ureadseq.h File Reference

Defines
#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++;}
#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)))
#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
#define	kListSequences   -1
#define	kOtherSeq   0
#define	kDNA   1
#define	kRNA   2
#define	kNucleic   3
#define	kAmino   4
#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
#define	kPIR   14
#define	kMSF   15
#define	kASN1   16
#define	kPAUP   17
#define	kPretty   18
#define	kMaxFormat   18
#define	kMinFormat   1
#define	kNoformat   -1
#define	kUnknown   0
#define	kASNseqentry   51
#define	kASNseqset   52
#define	kPhylipInterleave   61
#define	kPhylipSequential   62
#define	gPrettyInit(p)
#define	seqchecksum   CRC32checksum
Typedefs
typedef char	boolean
Functions
short	seqFileFormat (const char *filename, long *skiplines, short *error)
short	seqFileFormatFp (FILE *fseq, long *skiplines, short *error)
char *	listSeqs (const char *filename, const long skiplines, const short format, short *nseq, short *error)
char *	readSeq (const short whichEntry, const char *filename, const long skiplines, const short format, long *seqlen, short *nseq, short *error, char *seqid)
char *	readSeqFp (const short whichEntry_, FILE *fp_, const long skiplines_, const short format_, long *seqlen_, short *nseq_, short *error_, char *seqid_)
short	writeSeq (FILE *outf, const char *seq, const long seqlen, const short outform, const char *seqid)
unsigned long	CRC32checksum (const char *seq, const long seqlen, unsigned long *checktotal)
unsigned long	GCGchecksum (const char *seq, const long seqlen, unsigned long *checktotal)
short	getseqtype (const char *seq, const long seqlen)
char *	compressSeq (const char gapc, const char *seq, const long seqlen, long *newlen)
int	Strcasecmp (const char *a, const char *b)
int	Strncasecmp (const char *a, const char *b, long maxn)
Variables
prettyopts	gPretty

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Define Documentation

#define eASNerr   -10

#define eFileCreate   -7

#define eFileNotFound   -1

#define eItemNotFound   -4

#define eMemFull   -3

#define eNoData   -2

#define eOneFormat   -5

#define eOptionBad   -9

#define eUnequalSize   -6

#define eUnknownFormat   -8

#define false   0

#define gPrettyInit (  p   )

Value: { \ 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; }

#define is_lower (  c   )     ('a'<=(c) && (c)<='z')

#define is_upper (  c   )     ('A'<=(c) && (c)<='Z')

#define kAmino   4

#define kASN1   16

#define kASNseqentry   51

#define kASNseqset   52

#define kDNA   1

#define kEMBL   4

#define kFitch   7

#define kGCG   5

#define kGenBank   2

#define kIG   1

#define kListSequences   -1

#define kMaxFormat   18

#define kMinFormat   1

#define kMSF   15

#define kNBRF   3

#define kNoformat   -1

#define kNucleic   3

#define kOlsen   10

#define kOtherSeq   0

#define kPAUP   17

#define kPearson   8

#define kPhylip   kPhylip4

#define kPhylip2   11

#define kPhylip3   kPhylip4

#define kPhylip4   12

#define kPhylipInterleave   61

#define kPhylipSequential   62

#define kPIR   14

#define kPlain   13

#define kPretty   18

#define kRNA   2

#define kStrider   6

#define kUnknown   0

#define kZuker   9

#define max (  a, b   )     (a>b)?a:b

#define min (  a, b   )     (a<b)?a:b

#define NEWLINE   '\n'

#define seqchecksum   CRC32checksum

#define skipwhitespace (  string   )     {while (*string <= ' ' && *string != 0) string++;}

#define to_lower (  c   )     ((char)(is_upper(c) ? (c)+' ' : (c)))

#define to_upper (  c   )     ((char)(is_lower(c) ? (c)-' ' : (c)))

#define true   1

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Typedef Documentation

typedef char boolean

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Function Documentation

char* compressSeq (  const char  gapc, const char *  seq, const long  seqlen, long *  newlen )

unsigned long CRC32checksum (  const char *  seq, const long  seqlen, unsigned long *  checktotal )

unsigned long GCGchecksum (  const char *  seq, const long  seqlen, unsigned long *  checktotal )

short getseqtype (  const char *  seq, const long  seqlen )

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

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

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

short seqFileFormat (  const char *  filename, long *  skiplines, short *  error )

short seqFileFormatFp (  FILE *  fseq, long *  skiplines, short *  error )

int Strcasecmp (  const char *  a, const char *  b )

int Strncasecmp (  const char *  a, const char *  b, long  maxn )

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

added 31jan91 added 31jan91

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Variable Documentation

prettyopts gPretty

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