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//! \file us_pcsa_process.cpp #include <QApplication> #include <QtCore> #include <float.h> #include "us_pcsa_process.h" #include "us_util.h" #include "us_settings.h" #include "us_astfem_math.h" #include "us_astfem_rsa.h" #include "us_sleep.h" #include "us_math2.h" #include "us_lm.h" #include "us_solve_sim.h" #include ...
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//! \file us_data_model.cpp #include "us_data_model.h" #include "us_data_process.h" #include "us_data_tree.h" #include "us_util.h" #include "us_settings.h" #include "us_model.h" #include "us_noise.h" #include "us_editor.h" #define timeFmt QString("hh:mm:ss") #define nowTime() "T="+QDateTime::currentDateTime().toStrin...
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/* Copyright (c) 2012, Lambda Foundry, Inc., except where noted Incorporates components of WarrenWeckesser/textreader, licensed under 3-clause BSD See LICENSE for the license */ /* Low-level ascii-file processing for pandas. Combines some elements from Python's built-in csv module and Warren Weckesser's textreade...
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//! \file us_buffer_gui.cpp #include "us_buffer_gui.h" #include "us_gui_settings.h" #include "us_settings.h" #include "us_db2.h" #include "us_passwd.h" #include "us_constants.h" #include "us_investigator.h" #include "us_table.h" #include "us_editor.h" #include "us_util.h" #include "us_math2.h" #include "us_eprofile.h" ...
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/* Copyright (c) 2012, Lambda Foundry, Inc., except where noted Incorporates components of WarrenWeckesser/textreader, licensed under 3-clause BSD See LICENSE for the license */ /* Low-level ascii-file processing for pandas. Combines some elements from Python's built-in csv module and Warren Weckesser's textreade...
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//------------------------------------------------------------------------------ // // 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...
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//! \file us_proto_ranges.cpp #include "us_experiment_gui_optima.h" #include "us_extinction_gui.h" #include "us_table.h" #include "us_license.h" #include "us_license_t.h" #include "us_sleep.h" #include "us_util.h" #ifndef DbgLv #define DbgLv(a) if(dbg_level>=a)qDebug() #endif // Panel for Ranges parameters US_ExperG...
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/** \file gbwt_main.cpp * * Defines the "vg gbwt" subcommand for building, merging, and manipulating GBWT indexes * and GBWTGraphs. */ #include <omp.h> #include <unistd.h> #include <getopt.h> #include <set> #include "subcommand.hpp" #include "../gbwt_helper.hpp" #include "../gbwtgraph_helper.hpp" #include "../ha...
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//! \file us_mwl_species_fit.cpp #include <QApplication> #include "us_mwl_species_fit.h" #include "us_license_t.h" #include "us_license.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_util.h" #include "us_data_loader.h" #include "us_load_run_noise.h" #include "us_passwd.h" #include "us_images.h"...
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//------------------------------------------------------------------------------ // // 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...
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//! \file us_astfem_sim.cpp #include <QApplication> #include "us_license.h" #include "us_license_t.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_astfem_sim.h" #include "us_sim_params_gui.h" #include "us_math2.h" #include "us_astfem_math.h" #include "us_defines.h" #incl...
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//! \file us_report_gui.cpp #include "us_report_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" // Report GUI //ALEXEY_NEW_REPORT: an arg now is QMap < QString( wvl ), US_ReportGMP > ? //US_ReportGui::US_Repo...
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//! \file us_vhw_enhanced.cpp #include <QApplication> #include <QtSvg> #include "us_vhw_enhanced.h" #include "us_license_t.h" #include "us_license.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_matrix.h" #include "us_passwd.h" #include "us_constants.h" #include "us_astf...
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#include "recombinator.hpp" #include "decomposition_neighbors.hpp" #include "gref.hpp" #include "statistics.hpp" #include "algorithms/component.hpp" #include "algorithms/extract_subchain.hpp" #include "hash_map.hpp" #include <algorithm> #include <cmath> //#define debug_selected_haplotypes namespace vg { //--------...
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#include "gbwt_extender.hpp" #include "hash_map.hpp" #include <algorithm> #include <array> #include <cstring> #include <queue> #include <set> #include <structures/immutable_list.hpp> namespace vg { //------------------------------------------------------------------------------ // Numerical class constants. const...
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//------------------------------------------------------------------------------ // // 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...
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/** * \file * unittest/handle.cpp: test cases for the implementations of the HandleGraph class. */ #include "catch.hpp" #include "../handle.hpp" #include "../vg.hpp" #include "xg.hpp" #include "vg/io/json2pb.h" #include "bdsg/packed_graph.hpp" #include "bdsg/hash_graph.hpp" #include <handlegraph/util.hpp> #inc...
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/// /// \file snarls.cpp /// /// // #define debug #include <vg/io/protobuf_emitter.hpp> #include "snarls.hpp" #include "vg/io/json2pb.h" #include "subgraph_overlay.hpp" #include "crash.hpp" namespace vg { SnarlManager SnarlFinder::find_snarls_parallel() { // By default, just use a single thread, unless this f...
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#include <QApplication> #include "us_license_t.h" #include "us_license.h" #include "us_util.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_run_details2.h" #include "us_plot.h" #include "us_math2.h" #include "us_ramp_gui.h" #include "us_experiment_gui_ra.h" #include "us_select_triples_ra.h" #incl...
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/**************************************************************************** ** Form implementation generated from reading ui file '3dplot\mesh2mainwindowbase.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 c...
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/// /// \file integrated_snarl_finder.cpp /// /// #include "integrated_snarl_finder.hpp" #include "algorithms/three_edge_connected_components.hpp" #include "subgraph_overlay.hpp" #include <bdsg/overlays/overlay_helper.hpp> #include <structures/union_find.hpp> #include <array> #include <iostream> namespace vg { /...
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#include "us_add_refScan.h" #include <QTextStream> US_AddRefScan::US_AddRefScan() : US_Widgets() { setPalette( US_GuiSettings::frameColorDefault() ); dbCon = new US_DB2(); // Put the Run Info across the entire window QLabel* lb_run = us_banner(tr("Load the Run(s)")); pb_import = us_pushbutton(tr("...
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#include <cstdint> #include "genotyper.hpp" #include "traversal_finder.hpp" #include "cactus_snarl_finder.hpp" #include "path_index.hpp" #include "utility.hpp" #include "translator.hpp" //#define debug namespace vg { using namespace std; // genotyper: // use graph and reads to: // - Augment graph // - Find ultrabub...
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#include "catch.hpp" #include <stdio.h> #include <iostream> #include "../zip_code.hpp" #include "../integrated_snarl_finder.hpp" namespace vg{ namespace unittest{ using namespace std; TEST_CASE("One node zipcode", "[zipcode]") { VG graph; Node* n1 = graph.create_node("GCAAACAGATT"); In...
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#include <QApplication> #include "us_license_t.h" #include "us_license.h" #include "us_norm_profile.h" #include "us_load_auc.h" #include "us_passwd.h" #include "us_run_protocol.h" #include "us_solution.h" #include <QFileInfo> //Alt. constr. US_Norm_Profile::US_Norm_Profile( QString auto_mode ): US_Widgets() { us_a...
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//! \file us_eqmath.cpp #include "us_eqmath.h" #include "us_settings.h" #include "us_math2.h" #include "us_constants.h" #include <cfloat> const double dflt_min = (double)FLT_MIN; const double dflt_max = (double)FLT_MAX; // Main constructor: pass references to EditedData, ScanEdit, EqScanFit, // and EqRunFit object...
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///////////////////////////////////////// #include "us_protocol_dev_gui.h" #include "us_rotor_gui.h" #include "us_solution_gui.h" #include "us_extinction_gui.h" #include "us_table.h" #include "us_xpn_data.h" #include "us_license.h" #include "us_license_t.h" #include "us_sleep.h" #include "us_util.h" #include "us_crypto...
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#include "us_mpi_analysis.h" #include "us_math2.h" #include "us_astfem_math.h" #include "us_archive.h" #include "us_memory.h" #include "us_sleep.h" #include "us_util.h" #include "us_settings.h" #include "us_revision.h" #include <QtCore/QString> #include <cstdio> #include <mpi.h> #ifdef Q_OS_WIN #ifndef NOMINMAX #defin...
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/** \file * * Unit tests for gbwt_extender.cpp, which implements haplotype-aware gapless seed extension. */ #include "../gbwt_extender.hpp" #include "../gbwt_helper.hpp" #include "../io/json2graph.hpp" #include "../utility.hpp" #include "../vg.hpp" #include <bdsg/hash_graph.hpp> #include "catch.hpp" #include "sup...
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//! \file us_buoyancy.cpp #include <QApplication> #include <QDomDocument> #include <qwt_scale_div.h> #include "us_buoyancy.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_investigator.h" #include "us_run_details2.h" #include "us_math2.h" #include "us_util.h" #include "us_load_auc.h" #include "u...
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//! \file us_analyte_gui.cpp #include "us_analyte_gui.h" #include "us_passwd.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_investigator.h" #include "us_editor_gui.h" #include "us_table.h" #include "us_util.h" #include "us_db2.h" #include "us_constants.h" #include "us_editor.h" #include "us_math2...
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#include "path.hpp" #include <vg/io/stream.hpp> #include "region.hpp" #include "alignment.hpp" #include "crash.hpp" #include <sstream> // #define debug_simplify using namespace vg::io; namespace vg { const std::function<bool(const string&)> Paths::is_alt = [](const string& path_name) { // Really we want things ...
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//! \file us_ddist_combine.cpp #include <QApplication> #include <qwt_scale_div.h> #include "us_ddist_combine.h" #include "us_select_rundd.h" #include "us_license_t.h" #include "us_license.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_matrix.h" #include "us_constants.h" ...
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/** * \file mpmap_main.cpp: multipath mapping of reads to a graph */ #include <omp.h> #include <unistd.h> #include <ctime> #include <getopt.h> #include <thread> #include <atomic> #include <mutex> #include <list> #include "subcommand.hpp" #include "../utility.hpp" #include <vg/io/vpkg.hpp> #include "../algorithms/c...
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#include "crash.hpp" #include "zip_code.hpp" //#define DEBUG_ZIPCODE namespace vg{ using namespace std; // Make sure that the default / empty payload exists as a value that can be pointed to. constexpr std::pair<gbwtgraph::KmerEncoding::code_type, gbwtgraph::KmerEncoding::code_type> MIPayload::NO_CODE; void ZipCod...
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//! \file us_plot.cpp #include <QApplication> #include <QtSvg> #include "us_plot.h" #include "us_theme.h" #include "us_images.h" #include <QtPrintSupport> #include "us_colorgradIO.h" #include "qwt_picker_machine.h" #include "qwt_picker.h" #include "qwt_color_map.h" #define canvasBackground() canvasBackground().color(...
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/** * \file giraffe_main.cpp: G(ir)AF (Graph Alignment Format) Fast Emitter: a fast read-to-haplotypes mapper */ #include <omp.h> #include <unistd.h> #include <getopt.h> #include <fstream> #include <iostream> #include <cassert> #include <cstring> #include <ctime> #include <map> #include <optional> #include <vector> ...
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#include <cassert> // assert #include <limits> // std::numeric_limits<T> #include <memory> // std::unique_ptr #include <sstream> // std::ostringstream #include <string> // std::string #include <unordered_map> // std::unordered_map #include <vector> // std::vector #include <paral...
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#include <thread> #include <gbwtgraph/utils.h> #include "../io/save_handle_graph.hpp" #include "transcriptome.hpp" #include "../augment.hpp" #include "../utility.hpp" namespace vg { using namespace vg::io; using namespace std; // #define transcriptome_debug bool operator==(const Exon & lhs, const Exon & rhs) {...
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#include "controlpanelconfiguretab.h" #include "testcontrolpanel.h" #include "controlwindow.h" #include <algorithm> HelpDialogCheckInputWave::HelpDialogCheckInputWave(QWidget *parent) : QDialog(parent) { setWindowTitle(tr("Check Input Wave")); QLabel *label1 = new QLabel("Scans for a connected chip on Po...
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// // pinned_alignment.cpp // // Unit tests for pinned alignment and pinned multi-alignment functions in Aligner // #include <stdio.h> #include <unordered_set> #include "alignment.hpp" #include "support/test_aligner.hpp" #include "vg.hpp" #include "path.hpp" #include "catch.hpp" #include "vg/io/json2pb.h" #include "...
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//! \file us_ga_init.cpp #include "us_grid_editor.h" #include "us_matrix.h" #include "us_csv_loader.h" #include <cmath> // main program int main( int argc, char* argv[] ) { QApplication application( argc, argv ); #include "main1.inc" // License is OK. Start up. US_Grid_Editor w; w.show(); ...
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// // banded_global_aligner.cpp // // Contains objects to support Aligner in performing banded global alignment against // a graph. // #include "banded_global_aligner.hpp" #include "vg/io/json2pb.h" #include <array> //#define debug_banded_aligner_objects //#define debug_banded_aligner_graph_processing //#define...
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#include "ModularHH.h" #include "Common.h" #include "NeuroML.h" #include<algorithm> #include<numeric> #include<math.h> #include<cmath> #include<stdio.h> #include<chrono> //Linear interpolation from a -> b with respective parameter from 0 -> 1 static Real Lerp(Real a, Real b, Real ratio){ return a + (b-a)*ratio; }...
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//! \file us_experiment_main.cpp ///////////////////////////////////////// #include "us_com_project_gui.h" #include "us_rotor_gui.h" #include "us_solution_gui.h" #include "us_extinction_gui.h" #include "us_table.h" #include "us_xpn_data.h" #include "us_license.h" #include "us_license_t.h" #include "us_sleep.h" #include...
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/** * \file * constructor.cpp: contains implementations for vg construction functions. */ #include "constructor.hpp" #include "utility.hpp" #include "crash.hpp" #include "io/load_proto_to_graph.hpp" #include <IntervalTree.h> #include <cstdlib> #include <set> #include <tuple> #include <list> #include <algorithm> ...
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//#define DEBUG_ZIP_CODE_TREE //#define DEBUG_ZIP_CODE_SORTING #include "zip_code_tree.hpp" #include "crash.hpp" // Set for verbose logging from the zip code tree parsing logic //#define debug_parse // Set to compile in assertions to check the zipcode tree parsing logic //#define check_parse using namespace std; na...
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//! \file us_fematch.cpp //#include <QApplication> //#include <QtSvg> #include "us_fematch.h" #include "us_adv_dmgamc.h" #include "us_thread_worker.h" #include "us_license_t.h" #include "us_license.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_matrix.h" #include "us_co...
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#include <QApplication> #include <QCollator> #include <QKeyEvent> #include <QPainter> #include <QPdfWriter> #include <QPrinter> #include <QProgressDialog> #include <algorithm> //#include <QThread> #include "us_audit_trail_gmp.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #inclu...
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#include <stdio.h> #include <stdlib.h> #include <iostream> #include <set> #include "../io/json2graph.hpp" #include "../vg.hpp" #include "catch.hpp" #include "bdsg/hash_graph.hpp" #include "../integrated_snarl_finder.hpp" #include "random_graph.hpp" #include "../minimizer_mapper.hpp" #include "randomness.hpp" #include <...
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//! \file us_fit_meniscus.cpp //#include <QApplication> #include <QJsonDocument> #include <QJsonValue> #include <QJsonArray> #include <QJsonObject> #include "us_fit_meniscus.h" #include "us_license_t.h" #include "us_license.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_settings.h" #include "us...
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#include <stdio.h> #include <stdlib.h> #include <iostream> #include <set> #include "vg/io/json2pb.h" #include "../vg.hpp" #include "bdsg/hash_graph.hpp" #include "catch.hpp" #include "../snarls.hpp" #include "../cactus_snarl_finder.hpp" #include "../integrated_snarl_finder.hpp" #include "../genotypekit.hpp" #include "s...
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/// \file alignment.cpp /// /// unit tests for Alignments and their utility functions /// #include <iostream> #include <string> #include <google/protobuf/util/message_differencer.h> #include "vg/io/json2pb.h" #include <vg/vg.pb.h> #include "../alignment.hpp" #include "../vg.hpp" #include "../xg.hpp" #include "../ha...
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//#define debug_distance_indexing //#define debug_snarl_traversal //#define debug_distances //#define debug_subgraph //#define debug_hub_label_build //#define debug_hub_label_storage #include "snarl_distance_index.hpp" #include <unordered_set> #include "decomposition_neighbors.hpp" using namespace std; using namespac...
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#include "traversal_finder.hpp" #include "genotypekit.hpp" #include "algorithms/k_widest_paths.hpp" #include "cactus.hpp" #include "gbwt_helper.hpp" #include "haplotype_extracter.hpp" //#define debug namespace vg { using namespace std; string traversal_to_string(const PathHandleGraph* graph, const Traversal& travers...
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C++
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// // vg_algorithms.cpp // // // Created by Jordan Eizenga on 2/7/17. // // #include <stdio.h> #include <set> #include <random> #include "catch.hpp" #include "../algorithms/extract_connecting_graph.hpp" #include "../algorithms/extract_containing_graph.hpp" #include "../algorithms/extract_extending_graph.hpp" #incl...
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//! \file us_analysis_profile.cp #include "us_analysis_profile.h" #include "us_table.h" #include "us_license.h" #include "us_datafiles.h" #include "us_sleep.h" #include "us_util.h" #include "us_report_gmp.h" #ifndef DbgLv #define DbgLv(a) if(dbg_level>=a)qDebug() #endif // Constructor: build the main layout with ta...
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/// \file multipath_alignment.cpp /// /// unit tests for multipath alignment construction and utility functions /// #include <stdio.h> #include <iostream> #include <gbwt/dynamic_gbwt.h> #include "xg.hpp" #include "bdsg/hash_graph.hpp" #include "bdsg/overlays/path_position_overlays.hpp" #include "../haplotypes.hpp"...
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// // banded_global_aligner.cpp // // Unit tests for banded global aligner module. // #include <stdio.h> #include "catch.hpp" #include "support/test_aligner.hpp" #include "vg.hpp" #include "path.hpp" #include "banded_global_aligner.hpp" #include "../io/json2graph.hpp" #include "bdsg/hash_graph.hpp" #include "../al...
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//! \file us_exp_utils.cpp // This source file is meant to hold those portions of the // US_ExperimentMain class and its subclasses that are common // utility functions used by the class and its subclasses. // Thereby, the length of any one source file is reduced and the // us_experiment_main.cpp file contains only ve...
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#include <QPrinter> #include <QPdfWriter> #include <QPainter> #include <QProgressDialog> #include <QApplication> #include <QKeyEvent> //#include <QThread> #include "us_esigner_gmp.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_protocol_util.h" #include "us_run_proto...
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#include <string> #include <algorithm> #include <utility> #include <cstring> #include "cluster.hpp" #include "algorithms/subgraph.hpp" #include "algorithms/extract_containing_graph.hpp" #include "utility.hpp" //#define debug_mem_clusterer using namespace std; using namespace structures; namespace vg { //size_t...
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C++
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// // snarls.cpp // // Unit tests for SnarlManager and related functions // #include <stdio.h> #include <iostream> #include <sstream> #include <set> #include "vg/io/json2pb.h" #include "../io/json2graph.hpp" #include <bdsg/hash_graph.hpp> #include <vg/vg.pb.h> #include "catch.hpp" #include "support/random_graph.hpp"...
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C++
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/** * \file minimizer_mapper_from_chains.cpp * Defines the code for the long-read code path for the * minimizer-and-GBWT-based mapper (long read Giraffe). */ #include "minimizer_mapper.hpp" #include "logged_gap_alignment_scorer.hpp" #include "annotation.hpp" #include "banded_global_aligner.hpp" #include "crash.h...
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C++
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#include "vg.hpp" #include <vg/io/stream.hpp> #include "aligner.hpp" // We need to use ultrabubbles for dot output #include "genotypekit.hpp" #include "algorithms/id_sort.hpp" #include "algorithms/simplify_siblings.hpp" #include "cactus_snarl_finder.hpp" #include "augment.hpp" #include "algorithms/prune.hpp" #include <...
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C++
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/** * \file minimizer_mapper.cpp * Defines the code for the minimizer-and-GBWT-based mapper. */ #include "minimizer_mapper.hpp" #include "crash.hpp" #include "annotation.hpp" #include "gbwtgraph_helper.hpp" #include "path_subgraph.hpp" #include "multipath_alignment.hpp" #include "split_strand_graph.hpp" #include "...
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#include <QApplication> #include <qwt_scale_div.h> #include "us_license_t.h" #include "us_license.h" #include "us_util.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gui_util.h" #include "us_run_details2.h" #include "us_plot.h" #include "us_math2.h" #include "us_convert_gui.h" #include "us_conver...
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C++
200,000
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// // multipath_alignment_graph.cpp // #include "multipath_alignment_graph.hpp" #include "sequence_complexity.hpp" #include "reverse_graph.hpp" #include "banded_global_aligner.hpp" #include "explainer.hpp" #include "crash.hpp" #include "structures/rank_pairing_heap.hpp" #include "algorithms/extract_connecting_graph...
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C++
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// // multipath_alignment.cpp // #include "multipath_alignment.hpp" #include "haplotypes.hpp" #include <structures/immutable_list.hpp> #include <structures/min_max_heap.hpp> #include <type_traits> //#define debug_multiple_tracebacks //#define debug_search //#define debug_trace //#define debug_verbose_validation //#...
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//! \file us_experiment/us_experiment_gui_optima.cpp #include <QSslKey> #include "us_experiment_gui_optima.h" #include "../us_analysis_profile/us_analysis_profile.h" #include "us_rotor_gui.h" #include "us_solution_gui.h" #include "us_extinction_gui.h" #include "us_table.h" #include "us_xpn_data.h" #include "us_licens...
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C++
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// index_registry.cpp: index registry system implementation #include "index_registry.hpp" #include <algorithm> #include <iostream> #include <sstream> #include <vector> #include <map> #include <random> #include <thread> #include <mutex> #include <chrono> #include <cctype> #include <cstdio> #include <cerrno> #include <...
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C++
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#include "snarl_seed_clusterer.hpp" #include <algorithm> //#define DEBUG_CLUSTER //#define debug_distances //#define EXHAUSTIVE_CLUSTER_CHECK namespace vg { SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer( const SnarlDistanceIndex& distance_index, const HandleGraph* graph) : ...
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C++
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#include <QCollator> #include <QCoreApplication> #include <QDir> #include <QFileInfo> #include <QFontDatabase> #include <QJsonDocument> #include <QJsonObject> #include <QPainter> #include <QPdfWriter> #include <QPrinter> #include "us_reporter_gmp.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_gu...
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//! \file us_edit.cpp #include <QApplication> //#include <QDomDocument> #include <QToolTip> #include <QMessageBox> #include <QLineF> #include <qwt_scale_div.h> #include <qwt_scale_map.h> #include <qwt_picker_machine.h> #include "us_edit.h" #include "us_exclude_profile.h" #include "us_select_lambdas.h" #include "us_ri_...
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C++
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#include <QApplication> #include <QtSql> #include <qwt_scale_div.h> #include "us_xpn_viewer_gui.h" #include "us_xpn_export.h" #include "us_tmst_plot.h" #include "us_license_t.h" #include "us_license.h" #include "us_util.h" #include "us_settings.h" #include "us_gui_settings.h" #include "us_plot.h" #include "us_math2.h" ...
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C++
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#include <QCheckBox> #include <QCollator> #include <QDialog> #include <QDialogButtonBox> #include <QGroupBox> #include <QJsonArray> #include <QJsonDocument> #include <QJsonObject> #include <QJsonValue> #include <QScrollArea> #include <QTimer> #include <QXmlStreamReader> #include <QtNumeric> #include "../us_fematch/us_...
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C++
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/** * \file * surjector.cpp: implements a class that surjects alignments onto paths */ #include "surjector.hpp" #include "crash.hpp" #include "sequence_complexity.hpp" #include "alignment.hpp" #include "utility.hpp" #include "memoizing_graph.hpp" #include "multipath_alignment_graph.hpp" #include "reverse_graph.hp...
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C++
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// // snarl_distance_index.cpp // // Unit tests for SnarlDistanceIndex and related functions // //TODO: Tips at the end of the top-level chain? #include <stdio.h> #include <iostream> #include <sstream> #include <set> #include <algorithm> #include <vector> #include "../io/json2graph.hpp" #include <bdsg/hash_graph.hpp...
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C++
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/** * \file multipath_mapper.cpp * * Implements the MultipathMapper class */ //#define debug_multipath_mapper //#define debug_multipath_mapper_alignment //#define debug_validate_multipath_alignments //#define debug_report_startup_training //#define debug_pretty_print_alignments //#define debug_time_phases //#defin...
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C++
200,001
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#include <unordered_set> #include "mapper.hpp" #include "graph.hpp" #include "annotation.hpp" #include "statistics.hpp" #include "path.hpp" #include "alignment.hpp" #include "translator.hpp" #include "algorithms/subgraph.hpp" #include "algorithms/nearest_offsets_in_paths.hpp" #include "algorithms/jump_along_path.hpp" #...
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C++
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#include "alignment.hpp" #include "longest_overlap.hpp" #include "vg/io/gafkluge.hpp" #include "annotation.hpp" #include <vg/io/stream.hpp> #include <sstream> #include <chrono> using namespace vg::io; namespace vg { int hts_for_each(string& filename, function<void(Alignment&)> lambda, const PathPos...
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C/C++
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5
#import "UADSBaseOptions.h" @interface UADSShowOptions : UADSBaseOptions @end
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C/C++
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#import "UnityAds.h" @interface NSString (UnityAdsError) - (UnityAdsError)unityAdsErrorFromString; @end
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C/C++
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#import "UADSMetaData.h" @interface UADSPlayerMetaData : UADSMetaData - (void)setServerId:(NSString *)serverId; @end
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C/C++
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7
#ifndef SHD_GLOBAL_H #define SHD_GLOBAL_H typedef double shd_double; #define MPI_SHD_DOUBLE MPI_DOUBLE #endif // SHD_GLOBAL
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#import "UADSBaseOptions.h" @interface UADSLoadOptions : UADSBaseOptions @property (nonatomic, readwrite) NSString* adMarkup; @end
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/* File Maxfiles.h */ #ifndef MAXFILES_H #define MAXFILES_H /** * Add .max files here */ #include "HHmc.h" #endif /* !MAXFILES_H */
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C/C++
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/* File Maxfiles.h */ #ifndef MAXFILES_H #define MAXFILES_H /** * Add .max files here */ #include "RingIO.h" #endif /* !MAXFILES_H */
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141
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/* File Maxfiles.h */ #ifndef MAXFILES_H #define MAXFILES_H /** * Add .max files here */ #include "IOtwoHw.h" #endif /* !MAXFILES_H */
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C/C++
178
3
#import "UnityAdsExtendedDelegate.h" #warning "UnityAdsExtended.h" is deprecated and will be removed in the next major version please move to using "UnityAdsExtendedDelegate.h"
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#ifndef US_CSV_H #define US_CSV_H #include <qstring.h> #include <qstringlist.h> using namespace std; class US_Csv { public: static QStringList parse_line( QString qs ); }; #endif
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#ifndef eslGRAPH_INCLUDED #define eslGRAPH_INCLUDED #include "esl_config.h" extern int esl_graph_MaxBipartiteMatch(int **A, int M, int N, int ***opt_G, int *ret_nedges); #endif // eslGRAPH_INCLUDED
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6
// vbar for DNA .55, proteins .69 to .81 usually .72-.74 // k 1 to 4 float D_calc(float s, float vbar, float k); float s_calc(float D, float vbar, float k); float k_calc(float s, float D, float vbar);
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C/C++
204
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#ifndef eslALLOC_INCLUDED #define eslALLOC_INCLUDED #include <stdlib.h> extern void *esl_alloc_aligned(size_t size, size_t alignment); extern void esl_alloc_free(void *p); #endif // eslALLOC_INCLUDED
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C/C++
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9
#ifndef eslARR2_INCLUDED #define eslARR2_INCLUDED #include <stdlib.h> extern size_t esl_arr2_SSizeof(char **s, int dim1); extern void esl_arr2_Destroy(void **p, int dim1); #endif // eslARR2_INCLUDED
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C/C++
205
6
#include "esl_config.h" extern int esl_composition_BL62(double *f); extern int esl_composition_WAG (double *f); extern int esl_composition_SW34(double *f); extern int esl_composition_SW50(double *f);
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C/C++
215
14
#ifndef US_SAXS_CMDS_T_H #define US_SAXS_CMDS_T_H #include <map> #include <vector> #include <list> #include <stdio.h> #include <stdlib.h> #include <iostream> #include "us_saxs_util.h" using namespace std; #endif
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C/C++
226
9
#ifndef eslARR3_INCLUDED #define eslARR3_INCLUDED #include <stdlib.h> extern size_t esl_arr3_SSizeof(char ***s, int dim1, int dim2); extern void esl_arr3_Destroy(void ***p, int dim1, int dim2); #endif // eslARR3_INCLUDED
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C/C++
231
6
#ifndef mp_comp_MM_det_h__ #define mp_comp_MM_det_h__ /* Function Declarations */ void mp_comp_MM_det( double *Mdet_out, bool *MdetMsk_out, double *M_in, double *MdetThr_in, int *idx_in, int *numel_in ); #endif
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C/C++
237
10
#import "UMONPlacementContent.h" NS_ASSUME_NONNULL_BEGIN @interface UMONRewardablePlacementContent : UMONPlacementContent @property(nonatomic) BOOL rewarded; @property(strong, nonatomic) NSString *rewardId; @end NS_ASSUME_NONNULL_END