/* File: ureadseq.h
 *
 * Header for module UReadSeq
 */

#ifndef UREADSEQ_H
#define UREADSEQ_H

typedef char boolean;
#define NEWLINE '\n'
#define false 0
#define true 1
#define min(a, b) (a < b) ? a : b
#define max(a, b) (a > b) ? a : b
#define skipwhitespace(string)                                   \
	{                                                        \
		while (*string <= ' ' && *string != 0) string++; \
	}

/* NLM strings */
#define is_upper(c) ('A' <= (c) && (c) <= 'Z')
#define is_lower(c) ('a' <= (c) && (c) <= 'z')
#define to_lower(c) ((char)(is_upper(c) ? (c) + ' ' : (c)))
#define to_upper(c) ((char)(is_lower(c) ? (c) - ' ' : (c)))

/* readSeq errors */
#define eFileNotFound -1
#define eNoData -2
#define eMemFull -3
#define eItemNotFound -4
#define eOneFormat -5
#define eUnequalSize -6
#define eFileCreate -7
#define eUnknownFormat -8
#define eOptionBad -9
#define eASNerr -10

/* magic number for readSeq(whichEntry) to give seq list */
#define kListSequences -1

/* sequence types parsed by getseqtype */
#define kOtherSeq 0
#define kDNA 1
#define kRNA 2
#define kNucleic 3
#define kAmino 4

/* formats known to readSeq */
#define kIG 1
#define kGenBank 2
#define kNBRF 3
#define kEMBL 4
#define kGCG 5
#define kStrider 6
#define kFitch 7
#define kPearson 8
#define kZuker 9
#define kOlsen 10
#define kPhylip2 11
#define kPhylip4 12
#define kPhylip3 kPhylip4
#define kPhylip kPhylip4
#define kPlain 13 /* keep this at #13 */
#define kPIR 14
#define kMSF 15
#define kASN1 16
#define kPAUP 17
#define kPretty 18

#define kMaxFormat 18
#define kMinFormat 1
#define kNoformat -1 /* format not tested */
#define kUnknown 0   /* format not determinable */

/* subsidiary types */
#define kASNseqentry 51
#define kASNseqset 52

#define kPhylipInterleave 61
#define kPhylipSequential 62

typedef struct {
	boolean isactive, baseonlynum;
	boolean numright, numleft, numtop, numbot;
	boolean nameright, nameleft, nametop;
	boolean noleaves, domatch, degap;
	char matchchar, gapchar;
	short numline, atseq;
	short namewidth, numwidth;
	short interline, spacer, seqwidth, tab;
} prettyopts;

#define gPrettyInit(p)                                                \
	{                                                             \
		p.isactive = false;                                   \
		p.baseonlynum = true;                                 \
		p.numline = p.atseq = 0;                              \
		p.numright = p.numleft = p.numtop = p.numbot = false; \
		p.nameright = p.nameleft = p.nametop = false;         \
		p.noleaves = p.domatch = p.degap = false;             \
		p.matchchar = '.';                                    \
		p.gapchar = '-';                                      \
		p.namewidth = 8;                                      \
		p.numwidth = 5;                                       \
		p.interline = 1;                                      \
		p.spacer = 10;                                        \
		p.seqwidth = 50;                                      \
		p.tab = 0;                                            \
	}

#ifdef UREADSEQ_G
prettyopts gPretty;
#else
extern prettyopts gPretty;
#endif

#ifdef __cplusplus
extern "C" {
#endif

extern short seqFileFormat(const char *filename, long *skiplines, short *error);
extern short seqFileFormatFp(FILE *fseq, long *skiplines, short *error);

extern char *listSeqs(const char *filename, const long skiplines,
		      const short format, short *nseq, short *error);

extern char *readSeq(const short whichEntry, const char *filename,
		     const long skiplines, const short format, long *seqlen,
		     short *nseq, short *error, char *seqid);

extern char *readSeqFp(const short whichEntry_, FILE *fp_,
		       const long skiplines_, const short format_,
		       long *seqlen_, short *nseq_, short *error_,
		       char *seqid_);

extern short writeSeq(FILE *outf, const char *seq, const long seqlen,
		      const short outform, const char *seqid);

extern unsigned long CRC32checksum(const char *seq, const long seqlen,
				   unsigned long *checktotal);
extern unsigned long GCGchecksum(const char *seq, const long seqlen,
				 unsigned long *checktotal);
#ifdef SMALLCHECKSUM
#define seqchecksum GCGchecksum
#else
#define seqchecksum CRC32checksum
#endif

extern short getseqtype(const char *seq, const long seqlen);
extern char *compressSeq(const char gapc, const char *seq, const long seqlen,
			 long *newlen);

#ifdef NCBI

extern char *listASNSeqs(const char *filename, const long skiplines,
			 const short format, short *nseq, short *error);

extern char *readASNSeq(const short whichEntry, const char *filename,
			const long skiplines, const short format, long *seqlen,
			short *nseq, short *error, char **seqid);
#endif

/* patches for some missing string.h stuff */
extern int Strcasecmp(const char *a, const char *b);
extern int Strncasecmp(const char *a, const char *b, long maxn);

#ifdef __cplusplus
}
#endif

#endif /*UREADSEQ_H*/