Clustal Omega  1.2.0
clustal-omega.h
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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: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $
19  */
20 
21 #ifndef CLUSTALO_H
22 #define CLUSTALO_H
23 
24 
25 
26 #ifdef HAVE_OPENMP
27 #include <omp.h>
28 #endif
29 #include <stdbool.h>
30 
31 #include "clustal-omega-config.h"
32 
33 /* the following needs to be kept in sync with library_include_HEADERS of all
34  * subdir Makefile.am's
35  */
36 
37 /* hhalign */
38 #include "hhalign/general.h"
39 #include "hhalign/hhfunc.h"
40 
41 
42 /* clustal */
43 #include "clustal/log.h"
44 #include "clustal/util.h"
45 #include "clustal/symmatrix.h"
46 #include "clustal/tree.h"
47 #include "clustal/seq.h"
48 #include "clustal/mbed.h"
49 #include "clustal/weights.h"
50 #include "clustal/pair_dist.h"
51 #include "clustal/hhalign_wrapper.h"
52 
53 
54 
55 #define CLUSTERING_UNKNOWN 0
56 #define CLUSTERING_UPGMA 1
57 
58 /* weights will be computed if 1. but are not really used for now and they
59  * might slow things down. also, mbed's screws up branch lengths which will
60  * have a negative effect on weights
61 */
62 #define USE_WEIGHTS 0
63 
64 extern int iNumberOfThreads;
65 
66 /* output order */
67 enum {INPUT_ORDER = 0, TREE_ORDER};
68 
69 
76 typedef struct {
77  /* auto: Clustal (know what) is good for you
78  */
79  bool bAutoOptions;
80 
81  /* Distance matrix
82  */
84  char *pcDistmatInfile;
86  char *pcDistmatOutfile;
87 
88  /* Clustering / guide-tree
89  */
91  int iClusteringType;
93  int iClustersizes;
95  char *pcClustfile;
97  int iPairDistType;
99  bool bUseMbed;
101  bool bUseMbedForIteration;
103  char *pcGuidetreeOutfile;
105  char *pcGuidetreeInfile;
107  bool bUseKimura;
109  bool bPercID;
110 
111  /* HMMs
112  */
114  char **ppcHMMInput;
117  int iHMMInputFiles;
118 
119  /* Iteration
120  */
122  int iNumIterations;
124  bool bIterationsAuto;
126  int iMaxHMMIterations;
128  int iMaxGuidetreeIterations;
129 
130  hhalign_para rHhalignPara;
131 
132  /* changes here will have to be reflected in FreeAlnOpts(),
133  * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
134  */
135 } opts_t;
136 
137 
138 
139 extern void
140 PrintLongVersion(char *pcStr, int iSize);
141 
142 extern void
143 SetDefaultAlnOpts(opts_t *opts);
144 
145 extern void
146 FreeAlnOpts(opts_t *aln_opts);
147 
148 extern void
149 AlnOptsLogicCheck(opts_t *opts);
150 
151 extern void
152 PrintAlnOpts(FILE *prFile, opts_t *opts);
153 
154 extern void
155 InitClustalOmega(int iNumThreadsToUse);
156 
157 extern void
158 SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
159 
160 extern int
161 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
162  int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
163  int iClusteringType, int iClustersizes,
164  char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,
165  bool bUseMBed, bool bPercID);
166 
167 extern int
168 Align(mseq_t *prMSeq,
169  mseq_t *prMSeqProfile,
170  opts_t *prOpts);
171 
172 extern int
173 AlignProfiles(mseq_t *prMSeqProfile1,
174  mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
175 
176 #endif
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