sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
792287dbf0bc45bc4a4550f25c4b1d6c5d308d22d260665da9b95cdb872d289f | C | 3,123 | 149 | /* CrossCorr
* cross correlations
* MEX file
*
* batta 1999
*
* input: t1, t2: two time series to cross correlate in 1/10000 sec
* (assumed to be sorted)
* binsize: the binsize for the cross corr histogram in msec
* nbins: the number of bins
* output: C the cross correlation hi... |
64c7d4b982b4cf9a01e220cc36f676684e9fa004adf5a08b72d6697a328a9c20 | C | 3,389 | 111 | #include "mex.h"
/*
* TENSORPRODC
*
* See the help text in tensorprodc.m for a description.
*
* Author: Gunnar Farnebäck
* Medical Informatics
* Linköping University, Sweden
* gunnar@imt.liu.se
*/
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
int... |
4e5a3a8cc6b7a479d42fdbd3adb12bf34d5f8081adfec825969c94bdeec924a8 | C | 3,409 | 120 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <math.h>
#include "gfa.h"
/*******************************************
* Start looking for G_Islands *************
*******************************************
*/
void getGislands(int minGQ, int total_bases) {
register int i;
int ngs;... |
cb7f3dde212b7ca7acc72ce4b0f2410a2cff06d083215926fed283c6d20de0ae | C | 3,413 | 178 | /* do_intersect.c MEX file, engine for the interval_set intersection
function
INPUTS:
tstart1, tend1, tstart2, tend2, ... tstartN, tendN, start and stop
arrays for the objects to intersect
OUTPUTs Ostart, Oend
batta 2001
starting version
*/
/* modified fpbatta 2004/05/23 to allow intervals in ea... |
3d4c9f6d488610d4d9ff314b2dc783e24079325b78af13d3ee37b18fcc0b0d8a | C | 3,425 | 141 | /*
* utils.c - utility functions for libdeflate
*
* Copyright 2016 Eric Biggers
*
* 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 t... |
d1f56ed292b742fe5de05666b57b777ef9af1011f4030753c1c171d888587dbf | C | 3,515 | 180 | /* do_union.c MEX file, engine for the interval_set unionion
function
INPUTS:
tstart1, tend1, tstart2, tend2, ... tstartN, tendN, start and stop
arrays for the objects to union
OUTPUTs Ostart, Oend
batta 2001
starting version
*/
/* modified fpbatta 2004/05/23 to allow intervals in each set to b... |
2df0b60ec56888c0ad8d52a49c10156c4b9368256f7ff7f394b7b1e99c9c61b9 | C | 3,527 | 180 | /* do_intersect.c MEX file, engine for the interval_set intersection
function
INPUTS:
tstart1, tend1, tstart2, tend2, ... tstartN, tendN, start and stop
arrays for the objects to intersect
OUTPUTs Ostart, Oend
batta 2001
starting version
*/
/* modified fpbatta 2004/05/23 to allow intervals in ea... |
22264e681765f28daa67859c39d0c6e6502ca0f158b9be5445f4d870d4ea4343 | C | 3,540 | 149 | /*
Computes cross correlation between all rows in a matrix and a given
row vector.
Usage - [xcorr] = compute_xcorr(REGSMAT, PATMAT)
Where REGSMAT is a row vector from a regressors object and PATMAT is
the matrix from a pattern object.
% License:
%=====================================================================
... |
a72bad89d1b36300babc8cd87ac757b32beb780b2c026f11a7b0a16fa1639b6c | C | 3,548 | 95 | /* Include Files */
#include <math.h>
#include <stddef.h>
#include <stdlib.h>
#include <stdbool.h>
#include "comp_MM_eig_REls.h"
#include "eigL4x4real.h"
#include "rt_nonfinite.h"
void comp_MM_eig_REls(double *el1R ,double *el2R ,double *el3R ,double *el4R ,
bool *elRmsk,
... |
fbdb1435025455a117597ac15ce0eabd007e91f3d3b80a19ea2431ab1405ddab | C | 3,564 | 106 | /* working version of heat map displays in PostScript
* evolving toward eventual inclusion in Easel
*
* SRE, Thu Jan 25 09:51:18 2007 [Janelia] [Elgar, Enigma Variations]
*/
#include "p7_config.h"
#include <stdio.h>
#include <math.h>
#include "easel.h"
#include "esl_dmatrix.h"
/* dmx_Visualize()
* Incept: ... |
88727aa89df568e72375580a456da9d59b80bda6a043cf41561448f6d52c61cf | C | 3,575 | 87 |
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_vectorops.h"
#include <stdio.h>
static ESL_OPTIONS options[] = {
/* name type default env range toggles reqs incomp help d... |
85c55f08c968bf6c9cbb6b8fc8eeee918570ee00e2e1ebf8fc5dc7ac548a2446 | C | 3,583 | 174 | /* intervalMean_c.c C implementation of the intervalMean function.
inputs are:
1: array of timestamps for tsd to average
2: data array in a transposed format, so that time index is the
last one (major one)
3: array of timestamps for starting times of intervals
4: array of timestamps for end times of... |
dd793cf6785914d850b9d9247d34f6b4301ec253ba39f90de6e1070fa9a3a01d | C | 3,584 | 115 | /* Select <m> random lines from a file and print them.
*
* Uses a reservoir sample - O(m) in space, single pass on the input,
* never reads the entire input into memory.
*
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_getopts.h"
#include "e... |
3d8eac6d6c2be01a466b6cf7a1c54ffd211b759b4e5f5410f6f37b519d717716 | C | 3,586 | 85 | /* esl_subcmd : utilities for command line programs that take subcommands
*
* Extends esl_getopts to more complicated programs with subcommands.
*
* See also:
* esl_getopts : command line argument parsing
*/
#include "esl_config.h"
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_ge... |
690da4aa7df63b1d7a66058583ea5aaa37a58f723f4fa69e0c00f1cccdc8db73 | C | 3,636 | 77 | /* hmmconvert: converting profile HMM files to HMMER3 HMM format.
*
* SRE, Thu Oct 16 08:57:43 2008 [janelia] [Enigma MCMXC a.D.]
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "hmmer.h"
static E... |
48fcab7265e036f3c46d5bee8b3b45f4debfb242f902fefd3ab4a1927caa4570 | C | 3,668 | 53 | #include <omp.h>
#include <stdbool.h>
#include "mp_comp_MM_AIW.h"
#include "compute_M_AIW.h"
void mp_comp_MM_AIW(double *M_out, double *nM_out,
double *A_in , double *I_in , double *W_in ,
int *idx_in, int *numel_in )
{
int m = 16;
#pragma omp parallel for
for (int i=0... |
c606c2b155431d9ad4d75e52a4e809849b441d917919a413255cd91b744099c8 | C | 3,729 | 89 | /* Calculates pairwise %id for all aligned sequence pairs in MSA
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include "easel.h"
#include "esl_distance.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
static ESL_OPTIONS options[] = {
/* name type defa... |
c2d8d76bfdf770eb4b5e90cc3a120e988b3376d777e71100f1805dc8ba7bce82 | C | 3,805 | 167 | /* JPETH
* Joint Peri Event Time Histogram
* MEX file
* inspired from CrossCorr by francesco battaglia (header below)
* adrien peyrache 2007
*
* input: tref, t1,t2: three time series to cross correlate in 1/10000 sec
* (assumed to be sorted). Tref is the common reference.
* binsize: the ... |
3b610739ffa4780a613113322d9b4d778f92ec05e6f1638a8ad2fdf589837812 | C | 3,854 | 151 | #include "p7_config.h"
#include "easel.h"
#include "hmmer.h"
#include "p7_gbands.h"
#include "p7_gmxb.h"
P7_GMXB *
p7_gmxb_Create(P7_GBANDS *bnd)
{
P7_GMXB *gxb = NULL;
int status;
ESL_ALLOC(gxb, sizeof(P7_GMXB));
gxb->dp = NULL;
gxb->xmx = NULL;
gxb->bnd = bnd;
gxb->dalloc = 0;
gxb->x... |
51a135d444de2c65f1e8597b69f931273db1d9db9b49502dd72c0c1e243c107b | C | 3,994 | 199 | #include <math.h>
#include "mex.h"
double mymax(double x, double y)
{
if (x > y)
return x;
else
return y;
}
double absolute(double x)
{
if (x >= -x)
return x;
else
return -x;
}
void permuteInt(int *x, int p, int q)
{
int temp;
temp = x[p];
x[p] = x[q];
... |
38a411fa4df43d3281d25780592e59fb930ebb1989ea45ae28c34f0a4b5403be | C | 4,159 | 145 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <string.h>
#include "gfa.h"
/*****************************************************
* comparStartEnd routine for qsort ******************
* sort on the start then end position ***************
*****************************************************
... |
1cb2550444cd69aa7498341e3975d0464b32272a6f8e5d244ad63e762a0b89ca | C | 4,178 | 201 | /* CrossCorrSD_b
* cross correlations
* MEX file
*
* batta 1999
*
* input: t1, t2: two time series to cross correlate in 1/10000 sec
* (assumed to be sorted)
* binsize: the binsize for the cross corr histogram in msec
* nbins: the number of bins
* output: C the cross correlati... |
0052736b8b28645c3c20d059fd7b5460ea748aebd9f3ccd0fb86cff2c91126a6 | C | 4,253 | 212 | /* ETAverage event-triggered average
* MEX file
* fpbattaglia 2007
* input ev: an event time series
* t1 time series in 1/10000 sec
* (assumed to be sorted)
* d the values in the dataset
* binsize: the size of the bin in ms
* nbins: the number of bins to ... |
90138c0c932027b9d73495cdec2dd2ffd138933eb0c3caf367bc3be55b308021 | C | 4,376 | 216 | /* ETAverage event-triggered average
* MEX file
* fpbattaglia 2007
* input ev: an event time series
* t1 time series in 1/10000 sec
* (assumed to be sorted)
* d the values in the dataset
* binsize: the size of the bin in ms
* nbins: the number of bins to ... |
c51a68898e641b1fbd42201cca1c6196b259a0c33a184927f2354f0ad48d0643 | C | 4,378 | 211 | /* ETAverage event-triggered average
* MEX file
* fpbattaglia 2007, A Peyrache 2007-2016
* input ev: an event time series
* t1 time series in 1/10000 sec
* (assumed to be sorted)
* d the values in the dataset
* binsize: the size of the bin in ms
* nbins: t... |
829c54973a83710955436bfc1f88f233a21f9d883cbab234fb17ac3f12aded1f | C | 4,400 | 129 | /* hmmstat: display summary statistics for an HMM database.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "easel.h"
#include "esl_getopts.h"
#include "hmmer.h"
static ESL_OPTIONS options[] = {
/* name type default env range t... |
a2c80f128a17c54ad05382b64a51c6de03f9e57e46644afc210d4c666d25158c | C | 4,552 | 150 | #include "esl_config.h"
#include "easel.h"
#include "esl_composition.h"
/* Function: esl_composition_BL62()
*
* Purpose: Sets <f> to the background frequencies used in
* \citep{Henikoff92} to calculate the BLOSUM62
* substitution matrix. Caller provides space in <f>
* allocat... |
52e4f011e1ed28c3b9078b15a83b37580d414152bcbee0b43f26d5b1bdc81676 | C | 4,585 | 154 |
#include <stdio.h>
#include <errno.h>
#include <string.h>
#include "tools_CParser.h"
/* This function just allows someone to call the brandsTools.py function from within C
* It populates two strings : path to brandsTools and the path to the yaml file
* It then runs the command. It's designed to read a single YAML v... |
d5025e64d6a8b8086075519086760c55c417f139c35883e9cbb9227d76d2e1d1 | C | 4,684 | 162 | /* esl_bitfield : compact bit flags
*
* Contents:
* 1. ESL_BITFIELD
* 2. Unit tests
* 3. Test driver
*/
#include "esl_config.h"
#include <string.h>
#include "easel.h"
#include "esl_bitfield.h"
/*****************************************************************
* 1. ESL_BITFIELD
***********************... |
1c3dcc9f6aabb1e40e2e602149338a67fedf949a8c8254a07ba9d2cf4849800e | C | 4,762 | 160 |
#include <stdio.h>
#include <errno.h>
#include <string.h>
#include <redisTools.h>
/* This function just allows someone to call the redisTools.py function from within C
* It populates two strings : path to redisTools and the path to the yaml file
* It then runs the command. It's designed to read a single YAML value ... |
58d1da499efb25a3d1feb265a9e1837a6fc7a7aaace13f99634c6cf6f991cac3 | C | 4,784 | 171 | /* Vectorized routines for x86 AVX-512 instructions
*
* Most speed-critical code is in the .h file, to facilitate inlining.
*
* Contents:
* 1. Debugging/development routines
* 2. Unit tests
* 3. Test driver
*
* This code is conditionally compiled, only when <eslENABLE_AVX512> was
* set in <esl_... |
e778646b2f75512046a6c4525c4142fd487438306e27623bbee92e9dc7078dfe | C | 4,850 | 178 | #include "p7_config.h"
#include <ctype.h>
#include "easel.h"
#include "esl_mem.h"
#include "hmmer.h"
/* Function: fm_alphabetCreate()
*
* Synopsis: Produce an alphabet for FMindex.
*
* Purpose: Produce an alphabet for FMindex. This may end up being
* replaced with easel alphabet functions, but ... |
64f5ca0316a60c9f025564d9def6d383c55b0b64a84de0bb7cd252cc68434eaa | C | 4,857 | 154 | #include <math.h>
#include <matrix.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1i... |
c0b65d18455dadce27b66add7d537cf5a6966fc6a1d9a1cd35cc2f1d83ffb189 | C | 4,973 | 201 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <string.h>
#include <math.h>
#include "gfa.h"
/*******************************************
* Start looking for Short Tandem Repeats **
*******************************************
*/
/***************************************************... |
210a84a952608cb36a413ef710963ecb76651791467833a74a84033c2558250d | C | 5,014 | 207 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: compute_Retard_Params.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 29-... |
0b149d4ef34640e7b1156a8db0acd8f6768d745dd73f41dde8fd927c7f0041f6 | C | 5,061 | 226 | /* ETAverage event-triggered average
* MEX file
* fpbattaglia 2007
* input ev: an event time series
* t1 time series in 1/10000 sec
* (assumed to be sorted)
* d the values in the dataset
* binsize: the size of the bin in ms
* nbins: the number of bins to ... |
9a5e99899f6d579eab8aedcff8f0cd083e911a357171a6c0679554bfa43cd9ae | C | 5,069 | 161 | /*
Copyright (c) 2023, PyData Development Team
All rights reserved.
Distributed under the terms of the BSD Simplified License.
*/
#define _PANDAS_PARSER_IMPL
#include "pandas/parser/pd_parser.h"
#include "pandas/parser/io.h"
static int to_double(const char *item, const char *end, double *p_value,
... |
61d8e94df461ba58c030f5076c8a876f4100419795adbb0b3661599e22b67dcd | C | 5,080 | 227 | /* ETAverage event-triggered average
* MEX file
* fpbattaglia 2007
* input ev: an event time series
* t1 time series in 1/10000 sec
* (assumed to be sorted)
* d the values in the dataset
* binsize: the size of the bin in ms
* nbins: the number of bins to ... |
e3b647774ed2de219028d357f9ae146781e2d1ec4bf299870ae387cd657b7945 | C | 5,095 | 188 | #include "mex.h"
#include "math.h"
/* See prepare_displacement_matrices.m for documentation.
*
* Author: Gunnar Farnebäck
* Computer Vision Laboratory
* Linköping University, Sweden
* gf@isy.liu.se
*/
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
... |
9f591f8f639c2f9636f26fd3ecdaa46bf4258db9aacd831e3b93c3681e182fc0 | C | 5,187 | 230 | #include "p7_config.h"
#include "easel.h"
#include "esl_vectorops.h"
#include "p7_gbands.h"
P7_GBANDS *
p7_gbands_Create(void)
{
P7_GBANDS *bnd = NULL;
int init_segalloc = 4;
int init_rowalloc = 64;
int status;
ESL_ALLOC(bnd, sizeof(P7_GBANDS));
bnd->nseg = 0;
bnd->nrow... |
5127d50f10d7bbb7ce28da82fe997b9e344eef9880c4fa6f91a09b91bff51bc7 | C | 5,199 | 273 | /* Restrict_idx_align.c: MEX file that deals with the align case of
restrict: three possible behaviors are possible for this function:
'next': for each key, the first element equal of greater of
each key is returned
'closest': for each key, the element closest to the key is returned
'equal': if an elemen... |
a6d5de0c6632a5849abcd83716228e9e1eddc337abfe2b1058296237a0660a0f | C | 5,202 | 112 | /* easel - little utilities for biological sequence analysis
*
* A single program with many subcommands, subsuming the former Easel
* miniapps.
*
* For the implementations of individual miniapps:
* cmd_alistat.c alignment summary statistics
* cmd_downsample.c downsampling random subsets of things
* c... |
326357ba25ff39f8d45439186fdff05d1b6a4eddf71c8b6036c7ac474c8984d6 | C | 5,220 | 163 | /*
* Description:
* Computes the inverse of a symmetric matrix using the cholesky
* decomposition. We exploit the symmetric since P=L*L',
* inv(P)=inv_L*inv_L', more efficient than inv which uses
* LU decomposition.
*
*
* Author(s):
* Eric Blake
* Black River Systems
* blake@brsc.com
* 05/14/201... |
ab4f21f3e87448adacfa2847dbf1fa435f952db4ce1e664fec9ab8e87e136643 | C | 5,457 | 245 | #include <stdio.h>
#include <ctype.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include "linear.h"
int print_null(const char *s,...) {return 0;}
static int (*info)(const char *fmt,...) = &printf;
struct feature_node *x;
int max_nr_attr = 64;
struct model* model_;
int flag_predict_probability=0;
v... |
5f663e442a7363f12c403c07ae055fad4bd4ed97a7b7b7239bbe488562272a64 | C | 5,607 | 181 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include "gfa.h"
/******************************
* findMR Repeat Finder ****
*
*****************************/
void delMRep(int nreps, int toRemove) {//shifts stack down, but does not reset ndx
int i = 0;
for (i = toRemove; i < nreps; i++) {
mrep[i]... |
4d9e17f6584f8ab9ad7df916cb71592923349cb704ffc3929c172d9c3b4c8e6e | C | 5,654 | 182 | /* "Entropy weighting" to determine absolute sequence number to use in hmmbuild.
*
* Reference:
* L. Steven Johnson, "Remote Protein Homology Detection Using Hidden Markov Models",
* Ph.D. thesis, Washington University School of Medicine, 2006.
*
* SRE, Fri May 4 14:01:54 2007 [Janelia] [Tom Waits, O... |
1687c3e4203a7ed94d7d7e992a321eaa0a6c4f68a854a2582de036c11b76e713 | C | 5,664 | 217 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include "gfa.h"
/*******************************************
* A tract definition:
*
*Find all AT stretches of 4 to 9,
* regardless of A/T order.
*Find Longest A or AnTn run (NAs).
*Start at first A. Restart count at TA steps
*Find longes... |
245dbc197383f3ae98b1a4c9510e2d35b9912d5c35760c08e69b0abe029d55e9 | C | 5,676 | 189 | #include <math.h>
#include <matrix.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwSize *dimsout;
mwIndex indx;
int i, j, k, numdims;
int numelin, numrows;
mxClassID classid;
double *input1r, *input1i, *input... |
6559243aede11b99d70469bd6685a7f84051ce0bc3f6cf68737751825dbc0c78 | C | 5,694 | 174 | /* PAML interface.
*
* Ziheng Yang, "Phylogenetic Analysis by Maximum Likelihood" [Yang97]
* http://abacus.gene.ucl.ac.uk/software/paml.html
*/
#include "esl_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_vectorops.h"
#include ... |
5bc8e9ac352e7dd49a55e71425440ff48e228489503738d85f4a6a9ed7848d6b | C | 5,882 | 136 | /* Assigns sequence weights to an MSA.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msaweight.h"
#include "esl_random.h"
#define WGTOPTS "-g,-p,-b,-f"
static ESL_OPTIONS ... |
9418cd10d740733592ac1361985598dd7488178c93401a597a5b3ec8c5727f55 | C | 5,915 | 181 | #include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include "gfa.h"
/*******************************************************************
* findIR eXplorer (crux) *
* Program to locate possible cruciforms in nucleic acid sequence *
*************************************... |
cd4017601d02fd048eb828759b13af960cea37defd3c611c100e7a6c95c94714 | C | 5,940 | 236 | /*
Copyright © 2011 by Université catholique de Louvain.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files, to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribu... |
762a106c0a9f23989c8156e85918208bf279882fa9c46cead29e8c20f2d4b725 | C | 5,945 | 219 | /* This module is unfinished; don't try to use it for anything! */
/* Standard Smith/Waterman sequence alignment
*
* Contents:
*
*
*/
#include "esl_config.h"
#include "easel.h"
#include "esl_composition.h"
#include "esl_scorematrix.h"
#define eslSWAT_PROHIBIT -999999999
/* Function: esl_swat_Score()
* ... |
a3df82a5048f48e2f91f1bcd33e459f7677509f843143d7d1642e2ddc2bca1d5 | C | 6,122 | 149 | #include <stdio.h>
void print_usage(char arg0[]) {
fprintf(stderr, "\n\n");
fprintf(
stderr,
"************************ GFA2 ********************************************\n");
fprintf(
stderr,
"*****************************************************************************\n");
fprintf(
stderr,
"u... |
77eaef3d0a8e49c7f8321199211a101a97d857934b786646aa2e18998eac17a8 | C | 6,238 | 239 | /*
Copyright © 2011 by Université catholique de Louvain.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files, to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribu... |
9ed976e4c66478e8b6a8856424816147a971f75894c66f03274ab8119074dde0 | C | 6,371 | 213 | /*
* x86/cpu_features.c - feature detection for x86 CPUs
*
* Copyright 2016 Eric Biggers
*
* 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 lim... |
97298a8a7b540d5c86375fed0971b3cfa7052c3d2da70c4ba55e1ef0a3d6a6d3 | C | 6,420 | 173 | /*
Copyright (c) 2011-2013, ESN Social Software AB and Jonas Tarnstrom
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, t... |
f2cb109bb324d1e7eabb9cd4f8948c25536066e8b9292916353ee4683f446612 | C | 6,423 | 190 | #include "esl_config.h"
#include <stdio.h>
#include <sys/stat.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_distance.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_subcmd.h"
static ESL_OPTIONS cmd_options[] = {
/* name type default env r... |
ee3f9811747217571cc834c36d994f01b3e0f340537f1225ca10298be52f9665 | C | 6,556 | 204 | #include <math.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims, indx1, indx2, indx3;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1... |
462c4540c4cf45bc601492781c2fe66b17c07ed34a814b5bd4440128daab6ec9 | C | 6,631 | 156 | /* `easel index` - create SSI index for sequence file
*
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_regexp.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_ssi.h"
#include "esl_subcmd.h"
static ESL_OPTIO... |
d69c72e28d701c50f34764ad433d2a22d9f734b24d748182285d22605d9cef13 | C | 6,782 | 238 | /*
* The routine functions for 2-D Barnes-Hut Trees
*
* Copyright (c) 2014, Zhirong Yang (Aalto University)
* All rights reserved.
*
*/
#include "mex.h"
#include "barnes_hut.h"
#include <math.h>
#include <string.h>
#include <float.h>
#define MAX(a,b) ( (a) > (b) ? (a) : (b) )
#define MIN(a,b) ( (a) < (b) ? (a) ... |
b329c3574f35843809f02fcaae1620e9edaaafc1617abab9b3b17c0841f90e2f | C | 6,795 | 185 | /*
Copyright (c) 2011-2013, ESN Social Software AB and Jonas Tarnstrom
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, t... |
d0d321a37ea2a320da8ce053227343fa95fba6792665218c0f78755653ca6f16 | C | 6,909 | 316 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "gfa.h"
/***********************************************************
* procedure to create tab separated motif files **
* ================================================ **
***********************************************************... |
5262c6a10c6244c7b2ee00645bc89b07e71345d83edb2a9c44287583a4f03030 | C | 6,921 | 269 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: xzlartg.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47... |
4bf98fe046f15ab3877a2af97d3cd84305db9a52ca4cd0092b34a03991652ba1 | C | 6,948 | 225 | /* A cached profile database. Used by the hmmpgmd daemon.
*
* Contents:
* 1. P7_HMMCACHE : a daemon's cached profile database.
* 2. Benchmark driver.
* 3. Unit tests.
*/
#include "p7_config.h"
#include <stdlib.h>
#include <string.h>
#include "easel.h"
#include "hmmer.h"
#include "p7_hmmcache.h"
/******... |
0afbef1f628ad4042d56f4250b0aef013f841f1a00ee62fb89ea8679d9e9f1c2 | C | 7,136 | 279 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: compute_M_AIW.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 20-Jul-2022... |
3be7ea853fa9ed95922be30da38e95700216be1d31eb37470aee377685d2210f | C | 7,303 | 164 | /* Determine range of sequences for one of many parallel processes.
*
* EPN, Wed Mar 24 07:23:27 2010
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_fileparser.h"
#include "esl_keyhash.h"
#include "esl_regexp.h"
#incl... |
0743f9652bf2d29819b8f63d2ccbe5c41f25297eb4eedf65aa9c1dd8e145e8df | C | 7,324 | 251 | /* Vectorized routines for x86 Advanced Vector Extensions (AVX)
*
* Most speed-critical code is in the .h file, to facilitate inlining.
*
* Contents:
* 1. Debugging/development routines
* 2. Benchmark
* 3. Unit tests
* 4. Test driver
*
* This code is conditionally compiled, only when <eslENA... |
13967f25c780cfd33131334c6d46201b0c9da77371d2393f507dda7ecfcdbb58 | C | 7,480 | 235 | /* Quicksort.
*
* Differs from stdlib's qsort() in that Easel provides a standardized
* and reentrant way to sort arbitrary data arrays/structures by
* sorting an array of unique integer identifiers.
*
* Contents:
* 1. Quicksort algorithm
* 2. Unit tests
* 3. Test driver
* 4. Example
*/
#includ... |
9f5c584764dd533925a7706a06c99978428d18dd3765e2d9c964f160fc085875 | C | 7,690 | 274 | /*
smlr_mex.c:
This file contains the MEX optimized version of the Sparse
Multinomial Logistic Regression algorithm described in:
Krishnapuram, B., Figueiredo, M., Carin, L., & Hartemink, A. (2005)
“Sparse Multinomial Logistic Regression: Fast Algorithms and
Generalization Bounds.” IEEE Transactions on Patt... |
5e5488a02c93a403cf4017c6aaab2909ab84df5ca25e49d644cb6e3ad318843c | C | 8,021 | 298 | #include "mex.h"
/*
* r = POLYEXP_SOLVE_SYSTEM(BASIS, CONVRES_F, CONVRES_C, IS_REAL)
*
* Helper function for polyexp.m, solving equations of the form (3.9)
* in Gunnar Farnebäck's thesis "Polynomial Expansion for Orientation
* and Motion Estimation", when the basis functions are monomials. See
* polyexp.m for t... |
123a8cdd8db4a7e3521139c21da1b85e8a053a3f08e2489c2de9fd35b3c0a149 | C | 8,269 | 241 | /* General routines used throughout HMMER.
*
* Contents:
* 1. Miscellaneous functions for H3
* 2. Unit tests
* 3. Test driver
*
* SRE, Fri Jan 12 13:19:38 2007 [Janelia] [Franz Ferdinand, eponymous]
*/
#include "p7_config.h"
#include <math.h>
#include <float.h>
#include "easel.h"
#include "esl_getopts... |
f6af7195b96cb0024b271a18091462004fe1905b39764586a1377350aa8d3433 | C | 8,307 | 221 | /* HMMER search daemon
*/
#include "p7_config.h"
#ifdef HMMER_THREADS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <signal.h>
#ifndef HMMER_THREADS
#error "Program requires pthreads be enabled."
#endif /*HMMER_THREADS*/
#include "easel.h"
#include "esl_getopts.h"
#include "hmmer.h"
#include... |
ab7fb53d8b5b991200e986f20b66f71549a28bbe54b904f37ef81a4696780048 | C | 8,329 | 292 | /*
* arm/cpu_features.c - feature detection for ARM CPUs
*
* Copyright 2018 Eric Biggers
*
* 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 lim... |
20020469b0c4011d077bb0e64284b02c721dc406f7b5ebc7398744ab20cc3453 | C | 8,335 | 304 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: xztgevc.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47... |
32df3c4972dab25ad4287f48ec6a81ed133eeae29c0a2bf4f309bcda5d449e59 | C | 8,499 | 231 | /* Graph algorithms
*
* Contents:
* 1. Maximum bipartite matching
* 2. Unit tests
* 3. Test driver
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include "easel.h"
#include "esl_matrixops.h"
#include "esl_vectorops.h"
/* Function: esl_graph_MaxBipartiteMatch()
* Synopsis: Max... |
c1d3f46eae6d1d82dc5159c789bf9c4ddec6408b01af9615a70bdb9678cbf2bc | C | 8,513 | 222 | /* HMMER search daemon
*/
#include "p7_config.h"
#ifdef HMMER_THREADS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <signal.h>
#ifndef HMMER_THREADS
#error "Program requires pthreads be enabled."
#endif /*HMMER_THREADS*/
#include "easel.h"
#include "esl_getopts.h"
#include "hmmer.h"
#include... |
4e4041cf9899ff493f7df73ad3d1d160ddbd7c0e76c414ed98a25b35a54e7d0a | C | 8,576 | 315 | #include "mex.h"
#define DEBUG 0
#define DIMENSIONALITY 3
/*
* conv3_readable.c
*
* Perform convolution in 3 dimensions. Only real images and kernels
* are supported. An optimized version of this code is available as
* conv3.c.
*
* Call:
* result=conv3(signal,kernel)
* or
* result=conv3(signal,kern... |
0c42e9ac84e7630e5a40c4515ca6b43fdb6dcce44a0817f5cfbc79e8ef59fbb8 | C | 8,588 | 262 | /* Miscellaneous summary statistics calculated for HMMs and profiles.
*
* SRE, Fri May 4 11:43:20 2007 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_vectorops.h"
#include "hmmer.h"
/* Function: p7_MeanMatchInfo()
* Incept: SRE, Fri May 4 11:43:56 2007 [Janelia]
*
* Purpose: C... |
8e71e7d30a4338c4390ce02a0c3ee963480db00587fb3de93dc46f4bf4d6d9c5 | C | 8,648 | 343 | #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... |
a9fcac45eca0b460a890639a4049c59cbb1422a50d330329a6ed3c96b0946fff | C | 8,946 | 339 | #include "mex.h"
#include <string.h>
#define DEBUG 0
/*
* ARRAYLOOP
*
* See the help text in arrayloop.m for a description.
*
* Author: Gunnar Farnebäck
* Medical Informatics
* Linköping University, Sweden
* gunnar@imt.liu.se
*/
void mexFunction(int nlhs, mxArray *plhs[], int nrhs,... |
c1703069c1e4f613d2342b19574b806070bbad06cf221245ff5026239fd1dfed | C | 9,052 | 383 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: svd.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 29-Jul-2022 12:50:42
... |
cdc458995cd4c81d6d0b0176d079dafb22325e4cec7d279b9f214fa6761c286b | C | 9,083 | 215 | /* Translate DNA sequence into six frames, into individual ORFs.
*
*/
#include "esl_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_gencode.h"
#include "esl_getopts.h"
/*****************************************************************
* 1. Main loop for reading complete sequences with ReadSe... |
9a3aff9ad57b521998264f5a05c652454d26d8b71ad7f7e59c543c9ed153b8e6 | C | 9,111 | 399 | #include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <errno.h>
#include "linear.h"
#define Malloc(type,n) (type *)malloc((n)*sizeof(type))
#define INF HUGE_VAL
void print_null(const char *s) {}
void exit_with_help()
{
printf(
"Usage: train [options] training_set_f... |
91d0155e5e879527f9a5dbc53f01ea2400fbb80a75b9dda71d867cdd53d18cca | C | 9,227 | 262 | /*
* crc32.c - CRC-32 checksum algorithm for the gzip format
*
* Copyright 2016 Eric Biggers
*
* 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... |
4a9f71312253b251faf2bdd48df0c9fedf5d72a0793943362e9fad408b374bfb | C | 9,321 | 369 | /*
* Academic License - for use in teaching, academic research, and meeting
* course requirements at degree granting institutions only. Not for
* government, commercial, or other organizational use.
* File: compute_MM_polarLuChipman.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on :... |
62cd6b4dfa36685c0a9b61bbf49622436024699fa830da078acb23ab6f75d8de | C | 9,378 | 319 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "gfa.h"
/***********************************************************
* procedure to create gff(2) files of repeats **
* ================================================ **
* a flat tab-delimited file with 9 columns. Example: **
... |
507ac28a80ec992fbdde2162033923dbc13072d1053c2b0a6008aeeee07d677d | C | 9,502 | 257 | /* Simple statistics on a sequence file
*
* SRE, Sun Feb 24 15:33:53 2008 [UA5315 to St. Louis]
* from squid's seqstat (1994)
*
* Wish list:
* - add an option for printing sequence names only.
* This would facilitate using esl-seqstat in incantations (with
* esl-selectn and esl-sfetch) to extract su... |
05a44e50a47016734079c10e05ba628d067efda8741244aa94509876e2af39b9 | C | 9,531 | 335 | /* Heaps and priority queues.
* See TH Cormen, CE Leiserson, and RL Rivest, _Introduction to Algorithms_, MIT Press, 1999.
*
* Contents:
* 1. The <ESL_HEAP> object: creation, access.
* 2. Rest of the API: inserting, extracting values.
* 3. Debugging, development.
* 4. Internal functions.
* 5. Un... |
192bb3c1ee7167e8065dedc11afc9b5919ac7b1a018b2099400833740b061bae | C | 9,661 | 230 | /* Forward/Backward, generic, with bands.
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_sq.h"
#include "hmmer.h"
#include "p7_gbands.h"
#include "p7_gmxb.h"
int
p7_GForwardBanded(const ESL_DSQ *dsq, int L, const P7_PROFILE *gm, P7_GMXB *gxb, float *opt_sc)
{
int *bnd_ip = gxb->bnd->imem; ... |
88b3a566a81156c6dbeadb046acd25149e8cfe7dc2b4402a0f8888fcb280fa9d | C | 10,020 | 340 | /* Statistical routines for normal (Gaussian) distributions.
*
* Contents:
* 1. Densities and distributions
* 2. Generic API, interface to histogram module
* 3. Unit tests
* 4. Test driver
* 5. Example
*
* To-do:
* - incomplete API, by the standards of other Easel stats modules.
* Compare... |
f281ec0ff2b6733b90ad0bb760645efd01269cf7edf59d7d069b3d4e90346052 | C | 10,085 | 166 | #include "esl_config.h"
#include <string.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msaweight.h"
#include "esl_subcmd.h"
#define PREFOPTS "--conscover,--randorder,--origorder"
static ESL_OPTIONS cmd_options[] = {
/* name type defa... |
46a6ae23d5d9c646f1d186da72efed82c5fd17570f06afb952033393f2a540f8 | C | 10,166 | 221 | // Copyright (C) 2019 Andrea Vázquez Varela
// This program 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 3 of the License, or
// (at your option) any later version.
// This program is di... |
425cc037e8c4af9be1a085754f7a1fb9e4a05ea00b1a77187bf8f50bd66a2224 | C | 10,354 | 224 | /* hmmpress: prepare an HMM database for faster hmmscan searches.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "hmmer.h"
static ESL_OPTIONS options[] = {
/* name type default env... |
26ad76812dd58fe31b85ead89c5896926890d7a9bea8b518c93ce2c059b6fc90 | C | 10,367 | 224 | /* Mask sequences in a sequence flatfile.
*
* SRE, Sat Oct 31 09:58:56 2009 [Janelia]
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#include "esl_fileparser.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_sqio.h"
static c... |
897b9002979ee648f372234f91125cf461673df7e7671c97d652da262882c767 | C | 10,652 | 258 | #include "esl_config.h"
#include <string.h>
#include "easel.h"
#include "esl_buffer.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_subcmd.h"
#include "esl_mem.h"
#include "esl_rand64.h"
static ESL_OPTIONS cmd_options[] = {
/* name type default env range ... |
a1b7231e50f44455c3bcf043b872a1a49f0596607d8c7634844b564c20a95d9d | C | 10,668 | 328 | /* HMMLOGO, code to print values for building logos, or functions to inline
*
* Contents:
* 1. logo value functions
* 2. hmmlogo application
*/
#include "hmmer.h"
/*****************************************************************
* 1. logo value functions
****************************************************... |
bd578ce065c2de3e3528727d9db1c3f603d5f87d11e1d99fc6f1855e3b5fae14 | C | 10,677 | 427 | #include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.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)*size... |
f40f406a43414c9e564370b3573499a05a0e1e3a9b397b6db80ff3703ffba25d | C | 10,850 | 243 | /*
* =============================================================
* [FEAT THRESH CONF] = DSTUMP(WEIGHT,POS,NEG,SORTEDIX,EPSILON,TRAINPATS,SEED);
*
* Computes the feat, thresh, and conf for a weak hypotheses for a dataset on one AdaBoost round
*
* This is part of the Princeton MVPA toolbox, released under the
* ... |
fbe22583a5cd04851651279d8e25fa04f50bc653381ad708fe33b434209adac2 | C | 10,919 | 357 | /*
Copyright (c) 2016, PyData Development Team
All rights reserved.
Distributed under the terms of the BSD Simplified License.
The full license is in the LICENSE file, distributed with this software.
Copyright (c) 2005-2011, NumPy Developers
All rights reserved.
This file is derived from NumPy 1.7. See NUMPY_LICEN... |
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