sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
959b6da2c372e5bd96b0480dc31d068a81727111dd3be71222457d3000ebae87 | C++ | 26,589 | 787 | //------------------------------------------------------------------------------
//
// 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... |
207a8733d29494a0fe21b15540fdd4bfef746ab4ca08be934300131314320222 | C++ | 26,653 | 717 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
f584f2f9c84aa7b4eb4a34c0dc0d47b0967244edfb7b252bc212d39a5d879a02 | C++ | 26,745 | 716 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
30532974e03daceebba3032c8da8c614c5599ce3d1671c66581dd2963c2a2ca8 | C++ | 26,798 | 717 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
0f00b19e03ad56c79cea19a945a6ef1083c73a70b341eb07c5260d325040d795 | C++ | 26,838 | 718 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
c0986b1c40fb1f84018184c9e02ea9ea0a977025dd9913b586fb6483a58dcfad | C++ | 26,851 | 718 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
ee36fb57fd852537ef57fe58427532cf75a83bad563ecafcd13c96de86f0199a | C++ | 26,891 | 691 | #include "phase_unfolder.hpp"
#include "progress_bar.hpp"
#include "algorithms/disjoint_components.hpp"
#include <cassert>
#include <iostream>
#include <map>
#include <set>
namespace vg {
PhaseUnfolder::PhaseUnfolder(const PathHandleGraph& path_graph, const gbwt::GBWT& gbwt_index, vg::id_t next_node) :
path_grap... |
deb9af691d187b6a4b9169219104209d185c7d633c985627774a998676099706 | C++ | 26,924 | 724 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
1056adc08d571f5d69c53a1eab1ea9636df53b48c6be7e3861ab1db5e33a09a6 | C++ | 26,928 | 721 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
bf59995d1a18a1ca198133152336a3b8b0bda869e0ff41c7772d720d26e6d804 | C++ | 26,930 | 724 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
f9fa3d095d924437d0b08281057adeb32b4537d5e762533d6cad5088afe48b85 | C++ | 26,954 | 850 | #include "haplotypes.hpp"
#include "path.hpp"
#include "position.hpp"
namespace haplo {
// By default, should we warn when haplotype scoring fails?
bool warn_on_score_fail = false;
/*******************************************************************************
hDP_gbwt_graph_accessor
*******************************... |
258098ce19da3dd013397218c55ab8e5bee575ad09cb0c553405098510052d17 | C++ | 26,980 | 724 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
72a64758f30d3ae8e495b8195ba203c4fbadd57bfaeb30b96615dad8365d67ed | C++ | 26,988 | 722 | /*
movement sequences
references: https://www.omnicalculator.com/math/right-triangle-side-angle
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.mathsisfun.com/algebra/sohcahtoa.html
https://cplusplus.com/reference/cmath/asin/
*/
double rand_move() {
int num_directions = 4;
... |
19ef31a27f0d39fbc8fb88ce9c1d07f0038199d9b344151800e7b94e8e36a568 | C++ | 27,232 | 776 | // test_us_math2_unit.cpp - Unit tests for US_Math2 class
#include "qt_test_base.h"
#include "us_dataIO.h"
#include "us_math2.h"
#include "us_solution.h"
#include <QString>
#include <QTime>
#include <QVector>
#include <cmath>
#include <limits>
#include <random>
using namespace qt_matchers;
class TestUSMath2Unit : pub... |
78f93bb661fcfe609d0ac24a009ae7b0b9a5e8598b90b168409ae637c7dd4484 | C++ | 27,441 | 772 | //! \file us_rpscan.cpp
#include "us_rpscan.h"
#include "us_pcsa.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_sleep.h"
#include <qwt_scale_widget.h>
#include <qwt_scale_draw.h>
// Constructor: Regularization Parameter Scan widget
US_RpScan::US_R... |
fdfc92cc956326080853ff4caad5b1aaeb34860b34e6950e34290c6bc3445644 | C++ | 27,512 | 846 | //! \file us_select_rundd.cpp
#include "us_select_rundd.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_matrix.h"
#include "us_investigator.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_util.h"
#include "us_editor.h"
#include "us_constants.h"
#include "us_report.h"
#include "us_sleep... |
49ca0de305486eb2c5812b7a0c6cfa7126d9ca8aa437ae57976efc72b51c9f99 | C++ | 27,550 | 610 | //------------------------------------------------------------------------------
//
// 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... |
483bd41baceb90b6d80fb5dbcf1d0c851941e2896e956e9d2722db094930d5fe | C++ | 27,607 | 710 | /*
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... |
a993839bbb7a9027c00240c4c04cfef663a390b8c46593d4403c2ed17e4cfcac | C++ | 27,711 | 764 | /// \file multipath_alignment_graph.cpp
///
/// unit tests for the multipath mapper's MultipathAlignmentGraph
#include <iostream>
#include "../io/json2graph.hpp"
#include <bdsg/hash_graph.hpp>
#include <vg/vg.pb.h>
#include "../cactus_snarl_finder.hpp"
#include "../integrated_snarl_finder.hpp"
#include "../multipath... |
2aa855df1030223e0eefde6bea596d1ede2441d2dc2c42307a6708c79fd0907d | C++ | 28,199 | 879 | //! \file us_xpnhost.cpp
#include "us_xpnhost_db.h"
#include "us_newxpnhost_db.h"
#include "us_xpn_data.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_passwd.h"
#include "us_help.h"
#include "us_crypto.h"
#include "us_db2.h"
#define def_desc QString("place-holder")
#define def_host QString("19... |
4f9e49a244d25c32d07ebda2e258b87de2c22dab4b7715feba491939d396db23 | C++ | 28,223 | 883 | /*
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... |
7ced96a1154def89d33f1311fe1be0a1175f9159dc3a0e1abdfdd7557f9017b7 | C++ | 28,564 | 828 | //! \file us_tmst_plot.cpp
#include "us_tmst_plot.h"
#include "us_time_state.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_constants.h"
#include "us_images.h"
#include "us_editor.h"
#include <qwt_legend.h>
// constructor: residuals plot widget
US... |
8250521214cedc867240430271158058e002c2292ddaa5abb55bdab1fdd2cad5 | C++ | 28,772 | 631 | //------------------------------------------------------------------------------
//
// 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... |
714ab04b521365af4aa289e871a7e2fb4cfb79e950f7680e6b35c9fe9d63dbf1 | C++ | 29,051 | 821 | #include "functions.h"
GateConstStruct newGateConstStruct(uint32_t aFtype, float aX1, float aX2, float aX3,
float aX4, float aX5, float aX6,
float aX7, float aX8,float aX9,uint32_t bFtype, float bX1, float bX2, float bX3,
float bX4, float bX5, float bX6, float bX7, float bX8, float bX9... |
f4441167059f7220b9e985803aa9c00c9cbb98ca1a96ec45743a7d1bcbdeba34 | C++ | 29,155 | 523 | //------------------------------------------------------------------------------
//
// 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... |
d123b7ac6d4cc0f99850d7a759287ebf6877aa91f3b73bdaed3f025b9c2fcc48 | C++ | 29,159 | 742 | //------------------------------------------------------------------------------
//
// 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... |
2bf6c84af394b9d00b6b803a7c2ad3ae20b3f1564a315509d419dcbf02aaa9b4 | C++ | 29,341 | 844 | #include <bitset> // std::bitset
#include <cassert> // assert
#include <iostream> // std::cout
#include <map> // std::map<T,U>
#include <string> // std::string
#include <vector> // std::vector<T>
#include <seqan/sequence.h> // seqan::Dna5String
#include <graphtyper/graph/absolute_position.hpp>
#include <g... |
8d02ff9cf06b9a8924e5dee957729ce79344dfa90c656fa547d919f9469d1039 | C++ | 29,392 | 628 | #include "traversal_support.hpp"
#include "genotypekit.hpp"
//#define debug
namespace vg {
TraversalSupportFinder::TraversalSupportFinder(const HandleGraph& graph, SnarlManager& snarl_manager) :
graph(graph),
snarl_manager(snarl_manager) {
}
TraversalSupportFinder::~TraversalSupportFinder() {
}
int64_... |
898d5f3febafd7f4aaf0e17c4528a9338109df54fd5df5e256f91901aeddca52 | C++ | 29,627 | 792 | // mod.cpp: define the "vg mod" subcommand, which modifies vg graphs
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <string>
#include <vector>
#include <regex>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../cactus.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <h... |
25383974ac36689dc41444f91998efc8a5d8334c6eb261518d558b6cd0685dda | C++ | 29,668 | 550 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
5290b04dc07c74b006f0aae82dbda0a9ce91e7644e8f49c22f6a5d1e7de92d86 | C++ | 29,721 | 1,031 | #include "pm_worker.h"
// to add a new type
// define model generation routine:
// bool US_PM::"object"( int model_pos, vector < double > & params, vector < double > & params_left, set < pm_point > & model )
// insert into:
// enum objects
// init_objects()
// create_1_model()
// best_md0()
// also: bes... |
22f0ba2f618a7efcbf2460d12d2bcc01be6272d8abf54d3441bba6bf32cf922d | C++ | 29,734 | 790 | /** \file
*
* Unit tests for gaf_sorter.cpp, which provides tools for sorting GAF records.
*/
#include "../gaf_sorter.hpp"
#include "../utility.hpp"
#include <fstream>
#include <random>
#include <gbwt/gbwt.h>
#include "catch.hpp"
namespace vg {
namespace unittest {
//------------------------------------------... |
1e49fb4bb3851baf6df0a14ce7c7caa52faaf74091cbbf0d1d0e2c4b2ff245c6 | C++ | 29,776 | 1,013 | #include <QTimer>
#include "us_csv_loader.h"
#include "us_gui_settings.h"
#include "us_settings.h"
bool CSVSortFilterProxyModel::lessThan(const QModelIndex &left,
const QModelIndex &right) const
{
if (left.row() == 0 || right.row() == 0)
return false;
QVariant le... |
d1b0dedd55b9c7c9acae435c8ec34a6ba9e01edb17aa8e28280ab0d29c5cab67 | C++ | 29,824 | 676 | /**
* \file haplotype_indexer.cpp: implementations of haplotype indexing with the GBWT
*/
#include "haplotype_indexer.hpp"
#include <iostream>
#include <mutex>
#include <vector>
#include <string>
#include <vg/io/stream.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/path_cover.h>
#include "gbwt_helper.... |
3d4e4abc5b0010e182d5f14b126a6f075dd35e9703a1bdd753065083695780ad | C++ | 30,037 | 737 | #include "gbwtgraph_helper.hpp"
#include "gbwt_helper.hpp"
#include "gbzgraph.hpp"
#include <gbwtgraph/index.h>
#include <vg/io/alignment_io.hpp>
namespace vg {
//------------------------------------------------------------------------------
// Numerical class constants.
constexpr size_t MinimizerIndexParameters::... |
bf363c95bf447e008929359e9de0ac80d27774e9c4912a3930b1c83c3cbd52d2 | C++ | 30,215 | 503 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
8f15bec4f431ca716c9b31ba3b35b24cc9d156ff051cfd81a348351dd903badb | C++ | 30,231 | 954 | #include "us_mpi_analysis.h"
#include "us_math2.h"
#include "us_settings.h"
#include "us_tar.h"
#include "us_sleep.h"
#include "mpi.h"
// Analysis jobs with Supervisor and 2 or more Master+Workers parallel groups
void US_MPI_Analysis::pmasters_start()
{
// Determine group (0,...), worker count in group, rank within... |
e65c5a781d53a5b403aee1d54befdd738298208e46ce3cd4159093a0901625b6 | C++ | 30,253 | 902 | //! \file us_mrecs_loader.cpp
#include "us_mrecs_loader.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_editor.h"
#include "us_util.h"
// Main constructor for loading a single model records entry
US_Mr... |
a4a075a764cdb26247b23c03677a0803f7f32d2272a1ecbf66f10388b3e110cd | C++ | 30,279 | 617 | //------------------------------------------------------------------------------
//
// 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... |
1c5bb5db77280bcec40fdee06ceb7c0e95d84aa76ae3b2975ac4f70ef0712219 | C++ | 30,280 | 859 | //! \file us_eqfit_control.cpp
#include "us_eqfit_control.h"
#include "us_fit_worker.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_constants.h"
#include "us_math2.h"
#include "qwt_plot_marker.h"
// Main constructor with references to parameters from main GlobalEquil cl... |
a58887f85ec60f33717c59d3895f59f30810928d08d8d79ae3e6d2e84b91462e | C++ | 30,370 | 994 | #include "us_spectrum.h"
#include "qwt_plot_marker.h"
#include "us_csv_loader.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_settings.h"
#include <QtNumeric>
#include <algorithm>
#include <cmath>
int main(int argc, char *argv[])
{
QApplication application(argc, argv);
US_Spectrum w;
w.show(... |
e831d96ff116408cf94aead5a0c0a0093cd948115d3159d53ebffe1ab6cc3382 | C++ | 30,515 | 726 | //------------------------------------------------------------------------------
//
// 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... |
dbb68631f521646818d6063d108ef40069b0026bd046e335fe0a5a1406e4d8b4 | C++ | 30,704 | 699 | /**
* \file cluster_main.cpp: experimental snarl clustering test harness
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <iostream>
#include <cassert>
#include <vector>
#include <unordered_set>
#include <chrono>
#include "subcommand.hpp"
#include "../snarl_seed_clusterer.hpp"
#include "../gbwt... |
216c78bc987aa842ff92034d76d0864a46adefc33567adfdb61e07afea6cbec4 | C++ | 30,853 | 705 | //------------------------------------------------------------------------------
//
// 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... |
25dbc9eff807f2cfbfd5114716d409de6086ffffba6074995218f06c5251293c | C++ | 30,967 | 588 | //------------------------------------------------------------------------------
//
// 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... |
a5a9a223e29de99ce4531080b0fb52f77fb945d27227221de5e0e08eaef6d004 | C++ | 31,074 | 903 | //! \file us_show_norm.cpp
#include "us_2dsa.h"
#include "us_analysis_control_2d.h"
#include "us_adv_analysis_2d.h"
#include "us_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_gui_settings.h"
#include "us_memory.h"
#include "us_spectrodata.h"
#include "us_model.h"
#include "us_model_loader.h"
#inc... |
4b74e5d0bdd19b6443a89c9ab8d49607231039a5e46ceff6332df7dfe68ea5ab | C++ | 31,136 | 896 | //! \file us_eqreporter.cpp
#include "us_eqreporter.h"
#include "us_widgets.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_math2.h"
#include "us_editor.h"
#include "us_constants.h"
// Main constructor
US_EqReporter::US_EqReporter(
QVector< US_DataIO::EditedData >& dataList,
QVector... |
ab265c3d188a970c21953bfc8daac7d7325eafe65377770784f49791f8c4c0a8 | C++ | 31,142 | 747 | #include "mcmc_genotyper.hpp"
#include "subgraph.hpp"
#include <algorithm>
#include <random>
#include <chrono>
#include <utility>
#include "multipath_alignment.hpp"
// #define stdout_for_performance_script
// #define debug_mcmc
// #define debug_make_snarl_graph
// #define debug_karger_stein
// #define debug_proposal... |
48e89525c8f64be86c8baf3e0a1f2631e181eae75606257f8ded15713f87213e | C++ | 31,631 | 800 | #include "recombinator_haplotypes.hpp"
#include "kff.hpp"
#include <array>
#include <cmath>
//#define debug_selected_haplotypes
namespace vg {
//------------------------------------------------------------------------------
// Numerical class constants.
constexpr size_t Haplotypes::SUBCHAIN_LENGTH;
constexpr siz... |
167e921f1a9143453d58672516cf53cca375e16ae4a20fc9c06516d0db86510c | C++ | 31,646 | 948 | #include <QXmlStreamWriter>
#include <QXmlStreamReader>
#include <QBuffer>
#include <QDebug>
#include <QStringList>
#include <QMap>
#include <QJsonDocument>
#include <QJsonObject>
#include "us_ana_profile.h"
#include "qt_test_base.h"
using ::testing::_;
using ::testing::Not;
using ::testing::IsEmpty;
using ::testing:... |
c697bab096770e538ef4acd1944f93ec9bc57c37900e1e02c68598a905bf4c58 | C++ | 31,741 | 668 | ///////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// //
... |
2243aaee602142317489e9f88cdfec75fb0c3e63f646c0a3c848472ee43697ce | C++ | 31,932 | 756 | //------------------------------------------------------------------------------
//
// 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... |
6f60750f05ce29d852ba40a84fbc8724caefde7097b1d2b8f499498cb2a8d866 | C++ | 32,024 | 976 | /*
General functions
References: https://stackoverflow.com/questions/34218040/how-to-read-a-csv-file-data-into-an-array
https://iq.opengenus.org/split-string-in-cpp/
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.emathhelp.net/calculators/algebra-2/rotation-calculator/?px=20... |
82046c612243112e0810eac4ff44ae4c720e14553731886294d2287253eda649 | C++ | 32,025 | 976 | /*
General functions
References: https://stackoverflow.com/questions/34218040/how-to-read-a-csv-file-data-into-an-array
https://iq.opengenus.org/split-string-in-cpp/
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.emathhelp.net/calculators/algebra-2/rotation-calculator/?px=20... |
367c46ebf73757851cdbca3f7a360ea7564b997b0ab193b532498c1f1b6c2046 | C++ | 32,104 | 831 | #include "funnel.hpp"
#include "crash.hpp"
#include <cassert>
#include <cstring>
/**
* \file funnel.hpp: implementation of the Funnel class
*/
//#define debug
namespace vg {
using namespace std;
void Funnel::PaintableSpace::paint(size_t start, size_t length) {
// Find the last interval starting at or befor... |
6bd6156eab999248184b190606adfb8d44e817385d6fd9e32fd4311c60082d1d | C++ | 32,106 | 978 | /*
General functions
References: https://stackoverflow.com/questions/34218040/how-to-read-a-csv-file-data-into-an-array
https://iq.opengenus.org/split-string-in-cpp/
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.emathhelp.net/calculators/algebra-2/rotation-calculator/?px=20... |
d0709a03ab2d64d747adacf2c76cf6f61894558c25d70e9f98d3ce085067a5b7 | C++ | 32,112 | 787 | #include "gbwt_helper.hpp"
#include "utility.hpp"
#include <handle.hpp>
#include <gbwtgraph/utils.h>
#include <sstream>
#include <unordered_map>
namespace vg {
std::vector<std::string> parseGenotypes(const std::string& vcf_line, size_t num_samples) {
std::vector<std::string> result;
// The 9th tab-separate... |
2d8795a3db545a6870768ef9c267fd171960b8b4bd33b3ab275b9cee799fdbe1 | C++ | 32,190 | 977 | /*
General functions
References: https://stackoverflow.com/questions/34218040/how-to-read-a-csv-file-data-into-an-array
https://iq.opengenus.org/split-string-in-cpp/
https://www.mathsisfun.com/algebra/trig-finding-angle-right-triangle.html
https://www.emathhelp.net/calculators/algebra-2/rotation-calculator/?px=20... |
f99ff8b865a59f3a5977e093e412c60c596d7efbb2a4eed8233fd1763ee8e8ca | C++ | 32,386 | 746 | //------------------------------------------------------------------------------
//
// 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... |
7cbea163270efa54e2d5f495ec1506fc2e63d5b832ace9b3325fd03576996db6 | C++ | 32,496 | 974 | //! \file us_select_item.cpp
#include "us_select_item.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"
#include "us_failed_gmp_run_gui.h"
//! \brief Class for simple table widget display of
//! a list of item columns... |
5f5ee352cb072a22459642e6b425a4c6ee44f322cbc61d638f962a01cbc6c2d4 | C++ | 33,000 | 710 | // Verbatim copy of cctbx/eltbx/xray_scattering/it1992.cpp from the cctbx project
// (https://github.com/cctbx/cctbx_project), retained here as the reference transcription of
// International Tables Vol. C Table 6.1.1.4. It is NOT compiled into SOMO: it is parsed by
// perceiver/tools/gen_saxs_entries.py to generate s... |
c8ff0fb2176c88d2996361cfe52f6c0721af6430f320705db0bffd023de099c1 | C++ | 33,073 | 1,115 | //! \file us_widgets.cpp
#include <QtSvg>
#include "qwt_plot_canvas.h"
#include "us_widgets.h"
#include "us_gui_settings.h"
#include "us_theme.h"
#include "us_gui_util.h"
#include "us_settings.h"
#include "us_images.h"
#include "us_util.h"
US_Widgets::US_Widgets( bool set_position, QWidget* w, Qt::WindowFlags f ) :... |
2cc2cb915295a931e3393b1cf568f2d70ed6a9dac8be4cca818f743c2c5b9e49 | C++ | 33,286 | 589 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
8a32190f9444865f23a82491327eda7aa9b66d3b7588cce63a422e2394fee544 | C++ | 33,461 | 1,010 | /*
*
* Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* 1. Redistributions of source code must retain the above ... |
eb011a36efaa84ab7e44220ac72101d022aa979147ebc8e71260ab32ea5c8c05 | C++ | 33,474 | 698 | #include "three_edge_connected_components.hpp"
extern "C" {
#include "sonLib/sonLibList.h"
#include "sonLib/sonLibTuples.h"
#include "sonLib/3_Absorb3edge2x.h"
}
#include <structures/union_find.hpp>
#include <limits>
#include <cassert>
#include <iostream>
#include <sstream>
//#define debug
namespace vg {
namespace... |
b031b887ee121490594d58dcd0aef3bcfd69dbc5a833794f976f6a2f50472c84 | C++ | 33,565 | 1,083 | #include <cmath> // sqrt
#include <libgen.h> // dirname
#include <sstream> // std::ostringstream
#include <string> // std::string
#include <sys/stat.h> // mkdir
#include <vector> // std::vector
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/genomic_region.hpp>
#include <... |
ab916f75368d8bf656eadf1165c0c7e0425858ae03b0e985e67fbad7731e262d | C++ | 34,056 | 1,121 | #include "vg.hpp"
#include <vg/io/stream.hpp>
#include "aligner.hpp"
#include <vg/vg.pb.h>
#include "flow_sort.hpp"
#include <raptor2/raptor2.h>
namespace vg {
using namespace std;
FlowSort::FlowSort(VG& vg):vg(vg) {
}
std::unique_ptr< list<NodeTraversal> > FlowSort::max_flow_sort(const string& ref_name, bool ... |
4f5d573d33e2275460c9632cef1acf05c97c1fa400249c3cfae13bc18de9a6fd | C++ | 34,161 | 1,078 | #include "us_mpi_analysis.h"
#include "us_math2.h"
#include "us_settings.h"
#include "us_tar.h"
#include "us_sleep.h"
#include "mpi.h"
// Analysis jobs with Supervisor and 2 or more Master+Workers parallel groups
void US_MPI_Analysis::pm_cjobs_start()
{
// Determine group (0,...), worker count in group, rank within... |
b3029447c0ae5c84f1d21d0d2398fff4996bb49cd8699b61afaa3e32cad5ec6f | C++ | 34,184 | 1,174 | //! \file us_resplot_fem.cpp
#include "us_resplot_fem.h"
#include "us_fematch.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
#include "us_math2.h"
#include "us_constants.h"
#include "../us_autoflow_analysis/us_autoflow_analysis.h"
#include "../us_reporter_gmp/us_reporter_gmp.h"
#incl... |
156bed94ad0ac4294525312bdaab30e639a349fff6349b7920aa49c54927af81 | C++ | 34,399 | 1,081 | #include "utility.hpp"
#include "statistics.hpp"
#include <htslib/hfile.h>
#include <set>
#include <mutex>
#include <dirent.h>
#include <thread>
#include <cstdio>
#include <cmath>
#include <filesystem>
#include <fstream>
#include <iostream>
#include <cctype>
#include <locale>
// We don't define _GNU_SOURCE to get the... |
0909bcee4d032760a9e846ddd8aa4ed14976bd0a19722bf1fb9d9481c65ca46f | C++ | 34,431 | 1,156 | //! \file us_model_gui.cpp
#include "us_model_gui.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_constants.h"
#include "us_properties.h"
#include "us_investigator.h"
#include "us_util.h"
#include "us_passwd.h"
#include "us_associations_gui.h"
US_ModelGui::US_ModelGui( US_Model& current_model )
... |
3303dc2bd7a43654c5331c75a0f1dd2f86ef54e53bfe049fe36f165cff3cfc44 | C++ | 34,572 | 880 | //------------------------------------------------------------------------------
//
// 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... |
3b0ae736c515b79c4e971a72e0323db1702516008f86ae328a6382d69edbf988 | C++ | 34,635 | 1,004 | #include <stdio.h>
#include <stdint.h>
#include "Maxfiles.h"
#include "functions.h"
#include "NativeJSON.h"
// #include <mpi.h>
#define WRITE_OUTPUT 0
#define READ_OUTPUT 1
#define TIMING 0
#define TIME_SINGLE 0
#define MULTI_NODE 0
int main(int argc, char *argv[]) {
printf("start program\n");
double tStart, tEnd,... |
497d03c0ab03e60758dc0f4181b664be82b337c8ed00c263c2f7bfedb4def44e | C++ | 34,805 | 770 | /**
* @file dozeu_interface.hpp
* @author Hajime Suzuki
* @date 2018/03/23
*/
#include <cstdio>
#include <assert.h>
#include <utility>
#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 non-... |
34a0c46292e8a93473f0fc9e711abe2ae4ad47af5ceee20677f7abe67ae24be9 | C++ | 34,814 | 733 | //
// phased_genome.cpp
//
#include "phased_genome.hpp"
//#define debug_phased_genome
using namespace std;
namespace vg {
PhasedGenome::HaplotypeNode::HaplotypeNode(NodeTraversal node_traversal, HaplotypeNode* next, HaplotypeNode* prev) :
node_traversal(node_... |
85d4d8de36bcbfec395a664e062cc4efb06a6f386844f62ff62d4f713539f78e | C++ | 35,092 | 838 | //------------------------------------------------------------------------------
//
// 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... |
b1a89fa8acf2891bb3c494cb32045f37dc01320fec9d7bdeb27854bccb442fd3 | C++ | 35,232 | 991 | #include "NativeJSON.h"
#include "cJSON-1.7.1/cJSON.h"
#include "string.h"
bool ImportJsonFormula(cJSON *oFormula, Formula &fo, const char *filename, FILE *info_log, FILE *error_log){
if(!cJSON_IsObject(oFormula)){
fprintf(error_log, "file %s: Formula should be an object\n", filename);
return false;
}
cJSON... |
ae82b5e640f6e630cde0e8b77bcb58f766caab08a23ecca857e0df7b95c630f7 | C++ | 35,552 | 796 | #include "small_snarl_simplifier.hpp"
#include "cactus_snarl_finder.hpp"
namespace vg {
using namespace std;
SmallSnarlSimplifier::SmallSnarlSimplifier(VG& graph) : Progressive(), graph(graph), traversal_finder(graph) {
// create a SnarlManager using Cactus
CactusSnarlFinder site_finder(graph);
sit... |
4e74e491d54d3f389b22da1b4eb59b67e1b1caf896a36d7698f3ff8c47c7b1fd | C++ | 36,250 | 1,210 | //! \file us_rotor_gui.cpp
#include "us_rotor.h"
#include "us_rotor_gui.h"
#include "us_settings.h"
#include "us_util.h"
#include "us_db2.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
US_RotorGui::US_RotorGui(
US_Rotor::RotorCalibration& calibration,
bool new_calibration,
... |
5a28018b0d4aeec29d5e88b3d7c0b778c063a811e327930de8a027f8ada67d81 | C++ | 36,405 | 1,183 | #include <cassert>
#include <iostream>
#include <string>
#include <vector>
#include <seqan/basic.h>
#include <seqan/hts_io.h> // BamAlignmentRecord
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/haplotype_extractor.hpp>
#include <graphtyper/index/kmer_label.hpp>
#... |
47e6d475fa59bf03007723052738546c8db1743338f441f5c52f0c3589b1ba8d | C++ | 36,706 | 762 | // Unit tests for shell reduction (grpy_exposure.hpp + grpy_shell.hpp).
//
// The central property under test is HONESTY: the reported error bar must bound the true
// error, measured against an independently computed unreduced solve. A bar that
// understates is worse than no bar at all, so that check is the one that ... |
772325fcebad5b0c4c62457c2a85382748f37acaa8a9f29154372301454c484f | C++ | 37,617 | 809 | //------------------------------------------------------------------------------
//
// 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... |
26104dd57f5c34f31c277dc31ba816c4d2154c4f0fa8566c7aaf1054acf48199 | C++ | 37,692 | 1,371 | #include <iostream>
#include <limits>
#include <map>
#include <string>
#include <unordered_map>
#include <paw/parser.hpp>
#include <seqan/align.h>
#include <seqan/bam_io.h>
#include <seqan/file.h>
#include <seqan/seq_io.h>
#include <seqan/sequence.h>
#include <seqan/store.h>
#include <graphtyper/utilities/bamshrink.... |
4c90669cba2daafe6dd12dff93c3a8423a21658d6ba3d6915645a84cc4cf4d29 | C++ | 37,714 | 1,146 | //! \file us_project_gui.cpp
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_project.h"
#include "us_project_gui.h"
US_ProjectGui::US_ProjectGui(
bool signal_wanted,
int select_db_disk,
const US_Project& d... |
efc01ab889af137c466cb77f778e545ead799f5b9979d81fc9c08ce229c936b4 | C++ | 38,137 | 871 | //------------------------------------------------------------------------------
//
// 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... |
6d60f89536002e5295b0f07cc65b103dacec44406996bed1f16280f015100702 | C++ | 38,331 | 1,187 | //! \file us_properties.cpp
#include "us_properties.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_images.h"
#include "us_constants.h"
#include "us_model.h"
#include "qwt_arrow_button.h"
US_Properties::US_Properties( US_Model& mod, int access )
: US_WidgetsDialog( nullptr, Qt::WindowFlags()... |
724da9a73e1e49c76c8507af4b238bd519f40211e7de9bda3158481c560249b2 | C++ | 38,442 | 796 | #include "subcommand.hpp"
#include "../vg.hpp"
#include "../utility.hpp"
#include "xg.hpp"
#include "../algorithms/gfaz_to_handle.hpp"
#include "../io/save_handle_graph.hpp"
#include "../gfa.hpp"
#include "../gbzgraph.hpp"
#include "../gbwt_helper.hpp"
#include "../gbwtgraph_helper.hpp"
#include <vg/io/stream.hpp>
#in... |
1c77e1f90eb76fbda43c8d028b8951f0fc5c9091a2fd02c8cd4545d6976265f9 | C++ | 38,756 | 947 | //! \file us_eqmodel_control.cpp
#include "us_eqmodel_control.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
#include "us_math2.h"
#include "us_analyte_gui.h"
#include "us_buffer_gui.h"
#include "us_db2.h"
// Main constructor with references to parameters from main GlobalEquil clas... |
a7a09f01e091c9ed3ddbbd47a649343f596796fb8e9a8a319c1e9e5285e3e802 | C++ | 38,998 | 1,266 | //! \file us_mwl_data.cpp
#include "us_mwl_data.h"
#include "us_util.h"
#include "us_settings.h"
#include "us_math2.h"
#include "us_memory.h"
// Hold data read in and selected from a raw MWL data directory
US_MwlData::US_MwlData( )
{
clear(); // Clear internal vectors
curccx = 0; // C... |
3645137bf623513cf5e1710696718c5d4c3b77511a2206de0813a7f4f1478522 | C++ | 39,140 | 1,022 | /*********************************************************************
* Software License Agreement (BSD License)
*
* Copyright (c) 2011, Rice University
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following con... |
ea4be7ba5cc2824d5afdb7d146db989d01af87df0d58c8e87dcbfc4ded47a844 | C++ | 39,283 | 870 | //------------------------------------------------------------------------------
//
// 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... |
c944b832ca55276f3d5c33d10be76d67e2d34124ec4429e22a6fe13339dd74a3 | C++ | 39,361 | 1,255 | #include <string> // std::string
#include <unordered_map> // std::unordered_map
#include <vector> // std::vector
#include <seqan/basic.h>
#include <seqan/hts_io.h>
#include <seqan/sequence.h>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/haplotype_calls.hpp>
#include <graphtyper/graph/r... |
dcb659befc70d6bc8c4630bd461fc62b57670afb4f6c4fd9fe73db7c10a605d5 | C++ | 39,454 | 1,103 | #include <thread>
#include <vg/io/protobuf_iterator.hpp>
#include "packer.hpp"
#include "statistics.hpp"
#include "../vg.hpp"
//#define debug
using namespace vg::io;
namespace vg {
const int Packer::maximum_quality = 60;
const int Packer::lru_cache_size = 4096;
size_t Packer::estimate_data_width(size_t expected_cov... |
08911f85727f2856e872230ec53718f535b4a1975b4b25031a5c95f990a102b0 | C++ | 39,522 | 1,154 | #include "us_remove_ri.h"
US_RemoveRI::US_RemoveRI() : US_Widgets()
{
setPalette( US_GuiSettings::frameColorDefault() );
// Put the Run Info across the entire window
QLabel* lb_runInfoInt = us_banner( tr( "Load Exprimental Data" ) );
pb_import = us_pushbutton(tr("Import Experimental Data"));
p... |
3f3edb2ba6892eb6ec035f600640ca2ef991df0e3613cc89765b0bf812c6ddd4 | C++ | 39,697 | 1,024 | /** \file view_main.cpp
*
* Defines the "vg view" subcommand, which converts formats.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../multipath_alignment.hpp"
#include "../vg.hpp"
#include "../snarl_distance_index.hpp"
#includ... |
79d14163163e5b5f82cc817c7a170389e6ed02747c81236563ba77b43b6a547c | C++ | 39,860 | 859 | /// \file snarl_manager_decomposition.cpp
///
/// Unit tests for SnarlManagerDecomposition, and tests that check each
/// SnarlDecomposition implementation against the interface's laws and
/// against the other implementations.
#include "catch.hpp"
#include "../handle.hpp"
#include "../vg.hpp"
#include "../integrated_... |
ff9b2f03b33aeedaa0fdbc90e4ad0ebac083dfb488ebdf71d32ddaf44960dd34 | C++ | 40,053 | 976 | ///
/// \file position.cpp
///
/// Unit tests for Position and pos_t manipulation
///
#include "catch.hpp"
#include "surjector.hpp"
#include "aligner.hpp"
#include "bdsg/hash_graph.hpp"
#include "bdsg/overlays/path_position_overlays.hpp"
#include <vg/vg.pb.h>
namespace vg {
namespace unittest {
class TestSurjecto... |
0086af2b0f1dc3b31090dce620abddf1376bd37418c6599a644343aeefd75123 | C++ | 40,182 | 1,118 | //! \file us.cpp
#include <QtCore>
#include <QTcpSocket>
#include <QFontDatabase>
#include <QtWidgets/QApplication>
#include <QVersionNumber>
#include "us.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_theme.h"
#include "us_win_data.h"
#include "... |
c213b9ff89a3b1fff6ac44e696340180fe47866003eb756be4f2abdbb9057bb8 | C++ | 40,570 | 987 | /// \file unittest/xdrop_aligner.cpp
///
/// Unit tests for the XdropAligner class.
///
#include <iostream>
#include <string>
#include "../io/json2graph.hpp"
#include "../alignment.hpp"
#include "../vg.hpp"
#include <vg/vg.pb.h>
#include "test_aligner.hpp"
#include "catch.hpp"
#include "bdsg/hash_graph.hpp"
namespa... |
8bf3b65dc13497d856b39fef0014c20b82afbc81a5f609c6b74ec52d956c421e | C++ | 40,575 | 925 | #include "subcommand.hpp"
#include "../crash.hpp"
#include "../utility.hpp"
#include "../mapper.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <vg/io/protobuf_emitter.hpp>
#include "../io/save_handle_graph.hpp"
#include <gbwt/gbwt.h>
#include <gcsa/support.h>
#include "../region.hpp"
#include "../s... |
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