sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1053a0d1f4747fe3c78e33dc4d20c9b2ce00c8e5c388d374c358e41febe70d59 | C++ | 3,924 | 114 |
#include <ostream>
#include <iostream>
#include "sparse_union_find.hpp"
// #define debug
namespace vg {
using namespace std;
SparseUnionFind::SparseUnionFind(bool include_children, vector<size_t> node_ids) :
include_children(include_children), node_ids(node_ids), UnionFind(node_ids.size(), include_ch... |
6edc1443e62ded47163a58d39f279a6b5e6831eac4707c774b57069d32d360e9 | C++ | 3,938 | 107 | // =============================================================
// =============================================================
#include <iostream>
#include <iomanip> // cout precision
#include <math.h>
#include "VectorMatrix.h"
#include "NervousSystem.h"
using namespace std;
///////////////////////////////////////... |
a6bfad23a97299f7cc02c7be7209b9e4f1d1edb3eb42414211851103fce066a9 | C++ | 3,947 | 99 | //! \file us_advanced_fem.cpp
#include "us_advanced_fem.h"
#include "us_fematch.h"
#include "us_settings.h"
#include "us_gui_settings.h"
// constructor: advanced analysis control widget
US_AdvancedFem::US_AdvancedFem( US_Model* amodel,
QMap< QString, QString >& adv_vals, QWidget* p ) :
US_WidgetsDialog( p, Qt:... |
58174d26a9f0b35340c78d79e5d8576ead371de3bbacc49809d195a12fc7565c | C++ | 3,980 | 114 | /// \file interval_union.cpp
///
/// unit tests for IntervalUnion
///
#include "../interval_union.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
namespace vg {
namespace unittest {
TEST_CASE("IntervalUnion produces correct results on a small example", "[interval]") {
IntervalUnion i... |
dacf929777e7aec0eaa3bd8019649ccb5cee8dc6a6ffe3f314c9d03784485251 | C++ | 4,011 | 151 | // test_us_astfem_math.cpp
#include "qt_test_base.h"
#include "us_astfem_math.h"
#include "us_model.h"
#include "us_simparms.h"
#include <vector>
using ::testing::DoubleEq;
using ::testing::DoubleNear;
using ::testing::Eq;
class US_AstfemMathTest : public QtTestBase {
protected:
void SetUp() override {
Qt... |
c483d2b565a53f938c7b3b9d000add6545b98c3ba4db693999a08d97981d4dd7 | C++ | 4,014 | 172 | #include <Eigen/Core>
#include <Eigen/SparseCore>
#include <iostream>
#include <random> // Requires C++ 11
#include <SymEigsSolver.h>
#include <MatOp/DenseSymMatProd.h>
#include <MatOp/SparseSymMatProd.h>
using namespace Spectra;
#define CATCH_CONFIG_MAIN
#include "catch.hpp"
typedef Eigen::MatrixXd Matrix;
typedef... |
e0dd0e54adb1e4d39ae9f65ca49e1f19bfddadc7a7efbb956b3033470d41d080 | C++ | 4,080 | 162 | #include <string> // std::string
#include <vector> // std::vector
#include <seqan/hts_io.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/options.hpp>
#include <graphtyper/utilities/sam_reader.hpp>
namespace gyper
{
SamReader::SamReader(std::string con... |
f6fdfddf2333415a5c4948817431aee11309fe6fb6f70f8193cb26d40f68e78f | C++ | 4,103 | 137 | #include "progressive.hpp"
#include <vg/io/stream.hpp>
#include <iostream>
#include <chrono>
namespace vg {
using namespace std;
void Progressive::with_progress(bool show_progress, const std::string& task, const std::function<void(const std::function<void(size_t, size_t)>& progress)>& callback) {
if (!show_prog... |
28714330e1c5bee125372c3f5c32f7b7e7827bcf10454c5c4a51a054a6ace722 | C++ | 4,106 | 183 | #include "qwt3d_surfaceplot.h"
using namespace std;
using namespace Qwt3D;
/**
Initializes with dataNormals()==false, NOFLOOR, resolution() == 1
*/
#if QT_VERSION < 0x040000
SurfacePlot::SurfacePlot( QWidget* parent, const char* name )
: Plot3D( parent, name )
#else
SurfacePlot::SurfacePlot( QWidget *... |
d70ea8e890b4c3f262034e503f8f57b3e8fbd8f3e7f748705303be2b756756dd | C++ | 4,120 | 229 | #include "catch.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../flow_sort.hpp"
#include "../algorithms/gfa_to_handle.hpp"
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("sorts input graph using max flow approach", "[flow_sort]") {
SECTION("Sort simple graph") {
const strin... |
839deae80b3050c4e90bb1277b8c5f8d01e3a25cf4fe0a0453dc5fac7e2c5f18 | C++ | 4,136 | 122 | #include <gtest/gtest.h>
#include "qt_test_base.h"
#include <QDirIterator>
#include <QFile>
#include <QRegularExpression>
#include <QTextStream>
#include <QFileInfo>
#include <iostream>
class US_HelpPagesTest : public QtTestBase {
protected:
struct HelpCall {
QString file;
int line;
QString... |
2fdd716ea08d3bbc3ec0feff8c97b4b7f345cdd0d39439d5c90860e2d5489f02 | C++ | 4,138 | 103 | //------------------------------------------------------------------------------
//
// 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... |
579722151ba0f62e67b5b10fc7b18745da033441d7d648219ee98e598335b5b0 | C++ | 4,145 | 135 | //! \file us_images.cpp
#include "us_images.h"
#include <mutex>
// Get image as a pixmap
QPixmap US_Images::getImage( const QString& bname )
{
ensure_us3_gui_images_resources();
return QPixmap( expanded_name( bname) );
}
// Get image as a pixmap from type flag
QPixmap US_Images::getImage( int itype )
{
ensur... |
cc2b434c362f8d9ea687c49e79c4c0269c9a197ef2c802c808e943673a35ee2c | C++ | 4,151 | 140 | #include <gtest/gtest.h>
#include <gmock/gmock.h>
#include "mock_us_db2.h"
#include <memory>
using namespace testing;
class US_DB2_MockTest : public ::testing::Test {
protected:
void SetUp() override {}
void TearDown() override {}
};
// Example 1: Simple test with natural syntax
TEST_F(US_DB2_MockTest, Strin... |
8d655532a173566402a517d83cca169d820b9dc918908c6bd07aa7874b28dd53 | C++ | 4,157 | 142 | #include "dv_tools.h"
#include <iostream>
namespace dvtools {
int brokenStickVals(std::vector<double> &values, double random) {
/* torott palca egyszeru bemeneti ertekekkel
* visszateresi ertekek:
* 0-(noChoices-1): melyiket valassztottuk
* -1:... |
e88506a6b093ddb9e99f4ccc923f8986449792aba22bb1b930ff315eafba1770 | C++ | 4,164 | 145 | // subcommand.cpp: subcommand registry system implementation
#include "subcommand.hpp"
#include <algorithm>
#include <utility>
#include <vector>
#include <limits>
namespace vg {
namespace subcommand {
std::ostream& operator<<(std::ostream& out, const CommandCategory& category) {
switch(category) {
case PIPE... |
29f4280b55d025420039c9186ac1309b51dc50d72a21707cee716e577d833288 | C++ | 4,178 | 159 | /*
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... |
e3c305393c60bbab8228859854db7a2c03176e5f80c5d694a63a9f2527000534 | C++ | 4,206 | 113 | // test_us_utils_main.cpp - Google Test
#include "qt_test_base.h"
#include "us_defines.h"
#include "us_settings.h"
#include <QCoreApplication>
#include <QApplication>
#include <QCryptographicHash>
#include <QDir>
#include <QFile>
#include <QSettings>
#include <QStandardPaths>
#include <QTemporaryDir>
namespace
{
QByte... |
119a9af14790a463a66caf0ef80a47fb3f8d57a4fa5c7b2dd390ae66c1059872 | C++ | 4,208 | 114 | #include "contracting_graph.hpp"
#include <structures/union_find.hpp>
#include <iostream>
// #define debug
namespace vg{
using namespace std;
using namespace structures;
ContractingGraph::ContractingGraph(Graph graph)
:graph(graph),node_ids(graph.get_node_ids()){
#ifdef debug
c... |
2481e69d6e7b217ce6beaf01558ddcf747972d368184afece85843b158d58072 | C++ | 4,210 | 115 | #include <iostream>
#include <fstream>
#include <ctime>
#include <cstdio>
#include <csignal>
#include <getopt.h>
#include <sys/stat.h>
#include "google/protobuf/stubs/common.h"
#include "version.hpp"
#include "utility.hpp"
#include "crash.hpp"
#include "preflight.hpp"
#include "config/allocator_config.hpp"
#include "i... |
51c0d931fd9ec0fef992e065e8deba37b5250e08012459a7d41ccbd45da8a3e2 | C++ | 4,231 | 142 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/index/indexer.hpp>
#include <graphtyper/index/kmer_label.hpp>
#include <graphtyper/index/ph_ind... |
8cdc5a737fa50571eb0931990b883f36239133d6f2ea20e5ad272ee2751c5627 | C++ | 4,236 | 134 | /// \file packed_graph.cpp
///
/// Unit tests for the PackedGraph class.
///
#include <iostream>
#include <sstream>
#include "vg/io/json2pb.h"
#include "../split_strand_graph.hpp"
#include "../subpath_overlay.hpp"
#include "../utility.hpp"
#include "../handle.hpp"
#include "support/random_graph.hpp"
#include "../v... |
40466d68fdfccf820fa467b93a8093809acc8939069e65a42b7d6e08bc327fe2 | C++ | 4,250 | 156 | //! \us_failed_gmp_run_gui.cpp
#include "us_failed_gmp_run_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_help.h"
#include "us_crypto.h"
#include "us_db2.h"
US_FailedRunGui::US_FailedRunGui( QMap <QString, QString> run_details ) : US_Widgets()
{
//Get needed run pa... |
55ae3966af093e96900cd920cf7984be382a86e970c6cd92b0155776d1f24cbb | C++ | 4,259 | 118 | /// \file dagify.cpp
///
/// unit tests for the handle based dagify algorithm
///
#include "../handle.hpp"
#include "../algorithms/locally_expand_graph.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
namespace vg {
namespace unittest {
TEST_CASE("locally_expand_graph produces expected results", "[algorit... |
ffef3daefbfd38dc195702621fb1c1a873f8a3e8cd12d0262d6c5b4b9f0b8a7f | C++ | 4,278 | 117 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/index/kmer_label.hpp>
#include <graphtyper/typer/genotype_paths.hpp>
#include <graphtyper/typer/path.hpp>
#include <graphtyper/utilities/type_conve... |
2af53bc1ed6874f60be72a478b2f8926fc157a59310aafb8ce758118fe9bed23 | C++ | 4,282 | 183 | #include <Eigen/Core>
#include <Eigen/SparseCore>
#include <iostream>
#include <random> // Requires C++ 11
#include <GenEigsSolver.h>
#include <MatOp/DenseGenMatProd.h>
#include <MatOp/SparseGenMatProd.h>
using namespace Spectra;
#define CATCH_CONFIG_MAIN
#include "catch.hpp"
typedef Eigen::MatrixXd Matrix;
typedef... |
7cb134d90a05794cec9f0fde0c02530b1d31da2d9b3c0cb6d26e051c8b36793c | C++ | 4,308 | 131 | #include <vector>
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
std::vector <std::vector<int>> calculateVectors(std::vector<int> nodeColors,
IntegerMatrix edges,
bool directed,
bool weighted,
int numberOfWeights,
bool fromR = false) {
if(fromR == true) {
// Tran... |
5c87a4a5190c06ae99d479ea90d3c933f2af0878b1dce3a3e701b89f9eb3c939 | C++ | 4,345 | 154 | //------------------------------------------------------------------------------
//
// 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... |
a80efa8426fd561858a30c134c528893fc0986bb26f1ce5bb9cf40bc410dd6e2 | C++ | 4,346 | 136 | /** \file
*
* Unit tests for zstdutil.cpp, which implements wrappers for Zstandard compression.
*/
#include "../zstdutil.hpp"
#include "../utility.hpp"
#include <random>
#include <sstream>
#include "catch.hpp"
namespace vg {
namespace unittest {
//---------------------------------------------------------------... |
96c55079f15fac15d8fca9fb2d468f4c6ba0ee6747eec16707b65f4a23a874ee | C++ | 4,355 | 143 | /**
* \file scanner.cpp
* Implementations for traversing Protpbuf object trees
*/
#include "scanner.hpp"
namespace vg {
using namespace std;
// Specializations have to be defined in dependency order to avoid complaints of specialization after instantiation.
template<>
bool PositionIDScanner<Mapping>::scan(const... |
e2cf24dd10cdf91b6539bd3f668c417a748d3cd3cbf1a64000abd5f8e88d77ca | C++ | 4,380 | 194 | #include "LennardJones.hpp"
#include <iostream>
#include <iomanip>
#include <limits>
#include <cmath>
#include "GridayException.hpp"
LennardJones::LennardJones(GReal eps, GReal sig, GReal rcut) :
PairEnergy {},
mEps {eps},
mSig {sig},
mSigSq {sig * sig},
mRcut {rcut},
mRcutSq {rcut * rcut}
... |
0f88579c248a80e8026029c46ca1573e26bbbc222b93dc288fb8d9930a07939a | C++ | 4,414 | 140 | /**
* unittest/genotypekit.cpp: test cases for genotypekit modular genotyper pieces
*/
#include "catch.hpp"
#include "../genotyper.hpp"
#include "../snarls.hpp"
#include "../cactus_snarl_finder.hpp"
#include "../traversal_finder.hpp"
#include "../io/json2graph.hpp"
namespace vg {
namespace unittest {
TEST_CASE("tr... |
989bf42e670ad094a718fce7a6c45ad754e8502f83a568d757cb3b629f816318 | C++ | 4,445 | 126 | #include <Eigen/Core>
#include <iostream>
#include <iomanip>
#include <string>
using Eigen::MatrixXd;
using Eigen::VectorXd;
void eigs_sym_F77(MatrixXd &M, VectorXd &init_resid, int k, int m, double &time_used, double &prec_err, int &nops);
void eigs_gen_F77(MatrixXd &M, VectorXd &init_resid, int k, int m, double &ti... |
7a10179fe4781c5684ebba86a41ebc41a5395f46e268f96b3a7648f343a0fa1c | C++ | 4,446 | 177 | /// \file mem.cpp
///
/// unit tests for MEMs and their clustering algorithms
///
#include <iostream>
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include "../mem.hpp"
#include "../cluster.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
TEST_CASE( "ShuffledPairs loops over all pairs", "[mem]... |
eda95fdf9649cf8a30c800f59521b7fd1812c4f39ace88277ee924486c3e1e8e | C++ | 4,455 | 140 | /**
* \file
* unittest/vcf_buffer.cpp: test cases for the VcfBuffer and WindowedVcfBuffer
* which let us read through VCFs with context.
*/
#include "catch.hpp"
#include "../vcf_buffer.hpp"
#include "../utility.hpp"
#include "../path.hpp"
#include "vg/io/json2pb.h"
#include <vector>
#include <sstream>
#include ... |
44f622e5b2b62beb336101a15578e4a90829b6b13eb8a367166198c498c023ee | C++ | 4,508 | 220 | #include <qlayout.h>
#include <qframe.h>
#include <qslider.h>
#include <qcheckbox.h>
#include <qpushbutton.h>
#include "lightingdlg.h"
using namespace Qwt3D;
class Sphere : public ParametricSurface
{
public:
Sphere(SurfacePlot& pw)
:ParametricSurface(pw)
{
setMesh(41,31);
setDomain(0... |
3e068a7d01634093efb898ba20622597e88d076e60f9cbc571a12a9ff3349803 | C++ | 4,513 | 137 | //------------------------------------------------------------------------------
//
// 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... |
fa5518a6d0d753f2f163829389a6980f00ce4aa7c86ba1c13d2a39fe62cbdaa5 | C++ | 4,531 | 222 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4786 )
#endif
#include <stdlib.h> // qsort
#include <algorithm>
#include <float.h>
#include "qwt3d_types.h"
using namespace Qwt3D;
#ifndef QWT3D_NOT_FOR_DOXYGEN
namespace {
// convex hull
typedef double coordinate_type;
... |
67554520eaf95a4024f94816c7b0d3fbb8ff6115aa74fbcd505826efb8c65612 | C++ | 4,550 | 128 | /*
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... |
5429e37324b326dd12b2fcf1c613a22b277d49d1faf75485c9fe724c64c00463 | C++ | 4,554 | 146 | /*
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... |
9788824b15854f5294a0b558ff1803e5308f959a08050c7f991fd259093dedf2 | C++ | 4,571 | 114 | /*
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... |
52771b7cb461669e2442e951d35f745d411ccd90ea32054e1bfc90468e1434f8 | C++ | 4,576 | 164 | //! \file us_get_dbexp.cpp
#include "us_get_dbexp.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_GetDBExp::US_GetDBExp( QString& eID )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() ), expID( eID )
{
setWindowTi... |
e30dbc299ba365e86e6be0c440c7a102fa3d2247dbec45d25d5c5d068e7faa37 | C++ | 4,587 | 203 | #include <algorithm>
#include <cassert> // assert
#include <set>
#include <vector> // std::vector<Type>
#include <parallel_hashmap/phmap.h>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/typer/path.hpp>
namespace gyper
{
Path::Path(Graph const & graph,
KmerLabel const & l,
uint16_t ... |
bfc88f6613ac3483d98be54140ce61ddc9b0812f95719f1eb7c1c6583dce398b | C++ | 4,590 | 225 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4786 )
#endif
#include <float.h>
#include <stdio.h>
#include <qtextstream.h>
#include "qwt3d_surfaceplot.h"
#include "qwt3d_io_reader.h"
using namespace std;
using namespace Qwt3D;
const char* NativeReader::magicstring = "jk:1105189... |
68443949d3f307f24a6ba31194139813634ccafc2fb83bc9a7dc3ada9e49e70c | C++ | 4,600 | 225 | #include <qlayout.h>
#include <q3frame.h>
#include <qslider.h>
#include <qcheckbox.h>
#include <qpushbutton.h>
//Added by qt3to4:
#include <Q3GridLayout>
#include "lightingdlg.h"
// For some reson WIN32 is not picking up M_PI from math.h...
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
using names... |
0a0cbe6a723e7ca5024f923e53d7b096c2dfab9970f22afe21fcc17cb7413b1f | C++ | 4,604 | 190 | #include <Eigen/Core>
#include <Eigen/SparseCore>
#include <iostream>
#include <random> // Requires C++ 11
#include <GenEigsRealShiftSolver.h>
#include <MatOp/DenseGenRealShiftSolve.h>
#include <MatOp/SparseGenRealShiftSolve.h>
using namespace Spectra;
#define CATCH_CONFIG_MAIN
#include "catch.hpp"
typedef Eigen::M... |
f8e5ffdeee858bfea6232fd2f98a6671f96867f90d3ee9303b1b86b0753e024b | C++ | 4,613 | 193 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4305 )
#pragma warning ( disable : 4786 )
#endif
#include <float.h>
#include "qwt3d_plot.h"
using namespace Qwt3D;
namespace {
inline GLenum lightEnum(unsigned idx)
{
switch(idx) {
case 0:
return GL_LIGHT0;
case 1:
ret... |
50264f7afe782617f1b8e9a88870b22871b9acff2499e56b89d1bfb4ed86ca9d | C++ | 4,614 | 123 | // =============================================================
// =============================================================
#include <iostream>
#include <iomanip> // cout precision
#include <math.h>
#include "VectorMatrix.h"
#include "NervousSystem.h"
using namespace std;
///////////////////////////////////////... |
420d5b28e241cbb55ee528e47062bcb7e8a71025ff3191ddc3a03c6b2d91a2ba | C++ | 4,622 | 116 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph_serialization.hpp>
#include <graphtyper/index/kmer_label.... |
37e4a1a2adc043208b06fece22d5b3094b3bac2895d9c45ece658e2b4c6307ac | C++ | 4,629 | 161 | #include <fstream>
#include <string>
#include <unordered_set>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/typer/genotype_paths.hpp>
#include <graphtyper/typer/path.hpp>
#include <graphtyper/typer/primers.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graph... |
2e08c49ca85d5ba6f61f8a9471eb62f4d65a871d55c9689428bcb343243f7e6d | C++ | 4,648 | 171 | /// \file blocked_gzip_output_stream.cpp
///
/// Unit tests for BlockedGzipOutputStream
#include <vg/io/blocked_gzip_output_stream.hpp>
#include <vg/io/hfile_cppstream.hpp>
#include "catch.hpp"
#include <htslib/hfile.h>
#include <sstream>
namespace vg {
namespace unittest {
using namespace std;
using namespace v... |
80e7b253f3b3873d8c8a04c45b905b69233ec73a6482341a6b21d0977d33c83c | C++ | 4,672 | 139 | /**
* \file qual_adj_xdrop_aliigner.cpp: contains implementation of QualAdjXdropAligner
*/
#include "dozeu_interface.hpp"
// Configure dozeu:
// We want the full length bonus included
#ifndef DZ_FULL_LENGTH_BONUS
#define DZ_FULL_LENGTH_BONUS
#endif
// We want the quality adjusted versions of functions
#ifndef DZ_QUA... |
2f20e39adf14a63284089500d6ab87e3e6d8d5a4b981bd336b7dc4b9aa17e4fe | C++ | 4,678 | 150 | #include "us_help.h"
#include "us_settings.h"
// Null constructor
US_Help::US_Help( QObject* parent ) : QObject( parent ) { }
// Show a specified help page in US3 manual
void US_Help::show_help( const QString& helpFile )
{
// Create a new process each time. If show_help() is called multiple
// times from a proce... |
93f0df5d088451b4a708aa45c47e549d013bf44a423bbb8a6cfb6bfc4eb9599c | C++ | 4,688 | 190 | #include <Eigen/Core>
#include <Eigen/SparseCore>
#include <iostream>
#include <random> // Requires C++ 11
#include <SymEigsShiftSolver.h>
#include <MatOp/DenseSymShiftSolve.h>
#include <MatOp/SparseSymShiftSolve.h>
using namespace Spectra;
#define CATCH_CONFIG_MAIN
#include "catch.hpp"
typedef Eigen::MatrixXd Matr... |
81e0d86b54f49566c9c5177d6dcc2bc377b0cdb930c8e3ab1249d6b727e4994f | C++ | 4,695 | 155 | //////////////////////////////////////////////////////////////////////////////
// k-regular Network with Small-World block E-to-E
// Notice the range of degrees in each block!
//
// For a SW network with the same mean in- and out-degree for both neuron types
// set: kE <= kEold - NE*prob, where kEold is kE in an ... |
36609c0cbfbf896fde15b5a8bfad5c08add0ffbfd965d6115e8ef5a9597ceb5a | C++ | 4,697 | 130 | // Validate the native grid volume against (a) analytic geometry and (b) values measured with
// 3V (vossvolvox) Volume.exe, which it replaces. See DECISIONS.md.
// build+run: make gridvol (optionally: make gridvol DATA=/path/to/xyzr/dir)
#include <cmath>
#include <cstdio>
#include <fstream>
#include <sst... |
b671ad86afc1835ff769ab7a11567b9e67cb91703334b26ed3497bb05e56f7cc | C++ | 4,717 | 115 | //------------------------------------------------------------------------------
//
// 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... |
04871af83715bceb741b70dc83ad9bb66734935cdd811da315c0e7605c11ca2c | C++ | 4,733 | 123 | //------------------------------------------------------------------------------
//
// 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... |
8089d7787e852a694e7a35f1d92784d9b9ff3551cf677009cc151194e6c5d729 | C++ | 4,745 | 163 | #include "vectorizer.hpp"
using namespace std;
using namespace vg;
using namespace sdsl;
Vectorizer::Vectorizer(const PathPositionHandleGraph* x) : my_xg(x){
size_t rank = 1;
my_xg->for_each_handle([&](handle_t handle) {
id_to_rank[my_xg->get_id(handle)] = rank++;
});
}
Vectorizer::~Vector... |
7dc368ecf71b177f6ad58f5dddc6b4e345d07e1b3cd50965cf55294bb01c4b85 | C++ | 4,759 | 177 | // test_us_buffer.cpp
#include "qt_test_base.h"
#include "mock_us_db2.h"
#include "us_buffer.h"
#include "us_constants.h"
#include <QTemporaryFile>
#include <QTemporaryDir>
#include <QXmlStreamWriter>
#include <cstring>
using ::testing::_;
using ::testing::Return;
using ::testing::Eq;
using ::testing::DoubleEq;
using ... |
4c449fb76e2c9915ba5cc2d6542d6b4ddd940955b5573023f6cb5d56c3c7fad1 | C++ | 4,792 | 127 | #include <iostream>
#include <vector>
#include <graphtyper/index/ph_index.hpp>
#include <graphtyper/utilities/kmer_help_functions.hpp>
#include <graphtyper/utilities/type_conversions.hpp>
namespace gyper
{
template <typename TSequence>
std::size_t get_num_kmers(TSequence const & dna)
{
if (seqan::length(dna) < K)
... |
3f17cd5d2ecf8b96d89cd6ff7170814429952038b589fd4268ddf79ce1b8baff | C++ | 4,798 | 165 | #include "subcommand.hpp"
#include "../io/save_handle_graph.hpp"
#include "../handle.hpp"
#include "../xg.hpp"
#include "../utility.hpp"
#include "../snarls.hpp"
#include "../masker.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <gbwtgraph/gbz.h>
#include <unistd.h>
#include <getopt.h>
#include <s... |
b8af681b96b6506e278616954767731593fbf7bdfce57be0c5634fbcf9d3c42c | C++ | 4,802 | 137 | /**
* \file register_loader_saver_gfa.cpp
*/
#include <vg/io/registry.hpp>
#include "register_loader_saver_gfa.hpp"
#include "algorithms/gfa_to_handle.hpp"
#include "gfa.hpp"
#include "handle.hpp"
#include "bdsg/packed_graph.hpp"
#include "save_handle_graph.hpp"
#include <iostream>
namespace vg {
namespace io {
... |
493f5369838744b667e801c94fe021a55d8274f00ca56f6e352b4601ae7c4527 | C++ | 4,847 | 138 | #include "watchdog.hpp"
#include <iostream>
#include <cassert>
#include "memusage.hpp"
namespace vg {
using namespace std;
Watchdog::Watchdog(size_t thread_count, const duration& timeout) :
stop_watcher(false),
state(thread_count),
timeout(timeout),
memory_high_water_kb(get_max_rss_kb()),
watch... |
6c0a13c50e0c8720af381839052c4f2839d9b2635b72fe861d54eefaa119cd62 | C++ | 4,857 | 156 | /** \file circularize_main.cpp
*
* Defines the "vg circularize" subcommand
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../utility.hpp"
#include "../handle.hpp"
#include "../vg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
usin... |
6b6c46b07821ab8cef2713bb84ff7e9a2a0540b393596791bb6cfca6010157be | C++ | 4,884 | 127 | ///////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// //
... |
b3364fc0c1621d95ac2203ba2cf7476ec65a7f6808281c6e5cb5400055dad614 | C++ | 4,894 | 115 | //------------------------------------------------------------------------------
//
// 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... |
5bed1d49a0925b493302b44d6809b2af2ebfe789fd89efa20507cd262e43547d | C++ | 4,902 | 150 | #include "qbitmap.h"
#include "qwt3d_color.h"
#include "qwt3d_plot.h"
#include "enrichments.h"
using namespace Qwt3D;
/////////////////////////////////////////////////////////////////
//
// Bar
//
/////////////////////////////////////////////////////////////////
Bar::Bar()
{
configure(0, 1);
... |
fff8c1c44083e520c01211ea2ac189bb4e27633802480a693abdc19f86f6f2c3 | C++ | 4,905 | 195 | #include <algorithm> // std::generate_n
#include <cassert> // assert
#include <cstring>
#include <dirent.h>
#include <iomanip>
#include <iostream>
#include <random>
#include <sstream>
#include <string> // std::string
#include <sys/stat.h>
#include <unistd.h>
#include <utility>
#include <vector>
#include <graphtyper/... |
833e088d64e07c66e5c4f375bb67307493bad5a82ddce0369f4486924f8113a2 | C++ | 4,923 | 135 | #include "ssw_aligner.hpp"
namespace vg {
void SSWAligner::PrintAlignment(const StripedSmithWaterman::Alignment& alignment){
cout << "===== SSW result =====" << endl;
cout << "Best Smith-Waterman score:\t" << alignment.sw_score << endl
<< "Next-best Smith-Waterman score:\t" << alignment.sw_score_next_best ... |
a6aafed87462d5c54c55d60b23c10a55e1ab3a41c4a08652d03e4a74ed7a775c | C++ | 4,996 | 153 | #include "subcommand.hpp"
#include "../utility.hpp"
#include "../viz.hpp"
#include "../xg.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>
#include <unistd.h>
#include <getopt.h>
using namespace vg;
using namespace vg::subcommand;
void help_viz(char** argv) {
... |
5665496dae9a7c9208fe13e00a3be186f2b27605a18d364a27e074ecc123afa9 | C++ | 5,046 | 154 | //! \file us_font.cpp
#include "us_font.h"
#include "us_gui_settings.h"
US_Font::US_Font( QWidget* w, Qt::WindowFlags flags )
: US_Widgets( true, w, flags )
{
// Frame layout
setPalette( US_GuiSettings::frameColor() );
setWindowTitle( "Font Selection Dialog" );
setAttribute( Qt::WA_DeleteOnClose );
... |
e184e46f4f3ee4ea3c110b95c1e19c0a7a4642c3bb702417e7085e6880c0aaa2 | C++ | 5,059 | 162 | /*
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... |
2b261d11687f926d9da12944742f415a16295474588763bfe996b702345d66a9 | C++ | 5,063 | 223 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4305 )
#endif
#include "qwt3d_colorlegend.h"
using namespace Qwt3D;
/**
Contructs a legend object with an axis at the left
side. The legend resides in the top-right area
and has no caption. Scale numbering is shown.
*/
ColorLegend::C... |
43900962a4f9346a86ebd302147b6aaef40c35d0b73507cae54c43e9e3411e62 | C++ | 5,069 | 120 | //------------------------------------------------------------------------------
//
// 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... |
d3143fa03d50b2fa8502497acee524465d39829bfcbfe3b21baf1a972a199be0 | C++ | 5,090 | 161 | #include <getopt.h>
#include <string>
#include <vector>
#include "subcommand.hpp"
#include "../vg.hpp"
#include <vg/io/vpkg.hpp>
#include "../haplotype_extracter.hpp"
#include "../algorithms/find_gbwt.hpp"
#include <bdsg/overlays/overlay_helper.hpp>
using namespace vg;
using namespace std;
using namespace vg::subco... |
6003b214c98c3ac9e49e118b220a1938c69e810eb1978f83cf68d12dbed0e35c | C++ | 5,100 | 151 | ////////////////////////////////////////////////////////////////////////////////
// $Id: FIRFilter.cpp 6484 2022-01-03 16:59:03Z mellinger $
// Description: A finite impulse response (FIR) filter for temporal filtering.
//
// $BEGIN_BCI2000_LICENSE$
//
// This file is part of BCI2000, a platform for real-time bio... |
8558cdc90b961ca3e22a7cf6c2974038b2dae71007afebbc70bfa688d46561c9 | C++ | 5,106 | 217 | #include "ShiftedLJ.hpp"
#include <iostream>
#include <iomanip>
#include <limits>
#include <cmath>
#include "GridayException.hpp"
ShiftedLJ::ShiftedLJ(GReal eps, GReal sig, GReal rcut) :
PairEnergy {},
mEps {eps},
mSig {sig},
mSigSq {sig * sig},
mRcut {rcut},
mRcutSq {rcut * rcut}
{
... |
d6ac1eb5bce13e0ae91ce7c8511557a93f55ca4df47e2690c51c22a14c30ac19 | C++ | 5,133 | 131 | ////////////////////////////////////////////////////////////////////////////////
// $Id: TransmissionFilter.cpp 6484 2022-01-03 16:59:03Z mellinger $
// Author: juergen.mellinger@uni-tuebingen.de (custom change for bipolar montage: Filippo Costa)
// Description: A filter that returns a subset of input channels in it... |
93ea775fcb94ba43640a678562913416bd92ba4eea934e0a9eb6a4d6fc764c4d | C++ | 5,149 | 164 | // inject_main.cpp: define the "vg inject" subcommand, which lifts over alignments from the linear space
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <string>
#include <vector>
#include <set>
#include <subcommand.hpp>
#include "../crash.hpp"
#include "../utility.hpp"
#include "../alignment.hpp"... |
ae4ff299ede673a7ea8c948d362e88935d441509b64ed1a21c65a7276b685299 | C++ | 5,163 | 182 | //! \file us_exclude_profile.cpp
#include "us_edit_scan.h"
#include "us_settings.h"
#include "us_gui_settings.h"
US_EditScan::US_EditScan( US_DataIO::Scan& s,
const QVector< double >& r,
double invertValue, double left, double right )
: US_WidgetsDialog(... |
9d3e4df70be88adcc96ce2ec16f9c6c7d6d75822bd611d3282bf5e32a016095a | C++ | 5,185 | 169 | /// \file dinucleotide_machine.cpp
///
/// Unit tests for the DinucleotideMachine
///
#include <iostream>
#include <random>
#include "../dinucleotide_machine.hpp"
#include "../statistics.hpp"
#include "catch.hpp"
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespace std;
using bdsg::... |
f11ec91eee1366a10365fd76fed8b95dc251f82a5165d56fc6716431852f1f97 | C++ | 5,186 | 235 | #include <math.h>
#include <stdio.h>
#include <string.h>
#include <stdarg.h>
#include "tron.h"
#ifndef min
template <class T> static inline T min(T x,T y) { return (x<y)?x:y; }
#endif
#ifndef max
template <class T> static inline T max(T x,T y) { return (x>y)?x:y; }
#endif
#ifdef __cplusplus
extern "C" {
#endif
exte... |
b259942670fe9bd2be95567390c8e001da81a48e1068880c76bd6ea4ecbe0dd5 | C++ | 5,195 | 208 | // *******************************
// Various Random Number Utilities
//
// RDB 2/95
// *******************************
#include "random.h"
#include <stdlib.h>
#include <math.h>
#include <iostream>
using namespace std;
// A global random state
RandomState GRS;
// Functions to manipulate the global random state fo... |
bf7598521a6f4068d7ca6316d0ca0e1b0761c0ec2975599bc8c83f833f12eb3b | C++ | 5,195 | 132 | //------------------------------------------------------------------------------
//
// 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... |
f291b93bc672f5b5311f080ab574abb9b7e5696bd30bc25b384f257a1ebc0260 | C++ | 5,211 | 163 | /****************************************************************************
** Form implementation generated from reading ui file '3dplot\lightingdlgbase.ui'
**
** Created: Sun Mar 9 15:21:33 2008
** by: The User Interface Compiler ($Id: qt/main.cpp 3.3.8 edited Jan 11 14:47 $)
**
** WARNING! All chang... |
d829913c51dffece1343c6efe16ffb4d77387ccb3cafe44d8ee810a4f4848e8d | C++ | 5,240 | 161 | #include <torch/extension.h>
#include <c10/cuda/CUDAGuard.h>
#include <vector>
// CUDA forward declarations
std::vector<torch::Tensor> slice_acquisition_forward_cuda(
torch::Tensor transforms,
torch::Tensor vol,
torch::Tensor vol_mask,
torch::Tensor slices_mask,
torch::Tensor psf,
torch::IntArr... |
bb383c3aa8f017fefde8569396afc8caa7881f5eec2334fcb13b3c701e12e565 | C++ | 5,243 | 164 | #include "catch.hpp"
#include "../utility.hpp"
#include "../algorithms/component.hpp"
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespace std;
set<set<path_handle_t>> normalize(vector<unordered_set<path_handle_t>> result) {
set<set<path_handle_t>> return_val;
for (auto& comp_s... |
7bd711dd1071cbf265db895b493fa0315b26aa06cb6870f4f3105a136803c23c | C++ | 5,266 | 137 | //------------------------------------------------------------------------------
//
// 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... |
7f1a5fb957a422ab86080634ee00157f94795a960c15799228dc0e7865538eca | C++ | 5,267 | 162 | #include <QApplication>
#include "us_pseudo_absorbance.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_extern.h"
int main(int argc, char *argv[])
{
QApplication application(argc, argv);
#include "main1.inc"
// License is OK. Start up.
US_PseudoAbsorbance w;
w.show(); ... |
81db1676e4a69b4be5ff3f34bc76ca3aa1c71ab8c13bd3df9543c99fb47af85b | C++ | 5,271 | 176 | /** \file kmers_main.cpp
*
* Defines the "vg kmers" subcommand, which generates the kmers in a graph.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <set>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../vg_set.hpp"
#include "../kmer.hpp"
using namespace std... |
435f59e0f51a3827171635525e36566b71bc08824d6eb94b39cc296cbe8a17e9 | C++ | 5,349 | 164 | // Test ../include/LinAlg/UpperHessenbergQR.h and
// ../include/LinAlg/DoubleShiftQR.h
#include <Eigen/Core>
#include <Eigen/QR>
#include <LinAlg/UpperHessenbergQR.h>
#include <LinAlg/DoubleShiftQR.h>
using namespace Spectra;
#define CATCH_CONFIG_MAIN
#include "catch.hpp"
using Eigen::MatrixXd;
using Eigen::Vec... |
200e2b049678b3537c09cbf9beae27ac018f6b9685faae557d8154f91eae9a0d | C++ | 5,390 | 134 | #include "logged_gap_alignment_scorer.hpp"
#include <algorithm>
#include <cmath>
namespace vg {
LoggedGapAlignmentScorer::LoggedGapAlignmentScorer(const Alignment& standard, double gc_content)
: LoggedGapAlignmentScorer(standard, count_alignment_operations(standard), gc_content) {
// Nothing to do!
}
i... |
691481e4d38bf3ec8b56f52b712216e1bc3928f6eecf339b7cd822236043fbea | C++ | 5,393 | 109 | // coverage.cpp -- audit the "no hybridization and/or no SAXS coefficient" bottleneck.
//
// (A) Cross-validate somo.hybrid.new against somo.saxs_atoms: every hybrid type's saxs_name must
// resolve to a SAXS entry, else SAXS breaks for any atom of that type.
// (B) For given structures, perceive every atom and rep... |
b458d35f51c4fda3e34ddf2cd6d3285bd6dceba2c4a0718743a36640f53c28d0 | C++ | 5,394 | 146 | #include "designerworkaround.h"
namespace{
QString tr(const char* val)
{
return QObject::tr(val);
}
void setCheckable(QActionGroup* ag)
{
QList<QAction*> tmplist = ag->actions();
for (QList<QAction*>::iterator it=tmplist.begin(); it!=tmplist.end(); ++it)
(*it)->setCheckable(tr... |
0f30ffd402c4b6241174923e0c9234d47e6c5231af19dda25932ee87c6ddd489 | C++ | 5,407 | 177 | /** \file translate_main.cpp
*
* Defines the "vg translate" subcommand
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../translator.hpp"
#include <vg/io/stream.hpp>
using namespace std;
using namespace vg;
using namespace... |
01115c9b254bf3cd8b5282f6e335464bbc8d32ea18dadb2d242478d500d159b1 | C++ | 5,429 | 125 | /// \file traversal_clusters.cpp
///
/// Unit tests for traversal similarity, the metric behind -L/--cluster in vg deconstruct,
/// vg call and vg simplify.
///
/// These exercise weighted_traversal_similarity directly rather than through a caller, where a
/// similarity of 0 is indistinguishable from "these alleles re... |
ce2bd7085728f55249369ec2dfcb84f63ba8a123603eaa4cb1f3f4f74ee28811 | C++ | 5,433 | 171 | //! \file us_advanced.cpp
#include "us_advanced.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_help.h"
US_Advanced::US_Advanced( QWidget* w, Qt::WindowFlags flags )
: US_Widgets( true, w, flags )
{
// Frame layout
setPalette( US_GuiSettings::frameColor() );
setWindowTitle( "Advanced Se... |
97c6533ccc363953e23dfcc7eeeba6023ff87918d50481c7ef7c6b5324e7bbb0 | C++ | 5,436 | 120 | /**
* \file jump_along_path.cpp
*
* Contains implementation of jump_along_closest_path algorithm
*/
#include "jump_along_path.hpp"
//#define debug_algorithms
namespace vg {
namespace algorithms {
using namespace std;
vector<pos_t> jump_along_closest_path(const PathPositionHandleGraph* graph,
... |
86243b7b430f12352813101ddd56f80e27fe363f4fc87a6c23ce58c0791c6aeb | C++ | 5,504 | 138 | /**
* \file
* Allocator configuration procedure for jemalloc.
*/
#include "allocator_config.hpp"
#include <iostream>
#include <fstream>
#include <cstring>
#include <jemalloc/jemalloc.h>
extern "C" {
// Hackily define symbols that jemalloc actually exports.
// Somehow it gets a "je_" prefix on these relat... |
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