sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
92cbcd097071726012928292fd4badff13963e61f193221c88ed900c5e780c29 | C++ | 10,283 | 212 | /**
* \file back_translate.cpp
*/
#include "back_translate.hpp"
#include "../path.hpp"
#include "../snarls.hpp"
namespace vg {
namespace algorithms {
using namespace std;
/**
* Erase the items at the given indices in the given Protobuf repeated pointer field.
*/
template<typename RepeatedPtrField>
static void e... |
91d46f9da8d44f72fb9b571014d6e5548a36159359f7795f93196b9d97a6a9d0 | C++ | 10,367 | 272 | #include <getopt.h>
#include <string>
#include <vector>
#include <subcommand.hpp>
#include "../primer_filter.hpp"
#include "../snarl_distance_index.hpp"
using namespace std;
using namespace vg;
using namespace vg::subcommand;
void help_primers(char** argv) {
cerr << "usage: " << argv[0] << " primers [options] ... |
e26b78334087de9f8419e071af8b9fbd03b6cb4a132490cbc6dfb3763354d8d1 | C++ | 10,595 | 301 | /** \file vectorize_main.cpp
*
* Defines the "vg vectorize" subcommand, which turns graphs into ML vectors.
*/
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include "../vg.hpp"
#include "../vectorizer.hpp"
#include "../mapper.hpp"
#include... |
7c5ae0a5c40d5a01d4f24134ac73c05112aeffebfe9690623e03e731e347a51c | C++ | 10,623 | 372 | //! \file us_combined_plots_parms_gui.cpp
#include "us_combined_plots_parms_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_images.h"
US_CombPlotsGui::US_CombPlotsGui( QString combPlotsMask, QStringList type_method_list ... |
f5bb85d5f6b9e33a01648306c4c816f4cc143bb2ba605376416adb80a7725964 | C++ | 10,728 | 295 |
//using namespace std;
#include <armadillo>
using namespace arma;
//#include <vector>
#define DONT_USE_UNMAPPABLE_TUPLES
#include <nl-randvar.h>
#include <Delimited.hpp>
////////////////////////////////////////////////////////////////////////////////
const int MAXITERS = 20;
const int MAXDEPTH = 4;
// Initialized ... |
12bf20eefcc494ef7bf58dcba90fcdd0d2a028446851981dbfe1f079b0dd5ded | C++ | 10,771 | 343 | /*
* Copyright (C) 2022 Grupo de Neurocomputacion Biologica, Departamento de
* Ingenieria Informatica, Universidad Autonoma de Madrid.
*
* Authors:
* Garrido-Peña, Alicia
* Reyes-Sanchez, Manuel
* Sanchez-Martin, Pablo
*
* This program is free software: you can redistribute it and/or modify it
* un... |
cae81cd77dc5e49faad701273f41f1f4785e944f5a3fd67281c50f461189090b | C++ | 10,824 | 245 | // ProcessSolver: the GRPY program run as a subprocess, presented as a grpy::SolveFn.
//
// Driven by a FAKE GRPY program -- a script that replays a real golden report and the real
// progress banner -- so the parsing, the progress scraping and both failure paths are
// tested without needing a built GRPY. The report i... |
5a2bc3cb348c58b9559561f33bf0b8f0f623a00ccf18e1d9f8a61406ca889d16 | C++ | 10,887 | 347 | ///
/// \file vpkg.cpp
///
/// Tests for VPKG packaging format
///
#include "catch.hpp"
#include <vg/io/vpkg.hpp>
#include <bdsg/hash_graph.hpp>
#include <bdsg/packed_graph.hpp>
#include "xg.hpp"
#include "../vg.hpp"
#include "../snarl_seed_clusterer.hpp"
#include "../io/json2graph.hpp"
#include <gcsa/gcsa.h>
#inc... |
3df1e33f2c4db53802e16336e234f5940cb36e063abdfad0f1b05bd2f218b114 | C++ | 10,889 | 242 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
b0bc740ce3505ab8d95cde4a8fd97950161c120c5ee0d6d078e7b24b90e1f09a | C++ | 10,976 | 295 | //------------------------------------------------------------------------------
//
// 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... |
1f84361cec1b3a1b9fa793eba4f6de99e449b43398c5515c7516be1848254760 | C++ | 10,998 | 350 | #include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include <seqan/stream.h>
#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/grap... |
e00ec2efb5f2a01050f3f364f39c8fd1a0b95f1621385bdb4011c33775b8ee3f | C++ | 11,035 | 258 | /* * Copyright (c) 2016 Regents of the University of California. 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 copyright
* notice, ... |
a4f6d65e44e766c3c7530d90a4360d7e4f7cfa97348e8dc5306abea5512e8a71 | C++ | 11,042 | 387 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4305 )
#pragma warning ( disable : 4786 )
#endif
#include "qwt3d_plot.h"
using namespace std;
using namespace Qwt3D;
/**
Standard mouse button Function. Prepares the call to mouseMoveEvent
\see mouseMoveEvent()
*/
void Plot3D::mo... |
c5b2d2079d5bf317e55093dd53ab2009b5eacb8f2d4b692613b976249db6daae | C++ | 11,048 | 258 | /* * Copyright (c) 2016 Regents of the University of California. 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 copyright
* notice, ... |
ea6eb2b35f37342fb0b6ef31a2c4215620757014e74cba8865e5fafedabcd2b0 | C++ | 11,049 | 258 | /* * Copyright (c) 2016 Regents of the University of California. 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 copyright
* notice, ... |
026e1799bae660eb66f63e15cd6cc5d3d870c35b1d193b5378cd71bbcc55c4c6 | C++ | 11,076 | 316 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
ddcef621598f9946870017c9874ca7f30ff4441005b6af1ad68047715dec6be5 | C++ | 11,090 | 257 | /* * Copyright (c) 2016 Regents of the University of California. 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 copyright
* notice, ... |
1aa7ffb75060c5a4dff7fd0d180c5ea5c70fb8603b6af621fd9cbc7cb4fd6055 | C++ | 11,107 | 344 | /**
* \file
* constructor.cpp: contains implementations for vg construction functions.
*/
#include "vcf_buffer.hpp"
namespace vg {
using namespace std;
vcflib::Variant* VcfBuffer::get() {
if(has_buffer) {
// We have a variant
return &buffer;
} else {
// No next variant loaded.
... |
c1b0cdaa85529578d25517173f0c9bfe6e00bfc60cfb0442558241ae48b115c3 | C++ | 11,107 | 339 | #include "catch.hpp"
#include "../handle.hpp"
#include <bdsg/hash_graph.hpp>
#include "support/snarl_decomposition_fuzzer.hpp"
#include <vector>
#include <unordered_set>
namespace vg {
namespace unittest {
using ET = DecompositionEventType;
using Event = DecompositionEvent;
TEST_CASE("ReplaySnarlFinder replays eve... |
08d95677b9c04f331203b32d9a13aed107a6ad825236a312097310a9448e2be5 | C++ | 11,114 | 232 | #include "alignment_path_offsets.hpp"
//#define debug_mpaln_offsets
namespace vg {
namespace algorithms {
unordered_map<path_handle_t, vector<pair<size_t, bool> > >
alignment_path_offsets(const PathPositionHandleGraph& graph,
const Alignment& aln,
bool just_min,
... |
573934e268800d3b90916bca29eab93000c5dd848a3b71e8c1415c6e8083d544 | C++ | 11,130 | 296 | #include "shd.h"
// #define SHOW_MPI_TIMING
bool SHD::compute_amplitudes( vector < complex < float > > & Av )
{
// model should already be centered
#if defined( SHOW_MPI_TIMING )
double global_time_start = MPI_Wtime();
double time_start;
double time_end;
double rtp_time = 0e0;
double shbes_time = 0e... |
2c3e0eca11fdf6013cd2c1a9c02294cd746425c9954fb0ef2bbbb3962e5c9d74 | C++ | 11,194 | 324 | #include "qt_test_base.h"
#include <gmock/gmock-matchers.h>
#include "us_simparms.h"
#include "mock_us_db2.h"
#include <QTemporaryDir>
#include <QXmlStreamWriter>
#include <QXmlStreamReader>
#include <QFile>
#include <QDir>
using ::testing::_;
using ::testing::An;
using ::testing::Return;
using ::testing::SetArgRefere... |
f58d0f632a90e014a067a6c9a78105072091e7aa2c0b1f288aae94786ee7db78 | C++ | 11,264 | 237 | /**
* \file extract_extending_graph.cpp
*
* Implementation for the extract_extending_graph algorithm.
*/
#include "extract_extending_graph.hpp"
#include <structures/updateable_priority_queue.hpp>
#include "../crash.hpp"
//#define debug_vg_algorithms
namespace vg {
namespace algorithms {
using namespace structu... |
8dea847db41a3a5a75bc8e90214258621ec31b5a8c1afa216737b2cbdcdcd29f | C++ | 11,268 | 389 | #include <algorithm>
#include <iostream>
#include <numeric>
#include <cereal/archives/binary.hpp>
#include <cereal/types/vector.hpp>
#include <graphtyper/graph/absolute_position.hpp>
#include <graphtyper/graph/haplotype.hpp> // AlleleCoverage
#include <graphtyper/graph/reference_depth.hpp>
#include <graphtyper/graph/... |
cc684cc6debf7439689b8ea87c1163878f241ab3047160d360b08c7252c04fb7 | C++ | 11,270 | 372 | //! \file us_config.cpp
#include <QApplication>
#include "us_config.h"
#include "us_defines.h"
#include "us_license.h"
#include "us_license_t.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_constants.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "m... |
d33f4ad5e5c1350d2a80e48f30e781358f5f3aa94f93a9636d75ab2d5e05d119 | C++ | 11,275 | 263 | // SSSR on REAL coordinates, through the whole perception path (bond perception -> rings).
// The unit tests in sssr.cpp exercise the algorithm on hand-built graphs; this checks that what
// the perceiver actually derives from crystallographic coordinates has the ring count and sizes
// the chemistry demands. A wrong c... |
5b6c3b8d0bc9821f6e091bcb00f077c76e6cd05096371a7ac00f454ed64be5de | C++ | 11,287 | 319 | //------------------------------------------------------------------------------
//
// 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... |
185637187a13fb8224495fd6315559078c26ffc6125f0f234d9fdda25ce8b182 | C++ | 11,310 | 318 | // simplify_main.cpp: define the "vg simplify" subcommand, which removes small variation
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <list>
#include <fstream>
#include "subcommand.hpp"
#include <vg/io/vpkg.hpp>
#include "../vg.hpp"
#include "../small_snarl_simplifier.hpp"
#include "../rare_va... |
35482685d1577ca11c6f79a77e755de9f41aad503a1c5d7f9e330d87090c66e0 | C++ | 11,345 | 355 | /*
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... |
8c5a33bdecb73c1d45f2f45396e73094274c0e230f636ee2263f8b4486bd859a | C++ | 11,349 | 264 | /**
* \file path_subgraph.cpp: contains the implementation of PathSubgraph
*/
#include "path_subgraph.hpp"
#include "path.hpp"
#include <handlegraph/util.hpp>
#include <iostream>
namespace vg {
using namespace std;
PathSubgraph::PathSubgraph(const HandleGraph* base, const Path& path) : super(base), defining_... |
d77fd29cfe27058edf3238a84d78d6103b84a66fd156493937041635d1eda818 | C++ | 11,358 | 327 | //------------------------------------------------------------------------------
//
// 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... |
326ca5060c43fe0ae904d0dee5814af4a19739a5b2b075cf33524e569ae98b05 | C++ | 11,383 | 298 | #include "source_sink_overlay.hpp"
#include <handlegraph/util.hpp>
//#define debug
namespace vg {
using namespace std;
using namespace handlegraph;
SourceSinkOverlay::SourceSinkOverlay(const HandleGraph* backing, size_t length, id_t source_id, id_t sink_id,
bool break_disconnected) : node_length(length), backi... |
5857dc26adb8e4147123c36bb0516dfc4b561897ba0444801c8e070c017a54f1 | C++ | 11,418 | 357 | #include "abstractpanel.h"
#include "stimparamdialog.h"
#include "anoutdialog.h"
#include "digoutdialog.h"
#include "controlwindow.h"
#include "controlpanelconfiguretab.h"
ColorWidget::ColorWidget(QWidget *parent) :
QWidget(parent)
{
checkerboardIcon = QIcon(":/images/checkerboard.png");
QPixmap pixmap(16... |
8f5987d3e8364fd2f32c5d2bdbcec352184ed91a544aede37bad78550e62c2fe | C++ | 11,449 | 399 | // test_us_time_state.cpp - Unit tests for US_TimeState
#include <gtest/gtest.h>
#include <gmock/gmock.h>
#include "qt_test_base.h"
#include "mock_us_db2.h"
#include "us_time_state.h"
#include <QTemporaryDir>
#include <QXmlStreamWriter>
#include <QFile>
#include <QDataStream>
using ::testing::_;
using ::testing::Retur... |
cba411f5852fab53ce9c10a925fe30309c24784f8da8fd2f0e040d282ddd1257 | C++ | 11,472 | 351 | //! \file us_mpi_testdata.cpp
//! \brief Writes synthetic sedimentation velocity datasets for the
//! us_mpi_analysis regression tests.
//!
//! The data are simulated with the same simulation-parameter setup that
//! us_mpi_analysis uses for a dataset (initFromData, rotor stretch, bottom,
//! generated 1-second ... |
c514a218a710abeda771119d61ab03e8c08ced3a814a79993f2f341c1b39b658 | C++ | 11,493 | 507 | #include "catch.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../gfa.hpp"
#include "../algorithms/gfa_to_handle.hpp"
#include <bdsg/hash_graph.hpp>
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("Can import a simple graph from GFA", "[gfa]") {
const string graph_gfa = R"(H VN:Z:1.... |
b4c10d78514681e982db098d762ad84cdf3cc3e4bbc791131d6826081af3115b | C++ | 11,497 | 312 | /// \file packed_structs.cpp
///
/// Unit tests for bit-packed data structures
///
#include <iostream>
#include <random>
#include <unordered_set>
#include <sstream>
#include "vg/io/json2pb.h"
#include "catch.hpp"
#include "support/randomness.hpp"
#include <bdsg/internal/packed_structs.hpp>
namespace vg {
namespac... |
04e9e9e5d6b5776a3b35062698dea48c745f87648b48ab2d45a7ebdf7a09f31e | C++ | 11,522 | 251 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
f1e7c1ef2738d0db20bdc31eaa4a727ebb37aad2699c094ea9462b7f5472fd11 | C++ | 11,534 | 342 | /// \file path_index.cpp
///
/// Unit tests for the PathIndex class, which indexes paths for random access.
///
#include <iostream>
#include <string>
#include "../io/json2graph.hpp"
#include "../path_index.hpp"
#include <bdsg/hash_graph.hpp>
#include "catch.hpp"
namespace vg {
namespace unittest {
using namespace s... |
3f551abc9655d9b5def769357921254771d8d7f63b9a0168bce8615ead4a594c | C++ | 11,538 | 426 | #include <functional>
#include <string>
#include <string_view>
#include <vector>
#include <graphtyper/constants.hpp>
#include <graphtyper/typer/event.hpp>
#include <graphtyper/utilities/logging.hpp>
#include <graphtyper/utilities/options.hpp>
namespace
{
/*
std::vector<uint8_t>
get_phred_biallelic(uint32_t count, uin... |
202415bc44a7cc1d095719d4da725db677536a6ecbb113cf8cd8b8f4782fe610 | C++ | 11,584 | 489 | #if defined(_MSC_VER) /* MSVC Compiler */
#pragma warning ( disable : 4305 )
#pragma warning ( disable : 4786 )
#endif
#include "qwt3d_plot.h"
#include "qwt3d_enrichment.h"
using namespace Qwt3D;
/*!
This should be the first call in your derived classes constructors.
*/
#if QT_VERSION < 0x040000
... |
f170ce11e9e9348064c2583e6fe81d8eb1520a273ad5327f7df5cb32a21e6fa2 | C++ | 11,670 | 354 | #include "us3_file_test_base.h"
#include "us_project.h"
#include "mock_us_db2.h"
#include <QTemporaryDir>
#include <QDir>
#include <QFile>
#include <QFileInfo>
#include <QXmlStreamWriter>
#include <QDateTime>
#include <QRegularExpression>
using ::testing::_;
using ::testing::Return;
using ::testing::SetArgReferee;
usi... |
ddccb69411c9e333b91dd10a48f9434e00a8d488a0bf091e5c5b005b822759b5 | C++ | 11,738 | 364 | //! \file us_win_data.cpp
#include <QString>
#include <QObject>
#include <us_win_data.h>
/*! This namespace is used to configure data using C mechanisms instead
of a large C++ constructor. It is a convenience namespace used only
by \ref US_Win.
*/
namespace US_WinData
{
//! An array of processes
Process p... |
66e1dbe80ea784c8f5425ccf241ae80f4b23a48a0a7acdf6267079d433217e67 | C++ | 11,767 | 303 | /**
* \file zipcode.cpp: experimental zipcode 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 "../zip_code.hpp"
#include "../mapper.hpp"
#include "../annot... |
a0519f7a11c752df601e8edd91e4328e4f6b8c8cb3fda904d4b5c595a89d7658 | C++ | 11,809 | 355 | //! \file test_us_sim_cache.cpp
// test_us_sim_cache.cpp - Unit tests for US_SimCache
#include "qt_test_base.h"
#include "us_astfem_math.h"
#include "us_settings.h"
#include "us_sim_cache.h"
#include <atomic>
#include <cstring>
#include <memory>
namespace
{
// A simulation of a 4-scan, 10-point grid, filled with value... |
de50a066e106f7f24b82333a919f2282fdcfc52b1010a0ea75fdac28a4cea652 | C++ | 11,843 | 466 | //***************************************************************************
//
// Matlab C routine file: anaskel.cpp
//
// Written 8/04 by N. Howe
//
// Input:
// skel: shape to find skeleton for
//
// Output:
// dmap: directional maps
// exy: coordinates of endpoints
// jxy: coordinates of... |
893c56c8e468484cbe4551a094b43997f68e4c41fd833df650691ca625eecc0c | C++ | 11,851 | 315 | // gampcompare_main.cpp: defines a GAMP to GAM annotation function
#include <omp.h>
#include <unistd.h>
#include <getopt.h>
#include <string>
#include <vector>
#include <set>
#include <subcommand.hpp>
#include "../algorithms/alignment_path_offsets.hpp"
#include "../multipath_alignment.hpp"
#include "../alignment.hp... |
e65dfd558245b21306ec42e19213b2db0cb3fa25a885b2f5e3d382318308dbaf | C++ | 11,853 | 359 | #include <iostream>
#include <omp.h>
#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <numeric>
#include <fstream>
#include <cstdio>
#include <cstring>
#include <algorithm>
#include <math.h>
#include <sys/stat.h>
#include <unordered_map>
#include "dirent.h"
#include <chrono>
#include <omp.h>
#include <... |
83cb9a019d2d53a37d26b350b9ac0efdf70eef730d4ce620ec78809070ae0bf8 | C++ | 11,928 | 376 | // AUC reader status codes and destination-state guarantees.
#include "qt_test_base.h"
#include "us_dataIO.h"
#include "us_settings.h"
#include <QByteArray>
#include <QDir>
#include <QFile>
#include <QTemporaryDir>
namespace
{
// Byte offsets of the fixed-size header fields, derived from writeRawData():
// 4 magic +... |
a9e08febfe5cbe50c53e46b71b48eee846d8c387d2d3cf251f576e4e463f96e7 | C++ | 11,943 | 293 | #include "us_mpi_analysis.h"
#include "us_constants.h"
#include "us_math2.h"
#include "us_astfem_rsa.h"
#include "us_simparms.h"
void US_MPI_Analysis::_2dsa_worker( void )
{
bool repeat_loop = true;
MPI_Job job;
MPI_Status status;
// Use 4 here because the master will be reading 4 with the
// same... |
daf396be22f5f1cb570355f145a310ec904a5fbe7a364d85493f0a71e8323c4c | C++ | 12,005 | 252 | #include "expand_context.hpp"
namespace vg {
namespace algorithms {
using namespace std;
void expand_context_by_steps(const HandleGraph* source, MutableHandleGraph* subgraph,
int64_t dist, bool expand_forward, bool expand_backward) {
// let's make an O(1) lookup ... |
6d7cace8eb53a531e92cf64e43085ad8a1f41777594def929935933660e6e66c | C++ | 12,145 | 310 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
975dbf9f49e9664585de81763831e4042b849f36d527782cf2d63bb24afd1cf0 | C++ | 12,275 | 276 | #include "gfa.hpp"
#include "utility.hpp"
#include "path.hpp"
#include <sstream>
#include <gbwtgraph/utils.h>
namespace vg {
using namespace std;
/// Determine if a path should be written as a GFA W line or a GFA P line.
static bool should_write_as_w_line(const PathHandleGraph* graph, path_handle_t path_handle);
//... |
fbd71b89410b06760d638c568d0292ffc9a8eab66c74405d0d7979b5c19b3d41 | C++ | 12,364 | 416 | //! \file us_associations_gui.cpp
#include "us_associations_gui.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_constants.h"
US_PushButton::US_PushButton( const QString& text, int i )
: QPushButton( text ), index( i )
{
setFont( QFont( US_GuiSettings::fontFamily(),
US_... |
22d3f00c2c514ee9e2d728206adeb34df3c34a3302d345e17268d562aeeba7e4 | C++ | 12,380 | 1 | vector<float> ext_dir{1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01500000000000,0.985000000000000,1.01... |
2a23b54af2d113257505cb73c595610e45c0ed4c19efd5408f190630bd6a4d96 | C++ | 12,413 | 293 | /**
* \file simplify_siblings.cpp
*
* Defines an algorithm to merge nodes or parts of nodes with the same
* predecessors/successors.
*/
#include "simplify_siblings.hpp"
#include <unordered_set>
#include <map>
namespace vg {
namespace algorithms {
using namespace std;
bool simplify_siblings(handlegraph::Mutabl... |
42e2db24b160c8b8501ff0049f6526949e2962ddd09dcef8a19a8e96e708f879 | C++ | 12,426 | 341 | //------------------------------------------------------------------------------
//
// 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... |
936f84979c4d94de7a14763f0d6d62f813813cc266a00538447285cb0d7f3119 | C++ | 12,462 | 377 | //! \file us_noise_loader.cpp
#include "us_noise_loader.h"
#include "us_editor_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include <qwt_legend.h>
// constructor: load loader dialog
US_NoiseLoader::US_NoiseLoader( IUS_DB2* db, QStringList& mieGUIDs,
QStringList& nieGUIDs, US_Noise& ti_noise, US_... |
4fed7e0801357662f357c04b28ec8429d8a7c02648e72f01ed91f3138106f4ba | C++ | 12,527 | 343 | //! \file us_xpn_run_raw.cpp
#include "us_xpn_run_raw.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_util.h"
// Primary constructor to establish the dialog
US_XpnRunRaw::US_XpnRunRaw( QString& runDesc, QStringList& rdLists )
: US_WidgetsDialog( nullptr, Qt::WindowFlags() ), runDesc( runDesc ),... |
4744962b05ef955ee8760d8615ebe769143ea0c0407993434c74e6614c362c6b | C++ | 12,530 | 353 | //------------------------------------------------------------------------------
//
// 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... |
2e1b4e33698b897a997964b94096069dea6e9a56bb7b1abcb8153cb85cbbe3f5 | C++ | 12,533 | 303 | /** \file minimizer_main.cpp
*
* Defines the "vg minimizer" subcommand, which builds the minimizer index.
*
* The index contains the lexicographically smallest kmer in a window of w
* successive kmers and their reverse complements. If the kmer contains
* characters other than A, C, G, and T, it will not be indexe... |
25300f36a8a7c51f589deac4f2694ecbc7f49a65e8b75bf7ed144e1c1242d35c | C++ | 12,617 | 229 | // regression.cpp -- run the perceiver on a demo PDB and score against somo.residue.new.
// Usage: regression <pdb> [pdb2 ...]
#include <cstdio>
#include <string>
#include <vector>
#include <map>
#include <set>
#include "../pdb_lite.h"
#include "../../include/us_hydrodyn_perceive_hybrid.h"
#include "../residue_oracle.h... |
15973c3c8bb289c28bb1635c80deb575f0de197ca865e1eb17fd39bb5c055f7c | C++ | 12,619 | 319 | //------------------------------------------------------------------------------
//
// 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... |
66a62c991bec6e7ecf963f1360e33ba9efdb645b7614a4c73a3f48710c3c1087 | C++ | 12,634 | 430 | //! \file us_select_runid.cpp
#include "us_select_runid.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"
// Main construct... |
b9a3ab048507925f12788a57424e778b156c182ca0aa7d9783a6103ab939d6d3 | C++ | 12,664 | 415 | //! \file us_solution_gui.cpp
#include "us_solution_gui.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_investigator.h"
#include "us_buffer_gui.h"
#include "us_analyte_gui.h"
#include "us_solution.h"
#include "us_new_spectrum.h"
#include "us_editor_gui.h... |
4675bb2cce6d900215e7c57e9f8d813e0f61dbc0d28470171331403a5cdac604 | C++ | 12,686 | 431 | #include "qt_test_base.h"
#include "us_model.h"
#include "mock_us_db2.h"
#include "us_constants.h"
#include <QTemporaryDir>
#include <QTextStream>
#include <QXmlStreamWriter>
using ::testing::_;
using ::testing::Return;
using ::testing::SetArgReferee;
using ::testing::DoAll;
using ::testing::NiceMock;
using ::testing:... |
1e5dbdf2e57b88111fb82c1f4b79ac74f9fdea262ca27358035d7709d1939396 | C++ | 12,693 | 224 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 8553860;//2160220;//3813340;//3813340;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms b... |
f76e2fd8c2b2cf9d226a1f47dbb96a17d9973d7d4440de0a3a575e38cb447b11 | C++ | 12,748 | 371 |
#include <algorithm>
#include <cassert>
#include <cstdlib>
#include <ctime>
#include <iomanip>
#include <iostream>
#include <set>
#include <sstream>
#include <string>
#include "omp.h"
#include "FileUtils.hpp"
#include "GeneticMap.hpp"
#include "GenomeInterval.hpp"
#include "OspreyIBSParams.hpp"
#include "Variant.hpp... |
86817740a131466850ceba7bb1366304bab0a25089dc33401a68cbf9135ed7bd | C++ | 12,789 | 408 | //! \file us_sassoc.cpp
#include "us_sassoc.h"
#include "us_gui_settings.h"
#include "us_settings.h"
#include "us_constants.h"
#include "qwt_point_data.h"
#include "qwt_scale_engine.h"
US_Sassoc::US_Sassoc( double eq0, double eq1, double stoich1, double stoich2,
const QString& t_project, int t_... |
1f10bc4e2dc85f24acc4d25b14c54fb986d89e42ecc6c06d70ea95a2686f1465 | C++ | 12,797 | 349 |
#include <getopt.h>
#include "subcommand.hpp"
#include <vg/io/stream.hpp>
#include "../genotyper.hpp"
#include "../genotypekit.hpp"
#include "../variant_recall.hpp"
/**
* GAM sort main
*/
using namespace std;
using namespace vg;
using namespace vg::subcommand;
const string DEFAULT_TRAVERSAL_FINDER = "adaptive";
voi... |
78926197e23e2268d2e6a4ff14ed27a55b97e8db3662d04a0f99481597b3728d | C++ | 12,837 | 370 | /** \file chains_main.cpp
*
* Defines the "vg chains" subcommand, which extracts the handles in top-level chains from a distance index or a snarl file.
*
* NOTE: If a component (~chromosome) does not start with a shared node, the top-level chain is not unique.
* For example, if the component starts with edges (u, ... |
a51e6e582dda2e630699fc98bfb668ae6cd93f6240fae8a9774432c98c5b7b78 | C++ | 12,877 | 388 | //! \file us_tmst_viewer.cpp
#include "us_tmst_viewer.h"
#include "us_tmst_plot.h"
#include "us_select_item.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_investigator.h"
#include "us_passwd.h"
#include "us_db2.h"
#include "us_util.h"
#include "us_constants.h"
#include "us_u... |
cb5179f84ef4b72989c9417ab339d7c7e28a970f420a172e6c8a4d824fe3d829 | C++ | 12,882 | 303 | #include <iostream>
#include <unordered_set>
#include <vg/io/stream.hpp>
#include "chunker.hpp"
#include "algorithms/subgraph.hpp"
#include "vg.hpp"
#include "clip.hpp"
#include "crash.hpp"
//#define debug
namespace vg {
using namespace std;
PathChunker::PathChunker(const PathPositionHandleGraph* graph) : graph(gra... |
f826dcf2e53bef61fd18feaafedc533c2ae27de62330c2508c9eb807d61b71f3 | C++ | 12,931 | 491 | #include <cassert> // assert()
#include <cmath> // sqrt
#include <cstdint> // uint64_t
#include <cstdlib> // std::abs(int64_t)
#include <map> // std::map<Key, Value>
#include <numeric> // std::accumulate
#include <sstream> // std::ostringstream
#include <string> // std::string
#include <vector> // std::vector
... |
d75e320b953556416c8d155b063a5efcabb5d989431adcd839b39e7908b0e902 | C++ | 12,983 | 308 | #include "random_graph.hpp"
#include <random>
#include <time.h>
#include <iostream>
#include "randomness.hpp"
namespace vg {
namespace unittest {
using namespace std;
void random_graph(int64_t seq_size, int64_t variant_len, int64_t variant_count,
MutablePathMutableHandleGraph* graph) {
vector... |
f0a989405e4c56d1454b45cac17e53145316a2b1fb760b8528fc8baf428c6a7b | C++ | 12,994 | 439 | /// \file blocked_gzip_input_stream.cpp
///
/// Unit tests for BlockedGzipInputStream
#include <vg/io/blocked_gzip_input_stream.hpp>
#include <vg/io/blocked_gzip_output_stream.hpp>
#include <vg/io/hfile_cppstream.hpp>
#include "catch.hpp"
#include <google/protobuf/io/coded_stream.h>
#include <google/protobuf/io/gzi... |
98422d625b646856f07457e0e00859dda430705648acab6b71a5479530077587 | C++ | 13,061 | 354 | // test_us_memory_unit.cpp - Unit tests for US_Memory class
#include "qt_test_base.h"
#include "us_memory.h"
#include <QString>
#include <limits>
using namespace qt_matchers;
class TestUSMemoryUnit : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
}
void TearDown() ove... |
695443a353c8b8cbea5538aa8be329486f4ee65fede16f00f40b8de444a1c42a | C++ | 13,090 | 380 | //! \file us_spectrodata.cpp
#include "us_spectrodata.h"
#include "us_defines.h"
#include "us_settings.h"
#define LO_DTERM 0.2500 // low decay-term point (1/4)
// Provides raster data for QwtSpectrogram
US_SpectrogramData::US_SpectrogramData() : QwtRasterData()
{
rdata.clear();
xreso = 300.0;
yreso ... |
658f965cb1f720ecbe5c0bec622fce1b893f97128a33769b9ad76614aa8c60b1 | C++ | 13,146 | 286 | //------------------------------------------------------------------------------
//
// 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... |
c2348b7de588b4ac21524cc03cb275aa3fc9a4663ea0cf83f7f26f3c9eb1db65 | C++ | 13,165 | 224 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 3813340;//3813340;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement... |
83a2058b317ab7e88664d3b56fd5ef4dabef0cf208efa0b72383a41c9a1b9132 | C++ | 13,182 | 226 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 250000;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep between movements. e.g., 20ms between each movement command
i... |
bfbd10e29b13dba856c5513a9eac7c445d989c6ab26b40f13af1d11dd4ede104 | C++ | 13,248 | 226 | /*
General parameters
*/
#define PI 3.14159265
struct P {
double sim_time = 8460580;//8460580;//250000;//8460580;//8460580;//8485920;//250000;//1260120;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep bet... |
cb34ecf6373e9e3f006f0902460e476f40dfc261f52c02844194f2277761fc8e | C++ | 13,346 | 421 | /*
*
* 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 ... |
c2d5256a21fd12249c424eab2f8b2407ac8776dfaadcc56eb5f9697d5a076f40 | C++ | 13,381 | 449 | #include <algorithm>
#include <cassert>
#include <iostream>
#include <iterator>
#include <sstream>
#include <string>
#include <vector>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/var_record.hpp>
#include <graphtyper/utilities/logging.hpp>
std::ostream & operator<<(std::ostream & os, std::vector<cha... |
1fff96c09a1c2404b1bffa1322893a04e7fcbd1de4717190b32122719f12e200 | C++ | 13,392 | 452 | //! \file us_second_moment.cpp
#include <QApplication>
#include "us_second_moment.h"
#include "us_license_t.h"
#include "us_license.h"
#include "us_settings.h"
#include "us_gui_settings.h"
#include "us_gui_util.h"
//! \brief Main program. Loads translators and starts
// the class US_Convert.
int main( int ar... |
b146c4ddd295c290ef946533fa45ad98cb7b3fc8e1b82e9192fd1e983acbb746 | C++ | 13,479 | 415 | ///
/// \file stream_index.cpp
///
/// Unit tests for the GAMIndex which indexes seekable GAM files by node ID
///
#include <iostream>
#include "catch.hpp"
#include "../stream_index.hpp"
#include <vg/io/stream.hpp>
#include "../utility.hpp"
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE("BitS... |
396b62c3931f710155f457606fcae8e8a315d23429707a5edae8df360a6c8cc1 | C++ | 13,584 | 229 | /*
General parameters
*/
#define PI 3.14159265
struct P {
// general section
double sim_time = 3631180;//7000;//3631180;//1260120;//350000;//7000;//250000;//8485920;//8485920;//1440140;//1440140;//8553860;//131400;//8485920;//120000//29416*20;//60000*firing_bin;// sim run time in ms
int timestep = 20; // timestep... |
d94597b300e7ff1170135b649fa622be7c662bb644578dc59b053882da41e6fe | C++ | 13,614 | 354 | //------------------------------------------------------------------------------
//
// 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... |
8030abd9d5bbd2cf23113f7b766f39e36d6039a3a4f111862fe81629e431df23 | C++ | 13,620 | 485 | /**
* \file
* Implementations for algorithm explanation utilities.
*/
#include "explainer.hpp"
#include "log.hpp"
#include <structures/union_find.hpp>
#include <handlegraph/algorithms/copy_graph.hpp>
#include <bdsg/hash_graph.hpp>
#include <sstream>
#include <sys/stat.h>
#include <sys/types.h>
#include <errno.h... |
9dcc016ab8bd54ac6af7caf686afe6abf3b2ee0496f82a06af31d60a97f862ec | C++ | 13,655 | 348 | /// \file index_registry.cpp
///
/// unit tests for the vg-file-backed handle graph implementation
#include <iostream>
#include "../index_registry.hpp"
#include "catch.hpp"
namespace vg {
namespace unittest {
// expose the private functions to testing
class TestIndexRegistry : public IndexRegistry {
public:
us... |
05c33377923b618c5be2e5c1216d33bb4f6fe75daded6770fcb0fd718430914b | C++ | 13,790 | 475 | // test_us_util.cpp
#include <gtest/gtest.h>
#include <gmock/gmock.h>
#include "qt_test_base.h"
#include "us_util.h"
#include <QTemporaryFile>
#include <QDir>
#include <QFileInfo>
#include <QStandardPaths>
#include <QCoreApplication>
#include <QDateTime>
#include <QUuid>
using ::testing::_;
using ::testing::Return;
us... |
1780f8d24ac6155af45f875f4f207ea9ad11985f323b4ebcddd94496045d839f | C++ | 13,798 | 494 | //------------------------------------------------------------------------------
//
// 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... |
b2e429c1097a5ea3cdc28da9ce5de066ddcb02a90a37416a6e016ccead490acb | C++ | 13,830 | 402 | // test_us_crypto_unit.cpp - Unit tests for US_Crypto class
#include "qt_test_base.h"
#include "us_crypto.h"
#include <QString>
#include <QStringList>
#include <QByteArray>
#include <QTime>
#include <set>
using namespace qt_matchers;
class TestUSCryptoUnit : public QtTestBase {
protected:
void SetUp() override {
... |
24ff3b9cd665e084c7880b6ae4ae5f124386101d2752733da15a35d8d8aa8d23 | C++ | 13,852 | 374 | /// \file alignment.cpp
///
/// unit tests for Alignments and their utility functions
///
#include <iostream>
#include <string>
#include <unordered_map>
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include <vg/io/alignment_io.hpp>
#include <bdsg/hash_graph.hpp>
#include "../algorithms/back_translate.hpp"
#inclu... |
d756c8717ebe3333c9b9aec0431eb57e24872be278aaeaceebf5cc28b33cabe3 | C++ | 13,852 | 385 |
#include <cassert>
#include <climits>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>
#include "OspreyParams.hpp"
#include "format.hpp"
#include "version.hpp"
using namespace std;
namespace Osprey {
static int DEFAULT_THREADS =... |
dcc840cd4c0ac7df3cc44114c43610c8666811203de6bf0181ec3b39e64522f7 | C++ | 13,913 | 714 | #include "qt_test_base.h"
#include "us_vector.h"
#include <cmath>
#include <limits>
using namespace ::testing;
using namespace qt_matchers;
class US_VectorTest : public QtTestBase {
protected:
void SetUp() override {
QtTestBase::SetUp();
}
// Helper function to compare floating point vectors with... |
e11e687c0c4a385cfae3aaf2601f4daae0bed538e95100a3b75efd5d8deb17dd | C++ | 13,924 | 334 | #include "viz.hpp"
#include <regex>
#include <utility>
namespace vg {
Viz::Viz(PathHandleGraph* x, vector<Packer>* p, const vector<string>& n, const string& o, int w, int h, bool c, bool d, bool t) {
init(x, p, n, o, w, h, c, d, t);
}
void Viz::init(PathHandleGraph* x, vector<Packer>* p, const vector<string>& n,... |
13a756d27df200e407d9dbbc8fb0bd0654f200ffd6d7ef55a0ec94b054171310 | C++ | 13,944 | 347 |
#include <iostream>
#include <stdexcept>
#include <string>
#include <vector>
#include "vcf.h"
#include "Variant.hpp"
#include "format.hpp"
using namespace std;
namespace Osprey {
// BCF2 MISSING marker
/** Currently unused
static bool isMissing(float value) {
uint8_t* p = (uint8_t*) &value;
... |
2c2f1e3a17558893c782a71f94436e4692816cb82ab5632f0ccdcc4205b4fa90 | C++ | 13,954 | 367 | //------------------------------------------------------------------------------
//
// Intan Technologies RHX Data Acquisition Software
// Version 3.5.2
//
// Copyright (c) 2020-2026 Intan Technologies
//
// This file is part of the Intan Technologies RHX Data Acquisition Software.
//
// This program is free softw... |
aa844b8ba9c94080041b52253eb0704288efa1f8f37758c9e9e265b7eaa11ca0 | C++ | 13,985 | 285 | ////////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// ... |
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