#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include "ureadseq.h"
#include <gets_noOverflow.h>

Include dependency graph for readseq.c:

Go to the source code of this file.

Classes
struct	formatTable

Macros
#define	__NO_CTYPE

#define	kFormCount 30

#define	kMaxFormName 15

#define	kDupmatch -2

#define	USERINPUT_BUFFERSIZE 128

#define	USERINPUT_BUFFERSIZE_SEQ 256

#define	kMaxwhichlist 50

#define	kOptOkay 1

#define	kOptNone 0

#define	Exit(a) exit(a)

#define	exit_main(err)

#define	indexout()

Functions
const char *	formatstr (short format)

int	rs_isdigit (int c)

int	parseformat (char *name2)

static void	dumpSeqList (char *list, short format)

void	usage ()

void	erralert (short err)

int	chooseFormat (boolean quietly)

boolean	checkopt (boolean casesense, char sopt, const char smatch, short minword)

void	resetGlobals ()

int	readopt (char *sopt)

int	main (int argc, char *argv[])

Variables
const char *	title = "readSeq (1Feb93), multi-format molbio sequence reader.\n"

static char	inputfilestore [256]

static char *	inputfile = inputfilestore

const char *	formats [kMaxFormat+1]

const struct formatTable	formname []

const char *	kASN1headline = "Bioseq-set ::= {\nseq-set {\n"

const char	compl [] = " !\"#$%&'()*+,-./0123456789:;<=>?@TVGHNNCDNNMNKNNYRYSAABWNRN[\\]^_`tvghnncdnnmnknnyrysaabwnrn{\|}~"

boolean	chooseall = false

boolean	quietly = false

boolean	gotinputfile = false

boolean	listonly = false

boolean	closeout = false

boolean	verbose = false

boolean	manyout = false

boolean	dolower = false

boolean	doupper = false

boolean	doreverse = false

boolean	askout = true

boolean	dopipe = false

boolean	interleaved = false

short	nfile = 0

short	iwhichlist =0

short	nwhichlist = 0

short	whichlist [kMaxwhichlist+1]

long	whichSeq = 0

long	outform = kNoformat

char	onamestore [USERINPUT_BUFFERSIZE]

char *	oname = onamestore

FILE *	foo = NULL

Macro Definition Documentation

#define __NO_CTYPE

Definition at line 174 of file readseq.c.

#define kFormCount 30

Definition at line 204 of file readseq.c.

Referenced by parseformat().

#define kMaxFormName 15

Definition at line 205 of file readseq.c.

Referenced by parseformat().

#define kDupmatch -2

Referenced by parseformat().

#define USERINPUT_BUFFERSIZE 128

Definition at line 409 of file readseq.c.

Referenced by chooseFormat(), and main().

#define USERINPUT_BUFFERSIZE_SEQ 256

Definition at line 410 of file readseq.c.

Referenced by main().

#define kMaxwhichlist 50

Definition at line 457 of file readseq.c.

Referenced by readopt().

#define kOptOkay 1

Definition at line 487 of file readseq.c.

Referenced by readopt().

#define kOptNone 0

Definition at line 488 of file readseq.c.

Referenced by readopt().

#define Exit ( a ) exit(a)

Definition at line 718 of file readseq.c.

#define exit_main ( err )

Value:

{        \
  if (closeout) fclose(fout);   \
  if (closein) fclose(fin);   \
  if (*tempname!=0) remove(tempname);\
  Exit(err); }

Referenced by main().

#define indexout ( )

Value:

if (interleaved) {\
  if (noutindex>=outindexmax) {\
    outindexmax= noutindex + 20;\
    outindex= (long*) realloc(outindex, sizeof(long)*outindexmax);\
    if (outindex==NULL) { err= eMemFull; erralert(err); exit_main(err); }\
    }\
  outindex[noutindex++]= ftell(fout);\
  }

Referenced by main().

Function Documentation

const char* formatstr ( short format )

Definition at line 251 of file readseq.c.

References kASN1, kASNseqentry, kASNseqset, kMaxFormat, kPhylip, kPhylipInterleave, and kPhylipSequential.

Referenced by dumpSeqList(), and main().

int rs_isdigit ( int c )

Definition at line 265 of file readseq.c.

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

int parseformat ( char * name2 )

Definition at line 269 of file readseq.c.

References formname, kDupmatch, kFormCount, kMaxFormat, kMaxFormName, kNoformat, min, formatTable::num, rs_isdigit(), skipwhitespace, and to_lower.

Referenced by chooseFormat(), and readopt().

static void dumpSeqList	(	char *	list,
		short	format
	)

static

Definition at line 308 of file readseq.c.

References formatstr(), NEWLINE, and s.

Referenced by main().

void usage ( )

Definition at line 328 of file readseq.c.

References fputs(), kMaxFormat, kMinFormat, and title.

Referenced by main(), readopt(), and string2enum_or_die().

void erralert ( short err )

Definition at line 379 of file readseq.c.

References eASNerr, eFileCreate, eFileNotFound, eItemNotFound, eMemFull, eNoData, eOneFormat, ePipeStdin, eUnequalSize, and eUnknownFormat.

Referenced by main(), and readopt().

int chooseFormat ( boolean quietly )

Definition at line 412 of file readseq.c.

References gets_noOverflow(), kMaxFormat, kMinFormat, kNoformat, kPearson, outform, parseformat(), and USERINPUT_BUFFERSIZE.

Referenced by main().

boolean checkopt	(	boolean	casesense,
		char *	sopt,
		const char *	smatch,
		short	minword
	)

Definition at line 436 of file readseq.c.

References max, min, result, and Strncasecmp().

Referenced by readopt().

void resetGlobals ( )

Definition at line 470 of file readseq.c.

References askout, closeout, dolower, dopipe, doreverse, doupper, foo, gotinputfile, gPretty, gPrettyInit, interleaved, iwhichlist, kNoformat, listonly, manyout, nfile, nwhichlist, onamestore, outform, quietly, verbose, and whichSeq.

Referenced by main().

int readopt ( char * sopt )

Definition at line 490 of file readseq.c.

References askout, prettyopts::baseonlynum, checkopt(), closeout, prettyopts::degap, dolower, prettyopts::domatch, dopipe, doreverse, doupper, eFileCreate, eOptionBad, erralert(), foo, prettyopts::gapchar, gotinputfile, gPretty, prettyopts::interline, iwhichlist, kMaxwhichlist, kOptNone, kOptOkay, listonly, prettyopts::matchchar, max, prettyopts::nameleft, prettyopts::nameright, prettyopts::nametop, prettyopts::namewidth, nfile, prettyopts::noleaves, prettyopts::numbot, prettyopts::numleft, prettyopts::numright, prettyopts::numtop, prettyopts::numwidth, nwhichlist, outform, parseformat(), rs_isdigit(), prettyopts::seqwidth, prettyopts::spacer, prettyopts::tab, usage(), verbose, whichlist, and whichSeq.

Referenced by main().

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 720 of file readseq.c.

References askout, chooseFormat(), closeout, compressSeq(), prettyopts::degap, dolower, prettyopts::domatch, dopipe, doreverse, doupper, dumpSeqList(), eFileCreate, eItemNotFound, eMemFull, eOneFormat, ePipeStdin, erralert(), eUnequalSize, exit_main, foo, format(), formatstr(), fputc(), fputs(), prettyopts::gapchar, GCGchecksum(), gets_noOverflow(), getseqtype(), gotinputfile, gPretty, indexout, inputfile, inputfilestore, interleaved, prettyopts::interline, prettyopts::isactive, iwhichlist, kAmino, kASN1, kASNseqentry, kASNseqset, kDNA, kGCG, kMSF, kNoformat, kNucleic, kOtherSeq, kPAUP, kPhylip, kPhylip2, kPhylip4, kPIR, kPlain, kPretty, kRNA, listonly, listSeqs(), manyout, prettyopts::matchchar, nfile, prettyopts::noleaves, prettyopts::numbot, prettyopts::numline, prettyopts::numtop, nwhichlist, oname, outform, quietly, readopt(), readSeq(), readSeqFp(), resetGlobals(), rs_isdigit(), s, seq, seqchecksum, seqFileFormat(), skipwhitespace, title, to_lower, to_upper, usage(), USERINPUT_BUFFERSIZE, USERINPUT_BUFFERSIZE_SEQ, verbose, whichlist, whichSeq, and writeSeq().

Variable Documentation

const char* title = "readSeq (1Feb93), multi-format molbio sequence reader.\n"

char inputfilestore[256]

static

Definition at line 181 of file readseq.c.

Referenced by main().

char * inputfile = inputfilestore

static

Definition at line 181 of file readseq.c.

Referenced by main(), Helpfile::readHelp(), and Helpfile::writeXML().

const char* formats[kMaxFormat+1]

Initial value:

= {
    " 1. IG/Stanford",
    " 2. GenBank/GB",
    " 3. NBRF",
    " 4. EMBL",
    " 5. GCG",
    " 6. DNAStrider",
    " 7. Fitch",
    " 8. Pearson/Fasta",
    " 9. Zuker (in-only)",
    "10. Olsen (in-only)",
    "11. Phylip3.2",
    "12. Phylip",
    "13. Plain/Raw",
    "14. PIR/CODATA",
    "15. MSF",
    "16. ASN.1",
    "17. PAUP/NEXUS",
    "18. Pretty (out-only)",
    "" }