sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f82e45747d9a7134a3c10c0336b405e996f3b947f1a8caf4b0fde8816fd80b25 | C | 4,809 | 151 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
cf31fc4504ae3bcf68577d5fd33123d56aaeb8f0df33a333d6e773da1f8e0757 | C | 4,822 | 293 | /*
Copyright (c) 2014, Rafat Hussain
*/
#include "wtmath.h"
int upsamp(double* x, int lenx, int M, double* y)
{
int i;
if (M < 0) { return -1; }
if (M == 0)
{
for (i = 0; i < lenx; ++i) { y[i] = x[i]; }
return lenx;
}
const int N = M * (lenx - 1) + 1;
int j = 1;
int k = 0;
for (i = 0; i < ... |
9ea07abd1fa3203fb749c8029c3ac33ba14e14ee8c5e7dbd75b0539ec49bf64c | C | 4,916 | 165 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
119bbf0ae7f4c0c62b31c529286dc8e5277d545ef7b0a0ec885f0531115cbd59 | C | 4,980 | 169 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required by a... |
fecd0d18251d1ecc888dd68d79edca9d085ba305b6d17db5c37f3719efd9a029 | C | 5,058 | 194 | /*
* Copyright (c) 2011 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
c444e1ad849f58e255e18414968846e0e58be992c54a0e17a0dd6edb34b8c560 | C | 5,127 | 212 |
#include <zlib.h>
#include <string.h>
#include "memutil.h"
#include "util.h"
#include "impute.h"
#include "snp.h"
#include "err.h"
ImputeInfo *impute_info_new() {
ImputeInfo *impute_info;
impute_info = my_malloc(sizeof(ImputeInfo));
impute_info->buf_size = 1024;
impute_info->buf = my_malloc(impute_info->... |
6458696a05fbb5a62ab97c7077801ce903bc256f9ae3c3674601ee6608e16e4c | C | 5,167 | 238 |
#include <limits.h>
#include <string.h>
#include "memutil.h"
#include "chrom.h"
#include "util.h"
Chromosome *chrom_guess_from_string(char *str, Chromosome *chroms,
int n_chrom) {
Chromosome *match_chrom;
int i, j, longest_match, n1, n2;
fprintf(stderr, "guessing chromosome name from string %s\n",
... |
d7e3093c33c9dfc868074b442d9818f48fd95a4e462c75ef4cc24474dd09f32d | C | 5,361 | 171 | // ============================================================================
// gzstream, C++ iostream classes wrapping the zlib compression library.
// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU G... |
a51802cd962f82c0bfc46178fd5f29ab5c784a4f9b9a0fb4343cd6d0a596698e | C | 5,382 | 190 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
db580fb3952cba9d078c08dfee6195694165de20819ca0255ae423716044ac61 | C | 5,392 | 196 | /**
k2c_merge_layers.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <string.h>
#include <stdarg.h>
#include "k2c_include.h"
/**
* Element-wise sum of several tensors.
*
* :param output: output tensor.
* :param num_tensors: numb... |
3f44c0fec3ae7150d3a6e0c127675781fe40bcb8bb76880448406cc889e23de1 | C | 5,425 | 245 | /* Copy from "AnalyzeFMRI/src/spatial.c" since
"AnalyzeFMRI" is archived by CRAN. */
#include <math.h>
#include <R.h>
typedef int Sint;
#define SINT_MAX INT_MAX
/* functions for calculating spatial clusters and their properties by thresholding a statistic map/image. A neighbouthood matrix nmat is used to determin... |
59a5210a16b4696c18b3fc80a3470333db6bcca1a5f20f71261e3448d59f6184 | C | 5,497 | 224 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
cab8fc4a1f55373e23ef04cb15d7ddc8646793e0c6b3651241837f501036bac7 | C | 5,837 | 299 | #include "cwtmath.h"
static void nsfft_fd(const fft_object obj, fft_data* inp, fft_data* oup, const double lb, const double ub, double* w)
{
int i;
const int N = obj->N;
const int L = N / 2;
//w = (double*)malloc(sizeof(double)*N);
const int M = divideby(N, 2);
if (M == 0)
{
printf("The Non-Standard FFT Le... |
070839683fa248efb3afa047555263d561a0c449154f6feacb5b9ce7fdc79114 | C | 5,841 | 186 | /*
* Copyright (c) 2011 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
b9db6bfd0fde3b518990c13d718f6e6e050022a479c2e073b2753bde1b0c9e03 | C | 5,865 | 176 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
f1586b185068cd3d82e3d4ffa36db8147785b192174f4d9e71cd9ef7aaf62ac0 | C | 5,903 | 206 | /* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without li... |
06f14806dd0d1fa212d84a7cba644c259884a0981538a0acb9ae82e57349b6d3 | C | 5,952 | 311 | #include <stdio.h> // for printf
#include "pmatrices.h"
#include <stdlib.h> // for malloc and free
double **psdmatrix(int dim) // square double
{
int i;
double **m;
/* allocate pointers to rows */
m=(double **) malloc(dim * sizeof(double*));
if (!m) {
printf("allocation error in psdmatrix 1.\n");
exit(1);
}... |
33b4d2a92c8bb04fbdb4f5a3fac138fca6e88a84be11ed0e59d5266c3c6718cf | C | 5,959 | 179 | /****************************************************************************
* Copyright (C) 2014 by Taylor Arnold, Veeranjaneyulu Sadhanala, *
* Ryan Tibshirani *
* *
* This ... |
126f9397fb7485c88241161ffb990c030e2617649f3c6a297f7ce704bdba065f | C | 5,998 | 181 | /**
k2c_pooling_layers.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <string.h>
#include "k2c_include.h"
/**
* Global max pooling.
* works for 1D, 2D, or 3D inputs.
*
* :param output: output tensor.
* :par... |
29065ed0dd3c6073fdcb9a8f3d5478f11a2e8227c82c30ff12f15873b6431b9e | C | 6,321 | 144 | #include "cs.h"
/* breadth-first search for coarse decomposition (C0,C1,R1 or R0,R3,C3) */
static csi cs_bfs (const cs *A, csi n, csi *wi, csi *wj, csi *queue,
const csi *imatch, const csi *jmatch, csi mark)
{
csi *Ap, *Ai, head = 0, tail = 0, j, i, p, j2 ;
cs *C ;
for (j = 0 ; j < n ; j++) /*... |
620b3bc029b26542262f34d4e512ec002ad3e498135a7775363333e3976ae7d0 | C | 6,322 | 331 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <zlib.h>
#include "nuc.h"
#include "seq.h"
#include "util.h"
#include "memutil.h"
#include "err.h"
/**
* Expands the current sequence buffer, by doubling it's size
*/
void seq_expand(Seq *seq) {
seq->buf_sz = seq->buf_sz * 2;... |
09efdc8a95a1222cb89ff1f9744b8fa71fa10a8da0da3fc1aca212809f756509 | C | 6,399 | 240 | /*
* Copyright (C) 2010, Stefan Klanke
* F.C. Donders Centre for Cognitive Neuroimaging, Radboud University Nijmegen,
* Kapittelweg 29, 6525 EN Nijmegen, The Netherlands
*
*/
#include <buffer.h>
/* TODO: see if these can be optimized using compiler intrinsics etc. */
void ft_swap16(unsigned int numel, void *data... |
a97ebde31e9f6266283bdd77e2950445a6557a0d99c356cdb9144a2629aaf0f1 | C | 6,513 | 259 | #include <Python.h>
#include "pftypes.h"
#include "util.h"
#include <stdio.h>
//#include <libc.h> // for random and srandom, but on linux srandom is in stdlib.h
#include <stdlib.h>
#include "pmatrices.h"
void checkpoint(char *location)
{
FILE *dfile;
if ((dfile = fopen("debugFile", "a+")) == NULL) {
... |
814c0601d0111ed83943909f30b466cef269c12d0647af8fcd78fb652a18cecb | C | 6,557 | 223 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
06e43ac3fe2fe4ffbd6dedbff1dd0cfc0b5d6744b052d6198374566c7a1b7f03 | C | 6,633 | 249 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
e5f5b70d8f3929bd0bd1b551ab275b56995c5d73b2be5274fb6dbba62dec913a | C | 6,781 | 287 | /**
k2c_activations.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <stdio.h>
#include "k2c_include.h"
/**
* Linear activation function.
* y=x
*
* :param x: array of input values. Gets overwritten by output... |
2a5a412b7e3ae916a879d13b08fd571e588a1013965ac324644b2827dbaeb8c8 | C | 6,817 | 287 | /**
k2c_activations.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <stdio.h>
#include "k2c_include.h"
/**
* Linear activation function.
* y=x
*
* :param x: array of input values. Gets overwritten by output... |
930efb862e78bb26d18e06b2e323b3feb8b2219aee95c3820f35e0f689c0caf4 | C | 6,911 | 256 | # include <stdio.h>
# include <stdlib.h>
# include <malloc.h>
# include <time.h>
# include <math.h>
# include "ElectroMConst.h"
# include "FunAsser_ElePore.h"
void Cal_fi_Integ_SOR(double a, double E, double se, double si, double Cm, double Vm[Nthe + 1], double Vm_pr[Nthe + 1], double g1, double Vrest,
double ... |
ad08beca4becd30606fc35029437260c4e974f71a1db1d3a0d80d45276b3f182 | C | 6,911 | 261 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
0ecf5cecb56fce5d7557354e1efb8b0ee606f9eca8dedbf8f3ed2893fdf9481f | C | 7,110 | 198 | #include <mex.h>
#include <string.h>
#include <stdint.h>
/*
* [Values,Timestamps] = load_xdf_innerloop(Data, NumChannels, FormatString, SamplingInterval, LastTimestamp);
* MEX kernel that implements the inner loop of the load_xdf function.
*
* In:
* Data : byte array that contains the data of the chunk
*
* ... |
0593d2b3d5f7818282177574e9d04fa9ee2ea4e930922194390a95b6650f3483 | C | 7,528 | 311 | #include <stdio.h>
#include <math.h>
#include <stdarg.h>
#include <string.h>
#define K2C_MAX_NDIM 5
struct k2c_tensor
{
float *array;
size_t ndim;
size_t numel;
size_t shape[K2C_MAX_NDIM];
};
typedef struct k2c_tensor k2c_tensor;
void model(k2c_tensor A, k2c_tensor B, int reset_states) {
static float ls... |
78c05a409bba2132974abff1181c2e56902e1ef1b16c48213b62051501bc9e82 | C | 7,539 | 294 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
a650e540d84049e64a21648b0698e15257a8434de3f6c9ead6484008e6e7b905 | C | 7,584 | 327 | /* Created by Language version: 7.7.0 */
/* NOT VECTORIZED */
#define NRN_VECTORIZED 0
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#end... |
9c502945e96836bc79d2031d7d4aa937ba00ff1b857f0ab179721b2035bdde7b | C | 7,605 | 261 | #include "Rcplex2.h"
void setparams(CPXENVptr env, SEXP control, int isQP, int isMIP) {
int i, status, value;
const char *cur_parm;
SEXP names;
/* get list names */
PROTECT(names = getAttrib(control, R_NamesSymbol));
status = 1; /* avoid warning */
/* for each element in 'control' try to set the cor... |
67d0d58c87ab9cc3d29e6a802b76012c06bc84d382607f53db18ab5f473f3af0 | C | 7,629 | 286 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
ac1c6a66df650b938f879920f91bd0bb73c480a719e76ebc8eae287bc43d3e48 | C | 7,662 | 312 | /****************************************************************************
* Copyright (C) 2014 by Taylor Arnold, Veeranjaneyulu Sadhanala, *
* Ryan Tibshirani *
* *
* This ... |
f7cc3a8af6613f3ca10cdc47452ccb9558bb4a0bd42051f813a710b569321951 | C | 7,669 | 324 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
61b4388968b9b3874308402d85e98ed60cfdb3e804e64945143d7fc2cda48ed1 | C | 7,841 | 239 | /*
* Copyright (c) 2011 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
dae052bb6f394dad13373e888a633fb5e1fc1373d7a83028020300145d861adc | C | 7,853 | 376 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
aff818c833b7e4edfa69845d4e87b7969b7aff357fd36451df7d6560fea86623 | C | 7,912 | 314 |
#include <zlib.h>
#include <stdlib.h>
#include <getopt.h>
#include <string.h>
#include <hdf5.h>
#include <stdint.h>
#include "seq.h"
#include "util.h"
#include "memutil.h"
#include "chrom.h"
/*
* These values control size of chunks that are used for
* data transfer and compression. Changing them
* affects effc... |
53a8b4f871af36a463c720416553ea7f144a54d3afe58b9e7680d823d346276e | C | 8,029 | 390 | // Where did I steal this from? Yang I think. With lots of changes...
// And there is some code that I modified from Dave Swofford, below.
// Not GPL'd
#include "pftypes.h"
#include "pcomplex.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h> // for malloc and free
#include "pmatrices.h"
#include "util.h"
... |
71aca1332988eeb732831064793c53a12fb981efcf9e3a9b18a287f43625af3f | C | 8,326 | 289 | /* Performs fast detrended fluctuation analysis on a nonstationary input signal.
Useage:
Inputs
x - input signal: must be a row vector
Optional inputs:
intervals - List of sample interval widths at each scale
(If not specified, then a binary subdivision is constructed)
O... |
905237e639a1c216118502731bd9e897fe15d35c28ee0c668ff00ed2b3833ec3 | C | 8,362 | 287 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
b73dc2c20a2324bf0ffe93c29414bf67c35217af59e93a2bce6254ce794f793e | C | 8,372 | 281 | #include "Rcplex2.h"
void setparams(CPXENVptr env, SEXP control, int isQP, int isMIP) {
int i, status, value;
const char *cur_parm;
SEXP names;
/* get list names */
PROTECT(names = getAttrib(control, R_NamesSymbol));
status = 1; /* avoid warning */
/* for each element in 'control' try to set the cor... |
dc83b6db5758437b67fae119c4dd6a3dc7324d50b2f6f0278a5b9c1ac3060168 | C | 8,703 | 323 | /****************************************************************************
* Copyright (C) 2014 by Taylor Arnold, Veeranjaneyulu Sadhanala, *
* Ryan Tibshirani *
* *
* This ... |
303598bd026379d21229d417105218dc2f76f9e7db90d89617fec3faba4f7999 | C | 8,951 | 306 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
82e588e97320f96e1978f58ac1a67bc90cacc7d95dc38136658e6d749f20f85b | C | 9,136 | 366 | /*
Copyright (c) 2015, Rafat Hussain
*/
/*
This code is a C translation ( with some modifications) of Wavelet Software provided by
C. Torrence and G. Compo, and is available at URL: http://atoc.colorado.edu/research/wavelets/''.
*/
#include "cwt.h"
/*
static double factorial3(int N)
{
double factorial = 1;
for (i... |
832098a250493455c1dbf58055b126ead04f00dad5fd54e646c2b2ddffd360ec | C | 9,335 | 376 | /*
* Copyright (c) 2017 rxi
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to
* deal in the Software without restriction, including without limitation the
* rights to use, copy, modify, merge, publish, distri... |
ccff85790caf900211f8633030a459f5e3b105f8a63afe733386ea92724adca6 | C | 9,664 | 327 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
13fbb938219892d28590998c469a4bbbb681fc5d6f70943d099f6412229b6d55 | C | 9,857 | 299 | /*
* Copyright (c) 2011 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
4d2b398119e68f912208e128bf3e2845ee6d8f5982be3f24975fb6af17a67ad8 | C | 9,981 | 350 | /**
k2c_helper_functions.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "k2c_include.h"
/**
* Just your basic 1d matrix multipication.
* computes C = A... |
22d638773a0a64272fe4a9181a6a0d69fe6bdadd2dfe1b578fa9fcab0fd6073a | C | 10,130 | 419 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
b18ff70e173f50b2b6ae69f70780279b5a83018a1b85658529917a2b66e3b8a7 | C | 10,317 | 379 | #include <stdint.h>
#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <err.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include <time.h>
#include <unistd.h>
#include <stdbool.h>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
#define MAX(X, ... |
b0bdbb8a52f599de592f53efdedaa33b74107082020c316116d937b9326b0b29 | C | 10,597 | 377 | // The actual solving procedure is called using the function Rcplex
#include "Rcplex2.h"
int max_numcalls;
SEXP Rcplex2(SEXP numcols_p,
SEXP numrows_p,
SEXP objsen_p,
SEXP cvec,
SEXP bvec,
SEXP Amat,
SEXP Qmat,
SEXP lb_p,
SEXP ub_p,
SEXP Rsense,
SEXP Rvtype,... |
b7a0e98ecb2010e6f4f2fb3d469fb7a47ef43c4f90f47c8dd7c419919ce75c2c | C | 10,638 | 390 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
c4a4930bf9a2370e4ec55630729a23948ffe5ef0d8c373e278255e763abe57ea | C | 10,640 | 375 | // The actual solving procedure is called using the function Rcplex
#include "Rcplex2.h"
int max_numcalls;
SEXP Rcplex2(SEXP numcols_p,
SEXP numrows_p,
SEXP objsen_p,
SEXP cvec,
SEXP bvec,
SEXP Amat,
SEXP Qmat,
SEXP lb_p,
SEXP ub_p,
SEXP Rsense,
SEXP Rvtype... |
b7e2601dea499438cc82c75d8129a0f73238c629d0613b0b9db8d77ac3be2623 | C | 10,681 | 425 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
ae2fc3b5ca358ab93ef72da594ea1d42500d97ef8b5b40265496bd9b24aea3a1 | C | 10,850 | 404 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
8d38481a59bd3e249d6231fdade3ee669407d8fb3c9ea919efdc49c87a7f79bf | C | 11,405 | 366 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
cdad03ae3b73d5aba84e3fb11c873a264e0e8431108a8d2c262b2ac850aa6b8b | C | 11,772 | 291 | #include <stdio.h>
#include <math.h>
#include "util.h"
#include "gamma.h"
// PGF got these functions from John Huelsenbeck, who I believe got them from Ziheng Yang. They are GPL'd in MrBayes.
#define POINTGAMMA(prob,alpha,beta) PointChi2(prob,2.0*(alpha))/(2.0*(beta))
/*-------------------------------------------... |
4b8f6448d90c4baed39b36d7be8b9d9b252e7d672d3bd005681f63618196b230 | C | 11,813 | 338 | #include <string.h>
#include <unistd.h>
#include <stdlib.h>
#include <stdio.h>
#include <sys/stat.h>
#include <errno.h>
#include "bgzf.h"
#include "tabix.h"
#include "knetfile.h"
#define PACKAGE_VERSION "0.2.5 (r1005)"
#define error(...) { fprintf(stderr,__VA_ARGS__); return -1; }
int reheader_file(const char *heade... |
53e584069b9e349dcde0b7830e23ebc8ddf1aa314209024b810469cc73e7582c | C | 11,820 | 408 | /*-
* The MIT License
*
* Copyright (c) 2011 Seoul National University.
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the right... |
2e848710d3144220e6fc3b0955684881bf0a390900f42a2092168b04b1509f3f | C | 11,843 | 482 | /*
* Copyright (C) 2008, Robert Oostenveld & Christian Hesse
* F.C. Donders Centre for Cognitive Neuroimaging, Radboud University Nijmegen,
* Kapittelweg 29, 6525 EN Nijmegen, The Netherlands
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* for strerror */
#include "buffer.h"
#include <pt... |
b7b3860ac56f5eb88d169e1724764edc61e0fe90f1749e7dc1cf97ae090fa0a7 | C | 12,114 | 510 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
3af8f8aa1b96852316763250149b4580de16efeaa4ead8eff3d8e37fcf2ab4ab | C | 13,479 | 557 | /* Created by Language version: 7.7.0 */
/* NOT VECTORIZED */
#define NRN_VECTORIZED 0
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#end... |
490dc5ca3ce1603ab0996a78bd4e903c9d87985604a942a44ae14722bbcc19ad | C | 13,569 | 516 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
e0a44f53a90ac1956c187d31a7aee831d40ec87cb864d5e79e1c82172f1fc84f | C | 14,038 | 192 | #include <math.h>
#include <string.h>
#include "./include/k2c_include.h"
#include "./include/k2c_tensor_include.h"
void foobar(k2c_tensor* keras_tensor_8_input, k2c_tensor* keras_tensor_9_output) {
float lstm_fwork[80] = {0};
int lstm_go_backwards = 0;
int lstm_return_sequences = 0;
float lstm_state[20] = ... |
df0e67fac5233382aea984713a118180c7e393e8938e13d3ca23d633f7871357 | C | 14,060 | 329 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
0841a0243ec17298fbedd46e92fd0a29e5f259ae04728eb051284f240afc186b | C | 14,197 | 474 | /*
* Copyright (C) 2010, Stefan Klanke
* F.C. Donders Centre for Cognitive Neuroimaging, Radboud University Nijmegen,
* Kapittelweg 29, 6525 EN Nijmegen, The Netherlands
*/
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <fcntl.h>
#include <errno.h>
#include <socketserver.h>
/*******************... |
570fed64429c0e8d9215371ff9f3f2ee8851f6a05604e924924b6fa7a3c93fba | C | 14,320 | 573 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
32d1ee2e277c4e0373cc8074fb313f913a144661d2395ade51e277f7b151d259 | C | 14,957 | 608 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
c802eaf10d5969b14b0478e4027d01c5581cdb61a6f5fd6a576c91107550d219 | C | 15,190 | 402 | /**
k2c_recurrent_layers.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <stdio.h>
#include "k2c_include.h"
/**
* Cell for the LSTM layer.
* "units" is the dimension of the output space
*
* :param state: array... |
24e198bb058b499d8afb6d8c1c9077ceec80c3356cb149e67a6c7ad277aece2a | C | 15,497 | 543 | #include "pftypes.h"
#include <Python.h>
#include <numpy/arrayobject.h>
#include "p4_model.h"
#include "pmatrices.h"
#include "eig.h"
#include "proteinModels.h"
#include "defines.h"
#include "util.h"
p4_model *p4_newModel(int nParts, int doRelRates, int relRatesAreFree, int nFreePrams, int isHet, int *rMatrixNormaliz... |
65666980cf932089354b564cd23e1f4c08470a7dbcf7a703532fe88f9acb46ab | C | 15,634 | 333 | #include <stdio.h> // for printf
#include <stdlib.h> // for exit
#include "defines.h" // for N_LIKE
void logDetFillFxy(int *nUnambig, int *nAmbig, int *nDoubleGap, char *seq, int sNum1, int sNum2, int *refUnambigCountMatrix, int *refAmbigCountMatrix, int *allSymbolNums, int nTax, int nChar, int dim, int bigDim, doubl... |
52184491a10b2838ad14c38873ade7f60a89760da80248fb1ab5f1b7080f710d | C | 16,183 | 599 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
d086c3a6e472a25dc58b0cbf568658ecb5a62a7eed1037aa16785aed91a48e43 | C | 16,467 | 364 | #include "cs.h"
/* clear w */
static csi cs_wclear (csi mark, csi lemax, csi *w, csi n)
{
csi k ;
if (mark < 2 || (mark + lemax < 0))
{
for (k = 0 ; k < n ; k++) if (w [k] != 0) w [k] = 1 ;
mark = 2 ;
}
return (mark) ; /* at this point, w [0..n-1] < mark holds */
}
/* keep off-d... |
e3c983652015d566855364afb23690deff607703d58f559056088411386d0880 | C | 16,471 | 644 | // PGF got this from Dave Swofford. Thanks, Dave! It is not GPL'd,
// but it is gopyright by Dave. It is ok with Dave if it is used, as
// long as acknowledgement to Dave is given.
/* gamma.c
|
| This file contains miscellaneous routines related to statistical distributions including gamma
| and beta functions.
|
|... |
3471b34ed05aac03c6774c2bccb0287821a2fb4e9210245fea1dd9bb11e06114 | C | 16,884 | 434 | /**
k2c_convolution_layers.c
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under MIT License
https://github.com/f0uriest/keras2c
*/
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "k2c_include.h"
/**
* 1D (temporal) Padding.
*
* :param output: tensor to store padded output d... |
cdcd9e17263b4e246d9014138ec8cdab2bdcfe17dbbe1e4a8d84cb3b4ba3eb44 | C | 17,067 | 555 | /* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
2011 Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to dea... |
efcf24f4b8a70b472951c4d94bb943ef02bd936acf262f92efe37851bb62c8ba | C | 17,333 | 598 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
dcbef4f0077ecda6c6d1ea1a373abd92633209048bb820424eb1e5f78baf1778 | C | 18,281 | 632 | /* The MIT License
Copyright (c) 2008 Genome Research Ltd (GRL).
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use... |
7996ff069b6a711eab1c65c408065ac6253a57cec9b6e7ce0e350477403edf16 | C | 18,422 | 750 | /* Created by Language version: 7.7.0 */
/* NOT VECTORIZED */
#define NRN_VECTORIZED 0
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#end... |
0a47eaacb38e91de0ab273f91f60827981a647a5ebb8458f6d1c1547e6eae13d | C | 18,488 | 681 |
#include <zlib.h>
#include <string.h>
#include <math.h>
#include <stdio.h>
#include "util.h"
#include "vcf.h"
#include "memutil.h"
#define VCF_GTYPE_MISSING -1
const char *vcf_fix_headers[] =
{"#CHROM", "POS", "ID", "REF", "ALT", "QUAL",
"FILTER", "INFO", "FORMAT"};
/**
* Allocates memory for VCFInfo str... |
778d91df195cd4fa7c97cdbc03855a473b4fc6190eed6fd1c98003277a1ff464 | C | 18,576 | 278 | /*
Feeding experimentation device 3 (FED3)
Classic FED3 script
This script mimics the classic FED3 menuing system for selecting among the following programs
// FEDmodes:
// 0 Free feeding
// 1 FR1
// 2 FR3
// 3 FR5
// 4 Progressive Ratio
// 5 Extinction
// 6 Light tracking FR1 task
... |
f9084d0ca4b52df0fff4aaba7dbf1e2f4e303036ad959a2ae301545be2ca8d18 | C | 18,663 | 834 | // Copyright [1999-2017] EMBL-European Bioinformatics 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 required b... |
c479b15ff84bba988b8d64126d10234da795f31872023bc5fabed066a4e23931 | C | 19,085 | 651 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
d8e8ecb4d428ef7e423cb0c18ff9540c73cd1e51781e7dbb95a53146c4b6fb90 | C | 19,154 | 831 | /* PGF got this code from Dave L Swofford. Thanks Dave! He got it
from a book, and re-coded the fortran into c. This is not GPL'd; I
assume it is copyrighted by DLS. PGF added the newBrent() and
freeBrent() functions. And a little more tweaking.
It is OK with Dave that this code be used as long as ack... |
418a88b0ed7cfb23dc3042ea38b252228ccdc1d6b140a47b45127478b869d91f | C | 19,787 | 505 | #include "pftypes.h"
#include "eig.h"
#include <stdlib.h>
#include "pmatrices.h"
#include "pcomplex.h"
#include "linalg.h"
#include <stdio.h>
#include "util.h"
#include <math.h>
eig *allocEig(int theDim, double **theMat)
{
eig *anEig;
anEig = malloc(sizeof(eig));
anEig->complexEig = 0;
anEig->d... |
0c1a10d60c06e9ba5116bcec83e459163d4aa1ac802bacc34cd7340683d0ed7e | C | 20,417 | 725 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
e3a4ac3b32428f2f6cc16c5fa3a6df033983d89cd54a778d9405c3b82b618736 | C | 20,623 | 689 | /*
* Copyright (c) 2011 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
d33983a0246cfab80d659973e7aa649907f6de76ed3b38755005fff45206ac15 | C | 21,523 | 582 | /****************************************************************************
* Copyright (C) 2014 by Taylor Arnold, Veeranjaneyulu Sadhanala, *
* Ryan Tibshirani *
* *
* This ... |
dd4a3edea5120f502f9cd6408767f5064395961c899fd4cae7d5f7372ecf9885 | C | 22,513 | 322 | #include <stdio.h>
#include <math.h>
#include <time.h>
#include "./include/k2c_include.h"
#include "foobar.h"
float maxabs(k2c_tensor *tensor1, k2c_tensor *tensor2);
struct timeval GetTimeStamp();
float test1_keras_tensor_8_input_array[80] = {
+1.97848223e+00f,+4.39731327e-01f,-8.02321627e-01f,-1.94995153e+00f... |
ab5e57e0471f75e60c69a3597ba7c2c561aa5adb0f9011cfd9523fc25b9d3202 | C | 23,384 | 1,161 |
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <ctype.h>
#include <zlib.h>
#include <stdarg.h>
#include <stdio.h>
#include <errno.h>
#include "memutil.h"
#include "util.h"
#include "err.h"
/**
* Returns TRUE if the provided filename ends with ".gz", returns
* FALSE other... |
8e5ee35362ee4a3f44902acbec5fa1667695ee4c78b9828237cd6ce0273dbb62 | C | 23,961 | 735 | /*
* Copyright (C) 2008, Robert Oostenveld
* F.C. Donders Centre for Cognitive Neuroimaging, Radboud University Nijmegen,
* Kapittelweg 29, 6525 EN Nijmegen, The Netherlands
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "buffer.h"
#include <pthread.h>
#if defined TARGET_OS_Linux || def... |
36c338a1162e90d2fde45eef9d675208f485e5bc344e048cf8396a90808c4bc7 | C | 24,607 | 886 | # include <stdio.h>
# include <stdlib.h>
# include <malloc.h>
# include <time.h>
# include <math.h>
# include "ElectroMConst.h"
# include "FunAsser_ElePore.h"
void main()
{
clock_t start = clock(), finish;
FILE *fp, *fp1, *fp2, *fp3;
double fi_i[Nr_i + 1][Nthe + 1], fi_o[Nr_o + 1][Nthe + 1] = { 0 }, fi_i_... |
4a60cb3f90e99aead9c9555028dbb0a76dfdbd95fb82a8a096b28dc2d74e5492 | C | 24,760 | 676 | #include "pftypes.h"
#include "p4_tree.h"
#include "defines.h"
#include "p4_treeCopyVerify.h"
#include "p4_node.h"
void p4_copyCondLikes(p4_tree *treeA, p4_tree *treeB, int doAll)
{
int i, j;
p4_node *nA, *nB;
for(j = 0; j < treeA->nNodes; j++) {
i = treeA->preOrder[j];
if(i != NO_ORDER)... |
e73c0a7562225cb36eeca4a9d849cb445a932a8cb4bf948eb11135cfcfc81e57 | C | 26,227 | 685 | /*
* Copyright (c) 2012 The WebRTC project authors. All Rights Reserved.
*
* Use of this source code is governed by a BSD-style license
* that can be found in the LICENSE file in the root of the source
* tree. An additional intellectual property rights grant can be found
* in the file PATENTS. All contribut... |
aa07b15a5a9b557a6e5d4abb46b33a2fccf6859e410a355cd4b1baf5954add42 | C | 26,641 | 967 | #include <ctype.h>
#include <assert.h>
#include <sys/stat.h>
#include "khash.h"
#include "ksort.h"
#include "kstring.h"
#include "bam_endian.h"
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif
#include "tabix.h"
#define TAD_MIN_CHUNK_GAP 32768
// 1<<14 is the size of minimum bin.
#define TAD_LIDX_SHIFT 14
typedef... |
e317308100ca65e41c1d9ad411be056f099aa5553d4d9f1148a557f309b60c8b | C | 27,396 | 624 | #include "pftypes.h"
#include "p4_tree.h"
#include "p4_node.h"
#include "pmatrices.h"
#include "defines.h"
#include "util.h"
//static int getFirstLike;
//static int newtCount;
void p4_newtSetup(p4_tree *aTree)
{
int nNum, i, j;
p4_node *aNode;
// malloc cl2, if needed.
if(!aTree->root->cl2) {
... |
7e384280eb72c99e14dbebcdbebc2fd1e3f3c27f8081ce964f12881d5955398d | C | 28,680 | 1,001 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
... |
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