sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b6697bf9296730fb147a77a9a4da71847d8281d2a2f6aad2817ae2ff166e4ffb | C | 10,925 | 269 | /* Viterbi traceback; generic (non-SIMD) version.
*
* Contents:
* 1. Viterbi traceback
* 2. Example.
*
* SRE, Fri Aug 15 09:17:11 2008 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "hmmer.h"
/*****************************************************************
... |
bf0c3299a6e7323bdede7963ff5fdb01b9edc07aa79fd08f318bb7b4b5b66961 | C | 10,965 | 363 | /*
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... |
8edca32791752ff0c7f4c436bceeb7f6d9b454d708df7000f4ba3bb40538bdb4 | C | 11,058 | 372 | /* Dirichlet and Beta densities.
*
* Contents:
* 1. Dirichlet likelihood functions
* 2. Sampling from Dirichlets
* 3. Unit tests
* 4. Test driver
* 5. Example
*
* See also:
* esl_mixdchlet : mixture Dirichlets
* esl_gamma: Gamma densities
*/
#include "esl_config.h"
#inc... |
b808b63387a654e1096f1f6814a8de5be091f4b11e878f9fdbfa1babe631ac30 | C | 11,122 | 302 | /* Creating profile HMMs from single sequences.
*
* Contents:
* 1. Routines in the exposed API.
* 2. Experiment driver: generating HMMs for hmmsim tests
* 3. Unit tests.
* 4. Test driver.
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_vectorops.h"
#include "hmmer.h"
/*********************... |
e761d6ca1fdb431da604694ff27dd420897e4e28f989fce2c5c4daabf280e42f | C | 11,511 | 414 | /* Inflate the blocks of a BGZF file (BAM) on several threads; see
* bgzf_mt.h.
*
* Each block is inflated by libdeflate (vendored in libdeflate/: release
* v1.26, commit 92e6a0db9fa848d742f9eb286c92afc60f2c3dda of
* https://github.com/ebiggers/libdeflate, the files decompression and
* CRC32 need, unmodified; MIT... |
deb20e2e01a2365deaf60bb4bc5412e6122f8907800f270c39553398259a482b | C | 12,049 | 525 | #include "mex.h"
#define DEBUG 0
#define MAX_DIMENSIONALITY 4
/*
* CONV3
*
* Perform convolution in up to 4 dimensions. Only real kernels
* are supported but the signal may be complex.
*
* Call:
* result = conv3(signal, kernel)
* or
* result = conv3(signal, kernel, region_of_interest)
*
* signal ... |
c7c1e81602e7ba419709226378c9ac66424c62868b4cc34642b99084a1234954 | C | 12,154 | 451 | /*
* Copyright 2014 Google Inc. All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applica... |
52fae8ca1fae7aef173ff88946fa6547613ffdd69c04ec2655448ba085b71b94 | C | 12,193 | 283 | /* esl-histplot - collate data into a histogram and output xmgrace datafile.
*
* SRE, Tue Feb 21 14:18:05 2006
*/
/* Wish list
* - segfaults if you feed it nonnumeric data
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "ease... |
655371bb5173b21a32e9f9aee7036c6ba5b2ca427d323c8633dd2d6db49395cf | C | 12,239 | 338 | /* "null3" model: biased composition correction
*
* Contents:
* 1. Null3 estimation algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* See p7_domaindef.c -- null3 correction of per-seq and per-domain
* scores is embedded within p7_domaindef's logic; we split it out
* to a separ... |
6d5de932bc649a70f3270a1d3efc232896a7397f03598d37de3ce53306c15844 | C | 12,263 | 335 | /* esl-compstruct - calculate accuracy of RNA secondary structure predictions
*/
#include "esl_config.h"
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_wuss.h"
static char banner[] ... |
0afd9269f0a2adc7317f268f991e0c4c2acc6fa3edbbe262c6e8a2f0d2ebe68b | C | 12,301 | 672 | /* intervalFun_c.c C implementation of the intervalFun 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 i... |
5b895f8520ece3cc277d39da3f7320f271c8933d987de546b606db4e05e0ec2b | C | 12,401 | 288 | /* hmmalign: align sequences to a profile HMM
*/
#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 "esl_msa.h"
#include "esl_msafile.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_vectorops.h"
... |
494341414b670f430d89bec2add1d833e14ad84582e720992d6c643f75ff33b8 | C | 12,488 | 473 | #include "mex.h"
#include <string.h>
#define DEBUG 0
/*
* NEIGHBORHOODLOOP
*
* See the help text in neighborhoodloop.m for a description.
*
* Author: Gunnar Farnebäck
* Medical Informatics
* Linköping University, Sweden
* gunnar@imt.liu.se
*/
void mexFunction(int nlhs, mxArray *plh... |
9268faa7d84df25cdad69a69c1b799e80a6a62e06e470fc11e37e2a1ff65eac2 | C | 12,513 | 339 | /* Generalized single linkage clustering.
*
* Contents:
* 1. Single linkage clustering, generalized
* 2. Unit tests
* 3. Test driver
* 4. Example
*/
#include "esl_config.h"
#include <stdlib.h>
#include "easel.h"
#include "esl_cluster.h"
/******************************************************... |
f359053431700a30eb11c67265074fd9a3da62f614d358e5d197564ca09c3729 | C | 12,560 | 333 |
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <signal.h>
#include "brand.h"
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
// Parse command line ... |
d985d4f969c1816ff1d7bc97ea743ef6941437eb207dc805a0c6dedd7f50a250 | C | 12,724 | 243 | /* Input/output of HMMER3 HMMs in HMMER2 save file formats:
* for backwards compatibility.
*
* Contents:
* 1. Writing profiles in HMMER2 format.
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "hmmer.h"
#include "easel.h"
static int h2_multiline(FILE *fp, const ... |
854aa99b95eb12f4a46d1bcad690914a8acf47aa5ecd0829bfd7857e10e734c0 | C | 12,849 | 273 | /* hmmemit: sample sequence(s) from a profile HMM.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_dmatrix.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_random.h"
#include "esl_sq.h... |
cfa5b4b7c997dbb3b6a6daaaf2b69aec770b7ccf819e8a40a4c66cfffe09c7fe | C | 12,920 | 329 | /* Fetch an HMM from an HMM database (such as Pfam)
*
* SRE, Mon Jun 18 09:30:06 2007 [Janelia]
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_fileparser.h"
#include "esl_getopts.h"
#include "esl_keyhash.h"
#include "esl_ssi.h"
#include "hmm... |
76614cd670ae41815eb462ca7137e47a42a89af64014d0a26753c0376dde729b | C | 12,993 | 415 | /* Tracking cpu/system/elapsed time used by a process.
*
* Credits:
* - Thanks to Warren Gish for assistance.
* - Includes portable high-resolution timer code
* (C) 2012 David Robert Nadeau, http://NadeauSoftware.com/
* Creative Commons Attribution 3.0 Unported License
* http://creativecommons.o... |
d1c1a4152933202491d3c9af7c3a5783118967997a294f3dcb98f8ab6753a467 | C | 13,021 | 292 | /* hmmpgmd: hmmer deamon searchs against a sequence database.
*
* MSF, Thu Aug 12, 2010 [Janelia]
*/
#include "p7_config.h"
#ifdef HMMER_THREADS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <unistd.h>
#include <signal.h>
#include <pthread.h>
#include <setjmp.h>
#include <... |
56d810aa128c325062dde1f8b22e625f99e3d9a62d937d8c74ecfbd03f11ac53 | C | 13,049 | 427 | /* Functions to manipulate HMMD_SEARCH_STATUS objects.
* Contents: 1) Serialization and Deserialization routines
* 2) Debugging/Utility Functions
* 3) Unit Tests
* 4) Test Driver
* NPC 2/20/19 [Sparta]
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <stri... |
989e0d2e7a30a2a653794558fa7192fec372e928d8831fb48595cb8d209101ad | C | 13,057 | 343 | #include "mex.h"
#include "math.h"
/* RK4 is a function which performs one step of the Runge-Kutta 4 ray tracing
*
* EndPoint = RK4(StartPoint, GradientVolume, StepSize);
*
* inputs :
* StartPoint: 2D or 3D location in vectorfield
* GradientVolume: Vectorfield
* Stepsize : The stepsize
*
* outp... |
684dcb26b855fd0a6042c889cdde5962e1991a9549e50a04f2b1f37ade6d3dc5 | C | 13,093 | 443 | /* Simple master/worker data parallelization using POSIX threads.
*
* Contents:
* 1. The <ESL_THREADS> object: a gang of workers.
* 2. Determining thread number to use.
* 3. Examples.
*/
#include "esl_config.h"
#ifdef HAVE_PTHREAD
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <pt... |
fe5147087025d120a27a919971be0a59a0878576267efaaf88f651f6b862e7ba | C | 13,274 | 471 | /* Runtime detection of optional processor characteristics.
*
* Contents:
* 1. Checking for support of x86 vector code
* 2. Internal code used in those checks
* 3. Unit tests
* 4. Test driver
* 5. Example
*
* References:
* https://software.intel.com/en-us/articles/how-to-detect-new-instruction-su... |
d7316a5a2396ba40c76616b3fa9536d21ad55b17af92dd6e3f8c9cb27205bda9 | C | 13,386 | 608 | /* Simple matrix operations.
*
* Contents:
* 1. The matrixops API.
* 2. Debugging and development tools
* 3. Unit tests
* 4. Test driver
*
* Compare:
* esl_vectorops: simple vector operations
* esl_dmatrix: matrix algebra, double precision
*
* Note:
* Don't use <const> qualifier on i... |
aa9558cf5043f80e0764d268f14f62748de85adaa0e9a21b98771c876d1db276 | C | 13,442 | 358 | /* Mixture Dirichlet priors for profile HMMs.
*
* SRE, Sat Mar 24 09:12:44 2007 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_vectorops.h"
#include "hmmer.h"
/* Function: p7_prior_CreateAmino()
* Incept: SRE, Sat Mar 24 09:35:36 2007 [Janelia]
*
* Purpose:... |
712b929652d5b28020189ec4d9774ef7ec0aeca356753eefb47f3ce3e3de1277 | C | 13,735 | 401 | /* Clustering sequences in an MSA by % identity.
*
* Table of contents:
* 1. Single linkage clustering an MSA by %id
* 2. Internal functions, interface to the clustering API
* 3. Some internal functions needed for regression tests
* 4. Unit tests
* 5. Test driver
* 6. Example
*
* (Wonderin... |
0c1324519dcf74f3a728a48601eb9984fa8072631a70b28fad5d424d2fc7e877 | C | 14,128 | 370 | /* Fetch an MSA from a multi-MSA database (such as Pfam or Rfam).
*/
#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_mem.h"
#include "esl_ssi.h"
#include "esl_msa.h"
#incl... |
aef9976038d7a71d6ad06c167588fe7ca4600de4a5beabb74825e5d500cfe1c1 | C | 14,137 | 503 | /*
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, this list o... |
9f6ca3190c5ecec74a2f2ac629cb53526747b06bcf0b2eafe8f7ddc3293126d0 | C | 14,314 | 415 | /* p7_FLogsum() function used in the Forward() algorithm.
*
* Contents:
* 1. Floating point log sum.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*
* Exegesis:
*
* Internally, HMMER3 profile scores are in nats: floating point
* log-odds probabilities, with the log... |
abbb57cbbd75a006048c47dc40e91f362df9fd4e9749bb65b6114fa2f0f5dbdf | C | 14,490 | 503 | /*
* 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: xzggev.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47:... |
bafd2e92be5c223126a734a625b7b11b90fe736167d486d2958b427ce1ffebc4 | C | 14,495 | 328 | /* esl-mixdchlet : utilities for estimating new mixture Dirichlet priors
*
* Contents:
* 1. main : subcommand brokerage
* 2. fit : fit new mixture Dirichlet to count data
* 2. score : score count data with a mixture Dirichlet
* 3. gen : generate synthetic count data from a mixture Dirichlet
... |
61a8a9dd3c1ed57620712de24dd8e4d91d90cbb6d9296c3c80d0f550e348a5c8 | C | 14,710 | 411 | /* Portable aligned memory allocation.
*
* See esl_alloc.md for notes.
*
* Contents:
* 1. Portable(-ish) fallback implementation of aligned allocation.
* 2. esl_alloc_aligned(), esl_alloc_free() API calls
* 3. Benchmark driver
* 4. Unit tests
* 5. Test driver
*/
#include "esl_config.h"
#incl... |
bd6b3dc2df7d2888b771401256218ed89f03760b3538f1c3398f2a629948d92a | C | 15,545 | 391 | /* Shuffling or generating random sequences.
*
* SRE, Wed Jan 16 15:30:05 2008 [UA5230 to New York]
* from squid's shuffle (1995)
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_composition.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#in... |
a217d749fccac9ff7f241a34d808f9625233fbb1b472c82c97b78371b94960f2 | C | 15,631 | 425 | /* Posterior decoding algorithms; SSE versions.
*
* Contents:
* 1. Posterior decoding algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*/
#include "p7_config.h"
#include <stdio.h>
#include <math.h>
#include <x86intrin.h>
#include "easel.h"
#include "esl_sse.h"
#include "hmmer.h... |
fa32b1ff011eeea55c8944ec40f55dc36c33545c1b130652ca978444b35f9f85 | C | 15,689 | 430 | /* Posterior decoding algorithms; VMX versions.
*
* Contents:
* 1. Posterior decoding algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* SRE, Mon Aug 18 08:15:50 2008 [Janelia]
*/
#include "p7_config.h"
#include <stdio.h>
#include <math.h>
#ifndef __APPLE_ALTIVEC__
#include... |
8422ebf470bba937f7a39287cce5e2d4806ebea924fe9b2e2ac79bbf59ee35ce | C | 15,943 | 531 | /* Finding roots.
*
* Contents:
* 1. The ESL_ROOTFINDER object.
* 2. One-dimensional root finding.
* 3. Unit tests.
* 4. Test driver.
* 5. Examples.
*/
#include "esl_config.h"
#include <math.h>
#include "easel.h"
#include "esl_rootfinder.h"
/********************************************************... |
5ebae23e7f8fd30ce82f46005ab4a0a8591455f1598058ea6d3f122b42bd4ae0 | C | 16,341 | 472 | /* The Plan7 SCOREDATA data structure, which holds a compact representation
* of substitution scores and maximal extensions, used by nhmmer.
*
* Contents:
* 1. The P7_SCOREDATA object: allocation, initialization, destruction.
* 2. Unit tests.
* 3. Test driver.
*/
#include "p7_config.h"
#include <stdlib.h>... |
d163dbc84ea7821e169c61db272312611fb09e7adcec9252ba9d639282febfc0 | C | 16,541 | 438 | /* "null2" model: biased composition correction
*
* Contents:
* 1. Null2 estimation algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*
* See p7_domaindef.c -- null2 correction of per-seq and per-domain
* scores is embedded within p7_domaindef's logic; we split it ... |
07391284bde41a02f6d49013ceb4ac8e6aecbf21dbcffcff368e95f47d84bbbb | C | 16,607 | 424 | #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, numdims;
int numelin;
mxClassID classid;
double *input1r, *input1i, *output1r, *output1i... |
58b50ce649d97b76c249ca3a837ecfb50839992cb68826c8bb5e421cac596a5d | C | 16,736 | 557 | /* Threaded work queue.
*
* Contents:
* 1. Work queue routines
* 2. Examples.
*/
#include "esl_config.h"
#ifdef HAVE_PTHREAD
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <pthread.h>
#include "easel.h"
#include "esl_workqueue.h"
/****************************************************... |
103f05fe4f97aafba880a2c6f9c20860f75167299e23e5b047422c27f6abba8f | C | 17,022 | 531 | /*
* 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: xzhgeqz.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47... |
de1824a5d1a8425a9161bcdc3d77f4786c520b2ac3c69164ea212c330128bc07 | C | 17,500 | 527 | /* P7_GMX implementation: a generic dynamic programming matrix
*
* Contents:
* 1. The <P7_GMX> object
* 2. Debugging aids
* 3. Unit tests
* 4. Test driver
*/
#include "p7_config.h"
#include "hmmer.h"
/*****************************************************************
*= 1. The <P7_GMX> object.
*******... |
2929afb2b3d268382a541897e36c95a4026ecb6a8796a1b54e656b6dc7824251 | C | 17,568 | 502 | /* "null2" model, biased composition correction; VMX implementations.
*
* Contents:
* 1. Null2 estimation algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* SRE, Mon Aug 18 08:31:11 2008 [Janelia]
*/
#include "p7_config.h"
#include <stdlib.h>
#include <string.h>
#ifndef __APPL... |
b36864c9221073bdd45c8184b8b036ab1fa0468fea6fdf75dd36c968682b3670 | C | 17,568 | 495 | /* "null2" model, biased composition correction; SSE implementations.
*
* Contents:
* 1. Null2 estimation algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* SRE, Mon Aug 18 08:31:11 2008 [Janelia]
*/
#include "p7_config.h"
#include <stdlib.h>
#include <string.h>
#include <xmmi... |
58f4b09907345b25a58b70e3422bdcf7a64ff661196db2a96b33f39ec20d85c2 | C | 18,360 | 652 | /* Sequence and profile caches, used by the hmmpgmd daemon.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_stopwatch.h"
#include "hm... |
1dfa42088697275c3151989e7b71539ad43afc5265646d7dab7d6a9dc88edeb8 | C | 19,095 | 516 | #include "p7_config.h"
#include <sys/times.h>
#include <string.h>
#include "easel.h"
#include "hmmer.h"
static ESL_OPTIONS options[] = {
/* name type default env range toggles reqs incomp help docgroup*/
{ "-h", ... |
166332ff46d1cf681c9e7aeb01c45c3f87331af88485c4d927c1c4af27793b7e | C | 19,123 | 617 | /*
* 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: eigL4x4real.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 26-Jul-2022 1... |
44234a819e4d72520aec744a1a2799368574fb9ae8c6d316d1daf94937d560bb | C | 19,242 | 481 | /* Posterior decoding algorithms; generic versions.
*
* Contents:
* 1. Posterior decoding algorithms.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*/
#include "p7_config.h"
#include <math.h>
#include "easel.h"
#include "hmmer.h"
/******************************************... |
03534f83582a011966224cffdf6217eb3d7f53dc693a2ead3a677d9a96155d03 | C | 19,288 | 521 | /* Stochastic traceback of a Forward matrix; generic (non-SIMD) version.
*
* Contents:
* 1. Stochastic traceback implementation.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*
* SRE, Fri Aug 15 10:50:55 2008 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include... |
5404646ac5a68accf9e5d20b4f1edd80662dde6ce873a8fb317274b3dd522504 | C | 19,332 | 628 | /*
* 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: xhseqr.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47:... |
3a80aa950ce885b69bc177c41e889d2324f16ba3cce42abac857cb71aeb41127 | C | 19,976 | 594 | #include "functions.h"
GateConstStruct newGateConstStruct(uint32_t aFtype, float aX1, float aX2, float aX3,
float aX4, float aX5, float aX6,
float aX7, float aX8,float aX9,uint32_t bFtype, float bX1, float bX2, float bX3,
float bX4, float bX5, float bX6, float bX7, float bX8, float bX9... |
8a86766bfc7950d69eb26d83b1720c034772b52e4e8f50fc161dbae47aa45b37 | C | 19,994 | 639 | /*
* 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: eig.c
*
* MATLAB Coder version : 5.2
* C/C++ source code generated on : 19-Jul-2022 14:47:38
... |
eedb69bfa21f3dc6ba078898e5b728cd2178e5f730ae2f997680219bffacffeb | C | 20,310 | 539 | /* Summarizing results of a benchmark by plotting a ROC-like plot,
* including confidence intervals derived by Bayesian bootstrapping.
*
* The <.out file> from a profmark benchmark consists of lines:
* <E-value> <bitscore> <target_sequence> <query_model>
* Target sequence names are either
* decoy\d+ ... |
c6d335b4126ff3953a0cd81353dc7be0cd921e0d7d065c6a5759a69705a8fabd | C | 20,622 | 553 | /* Viterbi score implementation; VMX version.
*
* This is a SIMD vectorized, striped, interleaved, one-row O(M)
* memory implementation of the Viterbi algorithm, for calculating an
* accurate Viterbi score, without traceback.
*
* This implementation has full range and precision, so it may be used
* in any alig... |
5f8a090427fac37d97159fef84540eaf31875540fa6b00deba11d04feacaebd8 | C | 20,727 | 552 | /* Viterbi score implementation; SSE version.
*
* This is a SIMD vectorized, striped, interleaved, one-row O(M)
* memory implementation of the Viterbi algorithm, for calculating an
* accurate Viterbi score, without traceback.
*
* This implementation has full range and precision, so it may be used
* in any alig... |
e1388938524991cfd2b61f6b5443c9eccc6575fc2dbdbcd04801ba761cf4e825 | C | 20,812 | 672 | /* Function for conversion of binary data to MSA.
*
* Contents:
* 1. The <esl_msa_hmmpgmd2msa> function
* 2. Test driver
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "hmmer.h"
#include "hmmpgmd.h"
#include "esl_sqio.h"
/***********************************... |
c4e761562541f4472c9a04a0a29727d2a17446175c92bfa711570b3fa484c584 | C | 21,034 | 621 | /* SSE implementation of an optimized profile structure.
*
* Contents:
* 1. The P7_OMX structure: a dynamic programming matrix
* 2. Debugging dumps of P7_OMX structures
*
* See also:
* p7_omx.ai - figure illustrating the layout of a P7_OMX.
*
* SRE, Sun Nov 25 11:26:48 2007 [Casa de Gatos]
*/
#include... |
eac52ae2aa6380f07b85c866a9ccb5c2b6bbc44767d8e18655c75eaa002e3c77 | C | 21,172 | 641 | /* VMX implementation of an optimized profile structure.
*
* Contents:
* 1. The P7_OMX structure: a dynamic programming matrix
* 2. Debugging dumps of P7_OMX structures
*
* See also:
* p7_omx.ai - figure illustrating the layout of a P7_OMX.
*
* SRE, Sun Nov 25 11:26:48 2007 [Casa de Gatos]
*/
#include... |
370fd6867dd3e6f43e714cd3f293e188c37a33863282826846a4a1517967ea7d | C | 21,211 | 805 | /* General hidden Markov models (discrete, of alphabetic strings)
*/
#include "esl_config.h"
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_random.h"
#include "esl_vectorops.h"
#include "esl_hmm.h"
/* Function: esl_hmm_Create()
* Synopsis: A... |
f8b4181fa3fb195ffe5919a92f62ea7b8d2e13ca1358f48fbba1d5d9b8103a54 | C | 21,211 | 678 | /* Statistical routines for exponential distributions.
*
* Contents:
* 1. Routines for evaluating densities and distributions
* 2. Generic API routines: for general interface w/ histogram module
* 3. Routines for dumping plots for files
* 4. Routines for sampling
* 5. Maximum likelihood fitting
* ... |
6469c758a3289c719e1166554c92dced9f47f1e06b940a747c2b7ea44add0545 | C | 21,222 | 609 | #include "functions.h"
GateConstStruct newGateConstStruct(uint32_t aFtype, float aX1, float aX2, float aX3,
float aX4, float aX5, float aX6,
float aX7, float aX8,float aX9,uint32_t bFtype, float bX1, float bX2, float bX3,
float bX4, float bX5, float bX6, float bX7, float bX8, float bX9... |
92b979b47f5bb2dedacb62ba25e036c699b63f33e0c50402ec247fb609433fa7 | C | 21,356 | 559 | /* Vectorized routines for PowerPC processors, using Altivec/VMX intrinsics.
*
* Table of contents
* 1. SIMD logf(), expf()
* 2. Miscellaneous convenience functions.
* 3. Benchmark
* 4. Unit tests
* 5. Test driver
* 6. Example
*
*********************************************... |
fb17199ee0df8b1dd827125044c1def06ec7a7e6b5a89f4ac693c3472bf3e3ae | C | 21,522 | 661 | /* Statistical routines for stretched exponential distributions.
*
* Contents:
* 1. Evaluating densities and distributions
* 2. Generic API routines: for general interface w/ histogram module
* 3. Dumping plots for files
* 4. Sampling
* 5. ML fitting to complete data
* 6. ML fi... |
aa47aca9eeff559c569b5de80240ce8a84cc86d83a0c551824f28974b15b7cf9 | C | 21,672 | 642 | /* Routines for the P7_PROFILE structure - Plan 7's search profile
*
* 1. The P7_PROFILE object: allocation, initialization, destruction.
* 2. Access methods.
* 3. Debugging and development code.
* 4. Unit tests.
* 5. Test driver.
*
* See also:
* model... |
63a56d8cab1a31b411bcfd8d74c8ed161edce575fa7e5e57edf446ce5bf3592b | C | 22,163 | 573 | /* MSV algorithm; generic (non-SIMD) version.
*
* Contents:
* 1. MSV implementation.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*
* SRE, Fri Aug 15 10:38:21 2008 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_gumbel.h"
... |
2d9d6530fed0a78210632d1249aa6dcf0631a277dbc26ec962c54080bd0b7ebe | C | 22,248 | 494 | /* Fetch a sequence (or part of one) from a sequence flatfile.
*
* From squid's sfetch and ffetch
* SRE, Mon Mar 31 16:12:50 2008 [Janelia]
*/
#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_... |
dacdf40c58564af512c9df7fbd864dfd637b3c4f8f83b13c5f8d3b265a4637f2 | C | 22,718 | 604 | /* Emitting (sampling) sequences from an HMM, in either core or
* profile form.
*
* 1. Exported API: sequence emission routines.
* 2. Private functions.
* 3. Stats driver.
*
* SRE, Tue Jan 9 08:55:53 2007 [Janelia] [The Crystal Method, Vegas]
*/
#include "p7_config.h"
#include "easel.h"
#include "... |
63b18177f5a61b881c7439a011ca5e84fa87b730b633386d27b89da7ff5af2d1 | C | 22,894 | 575 | /* Shuffling, bootstrapping, permuting alignments, by column or row.
*
* Table of contents:
* 1. Shuffling or resampling columns ("horizontal" shuffling)
* 2. Shuffling residues within columns ("vertical" shuffling)
* 3. Permuting sequence order (i.e. by row)
* 4. Shuffling pairwise (QRNA) alignments... |
8e6cff765bf1b01d24d68fee561af6d0dffa49bef5eb09c7c88378e0fc5bfe38 | C | 22,899 | 805 | /* Statistical routines for mixtures of generalized extreme value distributions.
*
* Contents:
* 1. The ESL_MIXGEV object
* 2. Evaluating densities and distributions
* 3. Generic API routines: for general interface w/ histogram module
* 4. Dumping plots to xmgrace XY format
* 5. Sampling ... |
30829a354ea0e80f7c4eaf6b8cbc974174599ccd5a3dec1bfb3a0827cdac545f | C | 23,749 | 461 | /* Add mask line to a multiple sequence alignment
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#undef HMMER_THREADS
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_mpi.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msaweight... |
b58ca41c7a4215e9d533e637eb7398652580f5b0eb69984734d8407eff0df2a8 | C | 23,840 | 623 | /* Optimal accuracy alignment; generic version.
*
* Contents:
* 1. Optimal alignment accuracy fill.
* 2. Optimal alignment accuracy traceback.
* 3. Benchmark driver
* 4. Unit tests
* 5. Test driver
* 6. Example
*
* SRE, Fri Feb 29 12:48:46 2008 [Janelia]
*/
#include "p7_config.h"
#include <flo... |
d45ba0273cf6dab40370787d7fa8ef372cc542852ae00e11655807a5879e0251 | C | 23,969 | 642 | /*
* gcc -o generic_fwdback_rescaled_example -mssse3 -I. -I../easel -L../easel -L. generic_fwdback_rescaled.c -lhmmer -leasel
*/
#include "p7_config.h"
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_vectorops.h"
#... |
cea7f0e90672c6108da5f49dc40311177f783537cc3ac834d69200020229f085 | C | 24,008 | 589 | /* Defining domain number and coordinates in a significant hit by
* posterior sampling and clustering.
*
* SRE, Wed Jan 9 07:26:34 2008 [Janelia]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_cluster.h"
#include "esl_vectorops.h"
#include "hmmer.h"
/* Function: p7_spensemble_Create()
* Synopsis: ... |
3d9f118261670eb39cc6dfaf4ce0aa0ddeffac394c5cca25a2872b89d6635c23 | C | 24,119 | 855 | /*
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... |
d7b0a2e6ae3d2dc057d83c6a7152a546e2c3a97aaafeb88c787cb958b4fb3d60 | C | 24,520 | 706 | /* Statistical routines for Weibull distributions.
*
* Contents:
* 1. Routines for evaluating densities and distributions.
* 2. Generic API routines, for general interface w/ histogram module
* 3. Dumping plots to files
* 4. Sampling
* 5. ML fitting to complete data
* 6. ML fitt... |
480c52da4bd56ed4d1aad630ae84951b3c04a00d5466fff1421d1282f10c5c55 | C | 24,903 | 667 | /* Construction of new HMMs from multiple alignments.
*
* Two versions:
* p7_Handmodelmaker() -- use #=RF annotation to indicate match columns
* p7_Fastmodelmaker() -- Krogh/Haussler heuristic
*
* The maximum likelihood model construction algorithm that was in previous
* HMMER versions has been deprecat... |
cadcf6f66e3831f315d21ca2aa63092ef6227ac1788b24fd711ac881f63e7222 | C | 25,073 | 650 | /* VMX implementation of stochastic backtrace of a Forward matrix.
* (Compare generic version, p7_GStochasticTrace().)
*
* Contents:
* 1. Stochastic trace implementation.
* 2. Selection of steps in the traceback.
* 3. Benchmark driver.
* 4. Unit tests.
* 5. Test driver.
* 6. Example.
*
... |
19c97e194d1c8f38b5951bde3db849cbaa322ba0f607cb22dbb4b57b59051190 | C | 25,161 | 794 | /* A simple token-based file parsing system.
*
* Contents:
* 1. The ESL_FILEPARSER object and its API.
* 2. Private functions.
* 3. Unit tests.
* 4. Test driver.
* 5. Examples.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "ea... |
87bd93a27f50f3efe26ce3e8a617a6493bae6a9b79a6c123dd11e711eb4eb465 | C | 25,225 | 591 | /* The "brute" integration test.
*
* Create an entirely hand-specified profile HMM from given
* parameters; enumerate all paths and calculate either the sum
* (Forward score) or max (Viterbi score). Compare this to
* <p7_GForward()> and <p7_GViterbi()> results.
*
* The test exercises all possible transitions i... |
fa0f21a6c55450b96445904585685b254bbc65e7e9a3d7d1bed3cba8e91217fd | C | 25,320 | 650 | /* SSE implementation of stochastic backtrace of a Forward matrix.
* (Compare generic version, p7_GStochasticTrace().)
*
* Contents:
* 1. Stochastic trace implementation.
* 2. Selection of steps in the traceback.
* 3. Benchmark driver.
* 4. Unit tests.
* 5. Test driver.
* 6. Example.
*
... |
c0075d57f7701e9b375579cf535c61d8ccbde2c2f4e06ae57e0352a832a20c53 | C | 25,646 | 581 | /* esl-compalign - compare two multiple sequence alignments
*
*/
#include "esl_config.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_msa.h"
#include "esl_msafile.h"
#include "esl_vectorops.h"
#inc... |
e605aefd27c23d34558d3f2989fc25941ea068b157f1a6153e487c75fc749f3a | C | 25,777 | 1,220 | /*
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, this list o... |
d67dde5ce34d64644b5eb3c91ca7d1296e87428465392f084ea3f5fd3b88e7e7 | C | 25,782 | 777 | /* Functions for HMMD_SEARCH_STATS objects
* NPC, 1/10/19, Havahd, "Sparta"
*
* Contents:
* 1) Serialization and deserialization routines
* 2) Unit tests
* 3) Test driver
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "easel.h"
#include "esl_ssi.h"
#include "hmm... |
40bd7ef22e15e85cef78762a094353f2db119f38e7e575f4722c1ef886dfbc85 | C | 25,882 | 622 | #include "p7_config.h"
#include <stdio.h>
#if defined eslENABLE_SSE
#include <xmmintrin.h> /* SSE */
#include <emmintrin.h> /* SSE2 */
#endif
#include "easel.h"
#include "esl_getopts.h"
#include "hmmer.h"
#if defined eslENABLE_SSE
int
fm_getbits_m128 (__m128i in, char *buf, int reverse)
{
byte_m128 new;
new... |
4f3dda9d2e8540b689118a4b9095c1e8834917cd54402ccfab352556e7230b6a | C | 25,925 | 1,233 | /*
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, this list o... |
623deaead946585b79ddb0590d9ab147edd1cac38a005afacfba9fb28e22a1e2 | C | 25,929 | 818 | /* Statistical routines for gamma distributions.
*
* Contents:
* 1. Routines for evaluating densities and distributions
* 2. Generic API routines: for general interface w/ histogram module
* 3. Dumping plots for files
* 4. Sampling
* 5. ML fitting to complete data
* 6. Test driver
* 7. Example
... |
53948f2ee1414e0821f1b1b8d2ff787f2a7a4a11be03f9b40b59ca123c04eb71 | C | 25,983 | 749 | /* Architecture-independent functions used in FM-index range compuations
* and list management.
*
* Contents:
* 1. List management
* 2. Interval / range computation
* 3. Functions related to the original sequence
* 4. FM data initialization, configuration, and reading from file
*/
#include "p7_config.h"... |
94e84fc402bf2e87e5a131a166816c9c7fed2e0a12bca1b5ff3019fbc54eeaf0 | C | 26,084 | 756 | /* esl_red_black.c -- functions for implementing red-black trees */
#include "esl_config.h"
#include "easel.h"
#include "esl_red_black.h"
#define TEST_ITERATIONS 10000
//#define P7_CHECK_RED_BLACK // check tree for invariants after every change
#if defined(P7_CHECK_RED_BLACK) || defined(eslRED_BLACK_TESTDRIVE) // onl... |
4de37aab3fa7ff56e0413f03027ed735a9ec8dda2d1bccd7e7ab4d2edcb47cb0 | C | 26,214 | 755 | /* P7_BG: the null (background) model
*
* Contents:
* 1. P7_BG object: allocation, initialization, destruction.
* 2. Reading/writing residue backgrounds from files.
* 3. Standard iid null model ("null1").
* 4. Filter null model.
* 5. Benchmark driver.
* 6. Unit tests.
* 7. Test dr... |
65781e3c66a5f9ba148e9c3a4223808fc9929c92ade9af057eb3ef152b77dec1 | C | 26,710 | 827 | /* functions to manipulate P7_DOMAIN objects. Currently, most P7_DOMAIN objects are created/
* manipulated from within code that processes other data structures, but this is somewhat
* bad practice. For now, this file mostly contains serialization/deserialization code.
* NPC 2/8/19 [Mother Russia]
*/
#include "... |
8201eae6dfa4db1b0cd2a0e75529999566b60c24a46b8b0690fbf0e4ffa04631 | C | 26,943 | 690 | /* Vectorized routines for Intel/AMD processors, using Streaming SIMD Extensions (SSE).
*
* Contents:
* 1. SIMD logf(), expf()
* 2. Utilities for ps vectors (4 floats in a __m128)
* 3. Benchmark
* 4. Unit tests
* 5. Test driver
* 6. Example
*
**************************... |
23f7ff6a1b72dd995561a6a5b94f47678522a8c3ba985e8a0e8983523a8128e8 | C | 27,088 | 803 | /* Routines for manipulating evolutionary rate matrices.
*
* There is no specific object for this module. Rate matrix
* operations use square nxn ESL_DMATRIX data objects. (The rmx
* module essentially subclasses the dmx module.)
*
* An instantaneous rate matrix is usually denoted by Q. A
* conditional proba... |
8342651888db15dacb29e08d62fb6d6715f51e965fc9a8369dde18b3e13c544b | C | 27,098 | 733 | /* Vectorized routines for ARM processors, using NEON intrinsics.
*
* Table of contents:
* 1. SIMD logf(), expf()
* 2. Utilities for float vectors (4 floats in an esl_neon_128f_t)
* 3. Benchmark
* 4. Unit tests
* 5. Test driver
* 6. Example
*
***************************... |
52b2c4a63116cd7c7d3bebd9cc647b33371dcbdf8658f2d74b3d43208f849cb5 | C | 27,668 | 829 | /* Portable, threadsafe, 64-bit Mersenne Twister random number generator.
*
* Contents:
* 1. <ESL_RAND64> object
* 2. Base esl_rand64_*() number generators
* 3. Other sampling routines
* 4. Internal functions implementing Mersenne Twister MT19937-64
* 5. Debugging and development tools
* 6. B... |
cf270b9def13c742304ca1123a7d0a8188bf2f1e0b1a56d064d4713da8d162e6 | C | 27,840 | 712 | /* Viterbi algorithm; generic (non-SIMD) version.
*
* This implementation is modified from an optimized implementation
* contributed by Jeremy D. Buhler (Washington University in
* St. Louis).
*
* Relative to the implementation in HMMER2, Jeremy rearranged data
* structures to reduce the number of registers ne... |
be85b5298a29f53db9060157e84c27db38cff9d4e43375596b8106bc0a679165 | C | 27,877 | 886 | /* worker side of the hmmer daemon
*/
#include "p7_config.h"
#ifdef HMMER_THREADS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <unistd.h>
#include <signal.h>
#include <pthread.h>
#include <setjmp.h>
#include <sys/socket.h>
#ifdef HAVE_NETINET_IN_H
#include <netinet/in.h> ... |
a7f1651b9532af83bb2279bf3b10a8932e7d34e006992fa79e1cc3ab94f7cb44 | C | 28,138 | 641 | /* Calculations and simulations relevant to E-value calculations.
*
* Contents:
* 1. p7_Calibrate(): model calibration wrapper
* 2. Determination of individual E-value parameters
* 3. Statistics and specific experiment drivers
* 4. Benchmark driver
*
* SRE, Mon Aug 6 13:00:06 2007
*/
#include "p7_... |
17f65c7ba562efa777f34c426285a1bdfe752567da140cdfe4022c606767dd6b | C | 28,245 | 941 | /* Partial emulation of Perl hashes (associative arrays),
* mapping keys (ASCII char strings) to array indices.
*
* Contents:
* 1. The <ESL_KEYHASH> object.
* 2. Storing and retrieving keys.
* 3. Internal functions.
* 4. Benchmark drivers.
* 5. Unit tests.
* 6. Test driver.
* 7. ... |
bbe84d1508499fc1e47b258ba1d20ad80c20f870caf4370314e671b7ab5aeef6 | C | 29,105 | 840 | /* P7_GMXCHK implementation
*
* Checkpointed forward/backward dynamic programming matrix.
* Derived from P7_GMX structure; see p7_gmx.[ch]
*
* Contents:
* 1. The <P7_GMXCHK> object.
* 2. Debugging and testing tools.
* 3. Internal (static) routines.
* 4. Unit tests.
* 5. Test driver.
* 6. Referen... |
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