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#ifndef MSA_SEEN
#define MSA_SEEN
/***********************************************************************
* *
* msa.c *
* *
* Copyright (C) 2003 Douglas L. Theobald *
* *
* msa.c 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. *
* *
* msa.c is distributed in the hope that it will be useful, but *
* WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU *
* General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with msa.c in the file 'COPYING'; if not, write to the: *
* *
* Free Software Foundation, Inc., *
* 59 Temple Place, Suite 330, *
* Boston, MA 02111-1307 USA *
* *
* -/_|:|_|_\- *
* Douglas Theobald *
* Department of Chemistry and Biochemistry *
* UCB 215 *
* University of Colorado at Boulder *
* Boulder, CO 80309-0215 *
* *
* theobal@colorado.edu *
* dtheobald@hotmail.com *
* *
***********************************************************************/
#include "DLTutils.h"
#define MAXLINE 50
#define SEQ_NAME_LENGTH 8192
typedef struct
{
char filename[FILENAME_MAX]; /* MSA file name */
int distance;
int allocnum; /* number of sequences allocated in the MSA */
int alloclen; /* allocated length of the alignment */
int seqnum; /* number of actual sequences in the MSA */
int seqlen; /* actual length of the alignment */
int *checksum; /* GCG/MSF-style sequence checksums */
int msachecksum; /* MSA checksum */
int *flag; /* external boolean flag */
int *flag2; /* private boolean flag for MSA functions */
char **seq; /* pointer to an array of sequences */
char **name; /* pointer to an array of the sequence names */
double **dist; /* pointer to array of distances */
} MSA;
typedef struct
{
int arraynum; /* number of MSAs allocated in the MSAA */
int *flag; /* external boolean flag */
MSA **array; /* pointer to an array of the sequence names */
} MSAA;
/* ////////////////////////////////////////////////////////////////////// */
MSA
*getmsa(char *msafile_name);
int
isnexdist(char *msafile_name);
int
ismsf(char *msafile_name);
MSA
*MSAinit(void);
void
MSAalloc(MSA *msa, int seqnum, int alignment_len, int name_size);
MSA
*DISTalloc(MSA *msa);
void
DISTfree(MSA *msa);
MSAA
*MSAAalloc(int arraynum);
void
MSAfree(MSA **msa_ptr);
void
MSAAfree(MSAA **msas_ptr);
/* ////////////////////////////////////////////////////////////////////// */
void
MSAprint(MSA *);
void
MSAmultiprint(MSAA *msas);
MSA
*MSAcpy(MSA *msa1, MSA *msa2);
MSA
*MSAduplicate(MSA *msa);
MSA
*MSAduplicate_noflags(MSA *msa);
MSA
*MSAmult(MSA *msa, int multiply);
MSA
*MSAduplicate_empty(MSA *msa);
int
MSAseqeq(MSA *msa1, MSA *msa2, int *seq1, int *begin1, int *end1, int *seq2, int *begin2, int *end2);
MSA
*MSAdeldups(MSA *msa);
MSA
*MSAfixnamesphy(MSA *msa);
MSA
*MSAdelallgaps(MSA *msa, int begcol, int endcol, int logap, int upgap, double frac);
MSA
*MSAdelgap(MSA *msa);
MSA
*MSAmingap(MSA *msa);
MSA
*MSAmerge(MSAA *msas);
void
MSAcombine2(MSAA *msaa, int msa1_i, int msa2_i, int seq1_i, int seq2_i, int msao_i);
/* ////////////////////////////////////////////////////////////////////// */
int
GCGchecksum(MSA *msa, int seq);
int
GCGmultichecksum(MSA *msa);
void
reada2m(char *msafile_name, MSA *msa);
void
reada2m2(char *msafile_name, MSA *msa);
void
readaln(char *msafile_name, MSA *msa);
void
readnex(char *msafile_name, MSA *msa);
void
readnexd(char *msafile_name, MSA *msa);
void
nexus_dist(MSA *msa, char *filestr, int filesize, int format);
int
getvali(char *string, char *key, char delimiter, char **endptr);
char *
getvals(char *string, char *key, char delimiter, char **endptr);
double
getvald(char *string, char *key, char delimiter, char **endptr);
char
getvalc(char *string, char *key, char delimiter, char **endptr);
void
readphylip(char *msafile_name, MSA *msa);
void
readphylipd(char *msafile_name, MSA *msa);
int
phylip_dist_format(MSA *msa, char *filestr, int filesize);
void
phylip_dist(MSA *msa, char *filestr, int filesize, int format);
void
readmsf(char *msafile_name, MSA *msa);
/* ////////////////////////////////////////////////////////////////////// */
void
writea2m_seq(MSA *msa, int seqID, char *outfile_root);
void
writealn_seq(MSA *msa, int seqID, char *outfile_root);
void
writenex_seq(MSA *msa, int seqID, char *outfile_root);
void
writenexd(MSA *msa, char *outfile_root);
void
writea2m(MSA *msa, int begin, int window, char *outfile_root);
void
writealn(MSA *msa, int begin, int window, char *outfile_root);
void
writephylip(MSA *msa, int begin, int window, char *outfile_root);
void
writenex(MSA *msa, int begin, int window, char *outfile_root);
void
writepsib(MSA *msa, int begin, int window, char *outfile_root);
void
writefasta_explode(MSA *msa, int nfield);
#endif
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