#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"

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
	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. More...

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 ()

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
	)

Classes

Namespaces

Macros

Typedefs

Functions