1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
3 /*********************************************************************
4 * Clustal Omega - Multiple sequence alignment
6 * Copyright (C) 2010 University College Dublin
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.
13 * This file is part of Clustal-Omega.
15 ********************************************************************/
18 * RCS $Id: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $
30 #include "clustal-omega-config.h"
32 /* the following needs to be kept in sync with library_include_HEADERS of all
33 * subdir Makefile.am's
37 #include "hhalign/general.h"
38 #include "hhalign/hhfunc.h"
42 #include "clustal/log.h"
43 #include "clustal/util.h"
44 #include "clustal/symmatrix.h"
45 #include "clustal/tree.h"
46 #include "clustal/seq.h"
47 #include "clustal/mbed.h"
48 #include "clustal/weights.h"
49 #include "clustal/pair_dist.h"
50 #include "clustal/hhalign_wrapper.h"
54 #define CLUSTERING_UNKNOWN 0
55 #define CLUSTERING_UPGMA 1
57 /* weights will be computed if 1. but are not really used for now and they
58 * might slow things down. also, mbed's screws up branch lengths which will
59 * have a negative effect on weights
63 extern int iNumberOfThreads;
66 /** user/commandline options
68 * changes here will have to be reflected in ParseCommandLine()
69 * and during setup of the default opts
73 /* auto: Clustal (know what) is good for you
79 /** distance matrix input file */
80 char *pcDistmatInfile;
81 /** distance matrix output file */
82 char *pcDistmatOutfile;
84 /* Clustering / guide-tree
86 /** clustering type (from cmdline arg) */
88 /** pairwise distance method */
90 /** use mbed-like clustering */
92 /** use mbed-like clustering also during iteration */
93 bool bUseMbedForIteration;
94 /** guidetree output file */
95 char *pcGuidetreeOutfile;
96 /** guidetree input file */
97 char *pcGuidetreeInfile;
101 /** HMM input files. index range: 0..iHMMInputFiles */
103 /** number of provided HMM input files. not really a user
104 option but need for ppcHMMInput */
109 /** number of iterations */
111 /** determine number of iterations automatically */
112 bool bIterationsAuto;
113 /** maximum number of hmm iterations */
114 int iMaxHMMIterations;
115 /** max number of guidetree iterations */
116 int iMaxGuidetreeIterations;
118 /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
119 int iMacRam; /* FS, r240 -> */
121 /* changes here will have to be reflected in FreeAlnOpts(),
122 * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
131 PrintLongVersion(char *pcStr, int iSize);
134 SetDefaultAlnOpts(opts_t *opts);
137 FreeAlnOpts(opts_t *aln_opts);
140 AlnOptsLogicCheck(opts_t *opts);
143 PrintAlnOpts(FILE *prFile, opts_t *opts);
146 InitClustalOmega(int iNumThreadsToUse);
149 SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
152 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
153 int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
154 int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
158 Align(mseq_t *prMSeq,
159 mseq_t *prMSeqProfile,
161 hhalign_para rHhalignPara);
164 AlignProfiles(mseq_t *prMSeqProfile1,
165 mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);