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Classes
struct	prettyopts

Macros
#define	short int

#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	ePipeStdin -11

#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 /* 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 */

#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

Macro Definition Documentation

#define short int

Definition at line 8 of file ureadseq.h.

Referenced by AW_window::create_text_field(), gb_make_main_idx(), main(), and AW_window::refresh_toggle_field().

#define NEWLINE '\n'

Definition at line 12 of file ureadseq.h.

Referenced by dumpSeqList().

#define false 0

Definition at line 13 of file ureadseq.h.

#define true 1

Definition at line 14 of file ureadseq.h.

#define min	(	a,
		b
	)	(a<b)?a:b

Definition at line 15 of file ureadseq.h.

#define max	(	a,
		b
	)	(a>b)?a:b

Definition at line 16 of file ureadseq.h.

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

Definition at line 17 of file ureadseq.h.

Referenced by main(), parseformat(), readMSF(), readPAUPinterleaved(), readPAUPsequential(), readPhylipInterleaved(), readPhylipSequential(), and writeSeq().

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

Definition at line 20 of file ureadseq.h.

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

Definition at line 21 of file ureadseq.h.

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

Definition at line 22 of file ureadseq.h.

Referenced by main(), and parseformat().

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

Definition at line 23 of file ureadseq.h.

Referenced by CRC32checksum(), GCGchecksum(), getseqtype(), main(), Strcasecmp(), and Strncasecmp().

#define eFileNotFound -1

Definition at line 27 of file ureadseq.h.

Referenced by erralert(), readSeqMain(), and seqFileFormatFp().

#define eNoData -2

Definition at line 28 of file ureadseq.h.

Referenced by erralert(), and readSeqMain().

#define eMemFull -3

Definition at line 29 of file ureadseq.h.

Referenced by addseq(), erralert(), and main().

#define eItemNotFound -4

Definition at line 30 of file ureadseq.h.

Referenced by erralert(), and main().

#define eOneFormat -5

Definition at line 31 of file ureadseq.h.

Referenced by erralert(), and main().

#define eUnequalSize -6

Definition at line 32 of file ureadseq.h.

Referenced by erralert(), and main().

#define eFileCreate -7

Definition at line 33 of file ureadseq.h.

Referenced by erralert(), main(), and readopt().

#define eUnknownFormat -8

Definition at line 34 of file ureadseq.h.

Referenced by erralert(), readSeq(), readSeqFp(), and readSeqMain().

#define eOptionBad -9

Definition at line 35 of file ureadseq.h.

Referenced by readopt().

#define eASNerr -10

Definition at line 36 of file ureadseq.h.

Referenced by erralert().

#define ePipeStdin -11

Definition at line 37 of file ureadseq.h.

Referenced by erralert(), and main().

#define kListSequences -1

Definition at line 40 of file ureadseq.h.

Referenced by listSeqs(), readLoop(), readMSF(), readOlsen(), readPAUPinterleaved(), readPAUPsequential(), readPhylipInterleaved(), readPlain(), readSeq(), readSeqFp(), and readUWGCG().

#define kOtherSeq 0

Definition at line 43 of file ureadseq.h.

Referenced by getseqtype(), main(), seqFileFormatFp(), and writeSeq().

#define kDNA 1

Definition at line 44 of file ureadseq.h.

Referenced by getseqtype(), main(), seqFileFormatFp(), and writeSeq().

#define kRNA 2

Definition at line 45 of file ureadseq.h.

Referenced by getseqtype(), main(), seqFileFormatFp(), and writeSeq().

#define kNucleic 3

Definition at line 46 of file ureadseq.h.

Referenced by getseqtype(), main(), seqFileFormatFp(), and writeSeq().

#define kAmino 4

Definition at line 47 of file ureadseq.h.

Referenced by getseqtype(), main(), seqFileFormatFp(), and writeSeq().

#define kIG 1

Definition at line 50 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kGenBank 2

Definition at line 51 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kNBRF 3

Definition at line 52 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kEMBL 4

Definition at line 53 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kGCG 5

Definition at line 54 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kStrider 6

Definition at line 55 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kFitch 7

Definition at line 56 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPearson 8

Definition at line 57 of file ureadseq.h.

Referenced by chooseFormat(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kZuker 9

Definition at line 58 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kOlsen 10

Definition at line 59 of file ureadseq.h.

Referenced by readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPhylip2 11

Definition at line 60 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPhylip4 12

Definition at line 61 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPhylip3 kPhylip4

Definition at line 62 of file ureadseq.h.

#define kPhylip kPhylip4

Definition at line 63 of file ureadseq.h.

Referenced by formatstr(), main(), and seqFileFormatFp().

#define kPlain 13 /* keep this at #13 */

Definition at line 64 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPIR 14

Definition at line 65 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kMSF 15

Definition at line 66 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kASN1 16

Definition at line 67 of file ureadseq.h.

Referenced by formatstr(), main(), seqFileFormatFp(), and writeSeq().

#define kPAUP 17

Definition at line 68 of file ureadseq.h.

Referenced by main(), readSeqMain(), seqFileFormatFp(), and writeSeq().

#define kPretty 18

Definition at line 69 of file ureadseq.h.

Referenced by main(), and writeSeq().

#define kMaxFormat 18

Definition at line 71 of file ureadseq.h.

Referenced by chooseFormat(), formatstr(), parseformat(), readSeq(), readSeqFp(), and usage().

#define kMinFormat 1

Definition at line 72 of file ureadseq.h.

Referenced by chooseFormat(), and usage().

#define kNoformat -1 /* format not tested */

Definition at line 73 of file ureadseq.h.

Referenced by chooseFormat(), main(), parseformat(), resetGlobals(), and seqFileFormatFp().

#define kUnknown 0 /* format not determinable */

Definition at line 74 of file ureadseq.h.

Referenced by seqFileFormatFp(), and writeSeq().

#define kASNseqentry 51

Definition at line 77 of file ureadseq.h.

Referenced by formatstr(), main(), and seqFileFormatFp().

#define kASNseqset 52

Definition at line 78 of file ureadseq.h.

Referenced by formatstr(), main(), and seqFileFormatFp().

#define kPhylipInterleave 61

Definition at line 80 of file ureadseq.h.

Referenced by formatstr().

#define kPhylipSequential 62

Definition at line 81 of file ureadseq.h.

Referenced by formatstr().

#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=10;\
  p.numwidth=5;\
  p.interline=1;\
  p.spacer=10;\
  p.seqwidth=50;\
  p.tab=0; }

Definition at line 95 of file ureadseq.h.

Referenced by resetGlobals().

#define seqchecksum CRC32checksum

Definition at line 140 of file ureadseq.h.

Referenced by main(), and writeSeq().

Typedef Documentation

typedef char boolean

Definition at line 11 of file ureadseq.h.

Function Documentation

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

Definition at line 1151 of file ureadseq.c.

References format(), and seqFileFormatFp().

Referenced by main().

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

Definition at line 1165 of file ureadseq.c.

References ReadSeqVars::done, eFileNotFound, format(), getseqtype(), kAmino, kASN1, kASNseqentry, kASNseqset, kDNA, kEMBL, kFitch, kGCG, kGenBank, kIG, kMSF, kNBRF, kNoformat, kNucleic, kOlsen, kOtherSeq, kPAUP, kPearson, kPhylip, kPhylip2, kPhylip4, kPIR, kPlain, kRNA, kStrider, kUnknown, kZuker, ReadSeqVars::linestart, ReadOneLine, seq, and ReadSeqVars::sp.

Referenced by seqFileFormat().

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

Definition at line 1134 of file ureadseq.c.

References kListSequences, readSeq(), ReadSeqVars::seqid, and ReadSeqVars::seqlen.

Referenced by main().

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

Definition at line 1082 of file ureadseq.c.

References ReadSeqVars::addit, ReadSeqVars::allDone, ReadSeqVars::choice, ReadSeqVars::err, eUnknownFormat, ReadSeqVars::f, ReadSeqVars::filestart, ReadSeqVars::fname, ReadSeqVars::isseqchar, isSeqChar(), ReadSeqVars::isseqcharfirst8, kListSequences, kMaxFormat, kStartLength, ReadSeqVars::maxseq, ReadSeqVars::nseq, readSeqMain(), ReadSeqVars::seq, ReadSeqVars::seqid, and ReadSeqVars::seqlen.

Referenced by listSeqs(), and main().

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

Definition at line 1033 of file ureadseq.c.

References ReadSeqVars::addit, ReadSeqVars::allDone, ReadSeqVars::choice, ReadSeqVars::err, eUnknownFormat, ReadSeqVars::f, ReadSeqVars::filestart, ReadSeqVars::fname, ReadSeqVars::isseqchar, isSeqChar(), ReadSeqVars::isseqcharfirst8, kListSequences, kMaxFormat, kStartLength, ReadSeqVars::maxseq, ReadSeqVars::nseq, readSeqMain(), ReadSeqVars::seq, ReadSeqVars::seqid, and ReadSeqVars::seqlen.

Referenced by main().

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

added 31jan91

Definition at line 1583 of file ureadseq.c.

References prettyopts::atseq, prettyopts::baseonlynum, prettyopts::domatch, fputc(), prettyopts::gapchar, GCGchecksum(), getseqtype(), kAmino, kASN1, kDNA, kEMBL, kFitch, kGCG, kGenBank, kIG, kMaxseqwidth, kMSF, kNBRF, kNucleic, kOlsen, kOtherSeq, kPAUP, kPearson, kPhylip2, kPhylip4, kPIR, kPlain, kPretty, kRNA, kStrider, kUnknown, kZuker, prettyopts::matchchar, min, prettyopts::nameleft, prettyopts::nameright, prettyopts::nametop, prettyopts::namewidth, prettyopts::numleft, prettyopts::numline, prettyopts::numright, s, seqchecksum, ReadSeqVars::seqlen, prettyopts::seqwidth, skipwhitespace, prettyopts::spacer, prettyopts::tab, and tab().

Referenced by main().

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

Definition at line 1492 of file ureadseq.c.

References ReadSeqVars::seqlen, and to_upper.

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

Definition at line 1420 of file ureadseq.c.

References ReadSeqVars::seqlen, and to_upper.

Referenced by main(), and writeSeq().

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

Definition at line 1511 of file ureadseq.c.

References kAmino, kDNA, kNucleic, kOtherSeq, kRNA, min, and to_upper.

Referenced by main(), seqFileFormatFp(), and writeSeq().

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

Definition at line 1545 of file ureadseq.c.

References seq.

Referenced by main().

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

Definition at line 34 of file ureadseq.c.

References diff(), and to_upper.

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

Definition at line 48 of file ureadseq.c.

References diff(), and to_upper.

Referenced by checkopt().

Variable Documentation

prettyopts gPretty

Definition at line 31 of file ureadseq.c.

Referenced by main(), readopt(), and resetGlobals().

Classes

Macros

Typedefs

Functions

Variables

Macro Definition Documentation

Typedef Documentation

Function Documentation

Variable Documentation