sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
52e35294597bfd3da9762ef1d0b478485e17a00e03777c1c0ca5296587343577 | C++ | 5,533 | 207 | #include <vector>
#include <string>
#include <iostream>
#include <fstream>
#include <cstdio>
#include <cstdlib>
#include "StringUtils.hpp"
#include "FileUtils.hpp"
#include "Types.hpp"
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
namespace FileUtils {
using std::strin... |
addd6e8c202b64a2b125942df1c7e49286eb2d58542478371e0375ad2addd287 | C++ | 5,551 | 266 | #include <qbitmap.h>
#include "qwt3d_label.h"
using namespace Qwt3D;
bool Label::devicefonts_ = false;
Label::Label()
{
init();
}
Label::Label(const QString & family, int pointSize, int weight, bool italic)
{
init(family, pointSize, weight, italic);
}
void Label::init(const QString & family, i... |
312efb37dd00d9153a2fa5da9ee5e17af83de9c7d9ef1b09467b1e0f2c2126e4 | C++ | 5,581 | 158 | //------------------------------------------------------------------------------
//
// 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... |
afb7ffa32c50b99d851bef8bcf8af6263c7b6a6715d16129de942c5b8c81eadc | C++ | 5,612 | 151 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
a707930f423b4c2c6da2588d1e9cba9826c1e8e3ea3951e61bfdf0375f882850 | C++ | 5,618 | 173 | //! \file us_select_lambdas.cpp
#include "us_select_lambdas.h"
#include "us_settings.h"
#include "us_gui_settings.h"
US_SelectLambdas::US_SelectLambdas( QVector< int > lambdas )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() )
{
original = lambdas;
nbr_select = 0;
nbr_orig = original.size();
db... |
2e6448d044e49837cc7302f78cf4ccc3bee91819060c157e419851bf7f8bb19a | C++ | 5,631 | 174 | //! \file us_colorgradIO.cpp
#include "us_colorgradIO.h"
#include "us_defines.h"
int US_ColorGradIO::read_color_gradient( QString xmlfilename,
QList< QColor >& gcolors )
{
int rc = XFS_OK;
gcolors.clear(); // clear out the list
QList< int > cp... |
401a64a7bf578a6479c0ca02315b422a7cd10c0c4dc57fd121d3e9d2b756dfed | C++ | 5,653 | 158 | //------------------------------------------------------------------------------
//
// 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... |
93021b8b02570f4da9a50dca21de3abfb505c0a4f8c248cc9ac9d76eb32ae3c9 | C++ | 5,664 | 203 | #include "NlistMaker.hpp"
#include <cstdio>
#include <cmath>
#include <limits>
#include <queue>
#include <vector>
#include <fstream>
#include <iomanip>
NlistMaker::NlistMaker(const AtomTypeMap& typeMap,
const Framework& framework,
const ForceField& forceField) :
mAtomTyp... |
c05336d9b9803854fcf9d31308b76d2d90770c5368c52294592a36419bb5e7e4 | C++ | 5,664 | 173 | //! \file us_model_adpars.cpp
#include "us_model_adpars.h"
#include "us_settings.h"
#include "us_gui_settings.h"
// Main constructor with addition-parameters count and reference to params list
US_ModelAdPars::US_ModelAdPars(
int a_napars,
QList< double >& a_udpars )
: US_WidgetsDialog( nullp... |
b1b51a9fa3fa3b77815b540a1ced0ebd6ac3dc6b1eb3185d1d2c528192fe7631 | C++ | 5,671 | 157 | #include "feature_set.hpp"
#include <sstream>
namespace vg {
using namespace std;
void FeatureSet::load_bed(istream& in) {
// We want to read the BED line by line
string line;
while (getline(in, line)) {
// Turn each line into its own stream
stringstream line_stream(line);
... |
a76cc150d4d2a07eb15c0954a2daec6522abafc81e8cd865c4adca664d4825e7 | C++ | 5,686 | 109 | // emit_residue.cpp -- perceive a structure and emit a somo.residue entry (+ any new somo.hybrid
// lines) for a chosen residue, demonstrating "on-the-fly" generation for an unknown residue.
// Usage: emit_residue <pdb> <RESNAME> [resSeq]
#include <cstdio>
#include <fstream>
#include <set>
#include <sstream>
#include <... |
27371f31dc856f0f73110a6769411544055eab35a82206cc23268dd9fb003538 | C++ | 5,731 | 158 | /** \file
*
* Unit tests for various graph algorithms.
*/
// These are the algorithms we want to test.
#include "../algorithms/extract_subchain.hpp"
// Other includes.
#include <bdsg/hash_graph.hpp>
#include <random>
#include "catch.hpp"
namespace vg {
namespace unittest {
//----------------------------------... |
1b2b672a62b0e3f4736612476ff818799943fa2edf5473c7a25a2c688fcbb475 | C++ | 5,803 | 163 | #include "translator.hpp"
#include <vg/io/stream.hpp>
namespace vg {
using namespace std;
Translator::Translator(void) { }
Translator::Translator(istream& in) {
function<void(Translation&)> lambda = [&](Translation& trans) {
translations.push_back(trans);
};
vg::io::for_each(in, lambda);
bui... |
5fda17e0375c93456b70515be30aa40f15feb11153a56a523c9bd0064b95b11c | C++ | 5,830 | 168 | #include "varint.hpp"
#include <iostream>
#include <sstream>
#include <limits>
//#define DEBUG_VARINT
namespace vg {
using namespace std;
#ifdef DEBUG_VARINT
void write_byte_as_bits_to_stderr(size_t value) {
cerr << ((value & (1<<7)) ? "1" : "0")
<< ((value & (1<<6)) ? "1" : "0")
<< ((value &... |
9147aa4eadcc2490e232b109783cb48576736924d99845b9c5bb402e948be4bd | C++ | 5,834 | 185 | #include <string>
#include <iostream>
#include <iomanip>
#include <exception>
#include <regex>
#include "../Griday.hpp"
#include "../Vector.hpp"
#include "../Random.hpp"
std::vector<std::string>
split(const std::string& text, const std::string& delimiters = "\\s")
{
std::regex delimiter ("[" + delimiters + "... |
a999ff7bb47011351f55fec0b350bf334bcfa73be70bbbf2e3bad0be444dc645 | C++ | 5,901 | 195 | // Version 4 uses a different wavelength scale; versions 2 and 3 are unsupported.
#include "qt_test_base.h"
#include "us_crc.h"
#include "us_dataIO.h"
#include <QByteArray>
#include <QFile>
#include <QTemporaryDir>
#include <QtEndian>
namespace
{
// Header layout of a version 5 file, from writeRawData(): 4 magic + ... |
c31bc9ceb598d453d99ec6393d2d346e8eaeb9d50ee9255bc07aae5ba2f04c8a | C++ | 5,933 | 253 | #include "qwt3d_helper.h"
#include "qwt3d_autoscaler.h"
using namespace Qwt3D;
namespace
{
double floorExt( int& exponent, double x, std::vector<double>& sortedmantissi)
{
if (x == 0.0)
{
exponent = 0;
return 0.0;
}
double sign = (x > 0) ? 1.0 : -1.0;
double lx = log1... |
4cf78a53246620348029a34360bee329cba154673a9af143e5e6410fb03fcc7a | C++ | 5,963 | 1 | vector<float> ext_dir_initial{0,12.5939616406340,12.5939616406340,22.7838205293291,34.8769106806325,34.8769106806325,60,34.8769106806325,34.8769106806325,22.7838205293291,12.5939616406340,12.5939616406340,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,12.5939616406340,12.5939616406340,22.7838205293291,34.8769106806325,60,60,60,... |
c032c0c48c93ebeca6e8b7979631cfc87965bcbac1bb9c9cc4200880bf9e86d4 | C++ | 5,963 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,12.5939616406340,12.5939616406340,12.5939616406340,0,0,0,0,0,0,0,0,0,0,0,0,12.5939616406340,12.5939616406340,12.5939616406340,0,0,0,0,0,0,0,0,0,0,0,12.5939616406340,22.7838205293291,22.7838205293291,22.7838205293291,12.5939616406340,12.5939616406340,0,0,0,0,0,... |
1946c639c1374a95f982c71fba794a8bfaa38096374afafc64c5c8ffa2ad3a05 | C++ | 5,993 | 275 | #include <iostream>
#include <fstream>
#include <vector>
#include <cstdlib>
#include <algorithm>
#include <string>
#include <cmath>
/******************************************************************************
Codigo para tratar os dados fornecidos e transforma-los em um arquivo para
se calcular as magnetizações ... |
23addb3c3bdf3a09040ae336d9958d6f5e94889f2d1688dc5e3c7f899cd2d282 | C++ | 5,995 | 218 | // shared memory utility using shm_open
#include <QtCore>
#include <QCommandLineOption>
#include <QCommandLineParser>
#include <sys/types.h>
#include <pwd.h>
#include <unistd.h>
#include <set>
#include <csignal>
// includes required by shm_open ?
#include <sys/mman.h>
#include <sys/stat.h>
#include <fcntl.h>
#define... |
a4c935e5345f96eb59faf6516755925ac0922f527a3509ada7f7c1daed7dc722 | C++ | 5,997 | 110 | #include "kmer.hpp"
namespace vg {
namespace algorithms {
void for_each_kmer(const HandleGraph& graph, size_t k, size_t edge_max,
const std::function<void(const kmer_t&)>& lambda) {
graph.for_each_handle([&](const handle_t& h) {
// for the forward and reverse of this handle
... |
696cea88a5186ae945a04608ebf9129b3977bdc632fa4971f296469364b8a753 | C++ | 6,006 | 125 | // Offscreen exercise of the review dialog: construct it from a synthetic proposal, check it
// parses the block, rebuilds it faithfully, honours a hydration edit, and never offers a
// reserved bead colour. Run with QT_QPA_PLATFORM=offscreen -- no display needed.
#include <QApplication>
#include <QComboBox>
#include <... |
3167d6d9fcb75af4c61904aaed982584b5b306c72cda8fc86b624aef9af16546 | C++ | 6,054 | 216 | #include "qt_test_base.h"
#include "us_matrix.h"
#include <QVector>
using ::testing::_;
using ::testing::Return;
using ::testing::DoubleNear;
class TestUSMatrixUnit : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
// Set up test matrix (3x3 identity matrix)
ve... |
a9a85512426b06a04ee4f4445a39681f900f13e06ad0a2f8f77ac1dc442d4a45 | C++ | 6,061 | 229 | #include "us_editor.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#if QT_VERSION > 0x050000
#include <QtPrintSupport>
#endif
US_Editor::US_Editor( int menu, bool readonly, const QString& extension,
QWidget* parent, Qt::WindowFlags flags ) : QMainWindow( parent, flags )
{
file_extension = extension... |
7014124951b074c372cf4982822544ce1e1f517d7e95bb4ae3750b5d28af92ff | C++ | 6,149 | 164 |
#include <cstdlib>
#include <iostream>
#include <sstream>
#include <string>
#include "FileUtils.hpp"
#include "GeneticMap.hpp"
#include "format.hpp"
// Hack
#include "FileUtils.cpp"
#include "StringUtils.cpp"
using namespace std;
using namespace Osprey;
static const string EAGLE_GMAP_FILE_HEADER = "chr position CO... |
092e6f29b7441fa2dfab972eb25deb027d89a82a026c793aef9670c6a7166d3e | C++ | 6,161 | 194 | /** \file benchmark_main.cpp
*
* Defines the "vg benchmark" subcommand, which runs and reports on microbenchmarks.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../benchmark.hpp"
#include "../version.hpp"
#include "../gbwt_extender.hpp"
#incl... |
aa5e8aa3a91c0d6f6e3b48b6b946af285e05c2ee5220582afd596532cc208717 | C++ | 6,162 | 232 | // shared memory utility
#include <QtCore>
#include <QSharedMemory>
#include <QCommandLineOption>
#include <QCommandLineParser>
#include <sys/types.h>
#include <pwd.h>
#include <unistd.h>
#include <set>
#include <csignal>
#define TSO QTextStream( stdout )
#define TSE QTextStream( stderr )
// update if US_Global::Gl... |
2f9175bb13f927b098f05f12af493cbc6583233478c4ef2d4550c3e34176a365 | C++ | 6,228 | 178 | #include <algorithm>
#include <cassert>
#include <iostream>
#include <sstream>
#include <string>
#include <utility>
#include <vector>
#include <paw/station.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#include <grapht... |
71c98463cf31f2e716bab4f95dedddda94edfabf2ddee495bb191f46fec961f4 | C++ | 6,228 | 161 | #include <gtest/gtest.h>
#include "qt_test_base.h"
#include <QDirIterator>
#include <QFile>
#include <QRegularExpression>
#include <QTextStream>
class US_RegexTest : public QtTestBase {
protected:
struct PatternEntry {
QString file;
int line;
QString pattern;
QString context;
... |
df2e2ce6daf6cf1d186232d04496f03bb1be881e59bcac8ce6236a141b566ce5 | C++ | 6,228 | 192 | //! \file test_us_dataIO_edits.cpp
// Edit file round trips through US_DataIO::writeEdits and readEdits.
#include "qt_test_base.h"
#include "us_dataIO.h"
#include <QTemporaryDir>
namespace
{
US_DataIO::EditValues velocityEdits()
{
US_DataIO::EditValues ev;
ev.expType = "Velocity";
ev.runID = "demo-r... |
f3720aa930bf0b2963f9d5363efb13f086f7e7484b3d8dabca0924ffa1536298 | C++ | 6,242 | 185 | //! \file us_mwl_pltctrl.cpp
#include "us_mwlr_viewer.h"
#include "us_mwl_pltctrl.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
#ifndef ZSCAL_FACT
#define ZSCAL_FACT 0.008
#define RXSCL_FACT 0.032
#define RYSCL_FACT 0.900
#endif
// constructor: enhanced ... |
167b77d92931c9a016923e3805fa0a6bfe867d40a66b532ea3a3b96922810730 | C++ | 6,265 | 194 |
#include <string>
#include <algorithm>
#include <cstring>
#include <sstream>
#include "mem.hpp"
namespace vg {
using namespace std;
// construct the sequence of the MEM; useful in debugging
string MaximalExactMatch::sequence(void) const {
return string(begin, end);
}
// length of the MEM
int MaximalEx... |
1e46c62671447c1e48d84b0c6096bf225bd5ffc6c0c3999b738da8c043b09f00 | C++ | 6,269 | 136 | //------------------------------------------------------------------------------
//
// 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... |
ebde5e834350666f7677834e23b073486df8b67975ffaabfa222d069542203c2 | C++ | 6,288 | 198 | /**
* \file tree_subgraph.cpp
* Contains the implementation of the TreeSubgraph.
*/
#include "tree_subgraph.hpp"
#include <handlegraph/util.hpp>
#include <iostream>
namespace vg {
using namespace std;
TreeSubgraph::TreeSubgraph(const HandleGraph* super, vector<pair<int64_t, handle_t>>&& tree, size_t root_trim)... |
6d040091028eb1c655e5a7db6e1ef40f289d589633cba71434881ccafce0c1aa | C++ | 6,351 | 190 | //! \file us_mwls_pltctl.cpp
#include "us_mwl_spectra.h"
#include "us_mwls_pltctl.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include <qwt_legend.h>
#ifndef ZSCAL_FACT
#define ZSCAL_FACT 7.2
#define RXSCL_FACT 3.2
#define RYSCL_FACT 1.0
#endif
// Constructor: enhanced spectr... |
7711d0e2be0db5569cfb0b9ad4ba171f5261c04db81441c83e79fa5d27e854c5 | C++ | 6,357 | 135 | /**
* \file decomposition_comparison.cpp
* Names for the net graph elements of a snarl tree that every
* SnarlDecomposition implementation shares.
*/
#include "decomposition_comparison.hpp"
#include <algorithm>
#include <functional>
#include <string>
namespace vg::unittest {
/// Write a graph handle as its node... |
2ccf7e5f001c9b2a3b3c5ef092fdcbbbf636ecf448913545f2eb3919bace7bb2 | C++ | 6,408 | 239 | #include <string>
#include <vector>
#include <parallel_hashmap/phmap.h>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/index/ph_index.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/options.hpp>
#include <graphtyper/utilities/type_conversions.hpp>
namespace gyper
{
void PH... |
fbd3201edf9e1069fe00ffcf6ff06fbe5884b7d949f2bbcae87dc0ec48b965f2 | C++ | 6,414 | 233 | #include "version.hpp"
// Get the git version macro from the build system
#include "vg_git_version.hpp"
// Do the same for the build environment info
#include "vg_environment_version.hpp"
#include <htslib/hts.h>
#include <iostream>
#include <sstream>
// If the VG_GIT_VERSION deosn't exist at all, define a placehol... |
4d1accc6574d0424f6b9edf1554e4d584746d059927b4fef66b1177fa7a93fdd | C++ | 6,440 | 209 | #include <algorithm>
#include <cassert>
#include <cmath>
#include <iomanip>
#include <iostream>
#include <limits>
#include <sstream>
#include <string>
#include <graphtyper/typer/segment.hpp>
#include <graphtyper/utilities/graph_help_functions.hpp>
#include <graphtyper/utilities/logging.hpp>
namespace
{
std::vector<ui... |
55cc0ccff043273bf72d2c739c096398be587ef07914eb71ecb533485138d35d | C++ | 6,471 | 177 | #include "snarl_graph.hpp"
#include "algorithms/expand_context.hpp"
#include "annotation.hpp"
#include "gref.hpp"
#include "traversal_clusters.hpp"
//#define debug
namespace vg {
SnarlGraph::SnarlGraph(const HandleGraph* backing_graph, SnarlManager& snarl_manager, vector<const Snarl*> snarls) :
backing_graph(ba... |
2086b82dd76b14684284e3faaed87f2e7dd525d82aa004130b0e09b3da2f74e2 | C++ | 6,473 | 205 | /*
* HDF5Interface.cpp
*
* Created on: Dec 4, 2018
* Author: Florian Achermann, ASL
*/
#include "HDF5Interface.hpp"
#include <cmath>
#include <stdexcept>
namespace intel_wind {
namespace planning {
HDF5Interface::HDF5Interface()
: file_(),
sample_names_() {
}
HDF5Interface::~HDF5Interface() ... |
d96a5f2b096d920ac6c8f8ac524a807563ea1cbe86d070aa1705aab1f6e27c9b | C++ | 6,478 | 203 | #include "benchmark.hpp"
#include <vector>
#include <iostream>
#include <cassert>
#include <numeric>
#include <cmath>
#include <iomanip>
/**
* \file benchmark.hpp: implementations of benchmarking functions
*/
namespace vg {
using namespace std;
double BenchmarkResult::score() const {
// We comnpute a score in... |
6dd1c094ff39982ecbb9b8fd2a5334402ddbc6de92a869c6b4869531897abd54 | C++ | 6,503 | 245 | //! \file us_admin.cpp
#include "us_admin.h"
#include "us_license_t.h"
#include "us_help.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_crypto.h"
US_Admin::US_Admin( QWidget* w, Qt::WindowFlags flags )
: US_Widgets( true, w, flags )
{
setWindowTitle( "Change Master Password" );
setAttrib... |
33948b4ce308750b63d297da39f16fad41174fd787aced8e1a869eed0da33f67 | C++ | 6,539 | 268 | /** \file
*
* Unit tests for the FeatureSet, which keeps some BED-like regions in sync with
* changes to a graph.
*/
#include <iostream>
#include <sstream>
#include "../feature_set.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("FeatureSet can load and save a BED r... |
4e38c90b1e66af287152135787a26ddf43276bd647425486ca785dc26a9b33a1 | C++ | 6,561 | 211 | //! \file us_passwd.cpp
#include "us_passwd.h"
#include "us_global.h"
#include "us_settings.h"
#include <QApplication>
// Window to anchor (and center) the password dialogs against: the owner's
// top-level window if it has a parent, otherwise the currently active window.
// US_Passwd objects are normally created pare... |
2190b4db09c8119931f47dcb9989ddec59ecd97462482bc9850066c8c63222bc | C++ | 6,566 | 199 | /** \file ids_main.cpp
*
* Defines the "vg ids" subcommand, which modifies node IDs.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../vg_set.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <handlegraph... |
d6ad6727f34909ae3ced0baf0e474d1032dc52b5fb2ccd73c1d5553fdbe81764 | C++ | 6,585 | 179 | #include "catch.hpp"
#include "../handle.hpp"
#include "../utility.hpp"
#include <bdsg/hash_graph.hpp>
#include "support/randomly_flipped_nodes.hpp"
#include "support/randomness.hpp"
#include "support/random_graph.hpp"
#include <set>
#include <random>
namespace vg {
namespace unittest {
/// Get the canonicalized se... |
1abf2c1f008c504b0f07999081c258a2bbe56024c3e3f2617054346bb0ec09a0 | C++ | 6,605 | 158 | /// \file chain_items.cpp
///
/// unit tests for chaining logic
#include <iostream>
#include "../algorithms/chain_items.hpp"
#include "../integrated_snarl_finder.hpp"
#include "bdsg/hash_graph.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
/// Turn inline test data of read start, graph handle and of... |
a018438014b3aaa8be69f705d92498c398468037e5925b6b787dc0ec7f306cd3 | C++ | 6,639 | 187 | #include "snarl_decomposition_fuzzer.hpp"
#include <cassert>
#include <stack>
namespace vg {
namespace unittest {
using ET = DecompositionEventType;
SnarlDecompositionFuzzer::SnarlDecompositionFuzzer(
const HandleGraph* graph,
const HandleGraphSnarlFinder* finder,
const std::unordered_set<nid_t>& chains... |
1626e7491b676b58d2cd82ecc853bc3f0bdc3fc8665d1aae745fa6e87e7f56c6 | C++ | 6,646 | 179 | /// \file sample_minimal.cpp
///
/// unit tests for minimizer (sub)sampling
#include "../algorithms/sample_minimal.hpp"
#include "catch.hpp"
#include <iostream>
#include <unordered_set>
namespace vg {
namespace unittest {
TEST_CASE("minimizer subsampling samples all tied minimizers", "[giraffe]") {
// Say we ... |
cfe1d41540b8c327f2241c9cd92f325f36707b82901dd45d9821485b30f49329 | C++ | 6,656 | 198 | //! \file us_worker_calcnorm.cpp
#include "us_worker_calcnorm.h"
#include "us_util.h"
#include "us_settings.h"
#include "us_astfem_math.h"
#include "us_model.h"
#include "us_sleep.h"
#include "us_constants.h"
#include "us_memory.h"
// construct worker thread to calculate norms
WorkerThreadCalcNorm::WorkerThreadCalcNo... |
4ac44f1aa607b7dc06266d8a6192de551d6c4c954e2aa71f6c6989ee095177d8 | C++ | 6,681 | 304 | #include "qwt3d_scale.h"
using namespace Qwt3D;
Scale::Scale()
: start_p(0.), stop_p(0.),
majorintervals_p(0), minorintervals_p(0),
mstart_p(0.), mstop_p(0.)
{
}
/*! The function maps the double value at tic-position idx to a final
representation. The default return value is simply the tic values ... |
3769fdf7258ef16abdcc0f5c9c7fc179393c0da65abdbe3b5e77b6aafdf6929f | C++ | 6,688 | 180 | #include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/constructor.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/graph/haplotype_extractor.hpp>
... |
fbf68b027bc27a36cd83f3e6186879d83676eeedc5acf99811f369bf11bae828 | C++ | 6,766 | 243 | //! \file us_get_dbrun_ra.cpp
#include "us_get_dbrun_ra.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_db2.h"
#include "us_passwd.h"
// Primary constructor to establish the dialog
US_GetDBRunRa::US_GetDBRunRa( QString& r )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() ), runID( r )
{
setWi... |
931ab4d3642ae48b4dc25a6bf3469770a894f20bf57bda6b57813bd0110c37e1 | C++ | 6,840 | 162 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/utilities/kmer_help_functions.hpp>
#include... |
31e427f2a5aa7ed6ab8aa5835933c251dde5e6dba601fea2d1e2f4e591558ede | C++ | 6,858 | 273 | /**
*\file
* options.cpp: option parser system implementation
*/
#include "options.hpp"
namespace vg {
namespace subcommand {
void TickChainLink::reset_along_chain() {
reset_along_chain_parent();
}
bool TickChainLink::tick_along_chain() {
return tick_along_chain_parent();
}
void TickChainLink::reset_cha... |
3423b2ee4ee26e2d59a793e0c8a2be213de03e9ba74e1320bab5da15454f51b6 | C++ | 6,928 | 217 | /** \file
*
* Unit tests for kff.cpp, which provides tools for working with KFF files.
*/
#include "../kff.hpp"
#include "../utility.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
//------------------------------------------------------------------------------
namespace {
std::vector<std::strin... |
0e980e1c663dd51576fceac60577ccb67954566d9cf6b6e905872b803134eb59 | C++ | 6,971 | 165 | //------------------------------------------------------------------------------
//
// 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... |
ac0404c29f643dd9cd5a0e1534c173db785a8e1eafe1ed74cf2e90903140c4fa | C++ | 6,984 | 160 | /**
* \file nearest_offsets_in_paths.cpp
*
* Contains implementation of nearest_offsets_in_paths function
*/
#include "nearest_offsets_in_paths.hpp"
#include "../crash.hpp"
// #define debug
// #define debug_algorithms
namespace vg {
namespace algorithms {
using namespace std;
path_offset_collection_t nearest_o... |
e668d33be5065588d22c17290438570825a06fa6e0f3298fbb557e81a34d7eb8 | C++ | 6,991 | 158 | /** \file
* Implements the reference path distance function
*/
#include "ref_path_distance.hpp"
//#define debug_ref_path_distance
namespace vg {
namespace algorithms {
using namespace std;
int64_t ref_path_distance(const PathPositionHandleGraph* graph, const pos_t& pos_1, const pos_t& pos_2,
... |
3d4eda42ae9d145df2b71d9a3b85e3eff71c87da3452b93151f82b19ca789970 | C++ | 6,993 | 205 | ///////////////////////////////////////////////////////////////////////////////////////
// Implementation code for ER netwoks with exponentially decay of synapses activation
///////////////////////////////////////////////////////////////////////////////////////
using namespace std;
#include <iostream>
#include <... |
3ffb47d12bfbf35f5a64bae6266cceba4a3ab76c9558945a1727f71df70ac1a8 | C++ | 7,007 | 164 | //------------------------------------------------------------------------------
//
// 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... |
99914e66f121292d03855c2bddee86fbb299ff9f0840850538cf06ab75a139c6 | C++ | 7,063 | 217 | //! \file us_eqhistogram.cpp
#include "us_eqhistogram.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_math2.h"
#ifdef ARRAY_SIZE
#undef ARRAY_SIZE
#endif
#define ARRAY_SIZE 50
// Main constructor
US_EqHistogram::US_EqHistogram( double od_limit,
QVector< EqScanFit... |
a976ca302a42f2023603b2632e486b6ed441cf60cba4c77c5fd9fbb0ea18ba5b | C++ | 7,133 | 271 | #include <iomanip>
#include <sstream> // std::ostringstream
#include <string> // std::string, std::stol
#include <cereal/archives/binary.hpp>
#include <cereal/types/string.hpp>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#includ... |
8fab92c001a687e68420fa79d7052ad559448291b3339080305ea3df8c46ef4f | C++ | 7,135 | 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... |
df3e2d13b1adf58d425171a58e7b7c3ecfe0ba59b9cf9e22a96c1ff5c40b996a | C++ | 7,149 | 212 | ////////////////////////////////////////////////
// Implementation code for small-world netwok //
////////////////////////////////////////////////
using namespace std;
#include <iostream>
#include <math.h>
#include <fstream>
#include <cstdlib> // defines rand
#include <ctime> // defines time() function
... |
feddc5afce7f45dc9d8804296708f8be5aa2de1ade3fc3f9b8adef01e0df9f08 | C++ | 7,176 | 243 | /// \file stream.cpp
///
/// Unit tests for stream file external interface
#include <vg/io/stream.hpp>
#include <vg/io/protobuf_iterator.hpp>
#include <vg/io/protobuf_emitter.hpp>
#include <vg/vg.pb.h>
#include "catch.hpp"
#include <sstream>
#include <iostream>
#include <unordered_map>
namespace vg {
namespace u... |
cd22abf4c0086a8e15738131298c60cfe47d0426277238a955d7c351f285a401 | C++ | 7,181 | 273 | //! \file us_2dplot.cpp
#include "us_2dplot.h"
#include "us_settings.h"
#include "us_license_t.h"
#include "us_math2.h"
#include "us_util.h"
#include "us_license.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_run_details2.h"
#include "us_passwd.h"
#include "qwt_scale_engine.h"
//! \brief progr... |
1a94f154c6291c40371465941a2a6c23e40f5b49c707b04804d6f00b87f5a667 | C++ | 7,183 | 209 | #include <atomic>
#include "subgraph_overlay.hpp"
#include <handlegraph/util.hpp>
namespace vg {
using namespace std;
using namespace handlegraph;
SubgraphOverlay::SubgraphOverlay(const HandleGraph* backing, const unordered_set<nid_t>* node_subset) :
backing_graph(backing),
node_subset(node_subset) {
if... |
0ddfbd5b0b3f5a7802cac9c8471b9ef5c3df26b1674d7e0893cc1b7f8b1d394a | C++ | 7,197 | 290 | #include "ForceField.hpp"
#include <fstream>
#include <sstream>
#include <iomanip>
#include "LennardJones.hpp"
#include "Gaussian.hpp"
#include "ShiftedLJ.hpp"
ForceField::ForceField(const AtomTypeMap& map, const Cell& box) :
mAtomTypeMap {map},
mBox {box}
{
}
ForceField::ForceField(const ForceFiel... |
6100a27759199ad6dc0229a68d42d1c955c06b5c38a74f14aa8ea8436b61d224 | C++ | 7,197 | 163 | //
// snarls.cpp
//
// Unit tests for TraversalSupportFinder
//
#include <stdio.h>
#include <iostream>
#include <sstream>
#include <set>
#include "../io/json2graph.hpp"
#include <vg/vg.pb.h>
#include "catch.hpp"
#include "traversal_support.hpp"
#include "traversal_finder.hpp"
#include "../handle.hpp"
#include <vg/io... |
aef31b404187d65ce3cb8d1867780616a1362abbed29efa982028fb8bc287945 | C++ | 7,202 | 228 | // ************************************************************
// A neural network of phase model neurons
// (based on the Randall Beer CTRNN class)
//
// EOlivares
// 11/19 Created
// ************************************************************
#include "NervousSystem.h"
#include "random.h"
#include <stdlib.h>
#in... |
f66b8aad8d99fc0a029b4d75113697faec407b7ec8b1c6271b82a52ebfc603ff | C++ | 7,254 | 244 | /// \file dozeru_pinning_overlay.cpp
///
/// unit tests for the overlay that sockets handle graphs that may have
/// nodes with no sequence into the XdropAligner for pinning
///
#include <iostream>
#include "../dozeu_pinning_overlay.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
namespace vg {
namespace ... |
34ad0087a7ac75b9915b7f581b500ca782c6843dfc5dd92009c5028cdaf40248 | C++ | 7,287 | 281 | #include <fstream>
#include <iostream>
#include <sstream>
#include <seqan/bam_io.h>
#include <seqan/basic.h>
#include <seqan/seq_io.h>
#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/utilities/io.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <... |
9674dd36b55993d193fc47dfcbba72ea7cb9e04f499925a51b1e0bfcd9df3979 | C++ | 7,311 | 233 | #include <algorithm> // std::sort
#include <sstream> // std::stringstream
#include <string> // std::string
#include <vector> // std::vector
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/reference_depth.hpp>
#include <graphtyper/typer/genotype_paths.hpp>
#include <graphtyper/typer/variant_can... |
3593943ae4f9537fddaf1591d6ba05401c75bffeb16b73d765e60534a5e375cd | C++ | 7,341 | 237 | /** \file add_main.cpp
*
* Defines the "vg add" subcommand, which adds in variation from a VCF to an
* existing graph.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../variant_adder.hpp"
#include <vg/io/vp... |
d580209dcbbe69bea58c8a28630d50dd96146138cf17aa0afac29dac79b12ca9 | C++ | 7,362 | 323 | #include "Framework.hpp"
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include <sstream>
#include <iomanip>
Framework::Framework(AtomTypeMap& typeMap) :
mAtomTypeMap {typeMap}
{
//int n = mAtomTypeMap.getNumTypes();
//mAtomPositions.resize(n);
//mAtomIndices.resize(n);
}
void
Frame... |
da35b2f1c76a53cc3a4e284635f1b13688ab446c33206131e8c08e9c5ed0add2 | C++ | 7,369 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,7.06093269682636,13.6843655359258,17.4295012924159,37.4766596405907,22.3342988671423,24.9992871730106,24.4618806328896,18.4823626932923,9.44547123047548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3.59600305841730,12.2875352029154,17.4295012924159,18.7002223582052,36.37... |
417668da31ca459227d066853c0944f45a57f6dbdcbfc97038c633f15d2db25c | C++ | 7,370 | 1 | vector<float> ext_dir_initial{0,0,0,2.69653860717405,13.0581779638155,21.9656832022202,26.4360254588396,41.1105467722325,42.9838092059709,35.2552234226001,32.6592117408285,21.0140087590244,16.3180034351047,7.08537855583209,0,0,0,0,0,0,0,0,3.16362843641939,5.40670827487725,7.03648683782056,12.4184349007815,8.64237225025... |
79903eeec3edd0d0dfbc81d782e3942ef7b84a06908972288d2b1d3d958e84f7 | C++ | 7,370 | 1 | vector<float> ext_dir_initial{0,0,5.18457484342092,12.8095281009630,14.1177497347942,8.57207553091107,2.76813736457689,0,0,0,0,0,0,0,0.826242801167325,8.25995953044482,15.1838793576792,24.6484200229682,29.6346987241837,36.0653125936650,33.4321868308555,26.2128854414517,15.0967664554828,8.73786415816674,0.51737258604724... |
8999a741c427ac45d755d9051c821d1ba524310b750e572fd2c0eca0515a257e | C++ | 7,378 | 183 | #include "rare_variant_simplifier.hpp"
namespace vg {
using namespace std;
RareVariantSimplifier::RareVariantSimplifier(MutablePathDeletableHandleGraph& graph, VcfBuffer& variant_source) : Progressive(), graph(graph), variant_source(variant_source) {
// Nothing to do!
}
void RareVariantSimplifier::simplify() {
... |
31580e1ea80950847861349ca5021c1cbe734424ec82a4b25423645ccb9b2835 | C++ | 7,382 | 277 | // shared memory utility using sysv ipc
#include <QtCore>
#include <QCommandLineOption>
#include <QCommandLineParser>
#include <sys/types.h>
#include <pwd.h>
#include <unistd.h>
#include <set>
#include <csignal>
// includes required by sysv ipc
#include <sys/ipc.h>
#include <sys/shm.h>
#define TSO QTextStream( stdou... |
881722f75fdb8c90499ca70151e809c7e0bd12432c46acb97324d20903665cc9 | C++ | 7,396 | 246 | //! \file us_worker_2d.cpp
#include "us_worker_2d.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
WorkerThread2D::WorkerT... |
6209fe851d9c6364b0649f3f496c5668c504b44e1bb7815121512878c968df90 | C++ | 7,402 | 244 | //! \file us_exclude_profile.cpp
#include "us_exclude_profile.h"
#include "us_settings.h"
#include "us_gui_settings.h"
US_ExcludeProfile::US_ExcludeProfile( QList< int > includes )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() )
{
original = includes;
finished = false;
current.clear();
dbg_level = US... |
972c13107c07254a0ebf3f31927afc3a5aa788efcd814c492d762fff9d8cc36a | C++ | 7,413 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,0,0,0,2.20207549778845,8.40135057151993,14.1104729268175,19.2176277708706,29.8047619199130,18.6992264122024,20.1288398238711,17.1096904842092,12.7285214342429,3.73472488967162,0,0,0,0,0,0,0,3.62025334481099,4.18732909399698,3.04007945936854,0,0,0,0,0,0,0,0,0,0,6.7233344... |
7eb1581a3db91076d15e1448c997f1ce5269f64e061f3afc549c0ea1510e7b87 | C++ | 7,420 | 174 | /// \file site_traversal_finder.cpp
///
/// Unit tests for the traversal finders that implement both TraversalFinder
/// and SiteTraversalFinder.
///
/// PathTraversalFinder, GBWTTraversalFinder and FlowTraversalFinder each find
/// the walks through a site given either a Snarl, through TraversalFinder, or
/// the two ... |
701036098e06191ca3ea18b990e43f2af0d7fd6a0a7cc83386bc93d422eab51c | C++ | 7,472 | 245 | #include <qsplitter.h>
#include <qlayout.h>
#include <qcombobox.h>
#include <qaction.h>
#include <qslider.h>
#include <qcheckbox.h>
#include <qmenubar.h>
#include <qdatetime.h>
#include "axes.h"
#include "axesmainwindow.h"
#include "../../../include/qwt3d_function.h"
using namespace std;
using namespace... |
94a4410936041dabb5893ef6b07c11e78899c2ffd97c4a2bc61293bc314254b1 | C++ | 7,476 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,0,2.03491362605052,8.20896937538420,15.8763544380064,29.8047619199130,24.7603284059766,24.2344448420906,21.7688842469173,16.2151300079346,10.8743542817025,1.06327938928269,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6.63511347978181,19.9795910764909,23.1896046742352,34.258636... |
9e11ce8c0b50ea61c634ba887c48b6f739fa56db239feeafbe16cd52c699211f | C++ | 7,486 | 162 | #include "region_expander.hpp"
namespace vg {
RegionExpander::RegionExpander(const PathPositionHandleGraph* graph, const SnarlManager* snarl_manager) :
graph(graph), snarl_manager(snarl_manager)
{
// Nothing to do
}
map<pair<id_t, bool>, pair<uint64_t,uint64_t >> RegionExpander::expan... |
55a55fedfe9aabc39d6d09ac7f59dca473976dfa3687485f6d0fc6ef73bcc997 | C++ | 7,491 | 188 | /*
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... |
9c4dec3cc7683916eab7e435f140a62baaa41cc980d3ae8a3f44a804de3f999f | C++ | 7,520 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,0,0,6.40824061310890,18.9843569691234,23.0020126536974,27.5392311975295,22.6404889766808,19.1438345653237,16.1327504108453,10.1449694677216,2.15176787478274,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2.12550546453603,10.3815689059290,20.1006781382294,28.8407244255729,35.07481737... |
6d8751daf479a9a006ce1c22dd60a5201ec5a4094001c4489031a159175bf8c6 | C++ | 7,533 | 1 | vector<float> ext_dir_initial{0,0,0,0,0,0,0,1.92501771753426,8.64237225025455,14.6322499730935,16.4596483046550,15.7679158670480,17.8498751739897,15.7350310656833,9.35548866146556,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6.14795311199528,18.5378840255457,23.4649683068177,26.3934962227765,28.9578707655409,22.60927694... |
f8a5612bd54638fe07467bfbd3debb9a554a2914b56af79801772e37fb30fa7a | C++ | 7,534 | 1 | vector<float> ext_dir_initial{3.96102922193764,12.6418854668976,15.8855562845671,25.2231811654897,40.8673747688847,52.9532147559282,57.9453956910228,44.7647449491067,31.5490514869714,21.2494123630865,15.9033751216490,8.96609324097269,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.837653705695337,12.6192162614171,18.038730605858... |
1139d9b023adc14b1ee00533d75581d53617b1865aae9081200bcaaa5d027d3f | C++ | 7,576 | 218 | //////////////////////////////////////////////////////////////////////////////////
// Implementation code for reproducing parts of Fig.4 for one realization.
// Notice 1: For each panel, choose an appropriate parameter pNode
// By default here we set pNode=0.00005 to obtain panel (a). ... |
c47338d9246b031e039cdb651876ecff3f0c1709725aaea48b2d28adc2bb8e7d | C++ | 7,620 | 216 | //------------------------------------------------------------------------------
//
// 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... |
f0256334390cc84460ccbb25ffbde6d994f83939ba6a473183299a2425c911c4 | C++ | 7,675 | 219 | //////////////////////////////////////////////////////////////////////////////////
// Implementation code for reproducing parts of Fig.3
// Notice 1: For each phase (intermittent, semi-periodic, and periodic)
// choose an appropriate parameter pNode as the external input.
// By default her... |
c4dc3cda50b3ed7a11126cee81df5f813943020ca947c5dafb107a3e1f89a95f | C++ | 7,684 | 281 | //! \file us_ramp.cpp
#include "us_mwlramp.h"
#include "us_util.h"
#include "us_settings.h"
#include "us_editor.h"
US_mwlRamp::US_mwlRamp(): QObject()
{
}
bool US_mwlRamp::import_data( QString& mwldir, QLineEdit* lestat,
QVector< US_mwlRamp::RampRawData >& allData, QString& runID_xml_mwl )
{
bool status ... |
494832f66485f9460a800f157de387bac221474e1b4c33b12b5dd4ee44b770fd | C++ | 7,709 | 227 | #include "qt_test_base.h"
#include "us_settings.h"
#include <QSettings>
#include <QStandardPaths>
class US_SettingsTest : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
// Store original settings values to restore later
storeOriginalValues();
}
void Te... |
2c400c24d81dbb66fe3fa9e0d9f88502c2e44cf4e880ccfe7e87aeb3f6be41e9 | C++ | 7,767 | 209 | /** \file gamsort_main.cpp
*
* Defines the "vg gamsort" subcommand for sorting and shuffling GAM and GAF files.
*/
#include "subcommand.hpp"
#include "../alignment.hpp"
#include "../gaf_sorter.hpp"
#include "../stream_index.hpp"
#include "../stream_sorter.hpp"
#include <vg/io/stream.hpp>
#include <getopt.h>
usin... |
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