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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 <stdbool.h>

+

+#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;

+

+/* output order */

+enum {INPUT_ORDER = 0, TREE_ORDER};

+

+

+/** 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;

+    /** number of sequences in cluster */

+    int iClustersizes; 

+    /** file with clustering information */

+    char *pcClustfile; 

+    /** 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;

+    /** use Kimura corrected distance */

+    bool bUseKimura;

+    /** print percentage identity */

+    bool bPercID;

+

+    /* 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;

+    

+    hhalign_para rHhalignPara;

+

+    /* 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, int iClustersizes,

+               char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,

+               bool bUseMBed, bool bPercID);

+

+extern int

+Align(mseq_t *prMSeq, 

+      mseq_t *prMSeqProfile,

+	  opts_t *prOpts);

+

+extern int

+AlignProfiles(mseq_t *prMSeqProfile1, 

+			  mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);

+

+#endif