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年11月16日 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