sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0f6901e69db49bd26a8762d071b33d69ead924843e8ead429d476090f528c515 | C++ | 7,789 | 287 | #include "ChannelAnalyzer.hpp"
//#include <set>
#include <unordered_set>
#include <stack>
#include <vector>
#include <array>
#include <limits>
#include <algorithm>
#include <iostream>
#include <iomanip>
#include <cstdint>
// Hash function for unordered_set
namespace std
{
template<typename T, size_t N>
struct... |
234428eaf6807c521a8b6da4e7bac823d1ac373e3a89c50f8ffd472476b9c5be | C++ | 7,835 | 245 | /*
Copyright (c) 2006-2010, The Scripps Research 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 requir... |
e5150bf3b7db8d629893ee9e2957f0ee7aa51101cca5d371477ae63cf2bed385 | C++ | 7,842 | 232 | /** \file sort_main.cpp
*
* Defines the "vg sort" subcommand, which sorts graph nodes.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../stream_index.hpp"
#include "../flow_sort.hpp"
#include "../algorithms/gfaz_to_handle.... |
12ead2d0f9fa55ea9be8df591aba38052ea2ff332709282e30f90a8bbc44e079 | C++ | 7,859 | 222 | /**
* \file dozeu_pinning_overlay.cpp: contains the implementation of DozeuPinningOverlay
*/
#include "dozeu_pinning_overlay.hpp"
namespace vg {
using namespace std;
DozeuPinningOverlay::DozeuPinningOverlay(const HandleGraph* graph, bool preserve_sinks) : graph(graph), preserve_sinks(preserve_sinks) {
... |
29cd0c1937eb089e580abd9a9b0b708298887716d45965eba19da40f233469ec | C++ | 7,866 | 168 | /**
* \file extract_containing_graph.cpp
*
* Implementation for the extract_containing_graph algorithm.
*/
#include "extract_containing_graph.hpp"
//#define debug_vg_algorithms
namespace vg {
namespace algorithms {
using namespace structures;
void extract_containing_graph(const HandleGraph* source,
... |
5611d73762e14b8afec32885020702165a19a955076bd6017c12bb874f73ea40 | C++ | 7,867 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... |
384f0a752a806d4114a7cf2d7907a7b552f3fe6816032bbcea629f26a69bc0d1 | C++ | 7,875 | 229 | //////////////////////////////////////////////////////////////////////////////////
// Implementation code for ER netwok with a different connection probability in block E-to-E
//////////////////////////////////////////////////////////////////////////////////
using namespace std;
#include <ios... |
37833ab2d06372102786a0945cf14b9eec7003e02eef86e487cdc6e2f2011b11 | C++ | 7,886 | 199 | // Tests for the proposed-hydration lookup.
//
// The table is derived at run time from somo.residue rather than embedded, so these tests both
// exercise the derivation and record what the source data actually supports -- which is less
// than it first appears, because the per-atom values there are a hand distribution... |
f22292eeea87308690fbb1ec5c201823ebf8550970ac65dd101b29e839884718 | C++ | 7,908 | 230 | #include "pm_worker.h"
int npes;
int myrank;
int main( int argc, char **argv )
{
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &npes);
MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
MPI_Status mpi_status;
PM_WORKER *pm = (PM_WORKER*) 0;
pm_msg msg;
msg.type = PM_REGISTER;
vector < do... |
558a419fad547076877f6eb141b77996b44c74e0165a19692e8fc7cdd0db71c0 | C++ | 7,937 | 203 | #include "graph_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
GraphCaller::GraphCaller(SnarlCaller& snarl_caller,
SnarlManager& snarl_manager) :
snarl_caller(snarl_caller... |
1dfbb243c67dc2b5711a07b2557913db40c23bfe718a308ac790a33e620aba1b | C++ | 7,955 | 222 | /** \file bench_dist_query_main.cpp
*
* Defines the "vg bench-dist-query" subcommand, which benchmarks distance query speed across multiple indexes.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <fstream>
#include <filesystem>
#include <sstream>
#include <chrono>
#includ... |
b708af8703c3a3cf2df81cf0f4d66f72b038642692adbcc4a5391298f9cf243d | C++ | 8,018 | 219 | //! \file us_select_triples.cpp
#include "us_select_triples.h"
#include "us_settings.h"
#include "us_gui_settings.h"
//! Class to present a pair of lists (included, excluded) to allow the
//! user to select triples to be excluded (deleted)
US_SelectTriples::US_SelectTriples( QStringList& triples )
: US_WidgetsDia... |
f58ccaccbce6a5c2aec3fda614899acc62128c1f85c4448ef6a1597aecc3029d | C++ | 8,022 | 266 | //! \file us_gui_util.cpp
#include <QtSvg>
#include "us_gui_util.h"
#include "us_gzip.h"
#include "us_settings.h"
#if QT_VERSION > 0x050000
#include "qwt_plot_renderer.h"
#include "us_spectrodata.h"
#endif
// Save SVG+PNG or PNG file
int US_GuiUtil::save_plot( const QString& filename, const QwtPlot* plot )
{
int ... |
7767a5e882d7477d2947f1dc7ed97418e10cc3f18b6e707071abc07af4c5adc6 | C++ | 8,027 | 320 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4305 )
#pragma warning ( disable : 4786 )
#endif
#include "qwt3d_surfaceplot.h"
#include "qwt3d_enrichment_std.h"
using namespace std;
using namespace Qwt3D;
////////////////////////////////////////////////////////////////////////////... |
ef53c7940e54cf7531d7e181b1b3c4ca263df2a3d37be32fdafa1805cfabe558 | C++ | 8,046 | 193 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
274098aa3052b0f675509ef0ba71996b5d4a99ae51e804733ce68f4af5722c00 | C++ | 8,050 | 219 | //! \file us_select_triples_ra.cpp
#include "us_select_triples_ra.h"
#include "us_settings.h"
#include "us_gui_settings.h"
//! Class to present a pair of lists (included, excluded) to allow the
//! user to select triples to be excluded (deleted)
US_SelectTriplesRa::US_SelectTriplesRa( QStringList& triples )
: US_... |
9e1a83f9b751a721bcb9c6778e2a6460a75fb27b8fff3e7b455cef27d1754322 | C++ | 8,058 | 175 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
fec5a7e5ceb6cd19b9af51df51410170c01f37ed93b8c7558d9868d96d7a6308 | C++ | 8,061 | 224 | /**********************************************************************************************
* Arduino PID Library - Version 1.1.1
* by Brett Beauregard <br3ttb@gmail.com> brettbeauregard.com
*
* This Library is licensed under a GPLv3 License
*********************************************************************... |
2523064ca83cabfd21cb9a041a0f81d5a31a257338409c9b8e6498bcc8bbe994 | C++ | 8,145 | 271 | //! \file us_ri_noise.cpp
#include "us_ri_noise.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_matrix.h"
US_RiNoise::US_RiNoise( const US_DataIO::RawData& raw,
const QList< int >& Includes,
double left,
... |
046ea34647cb2c180e05970216a854ed34a61407e4c0a34b32e7fa49f3d1e3ab | C++ | 8,181 | 155 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
2f94e4b8bad7551a627266127f6a73ef7c247efe73547155b4b7658feece4bfd | C++ | 8,185 | 1 | vector<float> ext_dir_initial{{0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.228129,1.227010,0.935999,0.482537,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.143363,0.177148,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0... |
e4ea12f48c5c3067172478d75cdccb09b33569a8edb1a49e2c2f4e7408f2a5db | C++ | 8,199 | 355 | #include <time.h>
#include "qwt3d_plot.h"
#include "qwt3d_io_gl2ps.h"
#include "qwt3d_io_reader.h"
#if QT_VERSION < 0x040000
#else
#include <QImageWriter>
#endif
using namespace Qwt3D;
IO::Entry::Entry() : iofunc(0)
{
}
IO::Entry::~Entry()
{
delete iofunc;
}
IO::Entry::Entry(IO::Entry co... |
30966891527a833b5d926c05db6530cb0aad30841de2c8e30194ca416668bfa9 | C++ | 8,245 | 229 | /**
* \file memoizing_graph.cpp: contains the implementation of MemoizingGraph
*/
#include "memoizing_graph.hpp"
namespace vg {
using namespace std;
MemoizingGraph::MemoizingGraph(const PathPositionHandleGraph* graph) : graph(graph) {
}
bool MemoizingGraph::has_node(id_t node_id) const... |
51e2b9116390df75e17f7ef354aa0c3f50762e40ba830af85539f599049cc4d1 | C++ | 8,245 | 252 | #include "zstdutil.hpp"
namespace vg {
//------------------------------------------------------------------------------
// Public class constants.
constexpr int zstd_compress_buf::DEFAULT_COMPRESSION_LEVEL;
//------------------------------------------------------------------------------
zstd_compress_buf::zstd_co... |
abb406391d028daca0533d871e449c8df2db01b9b0e35016868fd33ad38ec7e9 | C++ | 8,291 | 312 | #include "shs.h"
void SHS::build( int max_harmonics,
shd_double delta,
shd_double max_x )
{
this->max_harmonics = max_harmonics;
x_t .clear();
y_t .clear();
y2_t.clear();
for ( shd_double tmp_x = 0; tmp_x <= max_x; tmp_x += delta )
{
x_t.push_back( ... |
58809509693f4b024a19f5d0e20c6817d3cab858db14f3126fa1bb78e8aa9654 | C++ | 8,298 | 230 | /// \file tree_subgraph.cpp
///
/// Unit tests for the TreeSubgraph, which defines a subgraph with a tree topology.
///
#include <iostream>
#include <string>
#include "vg/io/json2pb.h"
#include "../tree_subgraph.hpp"
#include "catch.hpp"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace... |
1fb3803ffda5b9bbaa84eb5dca019fdb47cc1ec151174099e7eab34e6edf5943 | C++ | 8,300 | 204 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
485f6d3d7c8178ff93716232ea06a4dea402c7b585fbb05a065bc2cd9aa41dac | C++ | 8,332 | 210 | /**
* \file
* Minimizer (sub)sampling algorithm implementation.
*/
#include "sample_minimal.hpp"
#include "../crash.hpp"
#include <deque>
#include <utility>
#include <iostream>
namespace vg {
namespace algorithms {
using namespace std;
//#define debug
void sample_minimal(size_t count, size_t element_length, ... |
c0933bd54cf407b78c0bfd9d6a4ff2d640d81544417199a6cc4c402dba0e327d | C++ | 8,339 | 257 | #include "gfaz_to_handle.hpp"
#include "../path.hpp"
#include <GFAz/core/codec/serialization.hpp>
#include <algorithm>
#include <cstring>
#include <fstream>
#include <tuple>
namespace vg {
namespace algorithms {
using gfaz::GFAZ_MAGIC;
using gfaz::NodeId;
bool GFAzParser::has_magic(const char* buffer, size_t lengt... |
fa4b1f12e0b882e2ddfe72dea2f2a306c099cbe3fd253e43fd1f2b7a0250b944 | C++ | 8,343 | 276 | #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <Python.h>
#include <numpy/arrayobject.h>
#include <stdint.h>
#include <iostream>
#include "convolution.hpp"
static PyObject *convolution(PyObject *self, PyObject *args);
static PyObject *convolution1(PyObject *self, PyObject *args);
static PyObject *slice_tes... |
0429037084a63ed3f2c1bd11cb90eecf06c44c9ac037aecfe9c90e656a6909b9 | C++ | 8,344 | 186 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ac932bdf4e9a289512997480eea3519352a16a73449a21ae0bc3068a05436208 | C++ | 8,379 | 228 | #include <iostream>
#include <sstream>
#include <string>
#include <vector>
#include <parallel_hashmap/phmap.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/typer/bucket.hpp>
#include <graphtyper/typer/event.hpp>
#include <graphtyper/typer/read.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <gra... |
7cd75da354fd86e54612c384bd9dfed3fd2b3ef6a16a5c57e5b2b11f1e63f84d | C++ | 8,391 | 196 | #include "gaf_output_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
GAFOutputCaller::GAFOutputCaller(AlignmentEmitter* emitter, const string& sample_name, const vector<string>& ref_paths,
... |
12ae3eeb47ba58199152e146eb1337cc41dacbf3c24c64bc3425fa5092f7e106 | C++ | 8,396 | 240 | //! \file us_delete_models.cpp
#include "us_delete_models.h"
#include "us_gui_settings.h"
// Constructor: remove-distributions dialog widget
US_DeleteModels::US_DeleteModels( QVector<IntegralDisSys>& adistros, QWidget* p ) :
US_WidgetsDialog( p, Qt::WindowFlags() ),
distros( adistros )
{
setObjectName( "U... |
ca33074e4490a232ebace54a5834fcd4247a2b69a6026a91cce5daf281744f11 | C++ | 8,425 | 347 | #include <math.h>
#include "qwt3d_color.h"
#include "qwt3d_plot.h"
#include "qwt3d_enrichment_std.h"
using namespace Qwt3D;
/////////////////////////////////////////////////////////////////
//
// CrossHair
//
/////////////////////////////////////////////////////////////////
CrossHair::CrossHair()
{... |
0593adb2c994a0244f8d57c759e4465f18a547ff28271af05bd3fe0a6ee9ac6e | C++ | 8,444 | 263 | //! \file us_abstractrotor_gui.cpp
#include "us_abstractrotor_gui.h"
#include "us_settings.h"
#include "us_license_t.h"
#include "us_util.h"
#include "us_db2.h"
#include "us_widgets.h"
#include "us_license.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
US_AbstractRotorGui::US_AbstractRotorGui(
bool signa... |
1fbd977f92da8af5eeb2b05555ffe02d8eba0cd00a8f1ca6c480bf3036154908 | C++ | 8,447 | 1 | vector<float> ext_dir_initial{{2.418941,10.772454,22.817637,38.056182,47.403656,51.267451,48.569655,40.073009,27.159467,17.714714,5.643129,0.130822,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.403227,1.926952,0.983769,0.000000,0.000000,0.000000,0.000000,0.000000,1.625102,7.637326,17.297724,4.291681,... |
971c3cd1264fbfdf85857758bead69c7f136f2defc2114ffbc6d5d4ef3dd1847 | C++ | 8,450 | 255 | /**
* unittest/chunker.cpp: test cases for the read filtering/transforming logic
*/
#include "catch.hpp"
#include "chunker.hpp"
#include "vg.hpp"
#include "xg.hpp"
#include "path.hpp"
#include "../io/json2graph.hpp"
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE(... |
54461a7b32e5ab33d899bff7b95d1a5845e63e16f85f63654e5631768b0402fb | C++ | 8,476 | 1 | vector<float> ext_dir_initial{{0.932444,1.537976,2.273668,0.751526,0.385351,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,2.521837,7.502246,10.171875,8.358875,8.588459,2.489002,0.779455,0.197028,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,5.141238,8.276877,10.210818,8.444244... |
574aa9e6794b6ec2d4fe465b975618ffe1359618d869cec9120bbc5939804234 | C++ | 8,476 | 1 | vector<float> ext_dir_initial{{3.545046,11.177108,10.783775,8.911644,7.318669,4.045267,1.535915,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,2.203112,4.458520,6.286495,6.878220,3.551117,2.235030,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.057451,15.440919,25.2763... |
291eef69050ad98d242677d4085770b3cbe2b0109996f716ef106d1ca30b3ff2 | C++ | 8,513 | 216 | // Unit tests for find_sssr(). Ring COUNT and SIZES drive the Durchschlag & Zipper ring-formation
// volume decrement, which is charged once per ring, so both must be exact -- a fused bicyclic
// must yield 2 rings, not the 3 simple cycles a full cycle enumeration finds.
//
// These run on hand-built adjacency, with no... |
596c4e6cc2709a3155b6803c19e3798a7181984730f2ab83834b15467849aef3 | C++ | 8,535 | 246 | //! \file us_remove_models.cpp
#include "us_remove_models.h"
#include "us_gui_settings.h"
// Constructor: remove-distributions dialog widget
US_RemoveModels::US_RemoveModels( QVector< DisSys >& adistros,
QWidget* p ) : US_WidgetsDialog( p, Qt::WindowFlags() ), distros( adistros )
{
setObjectName( "US_RemoveMo... |
0fd29a809f7607e77d7191b7df1819d97c70494d448ec97e2b830247721ced22 | C++ | 8,539 | 283 | //! \file us_sync_db.cpp
#include "us_sync_db.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_matrix.h"
#include "us_investigator.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_util.h"
#include "us_constants.h"
// Main constructor
US_SyncWithDB::US_SyncWithDB() : US_WidgetsDialog( n... |
56f3349696236ce5ed9e30ee0afab7126b55ed5fa2f7e13631ccadd0495d8bdf | C++ | 8,545 | 448 | #include <bitset> // std::bitset
#include <iomanip> // std::hex
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/type_conversions.hpp>
namespace gyper
{
/**
* @brief Converts a string/list of DNA bases to a unsigned 64 bit integer.
*
... |
1b98fd6bde592600dfa9b716aeb3d47e9ad439559b7f2fb2d601e856f2a43007 | C++ | 8,547 | 246 | //! \file us_remove_distros.cpp
#include "us_remove_distros.h"
#include "us_gui_settings.h"
// Constructor: remove-distributions dialog widget
US_RemoveDistros::US_RemoveDistros( QList< DisSys >& adistros,
QWidget* p ) : US_WidgetsDialog( p, Qt::WindowFlags() ), distros( adistros )
{
setObjectName( "US_Remove... |
d381d8bc38200c77b5adc20454fe173b3698ac4205a6a0c9a851e84cf6b05b9b | C++ | 8,547 | 386 | #include "qwt3d_axis.h"
using namespace Qwt3D;
Axis::Axis()
{
init();
};
Axis::~Axis()
{
}
Axis::Axis(Triple beg, Triple end)
{
init();
setPosition(beg,end);
}
void Axis::init()
{
detachAll();
scale_ = qwt3d_ptr<Scale>(new LinearScale);
beg_ = Triple(0.0, 0.0, 0.0);
end_ =... |
a22364d3ff05beabf4d0c5fef9c3cc41cbd3b5d057476f170d22b609bf124686 | C++ | 8,581 | 208 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
64e24450859da596165925c4572cdbf8ab5734bd2f0808a8ac45074e00627cf1 | C++ | 8,607 | 272 | //! \file us_mwl_run.cpp
#include "us_mwl_run.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_util.h"
// Primary constructor to establish the dialog
US_MwlRun::US_MwlRun( QString& runID, bool isRawMwl )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() ), runID( runID ), isRawMwl( isRawMwl )
{
... |
3ba3751a484e2ecd7a4a9c441513b8b9600fb247c8208d0d27501be7d13d3662 | C++ | 8,615 | 334 | // test_us_db2.cpp
#include "qt_test_base.h"
#include "mock_us_db2.h"
#include "us_db2.h"
#include <QString>
#include <QStringList>
#include <QVariant>
#include <QByteArray>
#include <memory>
using ::testing::_;
using ::testing::Return;
using ::testing::SetArgReferee;
using ::testing::DoAll;
using ::testing::StrictMoc... |
287b2545d7ab21cbdc3a8794b03ebe30aca82ac73b2665d209afac8ae071b9bb | C++ | 8,677 | 246 |
#include <cassert>
#include <climits>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>
#include "OspreyIBSParams.hpp"
#include "format.hpp"
#include "version.hpp"
using namespace std;
namespace Osprey {
static int DEFAULT_THREAD... |
f292512453abf8dc3caa81242b5f3c34314904a7b97b8259181bf91f2bd00316 | C++ | 8,688 | 228 | /**********************************************************************************************
* Arduino PID Library - Version 1.1.1
* Forked by Rick Hormigo 3/11/2020 to support external interval faster computation
* This forked version relays in a constant interval call that replaces the older sampling
* O... |
e97e8e6500f31b9065a153b961f80f01d2cebde8ae913f4a378c7f756a2b046b | C++ | 8,763 | 254 | ////////////////////////////////////////////////
// Implementation code for reproducing Fig.2 //
////////////////////////////////////////////////
using namespace std;
#include <iostream>
#include <math.h>
#include <fstream>
#include <cstdlib> // defines rand
#include <ctime> // defines time() function
... |
b56c39675b8377df28a1f15726e8381be26fe03ea699a0050eb4508b07118fcb | C++ | 8,764 | 302 | #include "us_refScan_dataIO.h"
int US_RefScanDataIO::writeRefData( const QString& file, RefData& data )
{
//define unions;
union union16 u16a, u16b;
union union32 u32a, u32b;
// Open the file for writing
QFile ff( file );
if ( ! ff.open( QIODevice::WriteOnly ) ) return CANTOPEN;
QDataStream... |
af3daa28e710752125ba523da92bbedc0380d48050b1a332818f0b5298929fd8 | C++ | 8,778 | 279 | #include "kff.hpp"
namespace vg {
//------------------------------------------------------------------------------
bool kff_is_trivial(const uint8_t* encoding) {
for (size_t i = 0; i < 4; i++) {
if (encoding[i] != i) {
return false;
}
}
return true;
}
std::string kff_invert(c... |
70be9ffeb4070bcd36d657e9005403f895751ee1eff9845c3ba0121b119ffe0d | C++ | 8,780 | 237 | //! \file us_sync_exper.cpp
#include "us_sync_exper.h"
#include "us_util.h"
#include "us_settings.h"
// Check synchronizing of experiment on database and local with raw data
US_SyncExperiment::US_SyncExperiment( US_DB2* a_db, QWidget* parent /*= 0*/ )
{
db = a_db;
parentw = parent;
dbg_level = US... |
ad27a4658216f96a8eb2b2cba37406a0b223fabb4cfdc35503bfcf302fe655fc | C++ | 8,786 | 237 | // test_us_crc_unit.cpp - Unit tests for US_Crc class
#include "qt_test_base.h"
#include "us_crc.h"
#include <QByteArray>
#include <limits>
using namespace qt_matchers;
class TestUSCrcUnit : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
}
void TearDown() override {
... |
5c8337e50f8940412ed5314c4df2c17b9c83bff48264650dba0fa8d002d5cfb9 | C++ | 8,837 | 239 | /**
* \file merge.cpp
*
* Defines an algorithm to merge parts of handles together.
*/
#include "merge.hpp"
#include <unordered_set>
#include <iostream>
namespace vg {
namespace algorithms {
using namespace std;
void merge(handlegraph::MutablePathDeletableHandleGraph* graph, const vector<pair<handle_t, size_t>>... |
69746202ffec1b93a312a66a7395ce1f5ec0e608cd9c556eca450206492fa45c | C++ | 8,947 | 234 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
f0824f2f71742513e339b30cbe4034233202249c29ad8215ac17bf730d15e234 | C++ | 8,953 | 307 | #include <algorithm>
#include <fstream>
#include <iostream>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/index/indexer.hpp>
#include <graphtyper/index/ph_index.hpp>
#include <graphtyper/utilities/logging.hpp>
namespace
{
bool entry_has_too_many_nonrefs... |
04af275bd7825512342ed3eac07084e4fe6e6c128f86bf4f989aab77a5a3e15c | C++ | 8,973 | 300 | ////////////////////////////////////////////////////////////////////////////////
// Authors: Costa Filippo
// Description: ADMFilter implementation
////////////////////////////////////////////////////////////////////////////////
#include "ADMFilter.h"
#include "BCIStream.h"
#include <iostream>
#include <fstrea... |
527c0633452b833fceb360487b6825f333684af828c8ea22a029511ac6db88c0 | C++ | 9,054 | 386 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4786 )
#endif
#include <time.h>
#include "qwt3d_openglhelper.h"
#include "../3rdparty/gl2ps/gl2ps.h"
#include "qwt3d_io_gl2ps.h"
#include "qwt3d_plot.h"
using namespace Qwt3D;
//! Provides a new VectorWriter object.
IO::Functor* Vect... |
32b299108c32ad06ab2e54e8f15fa823a1d67f8fa0829a56a993bdcf0608d297 | C++ | 9,057 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... |
3a75b8379f40f4fc148fc0116bc6fc8e897a0e309e23c033cdc9faf5ae5b326d | C++ | 9,057 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... |
180277b79f9fe1d6253882286090af8226a1ba909333b7523a51b636cc7e42df | C++ | 9,077 | 235 | /** \file combine_main.cpp
*
* Defines the "vg combine" subcommand
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <vg/io/vpkg.hpp>
#include <vg/io/message_iterator.hpp>
#include <vg/io/blocked_gzip_input_stream.hpp>
#include "subcommand.hpp"
#include "../handle.hpp"
#i... |
9901796bdd603241705825a9200bef1a9a0ff8dd9fce28bc0a3995a14afccbb0 | C++ | 9,113 | 178 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ddedaa4e06eaaa76d4ad4495e6d2b14bd1cd2e129bd888245037379d5e121668 | C++ | 9,139 | 223 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ac16268d3bc39c6e5a89d65a463386e09dda85add68a72cac3dbdf1753f99695 | C++ | 9,150 | 233 | /// \file dijkstra.cpp
///
/// Unit tests for the Dijkstra algorithm
///
#include <iostream>
#include <string>
#include "../handle.hpp"
#include "../io/json2graph.hpp"
#include "../vg.hpp"
#include "catch.hpp"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespac... |
09ea61d2fa89882aee0cdb28354e1247df121e461ba0e59d41b5aad9b9408ab4 | C++ | 9,212 | 237 | #include "advancedstartupdialog.h"
#include <QtWidgets>
AdvancedStartupDialog::AdvancedStartupDialog(bool &useOpenCL_, uint8_t &playbackPorts_, bool demoMode_, QWidget *parent) :
QDialog(parent),
useOpenCLDescription(nullptr),
useOpenCLCheckBox(nullptr),
synthMaxChannelsDescription(nullptr),
synthM... |
bf20b8f78469b036430fd9e4a52ed87ac9ee93a65488f49d13b39cfc372e93d8 | C++ | 9,232 | 183 | #include "walk.hpp"
#include <gbwtgraph/utils.h>
namespace vg {
namespace algorithms {
void for_each_walk(const HandleGraph& graph, size_t k, size_t edge_max,
const std::function<void(const walk_t&)>& lambda) {
graph.for_each_handle([&](const handle_t& h) {
// for the forward and ... |
a1ea42717444c946b17b975055394d68d4a21d7e7eb9458e8d1ed163ab6b15fa | C++ | 9,321 | 242 | /**
* unittest/distributions.cpp: test cases for distributions.hpp
*/
#include "catch.hpp"
#include "statistics.hpp"
namespace vg {
namespace unittest {
TEST_CASE( "Factorials are computed", "[distributions][factorial]" ) {
REQUIRE(factorial_ln(0) == Approx(log(1)).epsilon(1E-10));
// factorial_ln(1) is no... |
456a50f83e2be74406927149b958f93452f55a7fa503d5e15c09bc4356708f63 | C++ | 9,335 | 276 | /*********************************************************************
* Software License Agreement (BSD License)
*
* Copyright (c) 2010, Rice University
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions... |
93543ffc899e343a077ca5bb9ccc99dad346a3017cc352ecf8bf8cdd1fcfce40 | C++ | 9,364 | 227 | /** \file validate_main.cpp
*
* Defines the "vg validate" subcommand
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../alignment.hpp"
#include <vg/io/vpkg.hpp>
using namespace std;
using namespace vg;
using namespace vg::... |
0e6cd5b278b855134efce487a6e65e63e86e235a86aeb74d7860afb31b28c611 | C++ | 9,393 | 339 | #include <Eigen/Core>
#include <iostream>
#include "timer.h"
#include "ArpackFun.h"
using Eigen::MatrixXd;
using Eigen::VectorXd;
using Eigen::MatrixXcd;
using Eigen::VectorXcd;
using Eigen::Lower;
typedef Eigen::Map<VectorXd> MapVec;
void eigs_sym_F77(MatrixXd &M, VectorXd &init_resid, int k, int m,
... |
6ec7dcb7c7f42ed86979e2ace1c6bf62186c391406396512ed8983d2dc759439 | C++ | 9,434 | 241 | #include "dfs.hpp"
//#define debug
namespace vg {
namespace algorithms {
using namespace std;
// depth first search across node traversals with interface to traversal tree via callback
void dfs(
const HandleGraph& graph,
const function<void(const handle_t&)>& handle_begin_fn, // called when node orientatio... |
0524eb8f38633a1a250bf8493c4d407ffa5bfe8e432885af37c3e1de2d6b6e3f | C++ | 9,441 | 223 | //
// suffix_tree.cpp
//
//
// Created by Jordan Eizenga on 1/25/17.
//
//
#include <stdio.h>
#include <iostream>
#include <unordered_map>
#include "msa_converter.hpp"
#include "catch.hpp"
using namespace std;
namespace vg {
namespace unittest {
TEST_CASE("MSAConverter can build from each k... |
c866c60748eca0702f524c2cfca83237155e9efccdb4984e558175162540762a | C++ | 9,441 | 264 | /*!
* MyOptimizationObjective.cpp
*
* Created on: Nov, 21 2018
* Author: Florian Achermann, ASL
*/
#include "MyOptimizationObjective.hpp"
#include <limits>
#include <assert.h>
#include <iostream>
#include <boost/make_shared.hpp>
#include <ompl/config.h>
#include <ompl/base/goals/GoalRegion.h>
#include ... |
71880bb6391532088451c7a614a4fb615c0b6e441a05cd06f715fbfda8dc8541 | C++ | 9,459 | 276 | //! \file us_xpn_run_auc.cpp
#include "us_xpn_run_auc.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_util.h"
// Primary constructor to establish the dialog
US_XpnRunAuc::US_XpnRunAuc( QString& runID )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() ), runID( runID )
{
setWindowTitle( tr( "US... |
6aec7a6d15ad6c46bd503301d343677b5b3e0fde4eb88fc719adc34c99f8cbf4 | C++ | 9,470 | 233 | #include "algorithms/prune.hpp"
#include "hash_map.hpp"
#include "position.hpp"
#include "source_sink_overlay.hpp"
#include <stack>
namespace vg {
namespace algorithms {
/// Record a <=k-length walk in the context of a graph.
struct walk_t {
walk_t(uint16_t l,
const pos_t& b,
const pos_t& e... |
e950a751a574ba95f5e1f34a733561d49156d3fdbcea2ccf6220dc075b138e7b | C++ | 9,492 | 260 | //! \file us_vhwc_pltctl.cpp
#include "us_vhw_combine.h"
#include "us_vhwc_pltctl.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
#ifndef ZSCLF_CE // Plot scale adjusts: Contour/Points Envel/Integ
#define ZSCLF_CE 0.07
#define XSCLF_CE 0.13
#define YSCLF_C... |
5bd0e915d92aa66c68eea2763d5c64cc8008bc1c4816aa5699f9cc9f420e36cb | C++ | 9,534 | 315 | #include "GridMaker.hpp"
#include <cstdio>
#include <cmath>
#include <limits>
#include <vector>
#include <fstream>
#include <iomanip>
GridMaker::GridMaker(const AtomTypeMap& typeMap,
const Framework& framework,
const ForceField& forceField) :
mAtomTypeMap {typeMap},
... |
842b54978391abc4cee20bacea4ea9ae171ccb4a94d74aefc235f422270bb7b2 | C++ | 9,543 | 266 | /**
* \file mcmc_main.cpp: GFA (Graph Alignment Format) Fast Emitter:
* a new mapper that will be *extremely* fast once we actually write it
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <typeinfo>
#include <cassert>
#include <vector>
#include "subcommand.hpp"
#include <vg... |
b5514599516bf05bddd1553dc57a55d3f0ccb9c6b8f7a71ec55f9ecc4b0c0586 | C++ | 9,599 | 261 | #include <iostream>
#include "vg.hpp"
#include "haplotype_extracter.hpp"
#include "vg/io/json2pb.h"
#include "graph.hpp"
namespace vg {
using namespace std;
static id_t side_id(int64_t side) {
return abs(side);
}
static bool side_is_end(int64_t side) {
return side < 0;
}
static int64_t make_side(id_t id, b... |
051616ed0891379cff492b99a0da85bdb939018deb4d5277967b4686bc1634e7 | C++ | 9,669 | 301 | // g++ -fopenmp -O3 -Wall computeIBS.cpp -Iinclude -I/home/pl88/boost_1_58_0/install/include -Wl,-Bstatic -lboost_iostreams -lz -Wl,-Bdynamic -o computeIBS -L/home/pl88/boost_1_58_0/install/lib -L/n/groups/price/poru/external_software/zlib/zlib-1.2.11
#include <iostream>
#include <iomanip>
#include <sstream>
#include ... |
ef405722aec3a001271ddb26ff0cf1451969286e54078ccfdddbe373c61dc491 | C++ | 9,752 | 306 | //! \file us_worker_pc.cpp
#include "us_worker_pc.h"
#include "us_util.h"
#include "us_settings.h"
#include "us_astfem_math.h"
#include "us_astfem_rsa.h"
#include "us_model.h"
#include "us_sleep.h"
#include "us_math2.h"
#include "us_constants.h"
#include "us_memory.h"
// construct worker thread
WorkerThreadPc::Worker... |
3b9b47bc268314fef2dab486861875b13c7403422c149b88b718fd0810de1ba3 | C++ | 9,783 | 263 | #include "subcommand.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../utility.hpp"
#include "../packer.hpp"
#include "../gbwtgraph_helper.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <handlegraph/handle_graph.hpp>
#include <bdsg/overlays/overlay_helper.hpp>
#include <unistd.h>
#includ... |
ba0adae8143db70a68193f6f667f8211730208c38b5148e59019bfa6bec16790 | C++ | 9,787 | 300 | #include <typeinfo>
#include <cxxabi.h>
#include <cassert>
#include "option.hpp"
/// \file option.cpp: Definitions for our thing-doer-class-attached option
/// system
namespace vg {
using namespace std;
void Configurable::register_option(OptionInterface* option) {
// Turn into an offset from this
ptrdiff_t... |
7e71439e5554b349689dee29293c78a6cb1242631ba9aba1f0d9ba95a4321e12 | C++ | 9,796 | 248 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
80382207d7d093eca0524425907bc134b665d6c1d8c219b2b57bded509f4fab9 | C++ | 9,810 | 272 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ca4e771231766d99e6ef9df4b3f8b250556d4ae9f2135e7fa56e90aa910a42bc | C++ | 9,836 | 173 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
7864b22101bd5913fa901b11f1d71366d005b832c981587a6ba6ccc9790bb592 | C++ | 9,867 | 395 | #include <algorithm> // std::sort
#include <iostream> // std::cout, std::cerr, std::endl
#include <graphtyper/utilities/hts_reader.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/string.hpp>
#include <htslib/hfile.h>
#include <htslib/hts.h>
namespace gyper
{
HtsReader::HtsReader(HtsS... |
fda8373795bc7100806d5fb939f7c146324e90acb77db685082cb96b0a43f5e1 | C++ | 9,875 | 374 | #include "qt_test_base.h"
#include "us_stiffbase.h"
#include <algorithm>
#include <cmath>
class US_StiffBaseTest : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
stiffBase = std::make_unique<US_StiffBase>();
}
void TearDown() override {
stiffBase.reset(... |
ad8f8f3bb704b3723e38bf07c6a60ae716ae4441e618e368eae44ad7b28384ea | C++ | 10,020 | 232 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
e8abe21811610e5d5df15d0e7ecc27058d69416627986caa1c4c96c5fb240b24 | C++ | 10,022 | 306 | /** \file align_main.cpp
*
* Defines the "vg align" subcommand, which aligns a read against an entire
* graph.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../utility.hpp"
#include "../handle.hpp"
#include "../path.hpp"
#inclu... |
3a1f31bc34957466d0174725947b90cb100bfdce4ec0f9a4d846687c9403e236 | C++ | 10,038 | 245 | #include "vcf_genotyper.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
VCFGenotyper::VCFGenotyper(const PathHandleGraph& graph,
SnarlCaller& snarl_caller,
... |
932866edb7557a61e9d11bab67a22c51c0d99795942f1b0659db78632175268a | C++ | 10,040 | 259 | /// \file k_widest_paths.cpp
///
/// Unit tests for the Yen's K Widest Paths algorithm
///
#include <iostream>
#include <string>
#include "../algorithms/k_widest_paths.hpp"
#include "../handle.hpp"
#include "vg/io/json2pb.h"
#include "catch.hpp"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
namespace vg {... |
10bc54c67e9ca7b7d8121557344eb1b62964a7e04a62260920bca44b8d12a7ae | C++ | 10,066 | 289 | /// \file sampler.cpp
///
/// unit tests for the Sampler
#include <iostream>
#include <unordered_set>
#include <utility>
#include "../io/json2graph.hpp"
#include <bdsg/hash_graph.hpp>
#include "../sampler.hpp"
#include "../xg.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
TEST_CASE( "Sampler ca... |
0ffd5de82d254f282817dacb856c3682404a85f1ec865cb8af890e77d32647ac | C++ | 10,113 | 367 | #include "pm_worker.h"
void PM_WORKER::set_grid_size( double grid_conversion_factor, bool quiet )
{
// be careful with this routine!
// have to clear because any rtp data is now invalid
clear();
this->grid_conversion_factor = grid_conversion_factor;
one_over_grid_conversion_factor = 1e0 / grid_conversio... |
eddcd23109486b93dda78fe2f518be5300e07e70af9229d9aa5679d2fce722a8 | C++ | 10,152 | 250 | /**
* \file deletion_aligner.cpp
*
* Implements an aligner for global deletions
*
*/
#include "deletion_aligner.hpp"
//#define debug_deletion_aligner
namespace vg {
DeletionAligner::DeletionAligner(int8_t gap_open, int8_t gap_extension)
: gap_open(gap_open), gap_extension(gap_extension)
{
}
void Dele... |
9def79ed6aed24fb5bc2735372145536079e5b01c9272355bf18c1d42e0f16b1 | C++ | 10,179 | 281 | /**
* unittest/readfilter.cpp: test cases for the read filtering/transforming logic
*/
#include "catch.hpp"
#include "readfilter.hpp"
#include "xg.hpp"
#include "vg/io/json2pb.h"
#include "../io/json2graph.hpp"
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("read... |
2e34069ed3109061a9654d499abb7c11df3d2af4e331c59991c57961544f5393 | C++ | 10,195 | 235 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
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