Clustal Omega: src/clustal/seq.h Source File

00001 /*********************************************************************
00002  * Clustal Omega - Multiple sequence alignment
00003  *
00004  * Copyright (C) 2010 University College Dublin
00005  *
00006  * Clustal-Omega is free software; you can redistribute it and/or
00007  * modify it under the terms of the GNU General Public License as
00008  * published by the Free Software Foundation; either version 2 of the
00009  * License, or (at your option) any later version.
00010  *
00011  * This file is part of Clustal-Omega.
00012  *
00013  ********************************************************************/
00014 
00015 /*
00016  *  RCS $Id: seq.h 270 2011-11-16 07:27:31Z andreas $
00017  */
00018 
00019 #ifndef CLUSTALO_SEQ_H
00020 #define CLUSTALO_SEQ_H
00021 
00022 #include "squid/squid.h"
00023 
00024 #include "util.h"
00025 
00026 
00032 #define SEQTYPE_UNKNOWN kOtherSeq
00033 #define SEQTYPE_DNA kDNA
00034 #define SEQTYPE_RNA kRNA
00035 #define SEQTYPE_PROTEIN kAmino
00036 
00037 /* Alphabets are defined in squid.h: AMINO_ALPHABET, DNA_ALPHABET,
00038  * RNA_ALPHABET (all uppercase)
00039  */
00040 #define AMINOACID_ANY 'X'
00041 #define NUCLEOTIDE_ANY 'N'
00042 
00047 typedef struct {
00048     int nseqs; 
00049     int seqtype; 
00050     char *filename; 
00051     bool aligned; 
00057     char **seq;
00058     
00063     char **orig_seq;
00064     
00109     SQINFO *sqinfo; 
00110 } mseq_t;
00111 
00112 extern void
00113 AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll);
00114 
00115 extern void
00116 AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes);
00117 
00118 extern void
00119 SeqSwap(mseq_t *mseq, int i, int j);
00120 
00121 extern void
00122 DealignMSeq(mseq_t *mseq);
00123 
00124 extern const char *
00125 SeqTypeToStr(int seqtype);
00126 
00127 extern int
00128 ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, 
00129               int iSeqType,  int iSeqFmt,
00130               int iMaxNumSeq, int iMaxSeqLen);
00131 
00132 extern void
00133 NewMSeq(mseq_t **mseq);
00134 
00135 extern void
00136 FreeMSeq(mseq_t **mseq);
00137 
00138 extern void
00139 CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc);
00140 
00141 extern void
00142 LogSqInfo(SQINFO *sqinfo);
00143 
00144 extern int
00145 FindSeqName(char *seqname, mseq_t *mseq);
00146 
00147 extern int
00148 WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format);
00149 
00150 extern void
00151 DealignSeq(char *seq);
00152 
00153 extern void
00154 ShuffleMSeq(mseq_t *prMSeq);
00155 
00156 extern void
00157 SortMSeqByLength(mseq_t *prMSeq, const char cOrder);
00158 
00159 void
00160 JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd);
00161 
00162 bool
00163 SeqsAreAligned(mseq_t *prMSeq);
00164 
00165 #endif