sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
414fb9c4a93000cb697902f4089ea9b35256e38014fb10cdfa7a3645c57961fc | C | 5,028 | 132 | /* 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 ... |
5588c554974ab41d90230aa56f6bdf84286f58d5c79aa10bcea208623b8fe324 | C | 5,032 | 198 | #include "mex.h"
#include <stddef.h>
#if !defined(HAVE_OCTAVE) && ( !defined(MX_API_VER) || ( MX_API_VER < 0x07030000 ) )
typedef int mwIndex;
typedef int mwSize;
#endif
/*
% Copyright 2005-2016 CVX Research, Inc.
% See the file LICENSE.txt for full copyright information.
% The command 'cvx_where' will show where thi... |
7e0c029663f372120632146fefd29217fb7dd8bb81159f0db0b1948c889ab88a | C | 5,033 | 130 | /*
% [zhi,zlo] = quadadd(xhi,xlo,y)
% QUADADD Compute (zhi+zlo) = (xhi+xlo) + y.
% x an z are in double-double format (quad precision)
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function [zhi,zlo] = quadadd(xhi,xlo,y)
% This file is part of SeDuMi ... |
cd43926775c66ed48d181786fdc1e2c5c3187e249008f30e99234fb027ec65e1 | C | 5,107 | 168 | /***********************************************************************
* mexMatvec: compute
*
* mexMatvec(A,y,options)
*
* options = 0, compute A*y
* = 1, compute (y'*A)'
*
* Copyright (c) 2004 by
* K.C. Toh
* Last Modified: 120404
**************************************************... |
5dcc3baf102f15449f9387ccc60288654a6b89d9d9e58b68a779c2b75912e00b | C | 5,134 | 153 | /***********************************************************************
* mexinprod.c : C mex file to compute inner product of 2 vectors,
*
* Ax = mexinprod(blk,Avec,x,k,p);
* where Ax = Avec{p}(:,1:k)'*x
*
* SDPT3: version 3.0
* Copyright (c) 1997 by
* K.C. Toh, M.J. Todd, R.H. Tutuncu
* Last Modified:... |
851bc7ff61e798948b59e462c116ff98bdc7663bad20265f7c650c934ad7949c | C | 5,173 | 218 | /*
* ==============================================================
* matlab_bgl_all_sp_mex.c The mex interface to the matlab bgl wrapper.
*
* David Gleich
* 20 April 2006
* =============================================================
*/
/*
* 20 April 2006
* Initial version
*
* 19 February 2007
* Updated ... |
d7f1b6e44fee20ab41cef1d650776a039a2348935eb96bcbd294a4096139be3a | C | 5,204 | 186 | /* adler32.c -- compute the Adler-32 checksum of a data stream
* Copyright (C) 1995-2011, 2016 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* @(#) $Id$ */
#include "zutil.h"
local uLong adler32_combine_ OF((uLong adler1, uLong adler2, z_off64_t len2));
#define BASE 6552... |
961cdb9fbb0583d21c9b9855f149255090bdd879aba7c060a8d2a481190eb85f | C | 5,230 | 145 | /* 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 ... |
7b2aa3e9f8804cc5b4bccc61747f6fcc41e28303f926ecbeaa29f7c088179b25 | C | 5,266 | 145 | /*
% y = sqrtinv(q,vlab,K)
% SQRTINV Computes for PSD-cone, y = (Q / diag(sqrt(vlab)))', so that
% Y'*Y = inv(Q * diag(vlab) * Q').
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = sqrtinv(q,vlab,K)
% This file is part of SeDuMi 1... |
29521cef33c0e9b568f5d5e61d6267c9fc68dc91775c42c36c8e0d047ac9d669 | C | 5,283 | 140 | /* ************************************************************
% perm = sortnnz(At,Ajc1,Ajc2)
% SORTNNZ Sorts columns in At
% in increasing order of nnzs; only the nnzs between Ajc1 and Ajc2
% are considered for each column. If Ajc1 or Ajc2 is empty, we use
% the ... |
533956749a4049cf6e33146cbc6b09361e609ccb18ca845426f59244d342cb2d | C | 5,349 | 158 | /* 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 ... |
9de835527425e81739a5a8da51f1a12bd6539a38e59430a46a6cf01b91ec3782 | C | 5,391 | 174 | /**********************************************************************
* y = mextriang(U,b,options)
* Given nxn upper-triangular matrix U,
* options = 1 (default), solves U *y = b,
* = 2 , solves U'*y = b.
*
* Important: U is assumed to be dense.
**************************************... |
5a7f0016b7d8a99688882c597c90409f8562f4ba43d64318ad7d0e3a415145eb | C | 5,414 | 120 | #include <math.h>
#define FLOAT_T float
/* C implementation for sliding Jaccard similarity, based on Ziga Avsec's implementation.
* There are two functions here that are exported as Python functions through Numpy's amazing
* f2py module. In order to compile this module, make sure you have gcc and gfortran on your pa... |
34e3aea93d2f8144db87b67ecddd7b147f0a8626c7b9378a5c7799c4ea30d152 | C | 5,424 | 158 | // (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... |
b571b787ea71f6fb8feab02075d5e256248c3fbf542e2c8228b7c3db4330b200 | C | 5,491 | 158 | /* 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 ... |
fd11a9d3f30f17300bd93a2239bc2192eb6d9b89bba3901ebfcb4cafb102da56 | C | 5,564 | 138 | /*
perm = ordmmdmex(X)
Computes multiple-minimum-degree permutation, for sparse
Cholesky. X is a sparse symmetric matrix; only its off-
diagonal sparsity structure is used.
Invokes SPARSPAK-A Release III.
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster ... |
db7a11bab7f9959da5732188c18c7a06bec07ed5fa0a37d13cbbe127d2aeb60f | C | 5,611 | 138 | /* 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 ... |
305ff68420c76e4c79ee8d174c976d19e0d55a4cf52d14e1aaa21ea46fc712a6 | C | 5,618 | 167 | /* 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 ... |
43a6d28fc0df4e265f7f2084039c033e26acd2ddc3863f8801f771a4b24d7344 | C | 5,626 | 189 | #define _GNU_SOURCE
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include "medaka_common.h"
/** Allocates zero-initialised memory with a message on failure.
*
* @param num number of elements to allocate.
* @param size size of each element.
* @param msg me... |
cbc768deb0e9869533b98cd99b41fc7dc46d6dec1990e4e8f61d213d39ebd9e7 | C | 5,641 | 148 | /* 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 ... |
ad779c5886b130f565b0912300f11c7b1db86b0cedf94324fd70e771fef12c7b | C | 5,651 | 229 | #include <stdarg.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdint.h>
#include "htslib/kstring.h"
int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
{
va_list args;
int l;
va_copy(args, ap);
l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc ... |
98766e3bbdab2bc69befdc2b4da203634aadee330395136be821ae0c2977083f | C | 5,799 | 223 | /** @file mst_mex.c
* @copyright Stanford University, 2006-2008
* @author David F. Gleich
* The mex interface to the matlab bgl wrapper.
*/
/** History
* 2006-04-20: Initial version
* 2006-11-10: Altered the code to produce the correct number of edges
* in the minimum spanning tree by resizing the arrays. Th... |
ff3d2e00e31a4216c0ba2ec9b8f844d5ae73ab3b922924eddcac69c0e09f3640 | C | 5,882 | 138 | /*
% 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 Scien... |
976a07a85730331a3ea6ee3c852eb14fa3b575dd9003c43ba056379fd4df2eb1 | C | 5,910 | 203 | /* CCGEngine.c /*
/* This is a bare-bones C program whos purpose is to compute
Multi-unit cross correlograms quickly. Not intended for
use on its own. It is designed to be wrapped by a MATLAB
function.
Usage - [CCG, PAIRS] = CCGEngine(TIMES, MARKS, BINSIZE, HALFBINS)
TIMES ( is the name of a binary fi... |
9acfa87a89bb4ca5e6b50e993a372a59aa2ffdded58fc828b3c4a3aed354b580 | C | 5,953 | 212 | /** @file bfs_dfs_vis_mex.c
* @author David F. Gleich
* @date 2008-09-29
* @copyright Stanford University, 2006-2008
* The mex interface to the matlab bgl wrapper for bfs and dfs with a visitor.
*/
/** History
* 2006-05-30: Initial version
* 2007-02-19: Updated to use Matlab 2006b sparse matrix interface
* ... |
cdcd6ff33d053d0963b61ee972eebbb6a171178fb5281cc4825908a3ab62ccf4 | C | 5,983 | 159 | /* 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 ... |
70fc52a736ccdf6fbb5fb855b674f7489bff7fec637b913b15e466dca1ec7ab8 | C | 6,024 | 197 | /*
* Calculate cross-correlograms with a range of options.
* Called from chXcorr2.m.
*
* Copyright 2016 University of Surrey.
*
*/
#include "math.h"
#include "mex.h"
#include "matrix.h"
#define max(a,b) \
({ __typeof__ (a) _a = (a); \
__typeof__ (b) _b = (b); \
_a > _b ? _a : _b; })
/* structur... |
35b5ceb85ff8ba70fe268188de06c571b1b3459f5364b455049a759632205fec | C | 6,033 | 145 | /* ************************************************************
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)... |
84ca330d36082cfb7df18eafd6763836291d79d17ae469485bfd8fd6babd5ae0 | C | 6,037 | 250 | // (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
... |
732f12baaa10647e0993c868e615f24771c9837d92e225a04f051add2f8a13f5 | C | 6,041 | 154 | /* ************************************************************
% Ablkjc = partitA(At,blkstart)
% PARTITA Partition columns of A according to the subscripts listed in blkstart.
%
% SEE ALSO sedumi
% ******************** INTERNAL FUNCTION OF SEDUMI ********************
function Ab... |
1356e871c209ea825bfacd79fb597289cf847f17f135bfe8db1674860f756a71 | C | 6,161 | 168 | /* 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 ... |
ae2af8d21cec7a573153c1bedd6f4f325e5a7f4d6836ac92fcf9fe2b3d88dbbc | C | 6,185 | 250 | #include <stdarg.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdint.h>
#include "kstring.h"
int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
{
va_list args;
int l;
va_copy(args, ap);
l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. Se... |
92769918003a834aa53a370686b8616a76509bb0cc766af28d0460b6cb52524c | C | 6,213 | 207 | // isMatlabVer.c
// Compare Matlab version to specified number
// Match = isMatlabVer(Relop, N)
// INPUT:
// Relop: Comparison operator as string: '<', '<=', '>', '>=', '=='.
// N: Number to compare with as DOUBLE vector with 1 to 4 elements.
//
// OUTPUT:
// Match: Locical scalar, TRUE for matching compariso... |
c2c0cabbb5e607a9a670597f7ab7cd1c4f2cfd33192b2b271828db05703782ad | C | 6,220 | 145 | // This is the ``Mersenne Twister'' random number generator MT19937, which
// generates pseudorandom integers uniformly distributed in 0..(2^32 - 1)
// starting from any odd seed in 0..(2^32 - 1). This version is a recode
// by Shawn Cokus (Cokus@math.washington.edu) on March 8, 1998 of a version by
// Takuji Nishimur... |
b878e433d0d241dd9bbccfae44a3090ac07bcef0ab753383da2d313573863b99 | C | 6,263 | 202 | /*
* fast_kmeans_step.c - fast pairwise distance matrix
*
* This MEX file works, but comments and documentation in particular are
* a little slim ...
*
* Syntax:
* [assigns,bestdists,clustersizes,centroids] =
* fast_kmeans(waves,centroids,normsqr_waves,chunk)
*
* ##### NOTE #####... |
0802a7d5318a0121eb1d7afabed15279fb4a4070b77cabee077efddc813609a4 | C | 6,268 | 162 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
804f7cef695cda6150b24ff6de1965018a251e8fc13bcd59a7abc269cca32d7d | C | 6,269 | 192 | #include "mex.h"
#include "math.h"
int mindex3(int x, int y, int z, int sizx, int sizy, int sizz, int wrap)
{
int index;
if(wrap==1)
{
/* Positive modules */
x=(x % sizx + sizx) % sizx;
y=(y % sizy + sizy) % sizy;
z=(z % sizz + sizz) % sizz;
}
else if(wrap>1)
... |
8df252b0a770014ef1e9c6d168610d0555058e433ba3d63c1c5f433b12f48737 | C | 6,276 | 162 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
a1e7856c38f04dfccdfa97ab281904fd95b7cdfebd9f86ab8031eae9fdf1df64 | C | 6,296 | 168 | /*
% y = invcholfac(u,K, perm)
% INVCHOLFAC Computes y(perm,perm) = u' * u, with u upper triangular.
%
% SEE ALSO sedumi, getada3
% ******************** INTERNAL FUNCTION OF SEDUMI ********************
function y = invcholfac(u,K, perm)
% This file is part of SeDuMi 1.... |
68140a82582ede938159630bca0fb13a93b4bf1cb2e85b08943c26242cf8f3a6 | C | 6,323 | 205 | /* zpipe.c: example of proper use of zlib's inflate() and deflate()
Not copyrighted -- provided to the public domain
Version 1.4 11 December 2005 Mark Adler */
/* Version history:
1.0 30 Oct 2004 First version
1.1 8 Nov 2004 Add void casting for unused return values
Use switch s... |
f2c4973203f665c14dc1a94cfa5d628d3956aaf9728d3409574a9dc716a34442 | C | 6,341 | 192 | #include <stdio.h>
#include "simdxorshift128plus.h"
#if defined(__AVX2__)
/* used by xorshift128plus_jump_onkeys */
static void xorshift128plus_onkeys(uint64_t * ps0, uint64_t * ps1) {
uint64_t s1 = *ps0;
const uint64_t s0 = *ps1;
*ps0 = s0;
s1 ^= s1 << 23; // a
*ps1 = s1 ^ s0 ^ (s1 >> 18) ^ (s0 >> 5); // b, c... |
423edc9a45572844f30b21dc4916c99715499e8a4ae7626d4adbb6c44e0c5fc5 | C | 6,363 | 188 | /* 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 ... |
b0787d59c0c8d40b185e3d9b6a224c574ba31b19f5c63040c43474e8b4a83d50 | C | 6,409 | 207 | /* CCGEngine.c /*
/* This is a bare-bones C program whos purpose is to compute
Multi-unit cross correlograms quickly. Not intended for
use on its own. It is designed to be wrapped by a MATLAB
function.
Usage - [CCG, PAIRS] = CCGEngine(TIMES, MARKS, BINSIZE, HALFBINS)
TIMES ( is the name of a binary fi... |
c4494b831cb6aa0106449dacca6d4cca9d6ddbc4263fd408101e26e7f71a22b6 | C | 6,431 | 162 | /* ************************************************************
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)... |
eae3c1a58e56a13b8857e921dcff2778ac691deb05027d0ee3a7f46ce355b6bb | C | 6,535 | 193 | /******************************************************************
* mexProd2nz: compute the elements of P whose positions are
* specified by the variable list.
*
* P = mexProd2nz(blk,A,B,list), where P = A'*B.
*
* output: P is sparse, where
* P(i,j) = <ith column of A, jth column o... |
7ab3582eb3ff9c9c97b817aab118b25f51f82fbe3fce9c1d7794114d6553fba9 | C | 6,592 | 177 | /*
% y = vecsym(x,K)
% VECSYM For the PSD submatrices, we let Yk = (Xk+Xk')/2
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = vecsym(x,K)
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright... |
7b6c6225aeb3b41f65c96ba340e0266fdb65a756946ee05600883d6a4860eeca | C | 6,657 | 159 | /* 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 ... |
07b725c6e1a725205ac9dc6e5d1b5728501216edba7049c000f38e7f377abf85 | C | 6,756 | 171 | /* C file autogenerated by mexme.m */
#include <mex.h>
#include <math.h>
#include <matrix.h>
#include <stdlib.h>
#include <float.h>
#include <string.h>
/* Translate matlab types to C */
#define uint64 unsigned long int
#define int64 long int
#define uint32 unsigned int
#define int32 int
#define uint16 unsigned short
#... |
c93017aa4a8af8f863c95538e0b248df7c868a8e5972aaf544b2497fb9ee06b0 | C | 6,763 | 168 | /*
% y = givensrot(gjc,g,x,K)
% GIVENSROT
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = givensrot(gjc,g,x,K)
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Romanko
% Copyright (C) 2005 McMaster University, Hamil... |
255062b9926b4f3f73aed140a530a6337590a14d663f638e2e97cf3511735997 | C | 6,876 | 169 | /*
x = psdframeit(lab,frms,K);
Computes x = FRM*lab.
The frame "frms" is a product-form Householder reflection.
% 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)
% ... |
5eb70f799d791f4d4afe23b0d4f47c11b72db0d03e7f5bf044556ffc93a98e33 | C | 6,919 | 223 | /*
* $Id$
* 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
# elif defined(SPM_WIN32)
# define structStat struct _stati64
# define... |
a8554d035c97f6f006ba2daa2f1c7717ba0405fbf1272f290c55ba134f508a46 | C | 6,930 | 163 | /*
smult = adenscale(dense, d, qblkstart)
% 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 b... |
810975cec35367cdfd452bc21e705609b6ba5edce126378b1c5bf68e7220fc17 | C | 7,091 | 181 | /*% L = symbchol(X)
% SYMBCHOL Symbolic block sparse Cholesky factorization.
% L = symbchol(X) returns a structure L that can be used
% by the efficient block sparse Cholesky solver SPARCHOL.
% The fields in L have the following meaning:
%
% L.perm - Mu... |
8d2efc0fa4c419705de68c00e27765dfbb5cb6f708973ba28340e43428a8495d | C | 7,095 | 213 | #include "mex.h"
#include "math.h"
#include <string.h>
/* Coordinates to index */
int mindex3(int x, int y, int z, int sizx, int sizy) { return z*sizx*sizy+y*sizx+x;}
int mindex2(int x, int y, int sizx) { return y*sizx+x;}
/* The matlab mex function */
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxAr... |
cd5376acfdd65475c78c70590318e01708860e284bfb1c767b49bbbf4216ce0e | C | 7,268 | 227 | /* 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 ... |
d796215fc7c4b462d9279450fbc50ac2ac085c4dad8f9b54ae7965a9ebbe3bfa | C | 7,270 | 191 | /*
% 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 Scient... |
f7fdc9ef326a2683eb33c794face54e83c751ec17f3d1ba581847a62af36ddcd | C | 7,304 | 325 | /* zutil.c -- target dependent utility functions for the compression library
* Copyright (C) 1995-2017 Jean-loup Gailly
* For conditions of distribution and use, see copyright notice in zlib.h
*/
/* @(#) $Id$ */
#include "zutil.h"
#ifndef Z_SOLO
# include "gzguts.h"
#endif
z_const char * const z_errmsg[10] = {
... |
7e2e6a1a4332969ea0c01e4bfaeb240cbb5f05bab19774b829ccd9fd3c56cb69 | C | 7,316 | 190 | /* ************************************************************
% Apart = extractA(At,Ajc,blk0,blk1,blkstart[,blkstart2])
% EXTRACTA Fast alternative to
% Apart = At(blkstart(1):blkstart(2)-1,:).
% Instead of blkstart(2), it takes "blkstart2" (if supplied) or
% size(At,1)+1 (if neither blkstart(2) nor ... |
8df41cbb7180c1c86cad689b03b41cf34c155b3b40236e4fb7c155ff47769398 | C | 7,368 | 275 | #include <stdio.h>
#include <stdlib.h>
#include <windows.h>
#include "zlib.h"
void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
{
R->HighPart = A.HighPart - B.HighPart;
if (A.LowPart >= B.LowPart)
R->LowPart = A.LowPart - B.LowPart;
else
{
R->LowPart = A.LowPart - B.L... |
f0c55ace6d7775ce0ba8340c68b02170ad9f085c0ff517fd4df6109ac91d5f2a | C | 7,391 | 186 | /* inffas8664.c is a hand tuned assembler version of inffast.c - fast decoding
* version for AMD64 on Windows using Microsoft C compiler
*
* Copyright (C) 1995-2003 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*
* Copyright (C) 2003 Chris Anderson <christop@charm.net>
* Ple... |
8e2f98ccf9beed389b3b7fae6d85934a22a45878895bd7181c1d737c8e6c3d02 | C | 7,456 | 220 | #include "mex.h"
#include <stddef.h>
#include <math.h>
#if !defined(HAVE_OCTAVE) && ( !defined(MX_API_VER) || ( MX_API_VER < 0x07030000 ) )
typedef int mwIndex;
typedef int mwSize;
#endif
static const double MAX_GROWTH = 16;
/*
% Copyright 2005-2016 CVX Research, Inc.
% See the file LICENSE.txt for full copyright in... |
625fd641d49c711d3752ec61f2869606672e8efb24c42d629967132698590c8d | C | 7,487 | 215 | #include "mex.h"
#include "math.h"
#include <string.h>
/*
* Ne=vertex_neighbours_double2(Fa,Fb,Fc,Vx,Vy,Vz)
*
*/
/* Coordinates to index */
int mindex3(int x, int y, int z, int sizx, int sizy) { return z*sizx*sizy+y*sizx+x;}
int mindex2(int x, int y, int sizx) { return y*sizx+x;}
/* The matlab mex function */
voi... |
7da9424965e24cecec619c4e9afb9a5f03424fee1759e63d8e48578d51f5dbf5 | C | 7,517 | 225 | /* 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 ... |
7256394d1c48b968ad27f6c1d05fafabecf463470b1fe42775cd86e5625da321 | C | 7,584 | 231 | #include "mex.h"
#include "math.h"
#include "stdio.h"
#include <string.h>
/* Coordinates to index */
int mindex3(int x, int y, int z, int sizx, int sizy) { return z*sizx*sizy+y*sizx+x;}
int mindex2(int x, int y, int sizx) { return y*sizx+x;}
/* The matlab mex function */
void mexFunction( int nlhs, mxArray *plhs[], i... |
156ed42ca4eae80af9f7aaa58be1f3ec08501ee6fd9e01e6c6fd60eb1114dbe4 | C | 7,677 | 173 | /*
L.tmpsiz = choltmpsiz(L)
% 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 Netherla... |
ea3b92fde436d63a7bf00051ba4e0d608c0e6124a1e6e2ffc4783305f9d117b4 | C | 7,720 | 203 | /* 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 ... |
00bb9fa5203e3c0d89539dcbd5bfcfcbf6a0a9318362c5daf3bf8f7e3b8184a0 | C | 7,721 | 290 | #include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include <assert.h>
#include "htslib/tbx.h"
#include "htslib/bgzf.h"
#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 };
tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 };... |
3519026288bfede7108863531a254d8e64cf0461a10b8e77644a61886895e610 | C | 7,795 | 324 | /*
* ==============================================================
* astar_search_mex.c The mex interface to the astar_search
* wrapper.
*
* David Gleich
* 31 May 2006
* =============================================================
*/
/*
* 31 May 2006
* Initial version
*
* 19 February 2007
* Updated to u... |
57321c3cf62ab18af6744e11eb0e1a02c7359052a8260ad25f1f4c6f161760d4 | C | 7,796 | 213 | /* 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 ... |
5edc12c239b5ff095772524a22f468a05beb6d033719bc174de089e1780747fd | C | 7,902 | 184 | /*
L.split = cholsplit(L, cachesiz)
% 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 ... |
b5025ccdfc1ca51e7393c29a323f2b4c6074c612addb46199075d06e9f0a9405 | C | 7,935 | 254 | #include <math.h>
#include <stdlib.h>
#include "htslib/kfunc.h"
/* Log gamma function
* \log{\Gamma(z)}
* AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
*/
double kf_lgamma(double z)
{
double x = 0;
x += 0.1659470187408462e-06 / (z+7);
x += 0.9934937113930748e-05 / (z+6);
x -= 0.1385710331296526 /... |
cd887c4af6d20823bd15f24008b10acf01969b4165d7848656bde843a92428d7 | C | 8,146 | 291 | /*
Additional tools for Minizip
Code: Xavier Roche '2004
License: Same as ZLIB (www.gzip.org)
*/
/* Code */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "zlib.h"
#include "unzip.h"
#define READ_8(adr) ((unsigned char)*(adr))
#define READ_16(adr) ( READ_8(adr) | (READ_8(adr+1) << 8) )
#de... |
66b39c27042f6ad12cc12efb0c82cdf100c6640b5fa959b8b866e252966113a9 | C | 8,225 | 247 | /* ioapi.h -- IO base function header for compress/uncompress .zip
part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
Modifications for Zip64 support
Copyright (C... |
6a8f8e8a47b0fcabd78d009d60661b2d9c66a927f5c4bd2d743bd6814559813c | C | 8,247 | 243 | /* 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 ... |
d8ba5e4134208773650bb887ce92ed21ed84331eb21087f4ab55524de14e2812 | C | 8,254 | 205 | /* ************************************************************
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)... |
0f15e905a890216e5e4d5821e4716986658afa5aff4b309952a0568693f66570 | C | 8,298 | 331 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "../linear.h"
#include "mex.h"
#include "linear_model_matlab.h"
#ifdef MX_API_VER
#if MX_API_VER < 0x07030000
typedef int mwIndex;
#endif
#endif
#define CMD_LEN 2048
#define Malloc(type,n) (type *)malloc((n)*sizeof(type))
int print_null(const char... |
dceae37d45d1230b13e9269aa6269b68894aae066db389a0161921939d231802 | C | 8,461 | 295 | /*
* This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
* MD5 Message-Digest Algorithm (RFC 1321).
*
* Homepage:
* http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
*
* Author:
* Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
*
* ... |
3153a773b0f5244c2d3513226266bae0de985f4fe6977f071a34e8ffc8f9f130 | C | 8,507 | 252 | /* 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 ... |
b548d16bdc051cd4d134a6d56f366c7a695f3accb60812d55145f65e1c89941e | C | 8,577 | 202 | /*
% y = fwdpr1(Lden, b)
% FWDPR1 Solves "PROD_k L(pk,betak) * y = b", where
% where L(p,beta) = eye(n) + tril(p*beta',-1).
%
% SEE ALSO sedumi, dpr1fact, bwdpr1
% ********** INTERNAL FUNCTION OF SEDUMI **********
function y = fwdpr1(Lden, b)
% This file is ... |
5d3e0166c9b901fdb4e0ca36647de8c42477cb4753f650bf3e5b6a9f87612576 | C | 8,591 | 329 | /*
* David Gleich
* Copyright, Stanford Unviersity, 2007
*/
/**
* @file matlab_bgl_sp_mex.c
* Wrap a call to the libmbgl shortest path functions.
*/
/*
* 20 April 2006
* Initial version
*
* 19 February 2007
* Updated to use Matlab 2006b sparse matrix interface
*
* 1 March 2007
* Updated to use expand ma... |
950769163c41aff897ee41746a8685d9aa41073b1307f42da19dabe9d3fc8b85 | C | 8,594 | 233 | /* fitblk.c: example of fitting compressed output to a specified size
Not copyrighted -- provided to the public domain
Version 1.1 25 November 2004 Mark Adler */
/* Version history:
1.0 24 Nov 2004 First version
1.1 25 Nov 2004 Change deflateInit2() to deflateInit()
Use fixed-siz... |
355d76166e31af7756b30372957a10daa055365ad775b2b080f9bfa64a18229d | C | 8,672 | 298 | // (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... |
136c2fc045e9e33f553eec9f69ba777af7b643d54a89c77f4f50715aa3dc8df3 | C | 8,711 | 266 | /*
* FILE: CORE_library.c
* --------------------
* Common computational routines for Matlab CORE_function_ MEX files.
* Function descriptions can be found in CORE_library.h
*
* samar@cs.stanford.edu, 01/18/06
*/
#include <math.h>
#include <limits.h>
#include <float.h>
#include "CORE_library.h"
/* --------... |
11e317328ab3ad730b8b61531811e57644982d5de263d410c674bf59a1f45ec5 | C | 8,794 | 341 | // (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
... |
7781f188a883943ef11b0165fe314260f75a2d082aa3989361bd5dc7606bf43b | C | 8,999 | 282 | /***********************************************************************
* mexskron.c : * Find the matrix presentation of
* symmetric kronecker product skron(A,B), where
* A,B are symmetric.
*
* K = mexskron(blk,A,B,sym);
*
* sym = 1 if A=B
* = 0 otherwise
*
* (ij)-column = 0.5*svec(AUB + BUA)*xij, where... |
346422dd9abb2a00ddd34bcc2ad37a061254dea4451ab78451aa731d2d27635b | C | 9,142 | 283 | /* 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... |
7f0a2a1ad48d0d3d7799dce7a22631d87699eb7faa99680ad86c6f816d9665d8 | C | 9,214 | 360 | // (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... |
5f26cbe1d830f72702f5d365517cfed0560edd40fb77bd6c79da59b92f3922f7 | C | 9,235 | 214 | /* ************************************************************
% ADA = getada2(ADA, DAt,Aord, K)
% GETADA2 Compute ADA += DAt.q'*DAt.q
% IMPORTANT: Updated ADA only on triu(ADA(Aord.qperm,Aord.qperm)).
% Remaining entries are not affected.
%
% SEE ALSO sedumi, getada1, geta... |
3ff0842b645da7993bfea6d6731a8da5610adc7d7795f96b9293bfb915b9972b | C | 9,301 | 227 | /*
% z = psdinvjmul(xlab,xfrm, y, K)
% PSDINVJMUL solves x jmul z = y, with x = XFRM*diag(xlab)*XFRM'
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function z = psdinvjmul(xlab,xfrm, y, K)
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr... |
63d63c082bbbcc240c944c9f01c4ff84170a3d0dce6e7174a7f310af77d054b7 | C | 9,376 | 205 | /*
* Calculate cross-correlograms with a wide range of options.
* Called from chXcorr.m.
*
* Copyright 2016 University of Surrey.
*
*/
#include "math.h"
#include "mex.h"
#include "matrix.h"
#define INHIB_MULTIPLY 1
#define INHIB_SUBTRACT 2
#define MAX(A,B) ((A)>(B) ? (A) : (B))
#define A_TEMP_ARRAY mxCreateD... |
2c35d15c86c6a1dad6c3e08d121e0bc4d597c9b0491ffcae692e657eab62122a | C | 9,451 | 214 | /*
% Lden = finsymbden(LAD,perm,dz,firstq)
% FINSYMBDEN Updates perm and dz by inserting the
% last Lorentz trace columns (last columns of LAD). It creates the fields
% Lden.sign - +1 for "normal" columns, -1 for Lorentz trace columns
% Lden.first - First pivot column that will af... |
07168d5a426724d7961ec60d7ac9c91324541337cc7019709bf7f6d5a0b04648 | C | 9,501 | 357 | /*
Copyright (c) 2012-2013 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... |
7297bffb048b167f618e7192e4b70edadbdb73dbee63e80a51d1c2fe8367d7a4 | C | 9,532 | 388 | /*
* $Id: mat2file.c 5446 2013-04-24 16:56:51Z guillaume $
* John Ashburner
*/
#define _LARGEFILE_SOURCE
#define _LARGEFILE64_SOURCE
#define _FILE_OFFSET_BITS 64
#include <math.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <stdlib.h>
#include <stdio.h>
#include "mex.h"
#ifdef SPM_WIN32
#include <windows.h>
... |
41f314d38a15ef3be8bf58ec265485cef81e5d6471c12d065ad031d330f3c368 | C | 9,667 | 344 | /* Copyright (c) 2007
* Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne.
* 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... |
f06d6f8db0a585d30dd13e9f64a0e38fbedbc74f0b66cfbe3850c207366ea08f | C | 9,749 | 235 | /* ************************************************************
% Ablk = findblks(At,Ablkjc,blk0,blk1,blkstart)
% FINDBLKS Find nonzero blocks
% in A, with subscripts per column bounded bij Ablkjc([blk0,blk1]),
% block partitioned by blkstart.
% If blk0 < 1 (blk1 > size(Ablkjc,2)) then st... |
c6a1f604f55421fe7919c185bd9d58d12b23e9d14b7fe74c9a01b35a5b8d5a9a | C | 9,775 | 376 | // (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... |
4e80ad5e11fdcaeaf6c24a8d7ea045616e06fe1dda8a5243daad87df4480f506 | C | 9,839 | 286 | /* 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 ... |
e0e4b5d1ac98b59ea472bd7ca753eb86bcadfaab5a2e9d01c782b876fdc032d7 | C | 9,895 | 259 | #include "mex.h"
#include "cokus.cpp"
// Syntax
// [ X , XD , PQ ] = GibbsSamplerSWR( PQ0 , PQ1 , PQ2 , GAMMA , BURNIN , NS , LAG , SEED , OUTPUT );
// INPUTS
// [0] PQ0: NQ x D matrix of query word probabilities for each document according to topic model
// [1] PQ1: NQ x D matrix of query word proba... |
fcf8fc78a87abc8f46ff971d4a420f58a0f5dd82428c294528ace58d493f9065 | C | 9,972 | 305 | /******************************************************************
* mexProd2.c : C-MEX file to compute the product of two matrices.
*
* P = mexProd2(blk,A,B,type)
*
* input: blk = 1x2 cell array describing the block structure of A and B
* A = mxn matrix.
* B = nxp matrix.
* type ... |
5a40bc7002d91eec4a264012971550b9ae8bdc5761c17e1615c254a1e6b453c0 | C | 10,095 | 268 | /*
% [delta,h,alpha] = iswnbr(vSQR,thetaSQR)
% ISWNBR Checks feasibility w.r.t. wide region/neighborhood of Sturm-Zhang.
%
% SEE ALSO sedumi
% ********** INTERNAL FUNCTION OF SEDUMI **********
function [delta,h,alpha] = iswnbr(vSQR,thetaSQR)
% This file is part of SeDuMi 1.1 by Imre P... |
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