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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

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  ) 
 

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  )     ('a'<=(c) && (c)<='z')
 

#define is_upper  )     ('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,
 )     (a>b)?a:b
 

#define min a,
 )     (a<b)?a:b
 

#define NEWLINE   '\n'
 

#define seqchecksum   CRC32checksum
 

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

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

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

#define true   1
 


Typedef Documentation

typedef char boolean
 


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


Variable Documentation

prettyopts gPretty
 


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