sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
c9cbafe3bab10b7b3f3f690b6c28fd8ac7c70923b12bc0e2742351e38e68ab77 | C | 1,802 | 41 | bool TriangleTriangleIntersection(double *P1,double *P2,double *P3,double *O1,double *O2,double *O3, bool ignore_corners)
{
int i=0;
double A[3],B[3],C[3], E1[3], E2[3];
double inter_xyz[3];
bool check;
check=(mind(mind(P1[0],P2[0]),P3[0])>maxd(maxd(O1[0],O2[0]),O3[0]))||(mind(mind(P1[1],P2[1]),P3[... |
6abbf8ae68057aa07594247dfb9111bd2501c62d491fa91e7e072079b06b07ed | C | 1,823 | 69 | /*
* CORE_leadingedges.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_leadingedges.c
*
* samar@cs.stanford.edu, 01/20/06
*/
#include "matrix.h"
#include "mex.h"
#include... |
8163c6495f6ba6a47e05dc2d005f211e43f23306d4ce81732ff749c79c5e4e58 | C | 1,848 | 53 | /*
* FILE: CORE_mextools.c
* --------------------
* Common MEX utilities for Matlab CORE_function_ MEX files.
* Function descriptions can be found in CORE_mextools.h
*
* samar@cs.stanford.edu, 09/18/05
*/
#include "CORE_mextools.h"
// ------------------------------------------------------------------------
... |
6018237b3fb43fa32f93746d8b6f3eb6ac167f875e6e3b60c3897235329f10e4 | C | 1,866 | 55 | /*
* CORE_mindist.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
* COREmex CORE_mindist.c
*
* samar@cs.stanford.edu, 09/12/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_library... |
f392566a71f33eb593b168e72559998d19c131b3cf9f7ddff5887f187a58ad31 | C | 1,881 | 111 | #include "utils.h"
/*
* given log(a) and log(b), return log(a + b)
*
*/
double log_sum(double log_a, double log_b)
{
double v;
if (log_a < log_b)
{
v = log_b+log(1 + exp(log_a-log_b));
}
else
{
v = log_a+log(1 + exp(log_b-log_a));
}
return(v);
}
/**
* Proc to calculate the value o... |
7cbc2a1961cc69730ae1d408e3066bf21726bd3c57dbe56a2389a0a234c5bfe5 | C | 1,885 | 54 | /***************************************************************************
FindInInterval.c
--------------------
begin : June 2008
copyright : (C) 2008 by Michaël Zugaro
email : michael.zugaro@college-de-franc... |
4da1decacedd1a9cba4fadedcc52b4d86eaa2000f1412f44dd5d9ce5cc35fc50 | C | 1,887 | 97 | /** @file betweenness_centrality_mex.c
* @copyright Stanford University, 2007-2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper for the topological order func
*/
/** History
* 2007-04-20: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef in... |
b52655b35a9d122d2fa4bb9e9f11df68fc9a5439fffb4963c420a94c9faa99ec | C | 1,907 | 64 | /***********************************************************************
* mexexpand.c : C mex file
*
* z = mexexpand(blk,x);
*
* Input: blk = [n1, n2, ..., nk]
*
* Output: [x1 x1...x1, x2 x2...x2, ...., xk xk...xk]'
* n1 n2 nk
*
* SDPT3: version 3.0
* Copyr... |
229b43ab4c9a12e9aaaa0a2129151111fb22a6e92eee992dba3890408bd8b1b6 | C | 1,930 | 60 | #define _GNU_SOURCE
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include "medaka_bamiter.h"
#include "medaka_counts.h"
#include "medaka_read_matrix.h"
// Demonstrates usage
int main(int argc, char *argv[]) {
if(argc < 3) {
fprintf(stderr, "Usage %s <... |
d29f40ee24a8afe73cf69977db1510e5e0296b1da7185e0d991b1c10ee0ab343 | C | 1,937 | 68 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu)
// This file is part of MMLDA-C.
// MMLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
// option) any... |
83c0f42e27b13cfa85d49c420db7e0c3e4f066d4fd5d2ec52f8410f94f2eebd4 | C | 1,944 | 77 | /*
* $Id: zstream.c 6417 2015-04-21 16:03:44Z guillaume $
* Guillaume Flandin
*/
/* mex -O CFLAGS='$CFLAGS -std=c99' -largeArrayDims zstream.c */
/* setenv CFLAGS "`mkoctfile -p CFLAGS` -std=c99" */
/* mkoctfile --mex zstream.c */
/* miniz: http://code.google.com/p/miniz/ */
#define MINIZ_NO_STDIO
#define MINIZ_N... |
0abc74ef34f83eca02c92f2652c468ac5eefd786055a30956c37d907c52de88d | C | 1,947 | 68 | // (C) Copyright 2004, David M. Blei (blei [at] cs [dot] cmu [dot] edu)
// This file is part of LDA-C.
// LDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
... |
055f9ca1b4a849af1633b6ac3e86e9bf80b22a90c81772de15b78caf71b09179 | C | 1,964 | 68 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu), Xiuming Zhang
// This file is part of POLARLDA-C.
// POLARLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (a... |
2fbf176602da4745e2d7d866b0029d634fe37f311772e78a760f6020d7a5ffb6 | C | 1,978 | 54 | /***************************************************************************
MatchUpIndices.c - description
-------------------
copyright : (C) 2012 by Michaël Zugaro
email : mzugaro@andromeda.rutgers.edu
***********************... |
f9bc9d04c086391b4228f3e1a7e50de9a7473e79ca8181a9c1785dc94c4c7e83 | C | 1,999 | 63 | double nnz(double x)
{
if(absd(x)<1e-16) { return 1e-16; } else { return x; }
}
void LineLineIntersect(double *P1,double *P2,double *O1,double *O2,double *Val)
{
double inter_x, inter_y, SlopeA, SlopeB, t, disp, diso, OffsetA, OffsetB, temp;
int swap;
bool inter;
bool check;
check=(mind(P1... |
342808f0f3a630e8c9b0631e9bf038e8379779fdefa1e4aaa3d40419295dcc2e | C | 2,021 | 77 | /*
* $Id: zstream.c 6417 2015-04-21 16:03:44Z guillaume $
* Guillaume Flandin
*/
/* mex -O CFLAGS='$CFLAGS -std=c99' -largeArrayDims zstream.c */
/* setenv CFLAGS "`mkoctfile -p CFLAGS` -std=c99" */
/* mkoctfile --mex zstream.c */
/* miniz: http://code.google.com/p/miniz/ */
#define MINIZ_NO_STDIO
#de... |
04cc89afaf7ee4c2806f47456ad703bc70d8c6a0c52fb87a1db97ecd1f4f0c1a | C | 2,024 | 67 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu)
// This file is part of MMLDA-C.
// MMLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
// option) any... |
522948e716d985c80ac413eed4fe4c264acafd9fdf10836b47f097f51a9e050e | C | 2,034 | 67 | // (C) Copyright 2004, David M. Blei (blei [at] cs [dot] cmu [dot] edu)
// This file is part of LDA-C.
// LDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
... |
2d4968718aa5fa0654cfe2e6aec58f7051eb4a22fb14933bd5dd443617639846 | C | 2,058 | 53 | void SphereFrom4Points(double *PA, double *PB, double *PC, double *PD, double *Cx, double *Cy, double *Cz, double *L) {
double x1, x2, x3, x4;
double **a;
double m11, m12, m13, m14, m15;
int i;
a = malloc(4*sizeof(double *)); for (i=0;i<4;i++) { a[i] = malloc(4*sizeof(double)); }
x1=PA... |
3373f803c1464901c06861f37a701213dad139dc62d565648d9d379177b3ccfd | C | 2,069 | 55 | #include <lsl_c.h>
#include <stdio.h>
/**
* Example program that demonstrates how to resolve a specific stream on the lab network and how to
* connect to it in order to receive data.
*/
#define NCHANS 8
int main(int argc, char *argv[]) {
unsigned k, t; /* channel index */
lsl_streaminfo info; /* the streamin... |
ffffd7fcd6b19299e34cfd75f0432dd8a862ec1f5aa211ac85cdd1998bdeab37 | C | 2,096 | 55 |
#include <stdlib.h>
#include <stdbool.h>
#include <stdio.h>
/** Calculate which columns of an RNN output matrix should be considered
* variant.
*
* @param minor pileup minor indices (non-zero elements count insertion).
* @param reference reference sequence including gaps for insertion pileup
* columns.
* @param... |
1254a1ec6f6e7ea1acf3b4c13ac088a361da3ca86ed37850705c28b9bd63957d | C | 2,130 | 52 | /***************************************************************************
CountInIntervals.c
--------------------
begin : December 2009-2011
copyright : (C) 2009-2011 by Michaël Zugaro
email : michael.zugaro@... |
d3d9bf85be573640e987f70160ac50e493ad38a55bd7d82377e60d219a4a4b49 | C | 2,148 | 106 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "mex.h"
#ifdef MX_API_VER
#if MX_API_VER < 0x07030000
typedef int mwIndex;
#endif
#endif
void exit_with_help()
{
mexPrintf(
"Usage: libsvmwrite('filename', label_vector, instance_matrix);\n"
);
}
void libsvmwrite(const char *filename, const mxArr... |
6ee28d96db4cd77f4f7efcaedf51b27ee9eb907c61f66cb1096f14e5116f1cea | C | 2,209 | 65 | /***************************************************************************
copyright : (C) 2013 by Michaël Zugaro
email : michael.zugaro@college-de-france.fr
***************************************************************************/
/**********************************************... |
6ad6d576120bf9591a7955245211693ba5d98d5d8041e6b11446a85bb0d0ff8f | C | 2,251 | 87 | /*
* $Id: zstream.c 8044 2021-01-21 15:08:54Z guillaume $
* Guillaume Flandin
*/
/* mex -O CFLAGS='$CFLAGS -std=c99' -largeArrayDims zstream.c */
/* setenv CFLAGS "`mkoctfile -p CFLAGS` -std=c99" */
/* mkoctfile --mex zstream.c */
/* miniz: https://github.com/richgel999/miniz */
#define MINIZ_NO_STDIO
#define MIN... |
03d84ffb7af47d40f2fabfc52f2d80e5b848200a003e455cb722bbb3dddd036b | C | 2,286 | 115 | /*
* ==============================================================
* bfs_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 20 April 20020
* =============================================================
*/
/*
* 19 February 2007
* Updated to use Matlab 2006b sparse matrix interface
*
* 25... |
7b6e8df53f0cadb7ca5aec873e0ba087c9eb5026f85fc00cfc2073770753026e | C | 2,291 | 54 | #include <lsl_c.h>
#include <stdio.h>
#include <stdlib.h>
/**
* This example program offers an 8-channel stream, float-formatted, that resembles EEG data.
* The example demonstrates also how per-channel meta-data can be specified using the description field of the streaminfo object.
*
* Note that the app sends dat... |
932a1a17949a66988ea0174ed54d3681614b6fca448a484c6bb10127670688fe | C | 2,313 | 59 | #include <lsl_c.h>
#include <stdio.h>
int main(int argc, char* argv[]) {
int c; /* channel index */
lsl_xml_ptr desc,chns,chn,cap; /* some xml element pointers */
lsl_outlet outlet; /* stream outlet */
lsl_streaminfo info,inf; /* streaminfo objects */
lsl_inlet inlet; /* a stream inlet to get sample... |
fe08185c47878c983a07556a6d7fb38e5743530eb0ee60cf2d0e50260f6d3081 | C | 2,317 | 70 | // (C) Copyright 2018, Nanbo Sun (nanbosun@u.nus.edu), Xiuming Zhang
// This file is part of POLARLDA-C.
// POLARLDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (a... |
fa357004aef5ba024d647d8fcd7c4514ebc154aaf147a7bf374b5384fd66037c | C | 2,337 | 56 | #include <lsl_c.h>
#include <stdio.h>
#include <stdlib.h>
/**
* This example program offers an 8-channel stream, float-formatted, that resembles EEG data.
* The example demonstrates also how per-channel meta-data can be specified using the description
* field of the streaminfo object.
*
* Note that the app sends ... |
04f00e48af0899b7512d0eac9c85c37827cfb0fcc624aaffe8e32cf0ad279e7d | C | 2,342 | 58 | /* ************************************************************
MODULE sdmaux*.c -- Several low-level subroutines for the
mex-files in the Self-Dual-Minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)... |
1b26e5e132691661f042b6c693f864ae9421415d9aa5bdb7dd53b944c660dbdf | C | 2,364 | 60 | #include <lsl_c.h>
#include <stdio.h>
int main(int argc, char *argv[]) {
int c; /* channel index */
lsl_xml_ptr desc, chns, chn, cap; /* some xml element pointers */
lsl_outlet outlet; /* stream outlet */
lsl_streaminfo info, inf; /* streaminfo objects */
lsl_inlet inlet; /* a stream inlet to... |
c3140456cdd15233aac6da4cd59e98d56cc150f7c2e69b7a079fde87e1497e3d | C | 2,371 | 133 | /*
* ==============================================================
* components_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 21 April 20020
* =============================================================
*/
/*
* 19 February 2007
* Updated to use Matlab 2006b sparse matrix interface
... |
11dd0df8262cfa71b8e2e90844fe01fc2286cce706193362eb4d3eec43e7526b | C | 2,380 | 80 | // This file is part of Eigen, a lightweight C++ template library
// for linear algebra.
//
// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
//
// Eigen is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Softwar... |
5e54195a9f2d247e40d2d12369c70e8303cbd50f471c914024cabf86ba716a1e | C | 2,381 | 80 | #include "mex.h"
void revord(char *input_buf, int buflen, char *output_buf)
{
int i;
/* reverse the order of the input string */
for(i=0;i<buflen-1;i++)
*(output_buf+i) = *(input_buf+buflen-i-2);
}
void mexFunction( int nlhs, mxArray *plhs[],
int nrhs, const mxArray *prhs[]... |
477bfd6174b77780f52cca494ae1ad60e25af6696f1790f36c6788e3d5d56a2f | C | 2,412 | 63 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
8957b94a2db8218ab97848510c973453f56927478f0a5b64fc100698fc22d358 | C | 2,508 | 76 | /*
Copyright (c) 1994, 1996-1997, 2000, 2003 MEDICAL RESEARCH COUNCIL
All rights reserved
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1 Redistributions of source code must retain the above copyright notice,
this li... |
2968eb1287a44e9c627c6c6776aff9be2690b26b40e1ed7503f7374622f69fc2 | C | 2,546 | 84 | bool LineTriangleIntersection(double *A, double *B, double *C, double *P1, double *P2, bool ignore_corners, double *inter_xyz) {
bool intersect;
double T1[3], T2[3], N[3];
double l;
double Pline[3], Vline[3], P[3];
double P_2D[2], A_2D[2], B_2D[2], C_2D[2];
double mi[2], ma[2];
int i, j;
... |
14391303e8d85dce1bb103454705bdf909d2e7186fa50ad6a7795b23b178a2fe | C | 2,561 | 84 | /***************************************************************************
FindField.c - description
-------------------
begin : Wed May 22 2002
copyright : (C) 2002-2012 by Michaël Zugaro
email : mzugaro@and... |
5aecb330c22f37d67e5c451f62394f10db51f29eae4175b31f754540e539fb20 | C | 2,563 | 119 | /*
* David Gleich
* Copyright, Stanford Unviersity, 2007
*/
/**
* @file test_matching_mex.c
* Wrap a call to the libmbgl test_matching function.
*/
/*
* 8 July 2007
* Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#include... |
30d2e636c59a79b50e633a14037c5405960b25b36b3043b8f32326d4c6347059 | C | 2,614 | 75 | /*
* fast_kmeans_step.c - fast pairwise distance matrix
*
* Warning: this MEX file works, but is still being updated.
* Comments and documentation in particular are a little
* slim ...
*
* Syntax:
* [assigns,bestdists,clustersizes,centroids] =
* fast_kmeans(waves,centroids,normsqr... |
13ae64ddb226ffc5c4eafad9fcf09fe4b307a63cf8a320265360f50ad0fe8e32 | C | 2,617 | 94 | /** @file planar_drawing_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* Get extra sets of edges for a planar graph
*/
/** History
* 2008-10-05: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#include "m... |
668a549396b15d98539933f9320526f21a72a704d08ca0071181626f54625a95 | C | 2,623 | 128 | /*
* David Gleich
* Copyright, Stanford Unviersity, 2007
*/
/**
* @file dominator_tree_mex.c
* Wrap a call to the libmbgl shortest path functions.
*/
/*
* 12 July 2007
* Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#incl... |
5c11e1fc22e219cb986f6fa9e4ba939315227e84aef042737d38ec668b89b6d2 | C | 2,699 | 86 | /* compress.c -- compress a memory buffer
* Copyright (C) 1995-2005, 2014, 2016 Jean-loup Gailly, Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* @(#) $Id$ */
#define ZLIB_INTERNAL
#include "zlib.h"
/* ======================================================================... |
d768fb4458774cbf6e5da4d27f2bf3cc7afe179be069fe8a34965fe21b671bcb | C | 2,712 | 87 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
24adb9ec0fec520a67c3dcba4440b7766b73bc60f3f2e0d04b63687a6764c395 | C | 2,744 | 126 | // This library is free software; you can redistribute it and/or modify it
// under the terms of the GNU Library General Public License as published by
// the Free Software Foundation (either version 2 of the License or, at your
// option, any later version). This library is distributed in the hope that
// it will be ... |
9545285f1cb66559756a4eaa2fef8224d468c9e67c84598c126d43af79dc2f16 | C | 2,761 | 67 | /* ************************************************************
MODULE sdmaux*.c -- Several low-level subroutines for the
mex-files in the Self-Dual-Minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)... |
c1935020623bf49c06885bc23cd56274b39a9df9f9194ba26b2e6eefe0483724 | C | 2,766 | 75 | /* ************************************************************
MODULE sdmaux*.c -- Several low-level subroutines for the
mex-files in the Self-Dual-Minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)... |
87c5f6978bddbd55931de7545baec6eed218775bce95acbc6e358be0ad1a4f07 | C | 2,770 | 75 | /* ************************************************************
MODULE sdmaux*.c -- Several low-level subroutines for the
mex-files in the Self-Dual-Minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)... |
946aa814069c92876c9d34ab06f55eb261d96878379a2356285d5874138f63bc | C | 2,774 | 94 | /*
* CORE_pairdist.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_pairdist.c
*
* samar@cs.stanford.edu, 07/12/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_li... |
52e4f23a77a1a7d83caf1d1b905fc6330509ae338e0519b85a98953c5db36812 | C | 2,860 | 99 | /* hfile_net.c -- network backend for low-level input/output streams.
Copyright (C) 2013-2014 Genome Research Ltd.
Author: John Marshall <jm18@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to d... |
9d568d6bf79050d445ec7d43cb9d7ee3d34addcf6e0648da6d0e6323c2498d8f | C | 2,903 | 81 | #include "xorshift128plus.h"
uint64_t xorshift128plus(xorshift128plus_key_t * key) {
uint64_t s1 = key->part1;
const uint64_t s0 = key->part2;
key->part1 = s0;
s1 ^= s1 << 23; // a
key->part2 = s1 ^ s0 ^ (s1 >> 18) ^ (s0 >> 5); // b, c
return key->part2 + s0;
}
void xorshift128plus_jump(xorsh... |
e0630276f7af9d4b18505ad4c14654e4115ee2aa317e271a65e850613bbb9723 | C | 2,905 | 91 | #include <errno.h>
#include <string.h>
#include "medaka_bamiter.h"
#include "medaka_common.h"
// iterator for reading bam
int read_bam(void *data, bam1_t *b) {
mplp_data *aux = (mplp_data*) data;
uint8_t *tag;
bool check_tag = (strcmp(aux->tag_name, "") != 0);
bool have_rg = (aux->read_group != NULL);... |
69ea1f9ff62317b752a6e63c96cff702bc34f082708a7bcd8c767bc2c73b70e5 | C | 2,923 | 122 | /*
* ==============================================================
* path_from_pred.c A mex interface to the matlab bgl function
* to convert a predecessor array into a path
*
* David Gleich
* 17 April 2007
* =============================================================
*/
/*
* History
*
* 17 April 2007
*... |
31922aa982ee12fd28d1ce5fe6a94a3f07c2a941c821b566a881ca21845cdfaf | C | 2,966 | 93 | /* uncompr.c -- decompress a memory buffer
* Copyright (C) 1995-2003, 2010, 2014, 2016 Jean-loup Gailly, Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* @(#) $Id$ */
#define ZLIB_INTERNAL
#include "zlib.h"
/* ===============================================================... |
409031c31ef180d694ea5e98e893ae0e23006014779e9b36f18957851d4244b8 | C | 3,209 | 88 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
2a3b609533ce37b658817b9a1d21ac8f0f8012c1c14bbd5520f925d3003e84d6 | C | 3,398 | 109 | /** @file fruchterman_reingold_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2008-09-26: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#in... |
c4c5e9a86bad061e8b7f98f2a2e857f098b8ac4f200ebe0dadf1b07c7524f779 | C | 3,471 | 111 | #include "mex.h"
/*
Differences with built-in findstr:
- allows to search only the n first occurences of a pattern
- allows to search only in a substring (given an index of the beginning)
MATLAB hack:
- doesn't use mxGetString to prevent a copy of the string.
- assumes MATLAB stores strings as unsign... |
ca0b79a57cbe8a93fe4f00d8d2ca43043d090b62b8d2f4976650b8dbf2d4996c | C | 3,471 | 96 | /*
y = mJdetd(detd,K)
yields length(y)=sum(K.q) vector with y[k] = -detd(k)*J,
where J = [1, 0'; 0, -I].
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept.... |
37a54bc453a7aea80e0e409db004804c4fdd59bc8d42ce99df7ed7974f2d0e27 | C | 3,546 | 110 | #include "mex.h"
/*
* $Id: xml_findstr.c 6480 2015-06-13 01:08:30Z guillaume $
* Guillaume Flandin <guillaume@artefact.tk>
*/
/*
Differences with built-in findstr:
- allows to search only the n first occurences of a pattern
- allows to search only in a substring (given an index of the beginning... |
3ee1774bda0c8cb2994d2aebb5172c2ab16dabcbc242e687f1ff362d8b992952 | C | 3,550 | 176 | #include <stdlib.h>
#include <string.h>
#include "../linear.h"
#include "mex.h"
#ifdef MX_API_VER
#if MX_API_VER < 0x07030000
typedef int mwIndex;
#endif
#endif
#define Malloc(type,n) (type *)malloc((n)*sizeof(type))
#define NUM_OF_RETURN_FIELD 6
static const char *field_names[] = {
"Parameters",
"nr_class",
"n... |
5f816f9b229afd49308413264200760195c2014212c1cde850d0273ec2d12acb | C | 3,648 | 108 | /** @file planar_test_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2008-10-01: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#include "ma... |
6d79bc62ee91ce486aa3833ff6f677587abb65d62a6dea1a2303679b872f5494 | C | 3,656 | 110 | #include "mex.h"
/*
* $Id: xml_findstr.c 6480 2015-06-13 01:08:30Z guillaume $
* Guillaume Flandin <guillaume@artefact.tk>
*/
/*
Differences with built-in findstr:
- allows to search only the n first occurences of a pattern
- allows to search only in a substring (given an index of the... |
a2ad6d8a69fc5231f7b7636c031d87b607b6ceb513610b2e029e5f6c7f48cea9 | C | 3,679 | 153 | /** @file core_numbers_mex.c
* @copyright Stanford University, 2007-2008
* @author David F. Gleich
* Wrap a call to the libmbgl core_numbers function.
*/
/** History
* 2007-07-08: Initial version
* 2007-07-11: Updated for weighted cores
* 2007-07-30: Added option for removal times
*/
#include "mex.h"
#if ... |
c8ccad2a69126ae6cfdcc7db866d52e66e3ebdab51b3cf4651c0cf51d92b7bea | C | 3,718 | 174 | /*
* ==============================================================
* bfs_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 20 April 2006
* =============================================================
*/
/*
* 19 February 2007
* Updated to use Matlab 2006b sparse matrix interface
*
* 1 ... |
fe3c1d877a7d914cec63aea4d8aa48135c4a650e809f09c548d86be04099caa5 | C | 3,754 | 155 | /** @file betweenness_centrality_mex.c
* @copyright Stanford University, 2006-2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2006-04-23: Initial version
* 2007-02-19: Updated to Matlab 2006b sparse matrix interface
* 2007-02-22: Added edge centrality output
* ... |
52ff5004d1dd3140f7b731bcc6b974cfe3f72aca0956ddd2d2b63dbe40697fab | C | 3,789 | 149 | /** @file clustering_coefficients_mex.c
* @copyright Stanford University, 2006-2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2006-04-23: Initial version
* 2007-02-19: Updated to Matlab 2006b sparse matrix interface
* 2007-07-11: Update for weighted and directe... |
55166ee8e392e685d77a8320e4357fb59627f01abf0becc3c393163f81c2a164 | C | 3,810 | 134 | #include "mex.h"
#include "lfev.h"
void lfmxdata(lfdata *lfd, const mxArray *data)
{ const mxArray *tmp;
double *x, *sc, *xl;
int n, d, i, k;
char c, ststr[16];
n = lfd->n = mxGetM(mxGetField(data,0,"x"));
d = lfd->d = mxGetN(mxGetField(data,0,"x"));
x = mxGetPr(mxGetField(data,0,"x"));
for (i=0; i<d;... |
b74f8655adb70fc6bd3843556b6258ab81bf7b4714f0596699b6923b1e065a25 | C | 3,856 | 154 | /*
* David Gleich
* Copyright, Stanford Unviersity, 2007
*/
/**
* @file matching_mex.c
* Wrap a call to the libmbgl matching function.
*/
/*
* 8 July 2007
* Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#include "matlab_b... |
f5136c256fe9a6ba38d9e9825e855928cc34a96a25a73e64736e01e1e4ca0bbc | C | 3,875 | 128 | // (C) Copyright 2004, David M. Blei (blei [at] cs [dot] cmu [dot] edu)
// This file is part of LDA-C.
// LDA-C is free software; you can redistribute it and/or modify it under
// the terms of the GNU General Public License as published by the Free
// Software Foundation; either version 2 of the License, or (at your
... |
e4b43fa73fefc6ac6986fe6d405651271a2dc7f80cf53319c88d4492dc930f75 | C | 3,899 | 128 | /*=================================================================
* mexpp.c
*
* starting a locfit interface.
*
* $Revision: 1.5 $ */
#include "mex.h"
#include "lfev.h"
extern void lfmxdata(), lfmxevs();
design des;
lfit lf;
int lf_error;
void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[... |
d163066fa90659551e7a90b1cd3fffb7a9e96a13cb9546e1cd33c090b8715a12 | C | 4,014 | 212 | #include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include <errno.h>
#include "mex.h"
#ifdef MX_API_VER
#if MX_API_VER < 0x07030000
typedef int mwIndex;
#endif
#endif
#ifndef max
#define max(x,y) (((x)>(y))?(x):(y))
#endif
#ifndef min
#define min(x,y) (((x)<(y))?(x):(y))
#endif
void exi... |
ac9008dd046a9dace25994035d70b90012564250c13ca77a8407ab0bb96111ef | C | 4,055 | 186 | /*
* ==============================================================
* bfs_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 20 April 20020
* =============================================================
*/
/*
* 19 February 2007
* Updated to use Matlab 2006b sparse matrix interface
*
* 1 ... |
319ab87e7515ee09bde00185674003554a92fd40b19a208afe3925acf6fe1b0a | C | 4,064 | 105 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
e568bf28347e54c205e4492648f436b4c522e315f9dcd40ca239677f327ea8ea | C | 4,117 | 129 | /**********************************************************************
* mextriangsp: given upper triangular U,
* options = 1 (default), solves U *y = b (backward substitutions)
* = 2 , solves U'*y = b (forward substitutions).
*
* y = mextriangsp(Uinput,b,options)
*
* Important: U is ass... |
909a5bde29c6c74b5f5a4178de5e79b4fc9d09b201924d1c6b7abc85088ce59d | C | 4,128 | 116 | /* ************************************************************
MODULE sdmaux*.c -- Several low-level subroutines for the
mex-files in the Self-Dual-Minimization package.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)... |
1f3ff10d2224827598f7587a5bbc203b12981e7ff4785cc7b5d67af9528affc6 | C | 4,133 | 101 | /* Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions */
/*=========================================================================
Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are ... |
c1eb0b22fdc882145d3e152172d280c315388c250b0c7d8b9f71e2a785f382ec | C | 4,135 | 124 | /** @file kamada_kawai_spring_layout_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2008-09-26: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER *... |
0e6be70eaf51078638ff691ac15fc0ba08b9172a33bfe75e6024aaf880cc0446 | C | 4,152 | 153 | /*
Copyright (c) 2010 Genome Research Ltd.
Author: Andrew Whitwham <aw7@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list ... |
a71072ac81709b2c320560d0d894935f5b1d21c30c670a5befe0a77c4412db31 | C | 4,155 | 170 | /*
Copyright (c) 2009 Genome Research Ltd.
Author: Rob Davies <rmd@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of co... |
052e2a4e894f59e89e95dd7da8a73e446af68097916083b85e247ec06c5887ba | C | 4,163 | 158 | #include "htslib/vcf_sweep.h"
#include "htslib/bgzf.h"
#define SW_FWD 0
#define SW_BWD 1
struct _bcf_sweep_t
{
htsFile *file;
bcf_hdr_t *hdr;
BGZF *fp;
int direction; // to tell if the direction has changed
int block_size; // the size of uncompressed data to hold in memory
bc... |
f25861caafed86071cf8c6c65ac543ea7c376c53cce1093349d4e098f01bd79a | C | 4,204 | 110 | /*=================================================================
* mexlocfit.c
*
* starting a locfit interface.
*
/* $Revision: 1.5 $ */
#include "mex.h"
#include "lfev.h"
design des;
lfit lf;
int lf_error;
extern void lfmxdata(), lfmxsp(), lfmxevs();
void
mexFunction(int nlhs,mxArray *plhs[],int nrhs,const ... |
b918eebc7f36bacb658eb4fc17dfc6d2b639a888601351c3b5a13f63dbe7b640 | C | 4,222 | 136 | /*
* $Id$
* Guillaume Flandin
*/
#include <string.h>
#include "mex.h"
/*
* https://stackoverflow.com/a/37109258
* by polfosol: https://stackoverflow.com/users/5358284/polfosol
*/
static const char* B64chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
static const int B64index[256] =
... |
fcd0d1f0f7164b4014b58b4eb2ca6f65f724293c694ace49a4eae7f48a2b7430 | C | 4,259 | 124 | #ifndef lint
static char svnid[] = "$Id: nifti_stats_mex.c 253 2005-10-13 15:31:34Z guillaume $";
#endif
/*
* This is a Matlab mex interface for Bob Cox's extensive nifti_stats.c
* functionality. See nifti_stats.m for documentation.
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mex.h"
#in... |
37b694766f4d30b9b5bb0608ac197afd75b2c568d6638b67afdf5c50feec93a8 | C | 4,315 | 92 | #define FLOAT_T float
#define SIZE_T long
/*
* C implementation of row sliding, used to prepare input data for training.
*
*/
void runRow(const FLOAT_T * const restrict source, FLOAT_T *restrict dest,
SIZE_T numRows, SIZE_T numSourceCols, SIZE_T numDestCols, SIZE_T depth,
const int * const r... |
537efc3182631353244aa8ffeb6c4e8ca51f8698ce477ef79b7ff10174eaf1e8 | C | 4,364 | 147 | /************************************************************************
* mexschurfun(X,Y,options)
* options = 1, add Y to the diagonal of X (a square matrix)
* options = 2, add Y to X
* options = 3, X(i,j) = X(i,j)*Y(i)*Y(j)
************************************************************************/
#in... |
2ea074c653a6bb755c4c4433c96060ed3e72f0e1ae5076e7246eba07f044394d | C | 4,372 | 100 | #include "fastdelta.h"
#if defined(_MSC_VER)
/* Microsoft C/C++-compatible compiler */
#include <intrin.h>
#elif defined(__GNUC__) && (defined(__x86_64__) || defined(__i386__))
/* GCC-compatible compiler, targeting x86/x86-64 */
#include <x86intrin.h>
#elif defined(__GNUC__) && defined(__ARM_NEON__)... |
8c544ae19636faec30d8586329918c84316608dbdc00b983f5f8fd1be857e98d | C | 4,506 | 143 | /***********************************************************************
* mexqops.c : C mex file
*
* z = mexqops(blk,x,y,options);
*
* Input: blk = [n1, n2, ... nk]
* x = n-vector or k-vector
* y = n-vector, where n = n1+...+nk
*
* options = 1, z = k-vector, z(i) = <xi,yi>
* = 2... |
2407fbf7ca92a9100d6c8d201928cbd145f74f534a354af89696999c45821b94 | C | 4,573 | 122 | /*
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to 1.05R5)
% Dept. Econometrics & O.R., Tilburg University, the Netherlands.
% Supported by the Netherlands Organization for Sc... |
f3e544fea52fd87f0a2738883ef56610289ef7ae79c999eff928ffe0a053ac97 | C | 4,634 | 187 | /*************************************************************************
* MATLAB MEX ROUTINE inplaceprod.c
*
* > inplaceprod(A,B)
* performs inplace (i.e., without allocate array) complex array product
* > A(:) = A(:).*B(:);
*
* User must make sure A is not shared by other array.
* B must have the same size... |
18ff9426a663247000f152d619a9b4e3e17861422000b7d06ba7f77e26e347d2 | C | 4,655 | 135 | /** @file gursoy_atun_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2008-09-28: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER *... |
f72e6f3f96f13f3f314387ca455a97706e9df295c0ddd275196beea25a7c82f0 | C | 4,669 | 116 | /*
% y = qblkmul(mu,d,blkstart)
% QBLKMUL yields length(y)=blkstart(end)-blkstart(1) vector with
% y[k] = mu(k) * d[k]; the blocks d[k] are partitioned by blkstart.
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = qblkmul(mu,d,blkst... |
8ceb77529243c3c0738dd027630b94924756ac7b6d434d907edb7498fc509a2f | C | 4,700 | 143 | /*
bam_cat -- efficiently concatenates bam files
bam_cat can be used to concatenate BAM files. Under special
circumstances, it can be used as an alternative to 'samtools merge' to
concatenate multiple sorted files into a single sorted file. For this
to work each file must be sorted, and the sorted files must be given... |
49d5a4f0c338c2832f04589471ab6139dfce20f193532b3bfd1ecd95c81aebdd | C | 4,756 | 143 | /* Lindemann's precedence model.
*
* Copyright 2016 University of Surrey.
*
*/
#include "math.h"
#include "mex.h"
#define TEMP_ARRAY mxCreateDoubleMatrix((mwSize)length_c,(mwSize)1,mxREAL)
#define IN_ARRAY mxCreateDoubleMatrix((mwSize)n_sample,(mwSize)1,mxREAL)
void mexFunction(int nlhs, mxArray *plhs[], int n... |
56a6e355de5e03b9b0a2841d8eb54722cb7e4e07616f2ccf4ea673653a4a5e37 | C | 4,765 | 175 | /*
* $Id: init.c 6428 2015-05-06 14:09:04Z guillaume $
* Guillaume Flandin
*/
#ifndef MATLAB_MEX_FILE
# undef _LARGEFILE64_SOURCE
# define _LARGEFILE64_SOURCE
# include <stdio.h>
# include <sys/stat.h>
# if defined(__APPLE__)
# define structStat struct stat
# define getFileFstat fstat
# define getFilePos fgetpo... |
38e64fe182fb228e03b482d5e86a84b1dbbafe3303c491e8538178bc18e824f8 | C | 4,843 | 144 | /*
Copyright (c) 2010-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
4fd6ebe51ba1662f96f530db72510611b48854eedab2b3a92dc4fa5ef1dec7e1 | C | 4,915 | 131 | /*
y = blkmul(mu,d,nL)
yields length(y)=sum(nL) vector with y[k] = mu(k) * d[k].
length(mu)=length(nL), length(d)=sum(nL).
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamilton, CANADA (since 1.1)
%
% Copyright (C) 2001 Jos F. Sturm (up to... |
8ee0da78a1221a3c2036e22eed06c2faa27a671a46565a60e10111d4ee9c30ee | C | 4,917 | 165 | /*
* pufftest.c
* Copyright (C) 2002-2013 Mark Adler
* For conditions of distribution and use, see copyright notice in puff.h
* version 2.3, 21 Jan 2013
*/
/* Example of how to use puff().
Usage: puff [-w] [-f] [-nnn] file
... | puff [-w] [-f] [-nnn]
where file is the input file with deflate dat... |
ac3c0221e57281e1542fa94a99b5f6725bf60f50a22d4f7135196577be26d1c2 | C | 4,929 | 148 | /*
Written by Ru(by) Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
*/
#include "mex.h"
/* The computational routine */
/*function V_lam=Compute_V_lambda(params,V_same,V_diff,lambda)
neighborsys=double(params.neighborhood);%revise*/
void CBIG_MSHBM_V_lambda_Product(doub... |
7c6867443ee4940d86dce4cb5f25b757d5393b4c55cfd3581e70aed70df7490e | C | 4,947 | 185 | /*
Copyright (c) 2009-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this l... |
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