sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f7ee077b5208edaad340edf264169a70ab3786394a8f877f9104cd21b4086330 | C | 29,176 | 867 | /* RNA secondary structure markup in WUSS notation.
*
* <> : base pairs in stem-loops, i.e. <<<___>>>
* () : base pairs in helices enclosing multifurcation of all <> stems
* [] : base pairs in helices enclosing multifurc of at least one () helix
* {} : base pairs in helices enclosing even deeper mu... |
c61eeb082703c61af2e50a20d6f48ee243ac00427cc6194d35fcacec958cee55 | C | 29,500 | 921 | /* 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> ... |
a6f349bea3de618afb608be274a096cec7adfbe2917f3a8efd4f68bdb34c46dd | C | 29,908 | 1,182 | /*
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.
Written by Mark Wiebe (mwwiebe@gmail.com)
Copyright (c) 2011 by Enthought, Inc.
Copyright (c) 2005-2011, NumPy Deve... |
00764dccc67ee4fa86255286bf738ae2c04e8cf299145be6711e078ff8dbc857 | C | 30,136 | 968 | /* Statistical routines for generalized extreme value (GEV) distributions.
*
* Contents:
* 1. 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 or censored data
* 6. ... |
0e03d097395a55985ad565e0b50c9efdb48a76c3527aeb148500a99a9846f371 | C | 30,281 | 575 | /* daemon client.
*/
#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 <ctype.h>
#include <sys/socket.h>
#ifdef HAVE_NETINET_IN_H
#include <netinet/in.h> /* On FreeBSD, you need netinet/in.h ... |
d3fba0bcab37ed5a38e7823c61a032aa774f7784791e242f91e375bb21acb47b | C | 30,568 | 717 | /* i/o of multiple sequence alignment files in "aligned FASTA" format
*
* Contents:
* 1. API for reading/writing AFA format
* 2. Unit tests.
* 3. Test driver.
* 4. Examples.
*/
#include "esl_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#incl... |
54848066149aff29a4825b81f651435c975d2a6973313337c5717ee2ddd570ee | C | 30,905 | 750 | /* Construct a training alignment/test sequences set from an MSA.
*
* Usage:
./create-profmark <basename> <msa Stockholm file> <FASTA db>
For example:
./create-profmark pmark /misc/data0/databases/Pfam/Pfam-A.seed /misc/data0/databases/uniprot-7.0/uniprot_sprot.fasta
*
* This generates five output file... |
a53d0a0602bbd11765b4b594fb02f8d09e5db01614a5335a947189398965a1fc | C | 31,167 | 996 | /* 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... |
4c36065cad316ace48a5c7ee6fc22f68e10c3b939148fad94d5fb0c13a87fe86 | C | 31,527 | 708 | /* Construct consensus secondary structures from individually annotated
* secondary structures
*
* EPN, Mon May 11 06:49:37 2009
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include <limits.h>
#include "easel.h"
#include "esl_distanc... |
cf4a904cd15fd2e1f59bcb9746d76c7ce972c292d27ef3f388d5c77bd6cd96ab | C | 31,843 | 826 | /* Forward/Backward algorithms; generic (non-SIMD) versions.
*
* Contents:
* 1. Forward, Backward, Hybrid implementations.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "hmmer.h"
/**********... |
036eb942e52f43b8cfd5c14e86b0afadda0d25125c1d8171c7e9c3c64973d96f | C | 31,928 | 1,060 | /* Functions to manipulate P7_HIT objects.
* Contents: 1) Serialization and Deserialization routines
* 2) Unit Tests
* 3) Test Driver
* NPC 2/13/19 [The soothing whir of the air filter]
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#i... |
c42e602cde799bfac3c91f1e3ce081791046021786e592bf9b05ac8783c5d46f | C | 32,728 | 935 | /* Mixture Dirichlet densities
*
* Contents:
* 1. <ESL_MIXDCHLET> object
* 2. Likelihoods, posteriors, inference
* 3. Maximum likelihood fitting to count data
* 4. Reading/writing mixture Dirichlet files
* 5. Debugging and development tools
* 6. Unit tests
* 7. Test driver
* 8. Example
*
* ... |
762dbd9ebf3f27af8689243b2d435b24c5f6a11a3c2efb98911c836cb8c43e21 | C | 32,908 | 841 | /* Forward/Backward, checkpointed: generic (non-SIMD) demonstration version.
*
* Contents:
* 1. Forwards: checkpointed fill, Forwards nat score.
* 2. Backwards: linear-memory back pass, recovering posterior-decoded bands.
* 3. Benchmark driver.
* 4. Example main().
* 5. References.
*/
#include ... |
a4afbd1d5b5ea8cacb9e2ba76184bef1d629a1fc96ecd2cb76e80790d5aad854 | C | 33,264 | 926 | /* The SSV filter implementation; SSE version.
*
* Contents:
* 1. Introduction
* 2. p7_SSVFilter() implementation
*
* Bjarne Knudsen, CLC Bio
*/
/*****************************************************************
* 1. Introduction
*****************************************************************/
/* He... |
a39266ce904d4d362e50c6387188e5c3b1a32dfd697b4624d9610a49e1dfa484 | C | 33,301 | 907 | /* Variable-length binary prefix codes for integers
*
* Contents:
* 1. Exponential Golomb codes
* 2. Golomb-Rice codes
* 3. Elias delta code
* 4. Google varint codes
* 5. Unit tests
* 6. Test driver
* 7. Example
*
* See also:
* esl_huffman : Huffman coding
*/
#include "esl_config.h... |
b343b956c0eb42e33c74b9df19598c232a241a5e891f5983118a2af11f0a9528 | C | 33,637 | 859 | /* The MSV filter implementation; VMX version.
*
* A "filter" is a one-row, O(M), DP implementation that calculates an
* approximated nat score (i.e. in limited precision - here, uchar)
* and may have limited numeric range. It will return <eslERANGE> if
* its numeric range is exceeded, in which case the caller wi... |
ef10de1f7fe7df18c16d52aa021f73850fc49f86e26cf90261a8b9847fbff7ce | C | 33,900 | 686 | /* Map two multiple sequence alignments to each other.
*
* EPN, Tue Sep 23 13:39:03 2008
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include <limits.h>
#include "easel.h"
#include "esl_distance.h"
#include "esl_fileparser.h"
#include ... |
19849005f79664c83aa57b2a5603c536152e5c5f1bc4440e90f65be1fc9ecf09 | C | 33,918 | 959 | /* Multidimensional optimization using conjugate gradient descent.
*
* Can be used even without derivative information; falls back to
* a numeric gradient if analytic gradient is unavailable.
*
* Contents:
* 1. esl_min_ConjugateGradientDescent(), our optimizer
* 2. ESL_MIN_CFG, for optional configuration... |
346086278f12e80a2a4a1a5da1785e1d7b5c057d2b78e87735216fa9c471849f | C | 34,098 | 1,093 | /* Huffman coding, especially for digitized alphabets.
*
* Contents:
* 1. The ESL_HUFFMAN object
* 2. Huffman encoding
* 3. Huffman decoding
* 4. Debugging, development
* 5. Internal function, components of creating huffman codes
* 6. Example driver
*
* Useful emacs gdb tricks for displaying bit ... |
870615052a59542b4456542d270358bc21db493e3577810367f5f8ea12fc2743 | C | 34,509 | 1,155 | /* Pushdown stacks for integers, pointers, and characters.
*
* Contents:
* 1. The <ESL_STACK> object.
* 2. The main API, including pushing/popping.
* 3. Shuffling stacks.
* 4. Using stacks for thread communication [HAVE_PTHREAD]
* 5. Unit tests.
* 6. Test driver.
* 7. Example.
... |
22f5c7a37634677d0f81350135298f8e6d70e5ebd7097b0baeb047405c410298 | C | 34,515 | 828 | #include "p7_config.h"
#include <string.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_gumbel.h"
#include "esl_sq.h"
#include "hmmer.h"
/* hit_sorter(): qsort's pawn, below */
static int
FM_hit_sorter(const void *a, const void *b)
{
// return 2 * (((FM_DIAG*)a)->sortkey > ((FM_DIAG*)b)->sortkey) ... |
e14b4239fd436f6c68f74b24801cba42222da2de437e8ade55d8ff5968150f89 | C | 34,975 | 809 | /* I/O of multiple sequence alignments in PSI-BLAST format
*
* Contents:
* 1. API for reading/writing PSI-BLAST format
* 2. Unit tests.
* 3. Test driver.
* 4. Examples.
*/
#include "esl_config.h"
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include "easel.h"
#include "esl_alphabet.h"
#in... |
e72e3adfeb8dd9546cbe2831f225b580c8798dcfc501997644e371b5c2187613 | C | 35,165 | 877 | /* The MSV filter implementation; SSE version.
*
* A "filter" is a one-row, O(M), DP implementation that calculates an
* approximated nat score (i.e. in limited precision - here, uchar)
* and may have limited numeric range. It will return <eslERANGE> if
* its numeric range is exceeded, in which case the caller wi... |
0e2ddbf8ac4b5f738fd1309f5d3c8f08cf7f27f6641e0aff4d053f0c901f75bb | C | 35,466 | 1,277 | /* Please see velocity_segment.m for documentation.
*
* Author: Gunnar Farnebäck
* Computer Vision Laboratory
* Linköping University, Sweden
* gf@isy.liu.se
*/
#include "mex.h"
#include "matrix.h"
#include <stdlib.h>
#include <float.h>
#include <stdio.h> /* For DumpCandidateHeap */
#in... |
798aa7105952dce79fdd62b36c8a44137c9c766baa3a417c9f622a3883f2b3aa | C | 36,106 | 1,133 | /* Saving history in a line-based input stream
*
* Contents:
* 1. The <ESL_RECORDER> object
* 2. Using the <ESL_RECORDER>
* 3. Internal (static) functions
* 4. Benchmark driver
* 5. Unit tests
* 6. Test driver
* 7. Examples
*/
#include "esl_config.h"
#include <string.h>
#include "easel.h"
#in... |
258c2a9d71b2aa9e63a9c4324a4944db967e858151f6e7ba954f09147e20f684 | C | 36,169 | 911 | /* Viterbi filter implementation; VMX version.
*
* This is a SIMD vectorized, striped, interleaved, one-row, reduced
* precision (epi16) implementation of the Viterbi algorithm.
*
* It calculates a close approximation of the Viterbi score, in
* limited precision (signed words: 16 bits) and range. It may overflo... |
cb5b6fd9d189d096f7f18dafedc4c18dbce2a6acf3141f1788abe5035286f8bc | C | 36,781 | 785 | /* Optional support for MPI parallelization.
*
* Contents:
* 1. Communicating P7_OPROFILE, a score profile.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* SRE, Thu Jun 14 09:59:20 2007 [Janelia] [Tom Waits, Orphans]
*/
#include "p7_config.h"
#ifdef HMMER_MPI
#include <stdlib.... |
4686a965c9ac395d59f800639a8f6335c0432cde3e86d79ea61575ca282435a7 | C | 36,783 | 785 | /* Optional support for MPI parallelization.
*
* Contents:
* 1. Communicating P7_OPROFILE, a score profile.
* 2. Benchmark driver.
* 3. Unit tests.
* 4. Test driver.
*
* SRE, Thu Jun 14 09:59:20 2007 [Janelia] [Tom Waits, Orphans]
*/
#include "p7_config.h"
#ifdef HMMER_MPI
#include <stdlib.... |
ff2d599dfacbd7f72f82bb7a6d996606634b30f19446ce15e48581014ea0ac3d | C | 37,061 | 915 | /* Viterbi filter implementation; SSE version.
*
* This is a SIMD vectorized, striped, interleaved, one-row, reduced
* precision (epi16) implementation of the Viterbi algorithm.
*
* It calculates a close approximation of the Viterbi score, in
* limited precision (signed words: 16 bits) and range. It may overflo... |
81fe87734472824696102e350302aa5c533cb1fef6c96f0555c1a762de29ac9d | C | 37,367 | 891 | #include "p7_config.h"
#include "easel.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_mem.h"
#include <string.h>
#include "hmmer.h"
#include "divsufsort.h"
#define FM_BLOCK_COUNT 100000 //max number of SQ objects in a block
#define FM_BLOCK_OVERLAP 20000 //20 Kbases of overlap, at most, between adjasce... |
6eb46ee2f819ab4478504e391545dd602dfe807bf23ebd5fbe5e25c2ce007ebb | C | 37,980 | 951 | /* Optimal accuracy alignment; VMX version.
*
* Contents:
* 1. Optimal accuracy alignment, DP fill
* 2. OA traceback
* 3. Benchmark driver
* 4. Unit tests
* 5. Test driver
* 6. Example
*
* SRE, Mon Aug 18 20:01:01 2008 [Casa de Gatos]
*/
#include "p7_config.h"
#include <float.h>
#ifndef __APP... |
f216721c3440e991257346483480466b39b11baecbe0810b35e548a5847791d3 | C | 38,004 | 944 | /* Optimal accuracy alignment; SSE version.
*
* Contents:
* 1. Optimal accuracy alignment, DP fill
* 2. OA traceback
* 3. Benchmark driver
* 4. Unit tests
* 5. Test driver
* 6. Example
*
* SRE, Mon Aug 18 20:01:01 2008 [Casa de Gatos]
*/
#include "p7_config.h"
#include <float.h>
#include <xmm... |
0b46959bf10f2466bb171b7793fa9a72a9ff96635e978826e5b0f0a7aadb8edb | C | 38,624 | 1,281 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <stddef.h>
#include <ctype.h>
#include "gfa.h"
/********************************************************************
* Genomic Feature Analyzer; non-B motifs in nucleic acid sequence *
********************************************... |
ffc8bcfe96f26b67395dfcaf4892836b8d7bfdbdcf2956be36e288dc44c0069a | C | 38,806 | 1,245 | /*
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... |
cd17d012683360f3d05d19057b871b5dd5a9c4629bbb5cbfc60cd604c146b907 | C | 39,302 | 930 | #include "hmmer.h"
#include <string.h>
/* Check that esl exceptions, esl_fatal, -eslINFINITY, etc. are used
in the correct contexts!! */
/* Note that all calculations assume L is fixed. That is, for these
p-value and sensitivity calculations, a score for a sequence is
compared to the scores of seque... |
d6f5551d9daac925d2914eb977440adabf90e25986b65757397b51adc0047210 | C | 39,963 | 1,356 | /* Statistical routines for hyperexponential distributions.
*
* Contents:
* 1. The ESL_HYPEREXP object
* 2. Evaluating densities and distributions
* 3. Generic API routines: for general interface w/ histogram module
* 4. Dumping plots for files
* 5. Sampling
* 6. File input ... |
4c11f19225d7a217c87f6fcfa517d5db26aa8c464cb377cfd12a5b7c2dcc400d | C | 40,508 | 1,173 | #include <stdio.h>
#include <stdint.h>
#include "Maxfiles.h"
#include "MaxSLiCInterface.h"
#include "functions.h"
#define WRITE_OUTPUT 0
#define TIMING 0
#define TIME_SINGLE 0
#define READ_OUTPUT 1
int main(int argc, char *argv[]) {
printf("-----\n");
double tStart, tEnd, tKernelAll, tKernelSingle, tInitData, tIni... |
a32de606f81fa88cdada26b08baf1534c75e80a642623f01f828697eed494f20 | C | 40,611 | 1,160 | /* Foundation and miscellenea for the statistics modules.
*
* Contents:
* 1. Summary statistics (means, variances)
* 2. Special functions
* 3. Standard statistical tests
* 4. Data fitting.
* 5. Unit tests.
* 6. Test driver.
* 7. Examples.
* - driver for linear regression
* - driver f... |
cee0d1b5d487c750a356e426a1fa7906b44827f061ca7ee94137b85a27c8ca0e | C | 40,766 | 966 | /* hmmsim: scoring profile HMMs against simulated sequences.
*
* Main testbed for exploring the statistical behavior of HMMER3
* scores on random sequences.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#ifdef HMMER_MPI
#include "mpi.h"
#endif
#include "... |
85ce8a6d0c36e7264ab1e1c93e4d2fd97213c29d13d5d0acd882145f9199d9b4 | C | 42,103 | 1,588 | ///////////////////////////////////////////////////////////////////////////////
// //
// This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. //
// //
... |
be561865da8d240a9b65c3a2035366e6cbf6d92361600d42373b565220bf10c1 | C | 43,283 | 1,050 | /* Standardized pipeline for construction of new HMMs.
*
* Contents:
* 1. P7_BUILDER: allocation, initialization, destruction
* 2. Standardized model construction API.
* 3. Internal functions.
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#include "easel.h"
#include "esl_alphabet... |
c47d9af224625c4d1436b228e8b170fe21b144c4f5436f20662b901f1e1bef71 | C | 44,287 | 860 | /* nhmmscan: search sequence(s) against a profile HMM database, using nhmmer pipeline
*/
#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_sq.h"
#include "esl_sqio.h"
#include "esl_stopwatch.h"
#ifdef... |
1c4b1fc0cfd8f6e2dd335f3239885f43f0bb93bad5fbae1863432ab9fb809732 | C | 45,202 | 1,405 | /* Statistical routines for Gumbel (type I extreme value) 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 fit... |
43f5ec1a9ad01b32b387f97cc4a9bf1af7fad6ee0d3fd1adde75e16fc431a57e | C | 45,980 | 1,109 | /* I/O of multiple sequence alignments in A2M format (UCSC SAM)
*
* Contents:
* 1. API for reading/writing A2M format
* 2. Internal functions used by the A2M parser
* 3. Unit tests.
* 4. Test driver.
* 5. Examples.
*
* Reference:
* http://compbio.soe.ucsc.edu/a2m-desc.html
*/
#include "esl_confi... |
fd77707bd202f06f7faf9bfb84ebe580e4f145697bc234bab97aa80c69fc1686 | C | 46,487 | 1,058 | /* i/o of multiple sequence alignment files in Clustal-like formats
*
* Contents:
* 1. API for reading/writing Clustal and Clustal-like formats
* 2. Internal routines for Clustal formats.
* 3. Unit tests.
* 4. Test driver.
* 5. Example.
*
* This module is responsible for i/o of both eslMSAFILE_CLU... |
7c7dc9acc8542750103a4da4eb524e299ba6dd483b59c1b0b350085bbb8adf62 | C | 47,031 | 946 | /* Convert between sequence file formats
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <time.h>
#include "easel.h"
#include "esl_getopts.h"
#include "esl_mem.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_sq.h"
#include "esl_sqio.h"
#include "esl_wuss.... |
0188f0d58f6283f3a5a758cc8bec41cb2defc2160eeb051a35a19acfa786cc73 | C | 47,387 | 1,269 | #include <stdio.h>
#include <stdint.h>
#include "Maxfiles.h"
#include "MaxSLiCInterface.h"
#include "functions.h"
#define WRITE_OUTPUT 0
#define TIMING 0
#define TIME_SINGLE 0
#define READ_OUTPUT 1
int main(int argc, char *argv[]) {
printf("------\n");
double tStart, tEnd, tKernel, tInitMax, tInitData, tWrite, tRe... |
6ec009f472e5b0d207a168ea463ba97b71cba397b3ae69d55746da2cf5b7d414 | C | 47,616 | 1,121 | /* Model configuration:
* Converting a core model to a fully configured Plan7 search profile.
*
* Contents:
* 1. Routines in the exposed API.
* 2. Unit tests.
* 3. Test driver.
* 4. Statistics collection driver.
*
* Revised May 2005: xref STL9/77-81. (Uniform fragment distribution)
* ... |
176400410241eaa4ab1d5ea94d7d7073f19ca07f58edd82d7ad6aff85f47d52d | C | 48,445 | 1,271 | /* Definition of multidomain structure of a target sequence, and
* rescoring as a sum of individual domains, with null2 correction.
*
* Contents:
* 1. The P7_DOMAINDEF object: allocation, reuse, destruction
* 2. Routines inferring domain structure of a target sequence
* 3. Internal routines
*
* E... |
500f0b8ed52092486298b161985d38d169132195bd809703a8584c9e6aee1593 | C | 48,658 | 1,155 | /* Show statistics about a multiple sequence alignment file or MSA database.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_arr2.h"
#include "esl_arr3.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_... |
d622455fcee818390527c72fb76a78b17ff0a8d48930112ceb7a4641dc33302d | C | 48,960 | 1,184 | /* VMX implementation of Forward and Backward algorithms.
*
* Both profile and DP matrix are striped and interleaved, for fast
* SIMD vector operations. Calculations are in probability space
* (scaled odds ratios, actually) rather than log probabilities,
* allowing fast multiply/add operations rather than slow Log... |
5d6bacb64226f1f16ab00974f46cce7ee0d26e00aeb1b1957dfb80c244d6b8a7 | C | 49,160 | 1,900 | /* Operations on vectors of floats or doubles.
*
* Can operate on vectors of doubles, floats, or integers - appropriate
* routine is prefixed with D, F, or I. For example, esl_vec_DSet() is
* the Set routine for a vector of doubles; esl_vec_ISet() is for integers.
*
* Contents:
* 1. The vectorops API.
* ... |
e95f56465e1ff86b312759abb12b3cf234dc43e5853e76f12aab46c2636bbc20 | C | 49,242 | 1,441 | /* Portable, threadsafe Mersenne Twister random number generator
*
* 1. The ESL_RANDOMNESS object.
* 2. The generators, esl_random().
* 3. Debugging/development tools.
* 4. Other fundamental sampling (including Gaussian, gamma).
* 5. Multinomial sampling from discrete probability n-vectors.
* 6. Random dat... |
f4299b3a688b5768c3a8790339e47e02a6e6247d3675b0fafe412a1fc9bd995f | C | 49,357 | 1,208 | /*
* deflate_decompress.c - a decompressor for DEFLATE
*
* 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 limit... |
0bdd050932499e8d984e14af13b8f6d87229e7f6e8881ae7d595b51e177b72a8 | C | 49,476 | 1,017 | /* Saving optimized profiles in two pieces: MSV part and the rest.
*
* To accelerate hmmscan, which is limited by speed of HMM input,
* hmmpress saves an optimized profile in two pieces. One file gets
* a bare minimum of information needed to run the MSV filter.
* The other file gets the rest of the profile. Both... |
2b1d0a7846cad85f10bd2aa49089def0acba9d56904155e80864a763652d0438 | C | 49,806 | 1,307 | /* Construction of multiple alignments from traces.
*
* Contents:
* 1. API for aligning sequence or MSA traces
* 2. Internal functions used by the API
* 3. Test driver
*
* SRE, Tue Oct 21 19:38:19 2008 [Casa de Gatos]
*/
#include "p7_config.h"
#include "easel.h"
#include "esl_vectorops.h"
#include "hm... |
37d0fb42d1183eb034be59ae586f8d1b17178f070b2bdbbf031bbfac14eda336 | C | 50,144 | 1,021 | /* Saving optimized profiles in two pieces: MSV part and the rest.
*
* To accelerate hmmscan, which is limited by speed of HMM input,
* hmmpress saves an optimized profile in two pieces. One file gets
* a bare minimum of information needed to run the MSV filter.
* The other file gets the rest of the profile. Both... |
d6bcb8907a448eca96e511d68ba5a20efd007ae997b6334171ba3d8880b563a1 | C | 50,421 | 1,587 | /* Linear algebra operations in double-precision matrices.
*
* Implements ESL_DMATRIX (double-precision matrix) and
* ESL_PERMUTATION (permutation matrix) objects.
*
* Table of contents:
* 1. The ESL_DMATRIX object
* 2. Debugging/validation code for ESL_DMATRIX
* 3. Visualization tools
* 4. The ESL_... |
a665fedf0891324b1f270ce5665744412c6a95122c65398ada965101e8049e4b | C | 50,890 | 1,971 | #include "mex.h"
#define DEBUG 0
/*
* normconv.c
*
* Perform normalized convolution. Only real images and filters are
* supported, but at arbitrary dimensionality. Perform normalized
* convolution. Complex signals and basis functions are supported, at
* arbitrary dimensionality. The method is described in chapt... |
1b4d9e6b32fa626e6721bfe4945798146ad8ebbca58aa00d013b398ae096bae6 | C | 51,205 | 1,196 | /* SSE implementation of Forward and Backward algorithms.
*
* Both profile and DP matrix are striped and interleaved, for fast
* SIMD vector operations. Calculations are in probability space
* (scaled odds ratios, actually) rather than log probabilities,
* allowing fast multiply/add operations rather than slow Log... |
e9813c955410d058343966e2aac035fb8ea0d7d332cc16f5b553103df66eef2d | C | 51,300 | 1,794 | /*
* divsufsort.c for libdivsufsort-lite
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* 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 wit... |
b9c24784e33005977e50c084706fb4d6edff58a44367fec70fb986d7266022f5 | C | 52,153 | 1,238 | /* I/O of multiple sequence alignment files in SELEX format
*
* Contents:
* 1. API for reading/writing SELEX input.
* 2. Internal functions for a block of input lines.
* 3. Internal functions for parsing SELEX input.
* 4. Unit tests.
* 5. Test driver.
* 6. Examples.
*
* Notes:
* In SELEX, a ... |
bf9665be4a040ab2d504b229dcbb14cce482a287737b7a91fcff09e5fb0c8b49 | C | 52,222 | 1,494 | /* The Plan7 core HMM data structure.
*
* Contents:
* 1. The P7_HMM object: allocation, initialization, destruction.
* 2. Convenience routines for setting fields in an HMM.
* 3. Renormalization and rescaling counts in core HMMs.
* 4. Debugging and development code.
* 5. Other routines in the API.
* ... |
eb40801737f7bcba800db66a262b0efb0b049c952d4477f11810cbcae1ba2d28 | C | 54,244 | 1,578 | /* Pairwise identities, distances, and distance matrices.
*
* Contents:
* 1. Pairwise distances for aligned text sequences.
* 2. Pairwise distances for aligned digital seqs.
* 3. Distance matrices for aligned text sequences.
* 4. Distance matrices for aligned digital sequences.
* 5. A... |
c1e5889483bdc2cc73b73af5976225a3bc736ef5745898c0af6d01b3ead12192 | C | 56,234 | 1,325 | /* str*()-like functions for raw char arrays (non-NUL-terminated strings).
*
* esl_mem.md has additional notes.
*
* Contents:
* 1. The esl_mem*() API.
* 2. Unit tests.
* 3. Test driver.
*/
#include "esl_config.h"
#include <stdint.h>
#include <limits.h>
#include <string.h>
#include <ctype.h>
#includ... |
d961c3974210d883403e4d309e0c28c16b17f76ecc71c222cfcbb6c80d95a92c | C | 57,351 | 1,993 | /* esl_regexp.c: regular expression matching on strings.
*
* This is a wrapper around a modified version of Henry Spencer's
* regex library. Spencer's copyright notice appears below, after my
* wrappers, prefacing the section that includes his code. I believe
* you can obtain the original code from:
* ftp://ft... |
09c31110b423c656bce125094b2cdd4a7ce5ecf51270de772e8360f0e3075ad1 | C | 58,019 | 1,666 | /* P7_TRACE, the traceback structure.
*
* Contents:
* 1. The P7_TRACE structure
* 2. Access routines
* 3. Debugging tools
* 4. Creating traces by DP traceback
* 5. Creating faux traces from existing MSAs
* 6. Counting traces into new HMMs
* 7. Unit tests
* 8. Test driver
*
* Stylistic note:... |
e451691a53035afcbaf699c1b98ab8ea1c086aefa763a67f5d449027bd1d4da9 | C | 58,501 | 1,231 | /* Support for MPI parallelization.
*
* Contents:
* 1. Communicating optional arrays.
* 2. Communicating ESL_SQ (single biosequences)
* 3. Communicating ESL_MSA (multiple sequence alignments).
* 4. Communicating ESL_STOPWATCH (process timing).
* 5. Unit tests.
* 6. Test driver.
* 7. Examp... |
074ac9db4b5eb02f5ea20b9cd2f4952319dd783bcde1aa3aace44fb9f83faa66 | C | 59,305 | 1,288 | /* hmmscan: search sequence(s) against a profile HMM database
*
* To do:
* - in MPI mode, add a check to make sure ncpus >= 2. If 1, then we
* only have a master, no workers. See Infernal commit r3972 on the
* same point; and same note in hmmsearch.c's to do list.
*/
#include "p7_config.h"
#include <stdio... |
dbd184f8d6ddbcdae907add3484764ceecf47a53dceb067da89e1ab69b8befac | C | 60,437 | 1,906 | /* master side of the hmmpgmd daemon
* 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 <sys/socket.h>
#ifdef HAVE_NET... |
186880c45806c059e3500a91e57461604602c71dc40b2638df73fafc3a789f0c | C | 60,602 | 1,212 | /* Remove columns from a multiple sequence alignment.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <stdio.h>
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_arr2.h"
#include "esl_fileparser.h"
#include "esl_getopts.h"
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_msafile2.h"
#incl... |
fcfa41032071cbdc3a4c9e6f64490c15014302bae989c6b2574b7ce2529407a7 | C | 60,947 | 1,374 | /* esl_json : JSON data file parsing
*
* Inspired by Serge Zaitsev's Jasmine parser, https://github.com/zserge/jsmn
*
* Contents:
* 1. Full or incremental JSON parsing
* 2. ESL_JSON: a JSON parse tree
* 3. ESL_JSON_PARSER: precise state at each input byte
* 4. Accessing tokenized data
* 5. Debuggi... |
b3a3a100a3670a4c026cf260de56e99d2e5b264e63ba7893717920c1175c0252 | C | 63,302 | 1,181 | /* Genetic code tables for translation, whether canonical or noncanonical.
*
* Table of contents:
* 1. NCBI genetic code tables, in Easel digital form
* 2. ESL_GENCODE genetic code object
* 3. Reading and writing genetic codes in NCBI format
* 4. DNA->protein digital translation, allowing ambiguity chars... |
9742cc0be6ce22c1f1fb9362c83eee78a3462753a3da44431e96bdac3a18e717 | C | 63,714 | 1,966 | /* master side of the hmmpgmd daemon
* 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 <sys/socket.h>
#ifdef HAVE_NET... |
35aba0387f8997e8d6979837b3f56d29989ac627ae8091cb5d49781ceccce8db | C | 65,241 | 1,390 | /* Profile HMM construction from a multiple sequence alignment
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#ifdef HMMER_MPI
#include "mpi.h"
#endif
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_mpi.h"
#include "esl_msa.h"
#include "esl_m... |
5ddacbc7cc4c87628a23228673513213581c9697dcdd1e11a6fbd8b022e8210c | C | 65,777 | 1,431 | /* hmmsearch: search profile HMM(s) against a sequence database.
*
* To do:
* - in MPI mode, add a check to make sure ncpus >= 2. If 1, then we
* only have a master, no workers. See Infernal commit r3972 on the
* same point; and same note in hmmscan.c's to do list.
*/
#include "p7_config.h"
#include <stdi... |
206700419312c54f89c3f5061243a159e5875a4f500c38a21223d53746882a8f | C | 67,499 | 1,527 | /* Multiple sequence alignment file i/o
*
* Table of contents:
* 1. Opening/closing an ESL_MSAFILE.
* 2. ESL_MSAFILE_FMTDATA: optional added constraints on formats.
* 3. Guessing file formats.
* 4. Guessing alphabets.
* 5. Random MSA flatfile access.
* 6. Reading an MSA from an ESL_MSAFILE.... |
2a3c08b0ae351327a89ad6e446c5b743b08d8e735c6fbb3a7dde310db2346848 | C | 68,091 | 1,459 | /* Memory-efficient multiple sequence alignment i/o from Pfam format
*
* Legacy interface, now that ESL_MSAFILE is rewritten. Just enough
* of the old interface is retained to support --small option in
* various tools, for reading Pfam format in memory-efficient ways.
*
* Table of contents:
* 1. The ESL_MSAF... |
d24f9f53dd38a98afcb48536d2d9e821675bae79cd545cba4260987f90ad0c39 | C | 70,562 | 2,074 | /* Collecting and displaying histograms.
*
* 1. Creating/destroying histograms and collecting data.
* 2. Declarations about the binned data before parameter fitting.
* 3. Routines for accessing data samples in a full histogram.
* 4. Setting expected counts
* 5. Output and display of binned data.
* 6. Test... |
993a15a2265a5e3dc4e176dba30fdcc76921909ac4050177312cf1537f23c76c | C | 73,262 | 2,932 | /*
Copyright (c) 2009-2017 Dave Gamble and cJSON contributors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, m... |
e0559e81dbbcbdea1fca77e039b98c4bcaa3d7fa60f6599fb141ed68f7c6c094 | C | 73,791 | 2,188 | /* Phylogenetic trees.
*
* Contents:
* 1. The ESL_TREE object.
* 2. Newick format i/o
* 3. Tree comparison algorithms.
* 4. Clustering algorithms for distance-based tree construction.
* 5. Generating simulated trees.
* 6. Unit tests.
* 7. Test driver.
* 8. Examples.
*/
#include "esl_config.h... |
483c643c9b23683652ecca3b8b4dee3d1f9a41baf1ff489142af00a3782db130 | C | 75,540 | 2,494 | /*
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... |
11b417be1d990df5e6e0d9cb41ff1ecce0076dbe6ca2a8f8ca4bb6ca142457c0 | C | 75,553 | 1,874 | /* Sequence weighting algorithms.
*
* Implementations of ad hoc sequence weighting algorithms for multiple
* sequence alignments:
* PB weights: Henikoff and Henikoff, JMB 243:574-578, 1994.
* GSC weights: Gerstein et al., JMB 236:1067-1078, 1994.
* BLOSUM weights: Henikoff and Henikoff, PNAS 89:1091... |
4f45cff9225c810c7a47519d0a7f18de2f6a28ab598f207502212dd745e13f56 | C | 76,145 | 2,512 | /*
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... |
e62ce86be78369880bc83cb649f9dafbfcb7684622787836d63600c928c4d6ff | C | 76,272 | 1,534 | /* phmmer: search a protein sequence against a protein database
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.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_scorematrix.h... |
38959153d198b298c4ef33906a73aa2723b963bbbcd72e8a89d89c540f18ba0e | C | 77,336 | 2,114 | /* Generating, shuffling, and randomizing sequences.
*
* Contents:
* 1. Generating simple random character strings.
* 2. Generating iid sequences.
* 3. Shuffling sequences.
* 4. Randomizing sequences.
* 5. Generating iid sequences (digital mode).
* 6. Shuffling sequences (digital mode).
* 7. Ra... |
1f03af33bcd614e86350e976705bf6ccb79fdd972d28fbbdc01ceef75bd87f51 | C | 78,101 | 1,895 | /* I/O of multiple sequence alignment files in PHYLIP format(s)
*
* Contents:
* 1. API for reading/writing PHYLIP format alignment files
* 2. I/O of the interleaved variant of the format
* 3. I/O of the sequential variant of the format
* 4. Autodetection of format and its variants
* 5. Rectifying vali... |
e0feef1b59d64e1df574402a47d95a23e1aafc681cf161b34b46cf393da33145 | C | 79,338 | 2,087 | /* Routines for the P7_OPROFILE structure:
* a search profile in an optimized implementation.
*
* Contents:
* 1. The P7_OPROFILE object: allocation, initialization, destruction.
* 2. Conversion from generic P7_PROFILE to optimized P7_OPROFILE
* 3. Conversion from optimized P7_OPROFILE to compact score array... |
329c247ed69f55506f018c9337d76c592fcffb67a7f560379d9fec488e4db5b0 | C | 80,568 | 2,163 | /* Implements a somewhat more powerful command line getopt interface
* than the standard UNIX/POSIX call.
*
* Contents:
* 1. The ESL_GETOPTS object.
* 2. Setting and testing a configuration.
* 3. Retrieving option settings and command line args.
* 4. Formatting option help.
* 5. Private function... |
9de7892e970cdb5dfa4c8c4719ec2808a41e9f8046588008418470c19b8933c6 | C | 82,340 | 2,139 | /* Sequence/subsequence indices: fast lookup in large sequence files by keyword.
*
* Contents:
* 1. Using (reading) an SSI index.
* 2. Creating (writing) new SSI files.
* 3. Portable binary i/o.
* 4. Unit tests.
* 5. Test driver.
* 6. Example code.
*/
#include "esl_config.h"
#include <stdio.h>
#include ... |
df725d0fdefb3cd656ac8f5de5228ee04119d39977f4c6fc3a042dd0bebfb4f6 | C | 82,696 | 1,809 | /* esl_dsqdata : faster sequence input
*
* Implements a predigitized binary file format for biological
* sequences. Sequence data are packed bitwise into 32-bit packets,
* where each packet contains either six 5-bit residues or fifteen
* 2-bit residues, plus two control bits. Input is asynchronous,
* using POSIX... |
c834a45411feda4d243707426ac94e79c0ed60721c8ceec83a8d66217b34e2c2 | C | 82,909 | 2,157 | /* Routines for the P7_OPROFILE structure:
* a search profile in an optimized implementation.
*
* Contents:
* 1. The P7_OPROFILE object: allocation, initialization, destruction.
* 2. Conversion from generic P7_PROFILE to optimized P7_OPROFILE
* 3. Conversion from optimized P7_OPROFILE to compact score ar... |
4de802368348946199ba006a0675a7bdef31d1a2fc1a197cc496867e86819982 | C | 84,949 | 2,448 | /* Unaligned sequence file i/o.
*
* Contents:
* 1. An <ESL_SQFILE> object, text mode.
* 2. An <ESL_SQFILE> object, digital mode. [with <alphabet>]
* 3. Sequence reading.
* 4. Sequence writing.
* 5. Miscellaneous routines.
* 6. Sequence/subsequence fetching, random access [with <ssi>]
* 7.... |
f79faa7fd48af8b09ec2c5d16657b9019d86c6a720b5af11b05170c1745b6d4b | C | 87,102 | 2,198 | /* P7_TOPHITS: implementation of ranked list of top-scoring hits
*
* Contents:
* 1. The P7_TOPHITS object.
* 2. Standard (human-readable) output of pipeline results.
* 3. Tabular (parsable) output of pipeline results.
* 4. Benchmark driver.
* 5. Test driver.
*/
#include "p7_config.h"
#include <... |
7068e44a42530d466fbe62f3877d1b811c25456a18dfb1fa0e70e0c40cef97be | C | 87,322 | 2,218 | /* Formatting, transmitting, and printing single alignments to a
* profile.
*
* Contents:
* 1. The P7_ALIDISPLAY object.
* 2. The P7_ALIDISPLAY API.
* 3. Debugging/dev code.
* 4. Benchmark driver.
* 5. Unit tests.
* 6. Test driver.
* 7. Example.
*/
#include "p7_config.h"
#include <stdlib.h>
#... |
3b6562365b3fbdb7a87bb744e4708617b6c9afc546dfd4eb2286cb6fc88a8440 | C | 87,581 | 2,575 | /* Implements the standard digitized alphabets for biosequences.
*
* 1. ESL_ALPHABET object for digital alphabets.
* 2. Digitized sequences (ESL_DSQ *).
* 3. Other routines in the API.
* 4. Unit tests.
* 5. Test driver.
* 6. Examples.
*/
#include "esl_config.h"
#include <stdlib.h>
#include <... |
27156d292267c35139d8e146816a5a487a2a8b139ed60ec2adfd7aaea3cfcee5 | C | 89,073 | 1,823 | /* nhmmer: search profile HMM(s) against a nucleotide sequence database.
*/
#include "p7_config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.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_scor... |
deafc785d8950f4064876b2147e767088a46dd8b0542acc3c3bf4135217d52c0 | C | 89,285 | 1,771 | /* Optional support for MPI parallelization.
*
* Contents:
* 1. Communicating P7_HMM, a core model.
* 2. Communicating P7_PROFILE, a score profile.
* 3. Communicating P7_PIPELINE, pipeline stats.
* 4. Communicating P7_TOPHITS, list of high scoring alignments.
* 5. Benchmark driver.
* 6. Unit ... |
802ead0b1ad8b59a79108307cfb2a528f6a6a0105187cd15d2eb7bdfbdf44b4a | C | 89,331 | 1,810 | /* Merge alignments into a single alignment based on their reference (RF) annotation.
*
* Special care is taken to be consistent with missing data '~'
* annotation in two different contexts.
*
* First, from Infernal 1.1rc2 and later cmalign and cmsearch -A
* output alignments: '~' can occur in GC RF and SS_con... |
441fe529da7739ac9d839f83133d3277b71a71246b25aeba2d2d0f375f088fbb | C | 90,027 | 2,063 | /* H3's accelerated seq/profile comparison pipeline
*
* Contents:
* 1. P7_PIPELINE: allocation, initialization, destruction
* 2. Pipeline API
* 3. Example 1: search mode (in a sequence db)
* 4. Example 2: scan mode (in an HMM db)
*/
#include "p7_config.h"
#include <stdlib.h>
#include <stdio.h>
#includ... |
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