libfreecontact 1.0.21
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Classes | Namespaces | Macros | Typedefs | Functions
freecontact.cpp File Reference
#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_tfreecontact::_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_tfreecontact::_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 ()
 

Macro Definition Documentation

◆ _fill_pfi

#define _fill_pfi (   __i)
Value:
{\
pairfreq_t *pfi = &pairfreq(__i,0,0,0);\
for(uint16_t j = __i+1; j < __ali.alilen; ++j)\
{\
uint8_t ai = alik[__i];\
uint8_t aj = alik[j];\
if(ai < 21 && aj < 21)\
pfi[ j*pairfreq.d2 + ai*pairfreq.d3 + aj ] += ps_aliwk;\
} }

◆ CAN_VECW

#define CAN_VECW   0

Typedef Documentation

◆ g_fp_t

typedef float g_fp_t

Definition at line 38 of file freecontact.cpp.

Function Documentation

◆ glassofast_()

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 *   
)

◆ sgetrf_()

void sgetrf_ ( int *  M,
int *  N,
float *  A,
int *  LDA,
int *  IPIV,
int *  INFO 
)

◆ sgetri_()

void sgetri_ ( int *  N,
float *  A,
int *  lda,
int *  IPIV,
float *  WORK,
int *  LWORK,
int *  INFO 
)

◆ spotrf_()

void spotrf_ ( const char *  UPLO,
const int *  N,
float *  A,
const int *  LDA,
int *  INFO 
)