Wrapper for Clustal Omega.

[jabaws.git] / binaries / src / clustalo / src / clustal / seq.h

diff --git a/binaries/src/clustalo/src/clustal/seq.h b/binaries/src/clustalo/src/clustal/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 234 2011-04-13 05:26:16Z andreas $
+ */
+
+#ifndef CLUSTALO_SEQ_H
+#define CLUSTALO_SEQ_H
+
+#include "squid/squid.h"
+
+#include "util.h"
+
+
+/**
+ * int-encoded sequence types.
+ * these are in sync with squid's seqtypes and only used for
+ * convenience here
+ */
+#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'
+
+/**
+ * @brief structure for storing multiple sequences
+ *
+ */
+typedef struct {
+    int nseqs; /**< number of sequences */
+    int seqtype; /**< sequence type */
+    char *filename; /**< input file / source of sequences */
+    bool aligned; /**< true if all seqs are same length **/
+    
+    /** (working) sequence residues as char pointer.
+     * range for first index: 0--nseq-1.
+     * changes during alignment.
+     */
+    char **seq;
+    
+    /** original sequence residues as char pointer.
+     * range for first index: 0--nseq-1.
+     * only set during input
+     */
+    char **orig_seq;
+    
+    /**
+     * @brief Squid's sequence info structure.
+     * Index range: 0--nseq-1.
+     *
+     * extra data are available:
+     * int flags;
+     *
+     * name:
+     * char name[SQINFO_NAMELEN];
+     *
+     * database identifier:
+     * char id[SQINFO_NAMELEN];
+     *
+     * database accession no:
+     * char acc[SQINFO_NAMELEN];
+     *
+     * description:      
+     * char desc[SQINFO_DESCLEN];
+     *
+     * length of this seq, incl gaps in our case!:
+     * int len;
+     *
+     * start position on source seq (valid range: 1..len):
+     * int start;
+     *
+     * end position on source seq (valid range: 1..len):
+     * int stop;
+     *
+     * original length of source seq:
+     * int olen;
+     *
+     * kRNA, kDNA, kAmino, or kOther:
+     * int type;
+     *
+     * secondary structure string (index range: 0..len-1):
+     * char *ss;
+     *
+     * percent side chain surface access (index range: 0..len-1):
+     * char *sa;                  
+     * 
+     * @see squid.h
+     * @see LogSqInfo()
+     *
+     */
+    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 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);
+
+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);
+
+#endif