Mercurial > repos > clustalomega > clustalomega
annotate clustalomega/clustal-omega-0.2.0/src/hhalign/general.h @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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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 -*- */ |
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2 |
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3 /********************************************************************* |
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4 * Clustal Omega - Multiple sequence alignment |
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5 * |
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6 * Copyright (C) 2010 University College Dublin |
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7 * |
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8 * Clustal-Omega is free software; you can redistribute it and/or |
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9 * modify it under the terms of the GNU General Public License as |
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10 * published by the Free Software Foundation; either version 2 of the |
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11 * License, or (at your option) any later version. |
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12 * |
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13 * This file is part of Clustal-Omega. |
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14 * |
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15 ********************************************************************/ |
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16 |
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17 /* |
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18 * RCS $Id: general.h 241 2011-05-04 14:37:17Z fabian $ |
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19 */ |
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20 |
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21 |
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22 #ifndef GENERAL_H |
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23 #define GENERAL_H |
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24 |
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25 |
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26 #include "../clustal/log.h" |
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27 |
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28 /* |
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29 ***** Omega definitions************************************ |
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30 FS, 2010-02-19 |
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31 */ |
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32 enum {NO = 0, YES}; |
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33 enum {BASE10 = 10}; |
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34 enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7}; |
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35 enum {MAXWORD = 100, MAXLEN = 10000}; |
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36 enum {OVER_ALLOCATE = 2}; |
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37 enum {FAILURE = -1, OK}; |
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38 enum {F_OFFSET = 1}; |
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39 enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM}; |
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40 #define UNITY 1.00 |
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41 |
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42 /*#define MIN(a,b) ((a)<(b)?(a):(b))*/ |
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43 |
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44 |
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45 /* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */ |
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46 typedef struct { |
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47 |
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48 int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */ |
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49 |
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50 } hhalign_para; |
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51 |
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52 typedef struct { |
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53 /***public***/ |
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54 int n_display; |
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55 char **sname; |
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56 char **seq; |
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57 int ncons; |
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58 int nfirst; |
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59 int nss_dssp; |
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60 int nsa_dssp; |
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61 int nss_pred; |
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62 int nss_conf; |
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63 int L; |
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64 int N_in; |
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65 int N_filtered; |
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66 float *Neff_M; |
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67 float *Neff_I; |
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68 float *Neff_D; |
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69 float Neff_HMM; |
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70 char *longname; |
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71 char name[511]; |
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72 char file[511]; |
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73 char fam[511]; |
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74 char sfam[511]; |
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75 char fold[511]; |
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76 char cl[511]; |
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77 float lamda; |
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78 float mu; |
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79 /***private***/ |
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80 float **f; |
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81 float **g; |
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82 float **p; |
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83 float **tr; |
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84 float **linTr; |
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85 char trans_lin; |
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86 char *ss_dssp; |
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87 char *sa_dssp; |
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88 char *ss_pred; |
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89 char *ss_conf; |
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90 char *Xcons; |
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91 float pav[20]; |
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92 float pnul[20]; |
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93 int *l; |
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94 |
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95 } hmm_light; |
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96 |
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97 |
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98 #endif |
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99 |