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comparison clustalomega/clustal-omega-0.2.0/src/hhalign/general.h @ 0:ff1768533a07

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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author clustalomega
date Tue, 07 Jun 2011 17:04:25 -0400
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1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
2
3 /*********************************************************************
4 * Clustal Omega - Multiple sequence alignment
5 *
6 * Copyright (C) 2010 University College Dublin
7 *
8 * Clustal-Omega is free software; you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License as
10 * published by the Free Software Foundation; either version 2 of the
11 * License, or (at your option) any later version.
12 *
13 * This file is part of Clustal-Omega.
14 *
15 ********************************************************************/
16
17 /*
18 * RCS $Id: general.h 241 2011-05-04 14:37:17Z fabian $
19 */
20
21
22 #ifndef GENERAL_H
23 #define GENERAL_H
24
25
26 #include "../clustal/log.h"
27
28 /*
29 ***** Omega definitions************************************
30 FS, 2010-02-19
31 */
32 enum {NO = 0, YES};
33 enum {BASE10 = 10};
34 enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7};
35 enum {MAXWORD = 100, MAXLEN = 10000};
36 enum {OVER_ALLOCATE = 2};
37 enum {FAILURE = -1, OK};
38 enum {F_OFFSET = 1};
39 enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM};
40 #define UNITY 1.00
41
42 /*#define MIN(a,b) ((a)<(b)?(a):(b))*/
43
44
45 /* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */
46 typedef struct {
47
48 int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */
49
50 } hhalign_para;
51
52 typedef struct {
53 /***public***/
54 int n_display;
55 char **sname;
56 char **seq;
57 int ncons;
58 int nfirst;
59 int nss_dssp;
60 int nsa_dssp;
61 int nss_pred;
62 int nss_conf;
63 int L;
64 int N_in;
65 int N_filtered;
66 float *Neff_M;
67 float *Neff_I;
68 float *Neff_D;
69 float Neff_HMM;
70 char *longname;
71 char name[511];
72 char file[511];
73 char fam[511];
74 char sfam[511];
75 char fold[511];
76 char cl[511];
77 float lamda;
78 float mu;
79 /***private***/
80 float **f;
81 float **g;
82 float **p;
83 float **tr;
84 float **linTr;
85 char trans_lin;
86 char *ss_dssp;
87 char *sa_dssp;
88 char *ss_pred;
89 char *ss_conf;
90 char *Xcons;
91 float pav[20];
92 float pnul[20];
93 int *l;
94
95 } hmm_light;
96
97
98 #endif
99