seq.h

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/*********************************************************************
 * 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: seq.h 283 2013-06-10 17:42:14Z fabian $
 */

#ifndef CLUSTALO_SEQ_H
#define CLUSTALO_SEQ_H

#include "squid/squid.h"

#include "util.h"


#define SEQTYPE_UNKNOWN kOtherSeq
#define SEQTYPE_DNA kDNA
#define SEQTYPE_RNA kRNA
#define SEQTYPE_PROTEIN kAmino

/* Alphabets are defined in squid.h: AMINO_ALPHABET, DNA_ALPHABET,
 * RNA_ALPHABET (all uppercase)
 */
#define AMINOACID_ANY 'X'
#define NUCLEOTIDE_ANY 'N'

typedef struct {
    int nseqs; 
    int seqtype; 
    char *filename; 
    bool aligned; 
    char **seq;
    
    char **orig_seq;
    
  int *tree_order;

    SQINFO *sqinfo; 
} mseq_t;

extern void
AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll);

extern void
AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes);

extern void
SeqSwap(mseq_t *mseq, int i, int j);

extern void
DealignMSeq(mseq_t *mseq);

extern const char *
SeqTypeToStr(int seqtype);

extern int
ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, 
              int iSeqType,  int iSeqFmt, bool bIsProfile, 
              int iMaxNumSeq, int iMaxSeqLen);

extern void
NewMSeq(mseq_t **mseq);

extern void
FreeMSeq(mseq_t **mseq);

extern void
CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc);

extern void
LogSqInfo(SQINFO *sqinfo);

extern int
FindSeqName(char *seqname, mseq_t *mseq);

extern int
WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno);

extern void
DealignSeq(char *seq);

extern void
ShuffleMSeq(mseq_t *prMSeq);

extern void
SortMSeqByLength(mseq_t *prMSeq, const char cOrder);

void
JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd);

bool
SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile);

#endif