Clustal Omega  1.2.1
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"
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  */
80 
81  /* Distance matrix
82  */
87 
88  /* Clustering / guide-tree
89  */
95  char *pcClustfile;
103  bool bUseMbed;
107  bool bPileup;
115  bool bPercID;
116 
117  /* HMMs
118  */
120  char **ppcHMMInput;
124 
125  /* Iteration
126  */
135 
136  hhalign_para rHhalignPara;
137 
138  /* changes here will have to be reflected in FreeAlnOpts(),
139  * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
140  */
141 } opts_t;
142 
143 
144 
145 extern void
146 PrintLongVersion(char *pcStr, int iSize);
147 
148 extern void
150 
151 extern void
152 FreeAlnOpts(opts_t *aln_opts);
153 
154 extern void
156 
157 extern void
158 PrintAlnOpts(FILE *prFile, opts_t *opts);
159 
160 extern void
161 InitClustalOmega(int iNumThreadsToUse);
162 
163 extern void
164 SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
165 
166 extern int
167 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
168  int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
169  int iClusteringType, int iClustersizes,
170  char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,
171  bool bUseMBed, bool bPercID);
172 
173 extern int
174 Align(mseq_t *prMSeq,
175  mseq_t *prMSeqProfile,
176  opts_t *prOpts);
177 
178 extern int
179 AlignProfiles(mseq_t *prMSeqProfile1,
180  mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
181 
182 #endif
183 extern int
184 ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile);
Definition: clustal-omega.h:67
int ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile)
read pseudo-count 'fudge' parameters from file
Definition: clustal-omega.c:1466
bool bUseMbed
Definition: clustal-omega.h:103
bool bPileup
Definition: clustal-omega.h:107
int iMaxGuidetreeIterations
Definition: clustal-omega.h:134
bool bIterationsAuto
Definition: clustal-omega.h:130
char * pcDistmatOutfile
Definition: clustal-omega.h:86
int iClusteringType
Definition: clustal-omega.h:91
int Align(mseq_t *prMSeq, mseq_t *prMSeqProfile, opts_t *prOpts)
The main alignment function which wraps everything else.
Definition: clustal-omega.c:959
void FreeAlnOpts(opts_t *aln_opts)
free aln opts members
Definition: clustal-omega.c:163
char * pcClustfile
Definition: clustal-omega.h:95
void PrintLongVersion(char *pcStr, int iSize)
Print Long version information to pre-allocated char.
Definition: clustal-omega.c:149
hhalign_para rHhalignPara
Definition: clustal-omega.h:136
bool bPercID
Definition: clustal-omega.h:115
int iNumIterations
Definition: clustal-omega.h:128
void SetDefaultAlnOpts(opts_t *opts)
Sets members of given user opts struct to default values.
Definition: clustal-omega.c:189
int iHMMInputFiles
Definition: clustal-omega.h:123
void PrintAlnOpts(FILE *prFile, opts_t *opts)
FIXME doc.
Definition: clustal-omega.c:280
void SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq)
Defines an alignment order, which adds sequences sequentially, i.e. one at a time starting with seq 1...
Definition: clustal-omega.c:656
bool bUseKimura
Definition: clustal-omega.h:113
int iNumberOfThreads
Definition: clustal-omega.c:131
int AlignProfiles(mseq_t *prMSeqProfile1, mseq_t *prMSeqProfile2, hhalign_para rHhalignPara)
Align two profiles, ie two sets of prealigned sequences. Already aligned columns won't be changed...
Definition: clustal-omega.c:1418
bool bUseMbedForIteration
Definition: clustal-omega.h:105
void InitClustalOmega(int iNumThreadsToUse)
FIXME.
Definition: clustal-omega.c:621
char * pcDistmatInfile
Definition: clustal-omega.h:84
char ** ppcHMMInput
Definition: clustal-omega.h:120
int iTransitivity
Definition: clustal-omega.h:97
structure for storing multiple sequences
Definition: seq.h:47
Definition: clustal-omega.h:76
int AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMBed, bool bPercID)
Defines the alignment order by calculating a guide tree. In a first-step pairwise distances will be c...
Definition: clustal-omega.c:754
void AlnOptsLogicCheck(opts_t *opts)
Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, )) on Fatal logic error...
Definition: clustal-omega.c:231
bool bAutoOptions
Definition: clustal-omega.h:79
int iClustersizes
Definition: clustal-omega.h:93
Definition: clustal-omega.h:67
char * pcGuidetreeOutfile
Definition: clustal-omega.h:109
char * pcPosteriorfile
Definition: clustal-omega.h:99
char * pcGuidetreeInfile
Definition: clustal-omega.h:111
int iMaxHMMIterations
Definition: clustal-omega.h:132
int iPairDistType
Definition: clustal-omega.h:101