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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: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $
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19 */
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20
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21 #ifndef CLUSTALO_H
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22 #define CLUSTALO_H
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23
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24
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25
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26 #ifdef HAVE_OPENMP
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27 #include <omp.h>
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28 #endif
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29
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30 #include "clustal-omega-config.h"
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31
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32 /* the following needs to be kept in sync with library_include_HEADERS of all
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33 * subdir Makefile.am's
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34 */
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35
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36 /* hhalign */
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37 #include "hhalign/general.h"
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38 #include "hhalign/hhfunc.h"
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39
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40
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41 /* clustal */
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42 #include "clustal/log.h"
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43 #include "clustal/util.h"
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44 #include "clustal/symmatrix.h"
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45 #include "clustal/tree.h"
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46 #include "clustal/seq.h"
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47 #include "clustal/mbed.h"
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48 #include "clustal/weights.h"
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49 #include "clustal/pair_dist.h"
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50 #include "clustal/hhalign_wrapper.h"
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51
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52
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53
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54 #define CLUSTERING_UNKNOWN 0
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55 #define CLUSTERING_UPGMA 1
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56
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57 /* weights will be computed if 1. but are not really used for now and they
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58 * might slow things down. also, mbed's screws up branch lengths which will
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59 * have a negative effect on weights
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60 */
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61 #define USE_WEIGHTS 0
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62
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63 extern int iNumberOfThreads;
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64
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65
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66 /** user/commandline options
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67 *
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68 * changes here will have to be reflected in ParseCommandLine()
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69 * and during setup of the default opts
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70 *
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71 */
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72 typedef struct {
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73 /* auto: Clustal (know what) is good for you
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74 */
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75 bool bAutoOptions;
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76
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77 /* Distance matrix
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78 */
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79 /** distance matrix input file */
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80 char *pcDistmatInfile;
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81 /** distance matrix output file */
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82 char *pcDistmatOutfile;
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83
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84 /* Clustering / guide-tree
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85 */
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86 /** clustering type (from cmdline arg) */
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87 int iClusteringType;
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88 /** pairwise distance method */
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89 int iPairDistType;
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90 /** use mbed-like clustering */
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91 bool bUseMbed;
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92 /** use mbed-like clustering also during iteration */
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93 bool bUseMbedForIteration;
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94 /** guidetree output file */
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95 char *pcGuidetreeOutfile;
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96 /** guidetree input file */
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97 char *pcGuidetreeInfile;
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98
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99 /* HMMs
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100 */
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101 /** HMM input files. index range: 0..iHMMInputFiles */
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102 char **ppcHMMInput;
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103 /** number of provided HMM input files. not really a user
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104 option but need for ppcHMMInput */
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105 int iHMMInputFiles;
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106
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107 /* Iteration
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108 */
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109 /** number of iterations */
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110 int iNumIterations;
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111 /** determine number of iterations automatically */
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112 bool bIterationsAuto;
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113 /** maximum number of hmm iterations */
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114 int iMaxHMMIterations;
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115 /** max number of guidetree iterations */
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116 int iMaxGuidetreeIterations;
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117
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118 /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
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119 int iMacRam; /* FS, r240 -> */
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120
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121 /* changes here will have to be reflected in FreeAlnOpts(),
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122 * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
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123 */
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124 } opts_t;
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125
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126
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127
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128
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129
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130 extern void
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131 PrintLongVersion(char *pcStr, int iSize);
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132
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133 extern void
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134 SetDefaultAlnOpts(opts_t *opts);
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135
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136 extern void
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137 FreeAlnOpts(opts_t *aln_opts);
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138
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139 extern void
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140 AlnOptsLogicCheck(opts_t *opts);
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141
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142 extern void
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143 PrintAlnOpts(FILE *prFile, opts_t *opts);
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144
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145 extern void
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146 InitClustalOmega(int iNumThreadsToUse);
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147
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148 extern void
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149 SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
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150
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151 extern int
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152 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
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153 int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
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154 int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
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155 bool bUseMBed);
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156
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157 extern int
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158 Align(mseq_t *prMSeq,
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159 mseq_t *prMSeqProfile,
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160 opts_t *prOpts,
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161 hhalign_para rHhalignPara);
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162
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163 extern int
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164 AlignProfiles(mseq_t *prMSeqProfile1,
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165 mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
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166
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167 #endif
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