sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e456bdf010f0a297796b2feb5f936e77534b048454dec42354f76cdc20fa80a8 | C++ | 13,991 | 540 | #include "FourierAnalyzer.hpp"
#include <limits>
#include <iostream>
#include <iomanip>
#include <fstream>
#include "GridayException.hpp"
FourierAnalyzer::FourierAnalyzer(EnergyGrid& grid) : mGrid {grid},
mCoeff (1),
mMaxKx {0},
mMaxKy {0},
mMaxKz {0}
{
mCoeff[0] = this->calculateCoeff(0, 0, ... |
04834fbb99abce69f8d4f3cb5cf0dcc3c899b443b67069f41a4197f70dacf871 | C++ | 13,996 | 428 | //! \file us_theme.cpp
#include "us_theme.h"
#include "us_style.h"
#include "us_gui_settings.h"
#include "us_defines.h"
#include "us_settings.h"
#if QT_VERSION >= QT_VERSION_CHECK( 6, 5, 0 )
#include <QStyleHints>
#endif
namespace
{
QString applied_signature;
bool watcher_installed = false;
int sa... |
608eaf9f0f6880ac7769272913c8e8d19b1bb2fce4f7ebb3aec94160d53f2905 | C++ | 14,059 | 320 | /** \file describe_main.cpp
*
* Defines the "vg describe" subcommand, which attempts to identify and describe a file based on readily available information.
*
* TODO: Try identifying GAM, GAF, GFA, snarls...
* TODO: Can we get any useful information from graphs?
* TODO: Could we do this better with vg::io?
*/
#... |
210aacac400535691adea71e30448d67082709fc939fba906c02f7d0c63a8e95 | C++ | 14,087 | 333 | /**
* \file incremental_subgraph.cpp: contains the implementation of IncrementalSubgraph
*/
#include "incremental_subgraph.hpp"
//#define debug_incremental_subgraph
namespace vg {
using namespace std;
IncrementalSubgraph::IncrementalSubgraph(const HandleGraph& graph,
co... |
43f3d237e84b09fe785a0e5848315bb0097e9c02f11318f76cce7b9c34bdeca4 | C++ | 14,088 | 388 | ///
/// \file masker.cpp
///
/// Unit tests for the Masker class
///
#include "catch.hpp"
#include "../masker.hpp"
#include "../handle.hpp"
#include "../gbwt_helper.hpp"
#include "../gbwtgraph_helper.hpp"
#include <bdsg/hash_graph.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/utils.h>
#include <gbwtgraph... |
e490d02ce081d7ac6a8ac84016e953d8c857d1b9e2d933ce6a219f997a125f26 | C++ | 14,088 | 408 | //! \file us_combine_models.cpp
#include <QApplication>
#include "us_combine_models.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_passwd.h"
#include "us_editor.h"
#include "us_select_runs.h"
#include "us_model_loader.h... |
dbc4dcbb7c2b9d89ba206554fb95785b743b9a49c3d0f6f27ea191d2f3e5e037 | C++ | 14,092 | 284 | /// \file statistics.cpp
///
/// unit tests for statistics functions
///
#include "vg/io/json2pb.h"
#include "support/random_graph.hpp"
#include "catch.hpp"
#include "statistics.hpp"
#include <cmath>
namespace vg {
namespace unittest {
TEST_CASE("Summary statistics", "[statistics]") {
SECTION("Even number of... |
99bb068d2bebff27894f07d10d2f94b7477c4aec13e0493537e5b945ce1f081e | C++ | 14,146 | 394 | /*
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... |
0936bb2eda898e00a98c77df0730bd8c51a50486829db56d88e5fcbebf6e687a | C++ | 14,159 | 468 | /*---------------------------------------------------------------------------------------------
* Copyright (c) Unity Technologies.
* Copyright (c) Microsoft Corporation. All rights reserved.
* Licensed under the MIT License. See License.txt in the project root for license information.
*-------------------------... |
17da5cde0418ff4e90e3c8390352ea220f6f78514a8b61b6a408def073822e22 | C++ | 14,191 | 305 | // End-to-end: a complete somo.residue entry for a residue treated as non-coded.
// The individual stages are validated in psv.cpp, grid_volume.cpp and hydration.cpp; this checks
// that the orchestration produces a populated entry, that every unset field is visibly unset,
// and that the emitted numbers are the ones t... |
bd06e7af01369222d5fdeae440da4797e0b8e847a36077e47af68aeff3e6d057 | C++ | 14,236 | 226 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement command
int t = 0;... |
bcc424310feee3e1b97d203094824662f0196d4fe7c11d645cb9df9e90c50eab | C++ | 14,258 | 352 | // construct.cpp: define the "vg construct" subcommand.
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <memory>
#include "subcommand.hpp"
#include <vg/io/stream.hpp>
#include "../constructor.hpp"
#include "../msa_converter.hpp"
#include "../region.hpp"
#include <bdsg/hash_graph.hpp>
using namesp... |
5b2c403b48c68e5d83e885f37fe7fc24acefb65506597f03a22c02f5bf15e326 | C++ | 14,343 | 275 | //------------------------------------------------------------------------------
//
// 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... |
ff3083d5ececc87d905acfcf14dfb86808561d86ebb99d32dd4613fc4956f117 | C++ | 14,359 | 226 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 1323200;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement command
... |
f3baad8af325f5d06a82298c65cd9d15a75cbc899127ce14dc5664b754cba72e | C++ | 14,362 | 469 | //! \file us_select_runs.cpp
#include "us_select_runs.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_dataIO.h"
#include "us_util.h"
#include "us_editor.h"
#include "us_constants.h"
// Main constructor... |
79becd150379283ff569c6dd5e58ac508964c7d79ad51a211d017dc7f310dfd7 | C++ | 14,384 | 428 | //! \file us_plot_control_pc.cpp
#include "us_pcsa.h"
#include "us_plot_control_pc.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
// constructor: enhanced plot control widget
US_PlotControlPc::US_PlotControlPc( QWidget* p, US_Model* amodel )
: US_Widget... |
0044d6c33ee8bd59ee091439055da5e2ce327e86034a200874f241e4a1608058 | C++ | 14,405 | 235 | /*
General parameters
*/
#define PI 3.14159265
struct P {
// general section
double sim_time = 6000;//7000;//3813340;//3631180;//1260120;//350000;//7000;//250000;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // t... |
743c5c60132629a7aaa20c6887b540f829a992c01512be11dc66fb707de9b967 | C++ | 14,405 | 429 | //! \file us_plot_control_2d.cpp
#include "us_2dsa.h"
#include "us_plot_control_2d.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
// constructor: enhanced plot control widget
US_PlotControl2D::US_PlotControl2D( QWidget* p, US_Model* amodel )
: US_Widget... |
383c69aae5e11807296d44c813b700bcb7ffabb34299d999985fac4e322d7d13 | C++ | 14,420 | 323 | #include "vg_set.hpp"
#include <vg/io/stream.hpp>
#include "source_sink_overlay.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include "io/save_handle_graph.hpp"
namespace vg {
// sets of MutablePathMutableHandleGraphs on disk
void VGset::transform(std::function<void(MutableHandleGraph*)> lambda) {
/... |
fcf573f6b51532c9e1032112d4f49b29ecfe639fc4309836b21f236b42c7c6ab | C++ | 14,428 | 367 | // test_us_datafiles_unit.cpp - Unit tests for US_DataFiles class
#include "qt_test_base.h"
#include "us_datafiles.h"
#include <QString>
#include <QDir>
#include <QFile>
#include <QTextStream>
#include <QTemporaryDir>
#include <QXmlStreamWriter>
using namespace qt_matchers;
class TestUSDataFilesUnit : public QtTestBa... |
a49f957080c62fd6ec2d0ca37f581346744dd9c97c00efe6a48a8e27ae2b890f | C++ | 14,439 | 444 | /// \file packed_graph.cpp
///
/// Unit tests for the PackedGraph class.
///
#include <iostream>
#include <sstream>
#include <set>
#include "vg/io/json2pb.h"
#include "support/random_graph.hpp"
#include "support/randomness.hpp"
#include "bdsg/packed_graph.hpp"
#include "catch.hpp"
namespace vg {
namespace unitt... |
df49c315e6d855fe9c33ebdd6b97ab67627c02a63a409bb8d313682c4b45ee9c | C++ | 14,563 | 446 | //! \file us_scan_excl_gui.cpp
#include "us_scan_excl_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_images.h"
US_ScanExclGui::US_ScanExclGui( QStringList channels_desc, QList< int > scan_beg, QList< int > scan_end,
... |
8a0a31cdba4b14be83fc8f1a8eec2a421721bf33e2f26c06f9d8f83272c8fa79 | C++ | 14,576 | 519 | #include <cstdint>
#include <fstream>
#include <iostream>
#include <map>
#include <string>
#include <unordered_map>
#include <vector>
#include <paw/align.hpp>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/graph/haplot... |
20da5eeb7f0fe05cdb52214ebec900b660405134e7474d1b62dbf9610c814246 | C++ | 14,590 | 617 | #include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <time.h>
#include <math.h>
#include <vector>
#include <list>
#include <algorithm>
#include <numeric>
using namespace std;
int main(int argc, const char * argv[]) {
int i;
int j;
int l_begin;
int n_points;
i... |
7f4ec74df4e613aff7fd066aa6941be8289fbd4185702c533f8bfe087dade5de | C++ | 14,593 | 445 | //------------------------------------------------------------------------------
//
// 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... |
6e9a6eddd2ff1d025c301ee77d0f224cac5347ce50d3338a8d86463804ab5617 | C++ | 14,681 | 548 | //! \file us_ramp.cpp
#include "us_ramp.h"
#include "us_gui_settings.h"
#include "us_math2.h"
#include "us_util.h"
#include "us_settings.h"
#include "stdio.h"
#include <QDomDocument>
#include "us_crc.h"
#include "us_matrix.h"
#ifdef WIN32
#define round(x) floor( (x) + 0.5 )
#endif
// Generic constructor
US_Ramp::... |
b678fa96fe3732b13dd95a8187f92fb4b2f322b208cc7b7a0be41c7390ae8119 | C++ | 14,693 | 358 | /** \file depth_main.cpp
*
* Estimate sequencing depth from a (packed) alignment.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <algorithm>
#include <iostream>
#include <sstream>
#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include <vg/io/stream.hpp>
#include "../handle.hpp"
#incl... |
f0f00091cb92e2a6d1e462995f14758194c0a091119f2c03b5dddeae8319f99f | C++ | 14,705 | 260 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 1323200;//7000;//1200080;//8553860;//30000;//8460580;//8460580;//250000;//8460580;//8460580;//8485920;//250000;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run t... |
836b24addbd9ea5ee2cb270eaa910ef47963742881472fa32a10477a5de0c40a | C++ | 14,822 | 238 | /* configure the network */
/* neuron groups */
int EC_LI_II_Multipolar_Pyramidal=sim.createGroup("EC_LI_II_Multipolar_Pyramidal",
p.EC_LI_II_Multipolar_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate=sim.createGroup("MEC_LII_Stellate",
... |
303c9aed9d9e26acc3b4b9f91f180abf96f410bc940a0551ddefec8e79371907 | C++ | 14,922 | 226 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 250000;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement command
int t = 0; ... |
7b05a1e530bb31523b4ccd53e5e64b68798fdbaebffcb06d605bb57e8fe9be0d | C++ | 14,984 | 374 | /**
* \file
* msa_converter.cpp: contains a class that can construct VGs from clustal MSAs
*/
#include "vg.hpp"
#include "msa_converter.hpp"
//#define debug_msa_converter
namespace vg {
using namespace std;
MSAConverter::MSAConverter() {
// nothing to do
}
MSAConverter::~MSAConver... |
347fc96b809388e4ac800b9c614ffb81fbbf325f8ae925317ce4a53648c51af8 | C++ | 15,101 | 412 | //------------------------------------------------------------------------------
//
// 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... |
b05fccbf9d6bcd21166f13100b6d9d3643042c68971f6ae6ae5bd40a09f35530 | C++ | 15,127 | 316 | //------------------------------------------------------------------------------
//
// 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... |
3604fb609979348e75b0c295fb84f1729a0d5f5630582409fb4b0a18e318342c | C++ | 15,134 | 548 | //! \file us_widgets_dialog.cpp
#include "us_widgets_dialog.h"
#include "us_widgets.h"
#include "us_gui_settings.h"
#include "us_theme.h"
#include "us_images.h"
#include <QStyleFactory>
US_WidgetsDialog::US_WidgetsDialog( QWidget* w, Qt::WindowFlags f, bool set_style )
: QDialog( w, f )
{
if (set_style)
... |
ff9eca9c2f91e72a351e3fad7a38f8a303f5ddfe9e19d02e3c6a48b94bd65e7f | C++ | 15,164 | 406 | #include <cstdint>
#include "variant_recall.hpp"
#include "cactus_snarl_finder.hpp"
#include "traversal_finder.hpp"
#include "augment.hpp"
#include "translator.hpp"
#include "xg.hpp"
#include "utility.hpp"
#include "statistics.hpp"
#include "path_index.hpp"
using namespace xg;
namespace vg {
using namespace std;
... |
ee3533f5d6571a80d66eae5e5a6e90947f0867c5f3881cd4c8e67528f6f5b3bf | C++ | 15,224 | 436 | //! \file us_model_params.cpp
#include "us_model_params.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#define DbgLv(a) if(dbg_level>=a)qDebug()
// Constructor: remove-distributions dialog widget
US_ModelParams::US_ModelParams( QVector< DisSys >& adistros,
QWidget* p ) : US_WidgetsDialog( p, Qt::Window... |
5ef132f1f2dbc04bffccf72cb063b66a282f409549d91b228c92d0a152e0d664 | C++ | 15,227 | 355 | //------------------------------------------------------------------------------
//
// 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... |
5b87f382edf2dd4640011b06d5777eae9d5f152c81057fd8a135088536880073 | C++ | 15,333 | 319 | // Tests for the Durchschlag & Zipper psv engine.
//
// Three layers:
// 1. arithmetic -- the increment constants must reproduce the published GROUP increments
// (DZ94 Table 4), which is an independent check that the atomic table was transcribed right
// 2. synthetic molecules with real coordinates -- exercis... |
0b7ee133b336e860d1f9eb4535fb74bf908b38c21657066b2387938d281e7282 | C++ | 15,352 | 498 | //! \file us_loadable_noise.cpp
#include "us_loadable_noise.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_noise.h"
#include "us_util.h"
#include "us_investigator.h"
// Null constructor
US_LoadableNoi... |
13555a6fac2fe9b4e03fd158db2967fde05c0ae26dd5b5aa06ee10b4c5f3d35c | C++ | 15,372 | 508 | #include "shd.h"
// #define SH_TEST
#define SHOW_MPI_TIMING
#define RUN_SINGLE
#if defined( SH_TEST )
#include <sstream>
#endif
#if defined( RUN_SINGLE )
#include <time.h>
#endif
int world_size;
int world_rank;
void our_abort( MPI_Comm comm, int errno )
{
#if !defined( RUN_SINGLE )
MPI_Abort( comm, errno );
#en... |
7b16dbf8055f0e5145ca2e22d85850dd468d9d6e66d8482a002854a1b67fc8f7 | C++ | 15,398 | 529 | //------------------------------------------------------------------------------
//
// 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... |
2b04d6e591361c132674216f0422dc048015855f5af1cab23f63f12cd3c0e25c | C++ | 15,469 | 374 | /// \file path.cpp
///
/// unit tests for Paths and their utility functions
///
#include <iostream>
#include <string>
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include <bdsg/hash_graph.hpp>
#include <bdsg/overlays/reference_path_overlay.hpp>
#include "../path.hpp"
#include "../vg.hpp"
#include "catch.hpp"
n... |
3dafaba4812b98762a9a32c8bff2ab510c644503fdce72ef33c5159785a0a1ac | C++ | 15,472 | 341 | /**
* \file k_widest_paths.cpp
*
* Implementation of Yen's Algorithm over the bidirected graph.
*/
#include "k_widest_paths.hpp"
#include <structures/updateable_priority_queue.hpp>
namespace vg {
namespace algorithms {
using namespace structures;
//#define debug_vg_algorithms
pair<double, vector<handle_t>> wi... |
d84f8fc9de4cee1adff485ded848928ed1661ef762b2eedd618e1eedab36ccb6 | C++ | 15,531 | 386 | //------------------------------------------------------------------------------
//
// 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... |
46caf0357ca171e2304aec570ccbeafd8ebbd8f8490aaf277ff42beb5d501dc2 | C++ | 15,592 | 1 | vector<float> ext_dir{1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01... |
409c32976b98a3c63cc90a67cf500411feb23f02755c60bb57de4c02b988fdf1 | C++ | 15,598 | 505 | #include <QXmlStreamWriter>
#include <QXmlStreamReader>
#include <QBuffer>
#include <QDebug>
#include <QStringList>
#include <QMap>
#include <QDir>
#include <QFile>
#include <QTemporaryDir>
#include <QTemporaryFile>
#include "us_analyte.h"
#include "mock_us_db2.h"
#include "qt_test_base.h"
#include "us_constants.h"
u... |
d50d734ce6b5367fe969e94080e0950e4e91e427332ca17b764d5db5d46460e5 | C++ | 15,604 | 412 | //------------------------------------------------------------------------------
//
// 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... |
a0a025c30ae77fd2fc8eda0de3114c90bf74efd44eb95278d668f759a3b89632 | C++ | 15,639 | 640 | #include <iostream>
#include <ctime>
#include <string>
#include <sstream>
#include <vector>
#include <fstream>
#include "./include/nr3.h"
#include "./include/network.h"
#include "./include/forwardmethod.h"
#include "./include/InverseMethod.h"
#include "./include/LUdcmp.h"
using namespace std;
void SalvarDados (Rede b... |
1056a0d4650be27ede0bd684c0bcee5d9fee92d86d492a2d38f1a930c423d288 | C++ | 15,737 | 284 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
39889ddd08b06d9ed2bfe26ec736e5c25fb0655334c3cb73d1280358b9c621f8 | C++ | 15,745 | 491 | //! \file us_plot_control_fem.cpp
#include "us_fematch.h"
#include "us_plot_control_fem.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
// constructor: enhanced plot control widget
US_PlotControlFem::US_PlotControlFem( QWidget* p, US_Model* amodel )
: US... |
accb2cf0859121218fc6f0936dbb3c6ef6b1a168541a9bffa9e621af9c04c3de | C++ | 15,775 | 264 | /* configure the network */
/* neuron groups */
int EC_LI_II_Multipolar_Pyramidal=sim.createGroup("EC_LI_II_Multipolar_Pyramidal",
p.EC_LI_II_Multipolar_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate=sim.createGroup("MEC_LII_Stellate",
... |
e78b1c40745d350a59eccdae39e069d0ed5a4c2dc5054eee1830e4339e41eee3 | C++ | 15,776 | 264 | /* configure the network */
/* neuron groups */
int EC_LI_II_Multipolar_Pyramidal=sim.createGroup("EC_LI_II_Multipolar_Pyramidal",
p.EC_LI_II_Multipolar_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate=sim.createGroup("MEC_LII_Stellate",
... |
759326093c48735ba755928050e8d568141bff0dafcbb17620c13ea9594dccfc | C++ | 15,853 | 552 | //! \file us_data_process.cpp
#include "us_data_process.h"
#include "us_data_model.h"
#include "us_sync_exper.h"
#include "us_util.h"
#include "us_settings.h"
#include "us_datafiles.h"
// class to process operatations on data: upload/download/remove
US_DataProcess::US_DataProcess( US_DataModel* dmodel, QWidget* pare... |
b9d33df489802225c31252d0b530c7d90d328af5d429732f6241cdad19993f42 | C++ | 15,885 | 267 | /* configure the network */
/* neuron groups */
int EC_LI_II_Multipolar_Pyramidal=sim.createGroup("EC_LI_II_Multipolar_Pyramidal",
p.EC_LI_II_Multipolar_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate=sim.createGroup("MEC_LII_Stellate",
... |
acf8ba3cf8cbef993ef9a6de204b34cb715dd49bd6ab76a67fba955a4dbcfc07 | C++ | 15,992 | 411 | #include "graph_synchronizer.hpp"
#include "algorithms/extract_connecting_graph.hpp"
#include <iterator>
namespace vg {
using namespace std;
GraphSynchronizer::GraphSynchronizer(VG& graph) : graph(graph) {
// Because in general paths can overlap each other, and because we can't
// build a path index after a... |
84aa00b14ecc91dca851d6850acf7afbe76ea3ce66ea80e5e5d3b2949d4338b4 | C++ | 16,086 | 390 | //------------------------------------------------------------------------------
//
// 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... |
54029a9c1b2bf5901719749093c296b1d3ef2c30dac910dc6c8485826acc3fe8 | C++ | 16,187 | 503 | // g++ -fopenmp -O3 -Wall phaseImpMissing.cpp -Iinclude -I/home/pl88/boost_1_58_0/install/include -Wl,-Bstatic -lboost_iostreams -lz -Wl,-Bdynamic -o phaseImpMissing -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 <fstream>... |
9c999714cf66bde0b336c84cebe1e60570a76dc873d6b6062ce85541b5ede966 | C++ | 16,288 | 633 | #include "qwt3d_coordsys.h"
using namespace std;
using namespace Qwt3D;
CoordinateSystem::CoordinateSystem(Triple first, Triple second, COORDSTYLE st)
{
autodecoration_ = true;
axes = std::vector<Axis>(12);
setStyle(st);
setLineSmooth(true);
init(first,second);
setAxesColor(RGBA(0,0,0,1));
se... |
30b3fb2e71adfab6c3891b6702b1dde80e8d42de5d669403a9379f2c052aee23 | C++ | 16,351 | 596 | #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;
void SurfacePlot::createDataG()
{
createFloorData();
if (plotSt... |
a00ceb47083dddeed45bef798173a53e6a729e77d66dec5552b31e4eadcb1a66 | C++ | 16,359 | 664 | #include <algorithm>
#include <array>
#include <chrono>
#include <ctime>
#include <iterator>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/typer/alignment.hpp>
#include <graphtyper/utilities/io.hpp>
#in... |
727abb10781567ca6ca75b7c327e668fb51a113e872de2d2e3474bf8fe47dedc | C++ | 16,364 | 373 | /**
* \file
* unittest/source_sink_overlay.cpp: test cases for the source and sink node adding overlay.
*/
#include "catch.hpp"
#include "support/random_graph.hpp"
#include "../source_sink_overlay.hpp"
#include "../kmer.hpp"
#include "../vg.hpp"
#include "../io/json2graph.hpp"
#include <bdsg/hash_graph.hpp>
#in... |
74a1cb3e91ee89b7a3938e8da7730a41ea8e55cb3b73aece9b4405a98413c186 | C++ | 16,464 | 436 | //------------------------------------------------------------------------------
//
// 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... |
d82f129d654e29b3b3050bdafca7c9f006d863e4d56427174b2b22b4d16ffdd8 | C++ | 16,615 | 393 | /** \file
*
* Unit tests for utility classes and functions for working with GBWT, GBWTGraph, and GCSA2.
*/
#include "../gbwt_helper.hpp"
#include <gbwtgraph/utils.h>
#include "catch.hpp"
namespace vg {
namespace unittest {
//------------------------------------------------------------------------------
name... |
4a7e37e08f84f2b79890ead5d91116a09fe1f6381bc9cc5dc57c62de17b0b73a | C++ | 16,668 | 474 | //------------------------------------------------------------------------------
//
// 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... |
dc27a71e2ddf49d316f31825dce638e6063524b9e39304d5d9df262a59b1fc8e | C++ | 16,739 | 441 | /*!
* \file MySampler.cpp
* Allows sampling from an ellipsoid and also implements Dubins airplane adapted informed sampling.
*
* Created on: Feb, 04 2016
* Author: Daniel Schneider, ASL
* Florian Achermann, ASL
*
* Copy from OMPL (http://ompl.kavrakilab.org/classompl_1_1base_1_1PathLengthD... |
39958d438508ca3bf752db72d05e27ef2a3118fcf41364f4f561b92d777196be | C++ | 16,778 | 433 | //------------------------------------------------------------------------------
//
// 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... |
a5fa77f1128dafd6b1795511b0a92d07e6f3b5789b8cadc966c6ce727b38947c | C++ | 16,828 | 446 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/index/indexer.hpp>
#include <graphtyper/index/ph_index.hpp>
#include <graphtyper/utilitie... |
8ec3e6d98e769aba23b1ab9787af13e0ba4e60feaabff9c5e535225a3dfa8a57 | C++ | 16,854 | 308 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
367b923f48f2c0ee15e97511151f260e22b3e8b0afe516f218ac9a420ce62224 | C++ | 16,865 | 446 | ///////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// //
... |
dbafa2f0e125fdf44e734f3d6a587f84e9dc6aa09b2b7a4eb9effd19df5078fa | C++ | 16,941 | 610 | //! \file gui/us_license.cpp
#include "us_license.h"
#include "us_license_t.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_help.h"
#include "us_defines.h"
#include "us_http_post.h"
US_License::US_License( QWidget* parent, Qt::WindowFlags flags )
: US_Widgets( true, parent, flags )
{
setWind... |
9ee6a01c4fe479f26b525f9460a0af070599ab50ba641fd42290c4e68ef88971 | C++ | 16,999 | 565 | //! \file us_get_run.cpp
#include "us_get_run.h"
#include "us_experiment.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_db2.h"
#include "us_passwd.h"
#include "us_util.h"
#include "us_investigator.h"
// Primary constructor to establish the dialog
US_GetRun::US_GetRun( QString& run, bool inDB ) ... |
e4925d7d127f817866c5106ded9dcaeb1af28b3574c19c509f3afadb05f38ef8 | C++ | 17,008 | 432 | /** \file autoindex_main.cpp
*
* Defines the "vg autoindex" subcommand, which produces indexes needed for other subcommands
*/
#include <iostream>
#include <sstream>
#include <algorithm>
#include <cctype>
#include <unistd.h>
#include <getopt.h>
#include <htslib/hts.h>
#include <htslib/vcf.h>
#include <gbwt/utils.h>... |
1ab6247152cd8b4e5cabc5e084d63684d52b758b3a0e186897f2d63325a0795c | C++ | 17,085 | 483 | //! \file us_adv_analysis_2d.cpp
#include "us_2dsa.h"
#include "us_adv_analysis_2d.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include <qwt_legend.h>
// constructor: enhanced plot control widget
US_AdvAnalysis2D::US_AdvAnalysis2D( US_SimulationParameters* sim_par,
bool& loadDB, QWidget* p ) : US_W... |
bd124641b23f3fa724430ffd794aa106739ec267ba0d2bedd7dcf1924bb6fd64 | C++ | 17,127 | 464 | /** \file prune_main.cpp
*
* Defines the "vg prune" subcommand, which prunes the complex regions of the
* graph for GCSA2 indexing.
*
* By default, pruning removes the nodes touched by paths of length
* --kmer-length crossing more than --edge-max non-trivial edges. Graph
* regions shorter than --subgraph_min are... |
202c0be2510be81dfbd87b6eb1c39efcd8922a5a617b82c80a8641fe10e33044 | C++ | 17,129 | 496 | //! \file us_dmga_mc_stats.cpp
#include "us_dmga_mc_stats.h"
#include "us_math2.h"
// Class of static functions for DMGA-MC statistics
// Build a vector of iteration models from a DMGA-MC model
int US_DmgaMcStats::build_imodels( US_Model& model,
QVector< US_Model >& imodels )
{
imodels.clear();
QStringLi... |
8403f7e28a79a4dd078e5b36a112616c3373ff0e9a9380180687b4b31ee19382 | C++ | 17,213 | 357 | #include "legacy_caller.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
LegacyCaller::LegacyCaller(const PathPositionHandleGraph& graph,
SupportBasedSnarlCaller& snarl_caller,
... |
ffaf872ff6d0386a780b18044d8975d9a4153271d8ece9a154d90fd90726074b | C++ | 17,242 | 434 | /** \file augment_main.cpp
*
* Defines the "vg augment" subcommand, which augments a graph using a GAM as a first
* step before computing sites and calling variants.
*
* It presently only supports augmentation via pileup (as originally used by vg call).
*
* vg mod -i is an alternative, but as currently impleme... |
628bc6c102837c98412e42ffbada4302f94c084838df15bbdf4b4421859a5fe9 | C++ | 17,266 | 402 | /**
* \file load_proto_to_graph.cpp
* Implementation for backend-agnostic Protobuf loading.
*/
#include "load_proto_to_graph.hpp"
#include "../hash_map.hpp"
#include "../handle.hpp"
#include "../crash.hpp"
#include "load_proto_to_graph.hpp"
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include <vg/io/regist... |
d2db492555283beb66a54d4f53db581c3faf9339e5b8a58e63f79c469df7a1ca | C++ | 17,344 | 497 | #include "us_mpi_analysis.h"
#include "us_math2.h"
#include "us_settings.h"
#include "mpi.h"
// Parse XML routines
void US_MPI_Analysis::parse( const QString& xmlfile )
{
QFile file ( xmlfile );
if ( ! file.open( QIODevice::ReadOnly | QIODevice::Text) )
{
// Fail quietly - can't use udp yet
if (... |
b6f0136aee33d39204b93dfd671ed079eab2c0b9c4dfcc45a6968dd605682ffd | C++ | 17,353 | 427 | //------------------------------------------------------------------------------
//
// 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... |
473d08487e493b8d5c5ed18075f5765ec60086dbcae36c9d6bb9058c636e1826 | C++ | 17,373 | 395 | #include "masker.hpp"
#include <algorithm>
#include <unordered_set>
#include "integrated_snarl_finder.hpp"
//#define debug
namespace vg {
Masker::Masker(gbwtgraph::GBWTGraph& _graph, const SnarlManager* _snarl_manager) : graph(&_graph), snarl_manager(_snarl_manager) {
if (!snarl_manager) {
init_snarls(... |
3f1865d06a1ef3a18b12e30ff08bd53fe5bb2838f23b31bf82b5841cdd2fcd4c | C++ | 17,375 | 360 | //------------------------------------------------------------------------------
//
// 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... |
99f75ac4ee53725afe0b9b24c490beba4970f2d85e531000a74e215c7bf0ec94 | C++ | 17,399 | 367 | //------------------------------------------------------------------------------
//
// 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... |
1e07008375f84f51d1b0966e6f41f7ee8857a5afaf8a653d57440098cfe98fd7 | C++ | 17,464 | 365 | #include "kmer.hpp"
#include <atomic>
//#define debug
namespace vg {
const string SizeLimitExceededException::msg = "error: exceeded limit of size on disk";
const char* SizeLimitExceededException::what() const throw() {
return msg.c_str();
}
void for_each_kmer(const HandleGraph& graph, size_t k,
... |
92cbcfa3a238450136274b6cfd7ec92b6926b026166754a2e4d4d77e1770c33d | C++ | 17,498 | 710 | #include "shd_sh.h"
// #define USE_GSL
// #include <gsl/gsl_sf_bessel.h>
#include <iostream>
// #include <iomanip>
namespace nr {
bool plegendre( int l, int m, shd_double x, shd_double &result )
{
shd_double fact;
shd_double oldfact;
shd_double pll = 0e0;
shd_double pmm;
shd_doubl... |
0647e7bbd1607d43de9c04c40687838aecaf5ee32a330dad76f33c7433aa77dc | C++ | 17,590 | 481 | //------------------------------------------------------------------------------
//
// 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... |
036b1d692aeeea9ef60fe38788d73cc774b4f96557ccf698d214afa22706453e | C++ | 17,607 | 432 | ///
/// \file cactus_snarl_finder.cpp
///
///
//#define debug
#include "subgraph_overlay.hpp"
#include "handle.hpp"
#include "cactus_snarl_finder.hpp"
namespace vg {
using namespace std;
CactusSnarlFinder::CactusSnarlFinder(const PathHandleGraph& graph, const string& hint_path) :
graph(&graph) {
if (!hin... |
551d6f15539a8ac6e7e114d1f1e5ffc5b74518000414612e587045ccfb035bff | C++ | 17,619 | 443 | //------------------------------------------------------------------------------
//
// 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... |
e31cd165fbdf0198ef2ce0c0bda80d662415e52e3f290992d058f6167ef1add9 | C++ | 17,636 | 384 | //------------------------------------------------------------------------------
//
// 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... |
98fd94fc8e289b58deface64be3c9767ab9e732b82de734421733eae211f71b3 | C++ | 17,637 | 488 | //
// Tests for haplotype score functions
//
#include "catch.hpp"
#include "haplotypes.hpp"
#include "../io/json2graph.hpp"
#include "xg.hpp"
#include "vg.hpp"
#include <bdsg/hash_graph.hpp>
#include <numeric>
namespace unittest {
using namespace std;
using thread_t = vector<gbwt::node_type>;
vg::Path path_from_th... |
5a290e9de642982b5cfa7977d379fa0803001f54c8a364b3e46e77d75362ea63 | C++ | 17,853 | 492 | // test_us_dataio_unit.cpp - Unit tests for US_DataIO class
#include "qt_test_base.h"
#include "us_dataIO.h"
#include <QString>
#include <QVector>
#include <QByteArray>
#include <limits>
using namespace qt_matchers;
class TestUSDataIOUnit : public QtTestBase {
protected:
void SetUp() override {
QtTestBase... |
49e2dfa306dd740a7ba93a3ebd5df7aaecb91f3df334c911dfde97ffb129f025 | C++ | 17,939 | 501 | #ifdef __APPLE__
// We can't set _POSIX_C_SOURCE on OS X because it hides the non-POSIX dladdr() with no way to get it back.
// But we do need level 200809L features generally (for example, for EOWNERDEAD and ENOTRECOVERABLE on OS X).
// So we do it the Apple Way.
#define __DARWIN_C_LEVEL __DARWIN_C_FUL... |
1ee00634fda5bdf099a7de95ed618e147093c5a918b6883fcf494d8765d212fc | C++ | 17,953 | 571 | //! \file us_select_edits.cpp
#include "us_select_edits.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_dataIO.h"
#include "us_util.h"
#include "us_editor.h"
#include "us_constants.h"
// Main construct... |
8195f89d085d4dfcc85252b5137472e207e68f76fe2eb5a68166ecedd749b0b3 | C++ | 17,987 | 472 | //------------------------------------------------------------------------------
//
// 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... |
503e1ccf73a2fe10f26cac132b0f6545ff8aa06e00c1a8d7dde19f9c74fa8338 | C++ | 17,999 | 474 | #include <algorithm>
#include <array>
#include <chrono>
#include <fstream>
#include <H5Cpp.h>
#include <iostream>
#include <limits>
#include <memory>
#include <random>
#include <sstream>
#include <stdexcept>
#include <string>
#include <sys/stat.h>
#include <vector>
#include <ompl/base/PlannerStatus.h>
#include <ompl/b... |
80bf30804b2767c91a3ce9773675d7e06973186f6b1b1a75dd8e3cac91828c79 | C++ | 18,090 | 608 | //! \file us_solution_gui.cpp
#include "us_solution_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_buffer_gui.h"
#include "us_analyte_gui.h"
#include "us_solution.h"
#include "us_edit_spectrum.h"
#include "us_editor_gui.... |
983f630c5bcf8c89b6ace6ae55980c0054c63bb5ef10fef37935e6c963740634 | C++ | 18,276 | 518 | //
// xg.cpp
//
// Tests for xg algorithms
//
#include "catch.hpp"
#include "vg.hpp"
#include "xg.hpp"
#include "graph.hpp"
#include "../io/json2graph.hpp"
#include "algorithms/subgraph.hpp"
#include "bdsg/hash_graph.hpp"
#include <stdio.h>
namespace vg {
namespace unittest {
using namespace std;
TEST... |
5df1d6e6131006641339f0eae3165611b974bfef34d031a238b2f49eadaa8b77 | C++ | 18,302 | 447 | /*
Copyright (c) 2012 Daniel Forsberg
dannne.forsberg@outlook.com
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program... |
fcb250532b6f5ed8dc0b6d483a149eccf8040d2cc105bc72caad7df161cd931b | C++ | 18,314 | 459 | /// \file dagified_graph.cpp
///
/// unit tests for the overlay based dagify algorithm
///
#include <iostream>
#include "vg/io/json2pb.h"
#include "../dagified_graph.hpp"
#include "../split_strand_graph.hpp"
#include "support/random_graph.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
namespace vg {
name... |
83053d6334bd858f28f4598853807bc612fb538812a56b28d1f1aa1b066f0a4d | C++ | 18,404 | 396 | /**
* \file dagified_graph.cpp: contains the implementation of DagifiedGraph
*/
#include "dagified_graph.hpp"
//#define debug_dagify
namespace vg {
using namespace std;
DagifiedGraph::DagifiedGraph(const HandleGraph* graph, size_t min_preserved_path_length,
size_t max_num_du... |
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