sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
baf5ec3c7f0da788641aba69d32ea1300d48af7c2d73caa1c75381a4ea038b21 | C | 90,590 | 2,804 | /* esl_sq : a single biological sequence.
*
* Contents:
* 1. Text version of the ESL_SQ object.
* 2. Digitized version of the ESL_SQ object.
* 3. Other functions that operate on sequences.
* 4. Getting single sequences from MSAs.
* 5. Debugging, development tools
* 6. ... |
59300ba609e6dc5e9359e2a2aa0df104ff403aa13590a948c737153070601088 | C | 92,263 | 1,729 | /* jackhmmer: iterative search of a protein sequence against a protein database
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_dmatrix.h"
#include "esl_getopts.h"
#include "esl_keyhash.h"
#include "esl_msa.h"
#include "e... |
c40e22b8db9211d2062744575190db940bc6f39e62dcd7c0cf325ebd1bad685e | C | 96,252 | 2,635 | /* Easel's foundation.
*
* Contents:
* 1. Exception and fatal error handling.
* 2. Memory allocation/deallocation conventions.
* 3. Standard banner for Easel miniapplications.
* 4. Improved replacements for some C library functions.
* 5. Portable drop-in replacements for nonstandard C functions.
... |
cca711a7202fec3f73d93817f1341603532106775d9ef46e58a3f623fb2fb61d | C | 102,165 | 3,306 | /* Unaligned ncbi sequence file i/o.
*
* Contents:
* 1. An <ESL_SQFILE> object, in text mode.
* 2. An <ESL_SQFILE> object, in digital mode. [with <alphabet>]
* 3. Miscellaneous routines.
* 4. Sequence reading (sequential).
* 5. Parsing routines
*/
#include "esl_config.h"
#include <stdlib.h>
#in... |
1da3b49160c27bdf704962dddf498d81574e7c148d3940a9914b9582ec051710 | C | 115,083 | 2,715 | /* I/O of multiple sequence alignment files in Stockholm/Pfam format
* (Pfam format = always single block; Stockholm = multiblock allowed)
*
* Contents:
* 1. API for reading/writing Stockholm/Pfam input.
* 2. Internal: ESL_STOCKHOLM_PARSEDATA auxiliary structure.
* 3. Internal: parsing Stockholm line types... |
d7d4efec523d28279ab5a672b8593797d84066cbfa3d2ccc5e69621c3beb34c1 | C | 117,484 | 3,277 | /*::cexcerpt::header_example::begin::*/
/* An input parsing abstraction.
*
* Table of contents:
* 1. ESL_BUFFER object: opening/closing.
* 2. Positioning and anchoring an ESL_BUFFER.
* 3. Raw access to the buffer.
* 4. Line-based parsing.
* 5. Token-based parsing.
* 6. Binary (fread-like) parsing.
... |
ce694f0f7aa8ffd4d726d506f994001cc54c2c627cc307d6a836b8642d29d621 | C | 118,274 | 2,332 | /* Routines for manipulating sequence alignment score matrices,
* such as the BLOSUM and PAM matrices.
*
* Contents:
* 1. The ESL_SCOREMATRIX object.
* 2. Some classic score matrices.
* 3. Deriving a score matrix probabilistically.
* 4. Reading/writing matrices from/to files.
* 5. Implicit probabilis... |
de56bace10c407c88fc7551c84a86e1bcf4875ab73816c73260fe38e86530528 | C | 128,839 | 3,395 | /* Unaligned ascii sequence file i/o.
*
* Contents:
* 1. An <ESL_SQFILE> object, in text mode.
* 2. An <ESL_SQFILE> object, in digital mode.
* 3. Miscellaneous routines.
* 4. Sequence reading (sequential).
* 5. Sequence/subsequence fetching, random access
* 6. Internal routines shared by pa... |
9b8cd7ab9fff471539b7290ba5a34496edbe487b153624d03a694707acdee151 | C | 132,925 | 2,572 | /* Input/output of HMMs.
*
* Contents:
* 1. The P7_HMMFILE object for reading HMMs
* 2. Writing HMMER3 HMM files.
* 3. API for reading HMM files in various formats.
* 4. Private, specific profile HMM file format parsers.
* 5. Other private functions involved in i/o.
* 6. Benchmark drive... |
b5ce9709197475e7a0e9e0ceb34166a991b8a798277fad1c41623a6cdf4c6fa5 | C | 140,367 | 3,970 | /* Multiple sequence alignments.
*
* Contents:
* 1. The <ESL_MSA> object
* 2. Digital mode MSA's
* 3. Setting, checking data fields in an <ESL_MSA>
* 4. Miscellaneous functions for manipulating MSAs
* 5. Debugging, testing, development
* 6. Unit tests
* 7. Test driver
*/
#i... |
550a312e97acc3f6b93ab0eb6e750dfc693218fa20773affa88bce6f14df07f5 | C | 140,886 | 3,320 | /* Manipulate a multiple sequence alignment in various ways.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include <limits.h>
#include "easel.h"
#include "esl_arr2.h"
#include "esl_distance.h"
#include "esl_dmatrix.h"
#include "esl_filepa... |
63f2fd60837a0ff1fb2f46a55ad222e747f8d46aa16021ff6235a2bd100928fa | C | 142,677 | 4,170 | /*
* ANTIGRADIENT
*
* See the help text in antigradient.m for a description.
*
* Author: Gunnar Farnebäck
* Medical Informatics
* Linköping University, Sweden
* gunnar@imt.liu.se
*/
#include "mex.h"
#include <string.h>
#define RECURSION_SIZE_LIMIT 4
/* This can without cost be over... |
b6a400b56f6ef08006a115cb88b72f98f7d5c914214e9852c270e9d2a1e64f75 | C | 154,852 | 4,338 | #include "mex.h"
#include <string.h>
#define RECURSION_SIZE_LIMIT 4
/*
* ANTIGRADIENT
*
* See the help text in antigradient.m for a description.
*
* Author: Gunnar Farnebäck
* Medical Informatics
* Linköping University, Sweden
* gunnar@imt.liu.se
*/
/*************** 2D ***********... |
44d74a340a59d8e4c1717b5f1e93f5ff03c55679ece4201b05e9a84a5c98379f | C | 187,340 | 5,986 | /* $Id: gl2ps.c 173 2007-05-20 15:51:51Z krischnamurti $ */
/*
* GL2PS, an OpenGL to PostScript Printing Library
* Copyright (C) 1999-2006 Christophe Geuzaine <geuz@geuz.org>
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of either:
*
* a) the GNU Library Ge... |
389d60f25b86b885c2a226f7f0b9257334dd5f7fd4554fd27779aa0876bae45b | C | 200,000 | 5,380 | /* Generated by Cython 0.29.32 */
#ifndef PY_SSIZE_T_CLEAN
#define PY_SSIZE_T_CLEAN
#endif /* PY_SSIZE_T_CLEAN */
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSIO... |
60a1090fe019be60edde183e59b9b84791b9a0993c21b56b885b7fde1c67eebf | C | 200,000 | 4,844 | /* Generated by Cython 0.29.12 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
#error Cython... |
7734389ee64d8af19e0c0113eb2833c4c5e74b5cfb0bf3a2abb827828a8c9dda | C | 200,000 | 4,820 | /* Generated by Cython 0.29.23 */
/* BEGIN: Cython Metadata
{
"distutils": {
"depends": [
"/home/ruohawang2/miniconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h",
"/home/ruohawang2/miniconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ufuncobject.h... |
a3511a8c178055f7e8c2a18c3af3bce687ea749665a525ba6437064db39caeed | C | 200,000 | 4,237 | /* Generated by Cython 3.2.4 */
/* BEGIN: Cython Metadata
{
"distutils": {
"name": "dissect.PropsSimulator.simulator",
"sources": [
"dissect/PropsSimulator/simulator.pyx"
]
},
"module_name": "dissect.PropsSimulator.simulator"
}
END: Cython Metadata */
#ifndef PY_SSIZE_T... |
cee4275bcd7796bb3f8946a7d815ad886d78b4ace8ba7dd89b2a92f840e4f4da | C | 200,000 | 5,078 | /* Generated by Cython 0.29.32 */
/* BEGIN: Cython Metadata
{
"distutils": {
"name": "sift",
"sources": [
"/home/tomas/Projects/DrinkMoth2/sift.pyx"
]
},
"module_name": "sift"
}
END: Cython Metadata */
#ifndef PY_SSIZE_T_CLEAN
#define PY_SSIZE_T_CLEAN
#endif /* PY_SSIZE... |
fdf661409a3907dd4bfd1c730f03d1f5073f1c5139c5ac39163dc47146b618ef | C | 200,000 | 3,994 | /* Draw secondary structure diagrams given a postscript SS template.
* Initial development of this program was for SSU rRNA structures
* with templates derived from Gutell's CRW (Comparative RNA Website,
* http://www.rna.ccbb.utexas.edu/).
*
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#incl... |
5fbe613e35fcf19d88906be89c2178c3c20e59c9f1c6317235b40efca54672a4 | C++ | 46 | 3 | #define DENSE_VECTORS
#include <semproc.cpp>
|
b155006008f68adbaef29168f9a17f2ecc87631e5840fa6079ffe64a020f7a8c | C++ | 58 | 2 | #define MLP
#include<../resource-incrsem/src/semproc.cpp>
|
c596378030cb45c979f861c7979576789a8267ee8a565c982437e4c317285473 | C++ | 78 | 2 | #define MLP
#include<../resource-incrsem/src/linetrees2sm_semprocdecpars.cpp>
|
7e50d5e782a34de6a1f87b700b28988c504021d8493dbec79c05508ecb957fbc | C++ | 88 | 2 | #define DENSE_VECTORS
#include<../resource-incrsem/src/linetrees2sm_semprocdecpars.cpp>
|
fa3042f994b5dd365a31081c396c5ec67943725e6fc491fe1bef7a1fc3ef6753 | C++ | 113 | 7 | #define CATCH_CONFIG_MAIN
#include "test.hpp"
#include <graphtyper/constants.hpp>
#include <catch2/catch.hpp>
|
7912d5d3d73a18381951d77cb38a47c9b10c62182962e8fb2c8ea9ec19aa866c | C++ | 163 | 11 | #include "expr_mod.h"
using namespace std;
int main(int argc, char *argv[]){
dv_expr::ExpressionModell hema;
hema.load( std::string(argv[1]) );
return 0;
}
|
c8f0fe54f4f042b07e120ceffe0d9776ebd06089597fbde3fd0421f71a04b908 | C++ | 200 | 10 | #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;
|
b7db1406dc3f31a12209c0c6ac79db21f4610b8fb3c37f77e5edc809c1105ca8 | C++ | 203 | 5 | #include "qt_test_base.h"
// Static member definitions (put in qt_test_base.cpp)
std::unique_ptr<QCoreApplication> QtTestBase::app_ = nullptr;
std::unique_ptr<QApplication> GuiTestBase::app_ = nullptr;
|
82b5058d6c0d890deb194316228ac9c657cec4f56efbed60f521090c389d5336 | C++ | 212 | 14 | #include "stream_sorter.hpp"
/**
* \file stream_sorter.cpp
* StreamSorter: sort a stream of Protobuf messages in VPKG by node ID.
* Unplaced messages come first.
*/
namespace vg {
using namespace std;
}
|
e0438501d5a16f01dfd4268d8655998755836731c96a72360d67a346951e4b5d | C++ | 228 | 13 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <graphtyper/typer/variant.hpp>
#include <graphtyper/typer/vcf.hpp>
#include <catch2/catch.hpp>
// TODO
|
1ba6a297c385da1de4bd4c21252c926d66f8459614e906348aa7202067a2b07b | C++ | 288 | 16 |
#include <cstdlib>
#include <ctime>
#include "timestamp.hpp"
using namespace std;
string timestamp() {
struct tm tm;
char buffer[100];
const time_t now = time(NULL);
localtime_r(&now, &tm);
strftime(buffer, sizeof(buffer), "%c", &tm);
return string(buffer);
}
|
0edb1cb7fae44db2305aadd120992ca8054c9557d04226606570eb7878bb73a7 | C++ | 296 | 23 | #include <iostream>
#include <graphtyper/utilities/options.hpp>
namespace gyper
{
Options * Options::instance()
{
return _instance;
}
const Options * Options::const_instance()
{
return _instance;
}
Options::Options()
{
}
Options * Options::_instance = new Options;
} // namespace gyper
|
33128190af56c1ae7b61ed87fae25d927b4757c1ee14ac445dd504e14fdc6ba3 | C++ | 362 | 17 | #include "us_fematch.h"
#include "us_license_t.h"
#include "us_license.h"
// main program
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_FeMatch w;
w.show(); //!< \memberof QWidget
return applicati... |
57859480084f5e97662bafd180baee57bdb4f84a17def68121c09dce0504c4ef | C++ | 390 | 18 | //! \file us_integral_main.cpp
#include "us_integral.h"
#include "us_license.h"
#include "us_license_t.h"
// main program
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_Integral w;
w.show(); //!< \membero... |
14bfcd04634260406f0be3c4c43ae24229ebcd231166575a739b80a19227cc0c | C++ | 393 | 19 | //! \file us_2dsa_main.cpp
// the class US_2dsa.
#include "us_2dsa.h"
#include "us_license.h"
#include "us_license_t.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_2dsa w;
w.show(); //!< \memb... |
07971481ac7c80022041f69c356d37a71a97906bc1460e4e79edfd3623bf42ea | C++ | 401 | 20 | //! \file us_ddist_combine_main.cpp
#include "us_ddist_combine.h"
#include "us_license_t.h"
#include "us_license.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_DDistr_Combine w;
w.show(); //!< ... |
abbea60d91bf403dcc972fdeffaf97fe03f7a43f02a8b7fb7a99330dc8991e24 | C++ | 414 | 19 | //! \file us_convert_main.cpp
#include "us_convert_gui.h"
#include "us_license_t.h"
#include "us_license.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
//US_ConvertGui w("AUTO");
US_ConvertGui w;
w.show(); ... |
9e8055e9f8c571fcdd3b980c73e0348f5eaa55032c58ef3993d874b9aa48dab4 | C++ | 420 | 23 | #include "log.hpp"
#include <iostream>
#include <vector>
namespace vg {
namespace logging {
cerrWrapper info(const std::string& context) {
return cerrWrapper("[" + context + "] ", false);
}
cerrWrapper warn(const std::string& context) {
return cerrWrapper("warning[" + context + "] ", false);
}
cerrWrapper ... |
007b4979e5ffa50ef437a63760014242953b47647963ce31662b57f5c4a660e3 | C++ | 423 | 19 | //! \file us_pseudo3d_combine_main.cpp
#include "us_pseudo3d_combine.h"
#include "us_license_t.h"
#include "us_license.h"
// main program
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_Pseudo3D_Combine w;
w.show();... |
03d34a93d4dde7b3b250a3df44258c4fcd5f7e39e93c28953baf9d8613a9d37e | C++ | 427 | 19 | //! \file us_mwl_species_sim_main.cpp
// the class US_Convert.
#include "us_mwl_species_sim.h"
#include "us_license.h"
#include "us_license_t.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_MwlSpeciesSim w;
w.s... |
acc57c9acd6eed9f4cf801e37bdb84cf7a511a904360e404dc7a19df243503aa | C++ | 452 | 20 | //! \brief Main program. Loads translators and starts
// the class US_Convert.
#include "us_mwl_species_fit.h"
#include "us_license_t.h"
#include "us_license.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_... |
9996d0d0bfd0b8ae19c83381e3498fe29a4927da2aca9aaa6ede1306055c14d2 | C++ | 456 | 19 | #include "us_buoyancy.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Buoyancy. Loads translators and starts
// the class US_FitMeniscus.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up... |
74b400117bb0171305374f2cb866ea14f390d151ebc5df0ecc3e0b1a0664c1ab | C++ | 473 | 28 | //! \file us_protocol_dev_main.cpp
#include "us_protocol_dev_gui.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_ProtocolDevMain * w = new US_ProtocolDevMain;
w->show();
w->call_AutoflowDialogue();
if ... |
9bd8beb52721b2fea9d7fe134bfb3d8a97b32e29d16625e0e63018a9488e713e | C++ | 473 | 22 | //! \brief Main program for US_Edit. Loads translators and starts
//! the class US_FitMeniscus.
#include "us_edit.h"
#include "us_license_t.h"
#include "us_license.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
... |
d7718cea08fd7b813f5ed7ad4ca85c62bcc7b6634971b834867ac903e247eb8d | C++ | 476 | 22 | //! \file us_xpn_viewer_main.cpp
#include "us_xpn_viewer_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_XpnDataViewer.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
//US_XpnDataVi... |
df30586a081e96a5f791d9fb5342954e9f489a477fd27e705394d0c4620524b1 | C++ | 481 | 23 | #include <QApplication>
#include "us_model_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_ModelGui. Loads translators and displays
// the window.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
US_Model m;
... |
124751972893b4543c4a81512671338a6065b2197511a4e916f55d967cac8e99 | C++ | 496 | 27 | /**
* \file
* Allocator configuration procedure for mimalloc.
*/
#include "allocator_config.hpp"
#include <mimalloc.h>
namespace vg {
using namespace std;
void AllocatorConfig::configure() {
// mimalloc's default configuration is fine, so do nothing.
}
void AllocatorConfig::set_profiling(bool should_profil... |
dcf28de599ee731bd70aff3e06b26580531d284f64fe1564a9621220ea90c5b5 | C++ | 513 | 23 | //! \file us_predict2_main.cpp
#include <QApplication>
#include "us_predict2.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Predict2. Loads translators and starts
// the class US_Predict2.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
767bda3b88102971088e5df8bc24448d528ac3efe1c09ee2e56e5c064036550d | C++ | 523 | 23 | //! \file us_audit_trail_gmp_main.cpp
#include "us_audit_trail_gmp.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_audit_trail. Loads translators and starts
// the class
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.i... |
aa2c19f2c8455e01765b501bbf53c941ca1ccba392529d713bba2f14909c4128 | C++ | 524 | 22 | //! \file us_buffer_main.cpp
#include <QApplication>
#include "us_buffer_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Buffer. Loads translators and starts
// the class US_Buffer.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#incl... |
25d5bc3a95f8c479d82146964ecabcae7df654b3da18f8069d0fc37f9cdfcd2e | C++ | 525 | 23 | //! \file us_extinction_main.cpp
//
#include <QApplication>
#include "us_extinction_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_EXTINCTION. Loads translators and starts
// the class US_EXTINCTION
int main( int argc, char* argv[] )
{
QApplication application( argc... |
0f97dacc629da8ae2708e69044cba8f24026fdacd6737d0288c57a334f287a8a | C++ | 531 | 23 | //! \file us_rotor_main.cpp
#include <QApplication>
#include "us_rotor_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_RotorGui. Loads translators and starts
// the class US_FitMeniscus.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
ccecf4b2788de0fb29794e0d7a4456e9f27f37dfed4c621b730b231dac5c9a6c | C++ | 531 | 22 | //! \file us_project_main.cpp
#include <QApplication>
#include "us_project_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Project. Loads translators and starts
// the class US_Project.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#... |
79d613189c520231f26e5a6f85dd48cde4f34a6b04aba8698a74db032dafc1d6 | C++ | 537 | 22 | //! \file us_analyte_main.cpp
#include <QApplication>
#include "us_analyte_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_AnalyteGui. Loads translators and starts
// the class US_AnalyteGui.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
79d7e5d30ca01fce08ed147cc845dcf6dfe2e2ea893f679d9ac2e10bdb7b98bd | C++ | 537 | 22 | //! \file us_solution_main.cpp
#include <QApplication>
#include "us_solution_gui.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Solution. Loads translators and starts
// the class US_Solution.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
b724e841a479860846155f4c35df0e8bd3af9dec120eb74bad9f1599b4545161 | C++ | 544 | 22 | //! \file us_sassoc_main.cpp
#include <QApplication>
#include "us_sassoc.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Sassoc. Loads translators and starts
// the class US_Sassoc.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include ... |
85fa7ef74b51f6fad34a1154bed4a34712fc72395bbcb9a1cf11ae7bf08a7f9c | C++ | 545 | 23 | //! \file us_autoflow_analysis_main.cpp
#include "us_autoflow_analysis.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Analysis_auto. Loads translators and starts
// the class US_Analysis_auto
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );... |
b8c31fc5c778c719219a23e18ace420c77c57a694d0d6d5e9c5d552492fb810a | C++ | 553 | 23 | //! \file us_anapro_main.cpp
#include "us_analysis_profile.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_AnalysisProfileGui. Loads translators and starts
// the class US_AnalysisProfileGui
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
73ecd9ddc25441e3098899baae6cce6e0754de0e9f89e8bab09e418dcbbb269e | C++ | 561 | 22 | //! \file us_investigator_main.cpp
#include <QApplication>
#include "us_investigator.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_DB_TblInvestigator. Loads translators and starts
// the class US_DB_TblInvestigator.
int main( int argc, char* argv[] )
{
QApplication applic... |
28c616aa57e88af9e915e78c135e021715cb071a71e16e40d99bbe6c78242b8a | C++ | 581 | 25 | //! \file us_predict1_main.cpp
#include <QApplication>
#include "us_predict1.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Predict1. Loads translators and starts
// the class US_Predict1.
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
107689cc751a61bcd8f7bedc035c640dae0aaa6dd121e240460a3e2ac115516e | C++ | 586 | 21 | #include "us_editor_gui.h"
#include "us_gui_settings.h"
US_EditorGui::US_EditorGui() : US_WidgetsDialog( nullptr, Qt::WindowFlags() )
{
setWindowTitle( tr( "Analyte Details" ) );
setPalette( US_GuiSettings::frameColor() );
setAttribute( Qt::WA_DeleteOnClose );
QHBoxLayout* main = new QHBoxLayout( this );
... |
561cd8bb31cd6f629efc6b43a366a2b89304dfaa9ef87819a4c51ae8bd2da376 | C++ | 586 | 24 | //! \file us_experiment_main.cpp
#include "us_experiment_gui_optima.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_ExperimentMain. Loads translators and starts
// the class US_ExperimentMain
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
... |
a1c0af16c8ac4899b1fc3f394630109227d2a9b7743d8571d8ca29ddad11a969 | C++ | 596 | 28 | #include <cstdlib>
#include <sys/time.h>
#include "Timer.hpp"
Timer::Timer(void) {
update_time();
}
double Timer::update_time(void) {
struct timeval tv;
gettimeofday(&tv, NULL);
prevtime = curtime;
curtime = tv.tv_sec + 1e-6 * tv.tv_usec;
return curtime - prevtime;
}
unsigned long long Timer::rdtsc(void... |
9b0e8db98e08fba539a2b7ab033dc168585855a0a9b93786011bb2b8763eaf1f | C++ | 604 | 42 | #include <vector>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/ref.hpp>
namespace gyper
{
Ref::Ref(std::vector<char> && _seq) : seq(std::forward<std::vector<char>>(_seq))
{
}
Ref::Ref(std::vector<char> const & _seq) : seq(_seq)
{
}
Ref::Ref(std::initializer_list<char> l) : seq(l)
{
}
void Ref::cl... |
afb31c68f823b007f4b98a7308c81e84c8ea8e601a190ddc214c493f9c6e29a5 | C++ | 615 | 22 | #include "lightingdlgbaseimpl.h"
/*
* Constructs a lightingdlgbase which is a child of 'parent', with the
* name 'name' and widget flags set to 'f'
*
* The dialog will by default be modeless, unless you set 'modal' to
* TRUE to construct a modal dialog.
*/
lightingdlgbase::lightingdlgbase( QWidge... |
3c15a1e3a4de3ab43c0917cdafbf63b3e9975be7ed216c92a1a6a88b933c4415 | C++ | 619 | 28 | #include "id_sort.hpp"
#include <algorithm>
#include <vector>
namespace vg {
namespace algorithms {
using namespace std;
vector<handle_t> id_order(const HandleGraph* g) {
// We will fill and sort this
vector<handle_t> to_return;
g->for_each_handle([&](const handle_t& handle) {
// Collect all the... |
5ad651b4309f5795e16eef0b2255f0dc7e8ca7fb4bde4764cb06604d825fbd19 | C++ | 625 | 29 | /**
* \file register_loader_params_json.cpp
* Defines IO for a VG graph from stream files of Graph objects.
*/
#include <vg/io/registry.hpp>
#include "register_loader_params_json.hpp"
#include <iterator>
namespace vg {
namespace io {
using namespace std;
using namespace vg::io;
void register_loader_params_jso... |
d3716b3789836cb412b80c95fd3041549b8998162526575245908f2ff0ae19d3 | C++ | 629 | 31 | ///
/// \file sequence_complexity.cpp
///
/// Unit tests for SeqComplexity
///
#include "catch.hpp"
#include "../sequence_complexity.hpp"
#include <iostream>
namespace vg {
namespace unittest {
using namespace std;
TEST_CASE( "Sequence complexity can be identified", "[complexity]" ) {
string seq = "ACGTA... |
031313e2d2a32ec51ab093a8573bf21bc7372bdcaf9d9943d4d49927513affc2 | C++ | 641 | 25 | //! \file us_esigner_gmp_main.cpp
#include "us_esigner_gmp.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_eSigner. Loads translators and starts
// the class
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// L... |
f6018a162d0257bb8dc39bddc9d12a6292b2945fb64bfcb0474498196643812b | C++ | 643 | 31 | /********************************************************************
created: 2003/09/10
filename: main.cpp
author: Micha Bieber
*********************************************************************/
#include <qapplication.h>
#include "axesmainwindow.h"
int main( int argc, char** arg... |
49abf095047c64953e7e651f0dd849785cbe1249b576c3335127e4862d78ffbf | C++ | 647 | 32 | #include "qwt3d_gridmapping.h"
#include "qwt3d_surfaceplot.h"
using namespace Qwt3D;
GridMapping::GridMapping()
{
plotwidget_p = 0;
setMesh(0,0);
setDomain(0,0,0,0);
restrictRange(ParallelEpiped(Triple(-DBL_MAX,-DBL_MAX,-DBL_MAX),Triple(DBL_MAX,DBL_MAX,DBL_MAX)));
}
void GridMapping::setMesh(unsign... |
7d6fe18ca511b602b7bb6715124649251c3f49861d5b0d6c354888fc629a289f | C++ | 653 | 30 | /********************************************************************
created: 2003/09/10
filename: main.cpp
author: Micha Bieber
*********************************************************************/
#include <qapplication.h>
#include "enrichmentmainwindow.h"
int main( int argc, char**... |
68e0dfd91aa3dbbfb7ea52f1badcc305f325add066aa9662553cc39c69639fc6 | C++ | 671 | 24 | #include "next_pos_chars.hpp"
namespace vg {
namespace algorithms {
map<pos_t, char> next_pos_chars(const PathPositionHandleGraph& graph, pos_t pos) {
map<pos_t, char> nexts;
handle_t handle = graph.get_handle(id(pos), is_rev(pos));
if (offset(pos) < graph.get_length(handle)-1) {
++get_offset(pos... |
cf967d607617c2424bf980e9086d91de85869c87cfa51763b4332ab9e7ebe2ff | C++ | 672 | 26 | //! \file us_reporter_gmp_main.cpp
#include "us_reporter_gmp.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_Analysis_auto. Loads translators and starts
// the class US_Analysis_auto
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#incl... |
0d9c23564ede509a7e67be5f8999923f2b4031a85c3f785518e5017b53454387 | C++ | 693 | 28 | #include <algorithm>
#include <string_view>
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <graphtyper/utilities/hash_seqan.hpp>
namespace std
{
std::size_t hash<seqan::String<seqan::Dna>>::operator()(seqan::String<seqan::Dna> const & s) const
{
std::size_t hash_val = 0;
for (seqan::Iterator<seqa... |
f5a6b38f271fba8da366aa01aed6290ff82a7369e35796b9dc30aedaff613ddb | C++ | 734 | 30 | /**
* \file find_gbwtgraph.cpp
*/
#include "find_gbwtgraph.hpp"
#include "../gbzgraph.hpp"
namespace vg {
namespace algorithms {
const gbwtgraph::GBWTGraph* find_gbwtgraph(const HandleGraph* graph) {
if (!graph) {
// No graph means no translation.
return nullptr;
}
if (dynamic_cast<con... |
3b9793023c5137adf6778172cfd6610e1ee9bf3eea34360002fae5e2cc6a65cf | C++ | 736 | 32 | /********************************************************************
created: 2003/09/09
filename: main.cpp
author: Micha Bieber
*********************************************************************/
#include <qapplication.h>
#include "mesh2mainwindow.h"
int main( int argc, char **argv... |
32e5284e3d55ee3bbf786879da572db02c78e955e713e8288f7ab577201452c1 | C++ | 750 | 33 | #include <iostream>
#include <fstream>
#include "vg/io/json2pb.h"
#include <vg/vg.pb.h>
#include "vg.hpp"
using namespace std;
using namespace google::protobuf;
using namespace vg;
int main(int argc,char *argv[])
{
VG graph;
Node* n1 = graph.create_node("AAAACACGAAGGTGCTCACTGAAACATGGGAACCAAAG");
Node* n2... |
04d459d163c5079b07df029ff3f0fb1e4c2961d315ebe12cc7a3ba31d63124f5 | C++ | 757 | 24 | /*
Copyright (c) 2026, PyData Development Team
All rights reserved.
Distributed under the terms of the BSD Simplified License.
The full license is in the LICENSE file, distributed with this software.
*/
#include "pandas/moments.h"
#include "pandas/simd/moments_simd.hpp"
#include <optional>
#include <span>
Moments m... |
24f21b48ee06c8699c11c52c439309ec019bc749dd3cf61e6f94cbc8f9687391 | C++ | 759 | 24 | /*
Copyright (c) 2026, PyData Development Team
All rights reserved.
Distributed under the terms of the BSD Simplified License.
The full license is in the LICENSE file, distributed with this software.
*/
#include "pandas/moments.h"
#include "pandas/simd/moments_simd.hpp"
#include <optional>
#include <span>
Moments m... |
5c999e02f822b331cd99ce18a3460a1942d1ad9ae0cc5811394be4831244e9dd | C++ | 760 | 27 | //! \file us_esigner_gmp_main.cpp
#include "../us_esigner_gmp/us_esigner_gmp.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_eSigner. Loads translators and starts
// the class
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "m... |
57664c26d48ec167bfaf523d557fbda03016a90bcf6ac7636e36249d955c6f75 | C++ | 808 | 34 | //! \file us_experiment_main.cpp
#include "../us_com_project/us_com_project_gui.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_ComProjectMain * w = new US_ComProjectMain("US_MODE");
w->show();
// Create local... |
3737c316b481b6d41229212ff3d920822bcd14446bc1844ca2239a3cdd6b0bca | C++ | 815 | 30 | //! \file programs/us_license/us_license.cpp
//! \anchor licenseMain
#include "us_license.h"
/*! \brief Main program for us_license. Loads translators and starts
the class us_license
*/
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
// Set up language localization
QString lo... |
2fcf94a9db59f1f5fa7a9ba28e336bd24e5197d0acba4bb863e9832093b3e277 | C++ | 850 | 29 | //! \file us_esigner_gmp_main.cpp
#include "../us_esigner_gmp/us_esigner_gmp.h"
#include "us_license_t.h"
#include "us_license.h"
//! \brief Main program for US_eSigner. Loads translators and starts
// the class
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "m... |
ba8f740d3c691075404a5004115b8aae6773e46ee077c9c2f4f31647698394c0 | C++ | 852 | 48 | #include "randomgen.h"
gsl_rng * r;
void randomszam_inic(int seed, gsl_rng * rng){
//time_t timer;
r = (gsl_rng *) gsl_rng_alloc (gsl_rng_mt19937);
gsl_rng_set(r, seed);
}
int randomszam_mentes(const char * filename, gsl_rng * rng){
FILE *output;
output = fopen(filename, "a");
if(!output){
//std::ce... |
2d54f00363c29775c8dcec8c087a4627eb301d561a93db34e5c5c35feb01d2d0 | C++ | 874 | 27 | /*
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... |
8b2ff9423e9ce8f484b02769771abc0125696fa6c83967db04249f4a568053d4 | C++ | 892 | 41 | //! \file us_experiment_main.cpp
#include "us_com_project_gui.h"
int main( int argc, char* argv[] )
{
QApplication application( argc, argv );
#include "main1.inc"
// License is OK. Start up.
US_ComProjectMain * w = new US_ComProjectMain;
w->show();
// Create local "server" to register applic... |
cd85fc51ecbe9deb3b204fb8010feb9ad61f1d02e9675768baddd0017912619a | C++ | 900 | 49 | #include <string>
#include <iostream>
#include <iomanip>
#include <exception>
#include "../Griday.hpp"
#include "../Vector.hpp"
#include "../Random.hpp"
int
main(int argc, char* argv[])
try {
using namespace std;
if (argc < 3)
{
cerr << "./visit_maker GRID OUTPUT (blocking)"
<< e... |
efdf31b61615d250bfe5ca2a41cafa05215cdd14585a6f16e3c93953e9561af9 | C++ | 905 | 35 | #include <utility>
#include <cereal/archives/binary.hpp>
#include <cereal/types/utility.hpp>
#include <cereal/types/vector.hpp>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/genotype.hpp>
namespace gyper
{
Genotype::Genotype() : id(0), num(1), first_variant_node(0)
{
}
Genotype::Genotype(uint32_t c... |
fd709fa73a170dccd8c710f8fc2b9481cb225e6610e0963c2d18ce5a3c055bf7 | C++ | 906 | 33 | /**
* \file name_mapper.cpp: contains implementations for the NameMapper to convert
* between VCF and graph/FASTA contig names.
*/
#include "name_mapper.hpp"
namespace vg {
using namespace std;
void NameMapper::add_name_mapping(const string& vcf_name, const string& fasta_name) {
// Fill in both one-way map... |
97d7cd7b7a406f827106d7d7890dcc66d528d8043fdf08437f1926d7957419af | C++ | 908 | 32 | #include <iostream>
#include <sstream>
#include <graphtyper/graph/graph.hpp>
#include <graphtyper/graph/graph_serialization.hpp> // gyper::load_graph
#include <graphtyper/graph/sequence_extractor.hpp>
#include <graphtyper/utilities/io.hpp>
namespace gyper
{
void extract_to_fasta(std::string const & file_name, std::st... |
96c3843820cc57d6d703a275021c2a715da3d26151650cbff73fe9064f92508f | C++ | 927 | 28 | #include "approx_path_distance.hpp"
namespace vg {
namespace algorithms {
using namespace std;
size_t min_approx_path_distance(const PathPositionHandleGraph* graph, const pos_t& pos1, const pos_t& pos2, uint64_t max_search) {
auto nearest1 = nearest_offsets_in_paths(graph, pos1, max_search);
auto nearest2 = ... |
f4f24a23d7eb0fbc09a1c2c92c26743543c70355303081be9fd750f3a0acbcb0 | C++ | 948 | 42 | #include "GridayException.hpp"
#include <sstream>
GridayException::GridayException(const std::string& file, int line,
const std::string& msg)
: mDepth {0}
{
std::stringstream ss;
ss << "File: " << file << ", Line: " << line << ", Message: " << msg;
mMsg = ss.str()... |
9285cc009bdfea34c31bdf25f3b079d8ab1e86558501c2896686ea83b7ec3d53 | C++ | 955 | 44 | #include <climits>
#include <cstdio>
#include <fstream>
#include <iostream>
#include <stdio.h>
#include <string>
#include <graphtyper/constants.hpp>
#include <graphtyper/typer/vcf.hpp>
#include <catch2/catch.hpp>
TEST_CASE("Read the index test VCF file")
{
using gyper::Vcf;
std::string vcf_filename;
{
st... |
63dd11ec8d24e8907f23a420e1c0f6229c9b6a46dc9c5209643abba71314d79a | C++ | 958 | 38 | /*
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... |
d8d3d314df144d37bae795c62947764c7bdf3ad60772cf719947e3bc8b11ee84 | C++ | 960 | 36 | #define CATCH_CONFIG_RUNNER
// Make sure to grab catch relative to us
#include "../catch.hpp"
#include "../../io/register_libvg_io.hpp"
#include "../../utility.hpp"
#include "../../log.hpp"
using namespace vg;
/**
* Main function for unit test suite binaries.
*/
int main(int argc, char** argv) {
Logger logger("... |
efd1fe6b8b3240644201c132d91876f3604282044e910ebff45501dabc773c0e | C++ | 962 | 56 | #include <cstdint>
#include <set>
#include <graphtyper/constants.hpp>
#include <graphtyper/graph/snp_event.hpp>
#include <graphtyper/index/index_entry.hpp>
namespace gyper
{
IndexEntry::IndexEntry(uint32_t const s) : start_index(s)
{
}
IndexEntry::IndexEntry(uint32_t const s, uint32_t const i, bool const is_referenc... |
c53ea19f3cfe10664b3366ae73fa323dcd7ff717c6c7164d07a2d21814cf7cf2 | C++ | 997 | 39 | /**
* \file find_gbwt.cpp
*/
#include "find_gbwt.hpp"
#include "find_gbwtgraph.hpp"
#include <vg/io/vpkg.hpp>
#include "../gbzgraph.hpp"
namespace vg {
namespace algorithms {
const gbwt::GBWT* find_gbwt(const HandleGraph* graph) {
const gbwtgraph::GBWTGraph* typed_graph = find_gbwtgraph(graph);
if (!typed... |
3988815d365a2d7847790a8223da31f100f55856d0ab7c569f01232e81d2c4a9 | C++ | 1,010 | 50 |
#include <cstdarg>
#include <cstdio>
#include <cstdlib>
#include <sstream>
#include <string>
#include <vector>
#include "format.hpp"
std::string format(const std::string& format, ...)
{
va_list args;
va_start(args, format);
size_t len = std::vsnprintf(NULL, 0, format.c_str(), args);
va_end(args);
... |
223ebcc0840c5dd0b74c13dcd915293b88dba2ce6f0d7e8830a90cacd8602c40 | C++ | 1,041 | 36 | #include <cmath>
#include <iostream>
#include <stdint.h>
#include "convolution.hpp"
#include "integration.tcc"
double _convolution1(double *A, double *B, int t, double delta, int k) {
double y = 0.0;
double *C = new double[t+1];
for(int s=0;s<=t;s++){C[s] = A[t-s]*B[s];}
y = integration::integral<... |
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