libclustalo-dev 1.2.1-1 / usr / include / clustalo / hhalign / general.h

This file is indexed.

/usr/include/clustalo/hhalign/general.h is in libclustalo-dev 1.2.1-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */

/*********************************************************************
 * Clustal Omega - Multiple sequence alignment
 *
 * Copyright (C) 2010 University College Dublin
 *
 * Clustal-Omega is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License as
 * published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 *
 * This file is part of Clustal-Omega.
 *
 ********************************************************************/

/*
 * RCS $Id: general.h 290 2013-09-20 15:18:12Z fabian $
 */


#ifndef GENERAL_H
#define GENERAL_H


#include "../clustal/log.h"
#include <stdbool.h>

/*
***** Omega definitions************************************
 FS, 2010-02-19
*/
enum {NO = 0, YES};
enum {BASE10 = 10};
enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7};
enum {MAXWORD = 100, MAXLEN = 10000};
enum {OVER_ALLOCATE = 2};
enum {FAILURE = -1, OK};
enum {RETURN_OK = 0, RETURN_FROM_MAC, RETURN_FROM_VITERBI, RETURN_FROM_PRINT_ALI, RETURN_FROM_RNP, RETURN_UNKNOWN};
enum {REALLY_BIG_MEMORY_MB = 64000};
enum {F_OFFSET = 1};
enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM};
#define UNITY 1.00
enum {CALL_FROM_DONT_KNOW = -1, CALL_FROM_ALN_HMM, CALL_FROM_REGULAR};

/*#define MIN(a,b) ((a)<(b)?(a):(b))*/


/* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */
typedef struct {

    int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */
	bool bIsDna; /* indicates we're in nucleotide mode */
	bool bIsRna; /* indicates we're in nucleotide mode */
    double pca;
    double pcb;
    double pcc;
    double pcw;
    double gapb;
    double gapd;
    double gape;
    double gapf;
    double gapg;
    double gaph;
    double gapi;
    double pcaV;
    double pcbV;
    double pccV;
    double pcwV;
    double gapbV;
    double gapdV;
    double gapeV;
    double gapfV;
    double gapgV;
    double gaphV;
    double gapiV;

} hhalign_para;

/* 'scores' passed out from hhalign */
typedef struct{

	double forwardProb;
    double backwardProb;
    double hhScore;
    double sumPP;
    double *PP;
    int L;

} hhalign_scores;


typedef struct {
  /***public***/
  int n_display;
  char **sname;
  char **seq;
  int ncons;
  int nfirst;
  int nss_dssp;
  int nsa_dssp;
  int nss_pred;
  int nss_conf;
  int L;
  int N_in;
  int N_filtered;
  float *Neff_M;
  float *Neff_I;
  float *Neff_D;
  float Neff_HMM;
  char *longname;
  char name[511];
  char file[511];
  char fam[511];
  char sfam[511];
  char fold[511];
  char cl[511];
  float lamda;
  float mu;
  /***private***/
  float **f;
  float **g;
  float **p;
  float **tr;
  float **linTr;
  char trans_lin;
  char *ss_dssp;
  char *sa_dssp;
  char *ss_pred;
  char *ss_conf;
  char *Xcons;
  float pav[20];
  float pnul[20];
  int *l;

} hmm_light;


#endif

APT Browse - Built by Thomas Orozco.