/usr/include/clustalo/hhalign/general.h is in libclustalo-dev 1.2.1-2.
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
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