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[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / clustal-omega.h

diff --git a/website/archive/binaries/mac/src/clustalo/src/clustal-omega.h b/website/archive/binaries/mac/src/clustalo/src/clustal-omega.h
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-/* -*- mode: c; tab-width: 4; c-basic-offset: 4;  indent-tabs-mode: nil -*- */
-
-/*********************************************************************
- * Clustal Omega - Multiple sequence alignment
- *
- * Copyright (C) 2010 University College Dublin
- *
- * Clustal-Omega is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License as
- * published by the Free Software Foundation; either version 2 of the
- * License, or (at your option) any later version.
- *
- * This file is part of Clustal-Omega.
- *
- ********************************************************************/
-
-/*
- *  RCS $Id: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $
- */
-
-#ifndef CLUSTALO_H
-#define CLUSTALO_H
-
-
-
-#ifdef HAVE_OPENMP
-#include <omp.h>
-#endif
-
-#include "clustal-omega-config.h"
-
-/* the following needs to be kept in sync with library_include_HEADERS of all
- * subdir Makefile.am's 
- */
-
-/* hhalign */
-#include "hhalign/general.h"
-#include "hhalign/hhfunc.h"
-
-
-/* clustal */
-#include "clustal/log.h"
-#include "clustal/util.h"
-#include "clustal/symmatrix.h"
-#include "clustal/tree.h"
-#include "clustal/seq.h"
-#include "clustal/mbed.h"
-#include "clustal/weights.h"
-#include "clustal/pair_dist.h"
-#include "clustal/hhalign_wrapper.h"
-
-
-
-#define CLUSTERING_UNKNOWN 0
-#define CLUSTERING_UPGMA 1
-
-/* weights will be computed if 1. but are not really used for now and they
- * might slow things down. also, mbed's screws up branch lengths which will
- * have a negative effect on weights 
-*/
-#define USE_WEIGHTS 0
-
-extern int iNumberOfThreads;
-
-
-/** user/commandline options
- *
- * changes here will have to be reflected in ParseCommandLine()
- * and during setup of the default opts
- *
- */
-typedef struct {
-    /* auto: Clustal (know what) is good for you
-     */
-    bool bAutoOptions;
-
-    /* Distance matrix
-     */
-    /** distance matrix input file */
-    char *pcDistmatInfile;
-    /** distance matrix output file */
-    char *pcDistmatOutfile;
-    
-    /* Clustering / guide-tree
-     */
-    /** clustering type (from cmdline arg) */
-    int iClusteringType;
-    /** pairwise distance method */
-    int iPairDistType;
-    /** use mbed-like clustering */
-    bool bUseMbed;
-    /** use mbed-like clustering also during iteration */
-    bool bUseMbedForIteration;
-    /** guidetree output file */
-    char *pcGuidetreeOutfile;
-    /** guidetree input file */
-    char *pcGuidetreeInfile;
-    
-    /* HMMs
-     */
-    /** HMM input files. index range: 0..iHMMInputFiles */
-    char **ppcHMMInput;
-    /** number of provided HMM input files. not really a user
-       option but need for ppcHMMInput */
-    int iHMMInputFiles;
-
-    /* Iteration
-     */
-    /** number of iterations */
-    int iNumIterations;
-    /** determine number of iterations automatically */
-       bool bIterationsAuto;
-    /** maximum number of hmm iterations */
-    int iMaxHMMIterations;
-    /** max number of guidetree iterations */
-       int iMaxGuidetreeIterations;
-    
-    /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
-    int iMacRam; /* FS, r240 -> */
-
-    /* changes here will have to be reflected in FreeAlnOpts(),
-        * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc 
-        */
-} opts_t;
-
-
-
-
-
-extern void 
-PrintLongVersion(char *pcStr, int iSize);
-
-extern void
-SetDefaultAlnOpts(opts_t *opts);
-
-extern void
-FreeAlnOpts(opts_t *aln_opts);
-
-extern void
-AlnOptsLogicCheck(opts_t *opts);
-
-extern void
-PrintAlnOpts(FILE *prFile, opts_t *opts);
-
-extern void
-InitClustalOmega(int iNumThreadsToUse);
-
-extern void
-SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
-
-extern int
-AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
-               int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
-               int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
-               bool bUseMBed);
-
-extern int
-Align(mseq_t *prMSeq, 
-      mseq_t *prMSeqProfile,
-         opts_t *prOpts,
-      hhalign_para rHhalignPara);
-
-extern int
-AlignProfiles(mseq_t *prMSeqProfile1, 
-                         mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
-
-#endif