libfreecontact 1.0.21
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#include "config.h"
#include <omp.h>
#include <boost/format.hpp>
#include <cblas.h>
#include <iomanip>
#include <iostream>
#include <signal.h>
#include <stdio.h>
#include <sys/time.h>
#include <time.h>
#include <unistd.h>
#include "freecontact.h"
Go to the source code of this file.
Classes | |
class | freecontact::ct_vector< _Tp > |
class | freecontact::af_vector< _Tp > |
class | freecontact::pf_vector |
class | freecontact::cov_vector< _Tp > |
class | freecontact::_rawscore_calc_t |
Calculates raw score for an i,j contact. More... | |
class | freecontact::d2matrix< _Tp, _Tri, _Tci > |
2-dimensional matrix. More... | |
class | freecontact::_glasso_timer |
Namespaces | |
namespace | freecontact |
Macros | |
#define | CAN_VECW 0 |
#define | _fill_pfi(__i) |
Typedefs | |
typedef float | g_fp_t |
typedef float | freecontact::cov_fp_t |
typedef float | freecontact::fp_t |
typedef d2matrix< uint32_t, uint32_t, int > | freecontact::simcnt_t |
Functions | |
void | glassofast_ (int *, g_fp_t *, g_fp_t *, g_fp_t *, int *, int *, int *, g_fp_t *, g_fp_t *, g_fp_t *, g_fp_t *, int *, int *) |
void | spotrf_ (const char *UPLO, const int *N, float *A, const int *LDA, int *INFO) |
void | sgetrf_ (int *M, int *N, float *A, int *LDA, int *IPIV, int *INFO) |
void | sgetri_ (int *N, float *A, int *lda, int *IPIV, float *WORK, int *LWORK, int *INFO) |
static void | freecontact::_raw_score_matrix (map< string, ct_vector< fp_t > > &__raw_ctscore, map< string, vector< double > > &__apc_bg, map< string, double > &__apc_mean, const uint16_t __alilen, const string &__key, const _rawscore_calc_t &__fo) |
Calculate raw contact scores using given function and collect row/column/overall mean for APC calculation. | |
static vector< contact_t > | freecontact::_apc (const ct_vector< fp_t > &__raw_ctscore, const vector< double > &__apc_bg, const double __apc_mean, const uint16_t __mincontsep, bool __filt) |
static vector< contact_t > | freecontact::_raw_as_is (const ct_vector< fp_t > &__raw_ctscore, const uint16_t __mincontsep) |
static uint32_t | freecontact::_cache_holds_nseq (uint16_t __seqsize) |
static __m128i | freecontact::_mm_setzero_si128 () |
#define _fill_pfi | ( | __i | ) |
#define CAN_VECW 0 |
typedef float g_fp_t |
Definition at line 38 of file freecontact.cpp.
void glassofast_ | ( | int * | , |
g_fp_t * | , | ||
g_fp_t * | , | ||
g_fp_t * | , | ||
int * | , | ||
int * | , | ||
int * | , | ||
g_fp_t * | , | ||
g_fp_t * | , | ||
g_fp_t * | , | ||
g_fp_t * | , | ||
int * | , | ||
int * | |||
) |
void sgetrf_ | ( | int * | M, |
int * | N, | ||
float * | A, | ||
int * | LDA, | ||
int * | IPIV, | ||
int * | INFO | ||
) |
void sgetri_ | ( | int * | N, |
float * | A, | ||
int * | lda, | ||
int * | IPIV, | ||
float * | WORK, | ||
int * | LWORK, | ||
int * | INFO | ||
) |
void spotrf_ | ( | const char * | UPLO, |
const int * | N, | ||
float * | A, | ||
const int * | LDA, | ||
int * | INFO | ||
) |