851f299fdfdec1d3278582bf7a66aa | C/C++ | 599 | 11 | void p4_copyCondLikes(p4_tree *treeA, p4_tree *treeB, int doAll);
void p4_copyBigPDecks(p4_tree *treeA, p4_tree *treeB, int doAll);
void p4_copyModelPrams(p4_tree *treeA, p4_tree *treeB);
int p4_verifyIdentityOfTwoTrees(p4_tree *treeA, p4_tree *treeB);
int p4_verifyModelPrams(p4_tree *treeA, p4_tree *treeB);
int p4_ver... |
f9a9a21c048aa729368b20a9e7ac6d11428b9c3a34c7dd0bd83c664bc05932a8 | C/C++ | 618 | 25 | #pragma once
#include "../ovtk_base.h"
namespace OpenViBE {
namespace Toolkit {
class ISignalTrial;
class OVTK_API ISignalTrialSet : public IObject
{
public:
virtual bool addSignalTrial(ISignalTrial& signalTrial) = 0;
virtual bool clear() = 0;
virtual size_t getSignalTrialCount() const = 0;
virtual... |
7de3840e1da2aeb0145603d8d7761c4bd34e6bd83f8d55cda367861b6a57d8b1 | C/C++ | 622 | 23 | #pragma once
#if defined CSV_Shared
# if defined TARGET_OS_Windows
# define CSV_API_Export __declspec(dllexport)
# define CSV_API_Import __declspec(dllimport)
# elif defined TARGET_OS_Linux || defined TARGET_OS_MacOS
# define CSV_API_Export __attribute__((visibility("default")))
# define CS... |
9cf465aba1b84ccb063e8ef4d573234ec60ca30a247d2d540706b5ca79f20302 | C/C++ | 625 | 28 | #ifndef _RCPLEX_H
#define _RCPLEX_H
#include <ilcplex/cplex.h>
#include <stdlib.h>
#include <R.h>
#include <Rinternals.h>
#include <unistd.h>
#define my_error(x) { forceCplxClose = 1; error x; }
/* Global Variables */
extern CPXENVptr env;
extern CPXLPptr lp;
extern int numcalls;
extern int max_numcalls;
extern int ... |
f6b0b673c30431c4acde8e39410c4ef61af1c2f8d159bc30c23848312dcf5d25 | C/C++ | 625 | 32 | #ifndef BAMREADER_H
#define BAMREADER_h
#include "api/BamReader.h"
#include "api/BamWriter.h"
#include "Util.h"
class SVBamReader {
public:
Bamreader(const std::string filename, const std::string prefix, const int isize = 2000)
: m_bam(filename), m_prefix(prefix), m_isize(isize) {}
~Bamreader() { }
voi... |
271fe35f7df7fffb4c783fba4ffcb38d9d1ae7c03bad06b2a9650e32760a23ba | C/C++ | 627 | 25 | #pragma once
#include <ov_common_defines.h>
#if defined XML_Shared
# if defined TARGET_OS_Windows
# define XML_API_Export __declspec(dllexport)
# define XML_API_Import __declspec(dllimport)
# elif defined TARGET_OS_Linux
# define XML_API_Export __attribute__((visibility("default")))
# defi... |
aeea25d7f2aef65bd6de91651adefea5c4114aebb12f5f63053b218814106c16 | C/C++ | 628 | 16 | #pragma once
#define OVAS_Impedance_NotAvailable -2
#define OVAS_Impedance_Unknown -1
#define OVAS_Impedance_Zero 0
//___________________________________________________________________//
// //
// Global defines ... |
954c5c9d213fc94f76e9a0d95ff996b91d48c0fffa51ed542f7ff426e91f4cc8 | C/C++ | 629 | 35 | #ifndef SNOWMAN_BAM_SPLITTER_H__
#define SNOWMAN_BAM_SPLITTER_H__
#include "SeqLib/BamReader.h"
#include "SeqLib/BamWriter.h"
#include "Fractions.h"
class BamSplitter: public SeqLib::BamReader
{
public:
BamSplitter() {}
BamSplitter(uint32_t seed) : m_seed(seed) {}
void setWriters(const std::vector<st... |
16443e7101a5b077652613cd0e802f10b712a61da7db9128f73d73084ba64e5e | C/C++ | 633 | 33 |
#ifndef PROTEINSEQUENCEALIGNMENT_H
#define PROTEINSEQUENCEALIGNMENT_H
class ProteinSequenceAlignment : public SequenceAlignment {
public:
ProteinSequenceAlignment(CodonSequenceAlignment* from) {
Ntaxa = from->Ntaxa;
Nsite = from->Nsite;
taxset = from->taxset;
statespace = new ProteinStateSpace();
Data... |
b6311b5c8443f1444be4f4e4ff2493d86b605184e75f705d46f36841db87b457 | C/C++ | 633 | 29 | /*
* \author Christoph Veigl, Yann Renard
*
* \copyright AGPL3
*
*/
#pragma once
#include "../ovasCConfigurationBuilder.h"
#include <gtk/gtk.h>
namespace OpenViBE {
namespace AcquisitionServer {
class CConfigurationOpenEEGModularEEG final : public CConfigurationBuilder
{
public:
CConfigurationOpenEEGModular... |
b61b90e356d7a80e98b79cc8c16a2adf348118776e17edb7aee9d20348b0c828 | C/C++ | 640 | 25 | #pragma once
#include <ov_common_defines.h>
#if defined FS_Shared
# if defined TARGET_OS_Windows
# define FS_API_Export __declspec(dllexport)
# define FS_API_Import __declspec(dllimport)
# elif defined TARGET_OS_Linux || defined TARGET_OS_MacOS
# define FS_API_Export __attribute__((visibility("d... |
5a24e6495d3e6d8d41cceff6c48371842ae3060a6ff70d6b600ed85965358815 | C/C++ | 642 | 28 | #pragma once
#include "defines.h"
namespace XML {
class XML_API IWriterCallback
{
public:
virtual ~IWriterCallback() { }
virtual void write(const char* sString) = 0;
};
class XML_API IWriterCallBack : public IWriterCallback { };
class XML_API IWriter
{
public:
virtual bool openChild(const char* name) = ... |
40476f9296befc498506ef00c7b592ed2185284d95b39a028b9f0d35039ab1c7 | C/C++ | 643 | 33 | /**
* SPDX-FileCopyrightText: Inria <thomas.prampart@inria.fr>
* SPDX-License-Identifier: AGPL-3.0-only
*/
#pragma once
#include <any>
#include "ov_common_defines.h"
#include "../CIdentifier.hpp"
#include "parameterTraits.h"
namespace OpenViBE {
namespace Parameters {
/**
* @brief Get the correspondance map b... |
a979c01a2b00b19382fa9f894b8654a03d84a710bc6f7ad849ca1e620068943c | C/C++ | 645 | 26 | /*
# =============================================================================
# Copyright (c) 2016 - 2021 Blue Brain Project/EPFL
#
# See top-level LICENSE file for details.
# =============================================================================.
*/
/**
* @file nrn_stats.h
* @date 25th Dec 2014
* @brie... |
15a46bbb7db26a82146a0a9c60fa29e7d36d40a6cf36c683357e25cd995c8aca | C/C++ | 647 | 30 | //-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// PrimerScreen - Singleton class to filter sequences
// that match a database of primer seq... |
4f911f70dc5f89aeafa48243a06d72439ed1db2a8cb6f26a3c3a9d22d56ff1c5 | C/C++ | 649 | 25 | // PGF got this from Dave Swofford. Thanks, Dave! It is not GPL'd, obviously.
/* gamma.h, now paupgamma.h
|
| Prototypes for functions relating to gamma and other statistical distributions.
|
| Copyright (c) 1998 by David L. Swofford, Smithsonian Institution.
| All rights reserved.
*/
#ifdef __cplusplus
extern "C" ... |
1af67b5203d347082e3abea6ecd035895b25caefef90e967fff6262870f3e8cc | C/C++ | 657 | 23 |
#define WARPSIZE 32
#define DIMENSION 3
#define MARK 2
#define SEED 3
#define ACTIVE 1
#define FARP 0
#define STOP 4
#define ALIVE 5
#define TOBEALIVE 6
#define TETMEMLENGTH 4
#define EDGEMEMLENGTH 3
#define VERTMEMLENGTH 6 //must be even number and best be odd*2 to avoid shared... |
26369292481dfefb18bdc6fda859add757586cf73c895e34df0b044a6fd3c00b | C/C++ | 664 | 23 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL license
//-----------------------------------------------
//
// index - Build a BWT/FM-index for a set of reads
//
#ifndef INDEX_H
#define INDEX_H... |
352093addf595a30fc5bbb0ef7aaacc4fd71a02c6ffa094f264f3c3dcbd21c03 | C/C++ | 667 | 32 | #pragma once
#include "ovtk_defines.h"
#include <openvibe/ov_all.h>
namespace EBML {
class IWriter;
class IWriterCallback;
class IWriterHelper;
class IReader;
class IReaderCallback;
class IReaderHelper;
} // namespace EBML
namespace OpenViBE {
namespace Toolkit {
template <class THandledType>
class TScopeHandle
{
... |
878a9dc530a14d611ebdf81a6fa2e3be6cb32b7d490670968ef1b14bb7cb1d76 | C/C++ | 669 | 11 | /*************************************************************************************/
/* linpack.h */
/*************************************************************************************/
/******************************************************... |
6f4d6fd84d5768777a4dfda2c52997ffbaca1ab3d4caab1971117026d7cda14a | C/C++ | 676 | 27 | #pragma once
#include "ovkTKernelObject.h"
#include <vector>
#include <mutex>
namespace OpenViBE {
namespace Kernel {
class CKernelObjectFactory final : public TKernelObject<IKernelObjectFactory>
{
public:
explicit CKernelObjectFactory(const IKernelContext& ctx) : TKernelObject<IKernelObjectFactory>(ctx) {}
... |
bdef87d7d722d21b7b21523ec5c76bdf334f95b4b9bc7982b333a54cd2d37f9f | C/C++ | 678 | 17 | #pragma once
#include <cstddef> // for size_t
#include <cstdint> // for uint64_t
#define TIMESTAMP_INVALID 0xFFFFFFFFFFFFFFFF ///< Define a constant representing an invalid timestamp value.
using sampleType = float; ///< Define an alias for the data type used to store samples (single-precision floating-point).
u... |
d69781b4dd180a58b9f36afc3f2d1684021790d3b3c77bc00d014e7c399b9f13 | C/C++ | 683 | 22 | #pragma once
#include "ITrackerPlugin.h"
namespace OpenViBE {
namespace Tracker {
/**
* \class TrackerPluginCountStimulations
* \brief Example of a Tracker plugin that processes given tracks. It counts the occurrences of different stimulations in each stimulation stream.
* \author J. T. Lindgren
*
*/
class Tra... |
51c7d954cf7b8189ea2759652d20cb68fa4df09f1ecec3e06ea668d5c6134eda | C/C++ | 690 | 14 | #pragma once
// Boxes
//---------------------------------------------------------------------------------------------------
#define OVP_ClassId_MouseControl OpenViBE::CIdentifier(0xDA4B4EEB, 0x64FC6A16)
#define OVP_ClassId_MouseControlDesc OpenViBE::CIdentifier(0xB6B65C98, 0xA756ED0E)... |
19be8e0f3523f621c53e7d5f1171e1528410397cef34fb94802455610e0af1a8 | C/C++ | 695 | 23 | //-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// BWT - All functions that use a BWT include this file
// it simple typedefs the BWT name t... |
0939b68e59e116f013d980ff66a63bbcbdf087eece264e140f7749976911226f | C/C++ | 696 | 25 | #pragma once
#include <ov_common_defines.h>
#if defined System_Shared
# if defined TARGET_OS_Windows
# define System_API_Export __declspec(dllexport)
# define System_API_Import __declspec(dllimport)
# elif defined TARGET_OS_Linux || defined TARGET_OS_MacOS
# define System_API_Export __attribute_... |
ffd10c025c7875d5188fb8a3b0da7f447f61bc2784b7f2d2311441ed433d63d4 | C/C++ | 698 | 30 | #ifndef SNOWMAN_POWER_LAW_SIM_HH
#define SNOWMAN_POWER_LAW_SIM_HH
#include <fstream>
#include "SeqLib/GenomicRegionCollection.h"
#include "SeqLib/BWAWrapper.h"
void PowerLawSim(faidx_t* findex, int num_breaks, double power_law, SeqLib::GRC& grc,
std::ofstream& outfasta, std::ofstream& events);
std::vector<int> d... |
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