void Parser::applyState(
std::stack<std::string> &frameStack,
std::stack<std::string> &pStack, std::list<int> &output,
int &s, std::string &a, int &ip, int &ip2, std::string &action
)
{
//=========================================================
action = popStack(frameStack);
ip2 = val(popStack(frameStack));
ip = val(popStack(frameStack));
a = popStack(frameStack);
s = val(popStack(frameStack));
//=========================================================
writeSeq(output, popStack(frameStack));
writeSeq(pStack, popStack(frameStack));
//=========================================================
this->pushState(frameStack, pStack, output, s, a, ip, ip2, action);
}
extern int main( int argc, char *argv[])
#endif
{
boolean closein = false;
short ifile, format, err = 0, seqtype = kDNA,
nlines=0, seqout = 0, phylvers = 2;
long atseq, nseq, i, skiplines, seqlen, seqlen0=0; /* changed atseq and nseq from short to long - James J (UQ) */
unsigned long checksum= 0, checkall= 0;
char *seq=NULL, *cp=NULL, *firstseq = NULL, *seqlist=NULL,
*progname;
/*char tempname[] = "readseqXXXXXX";*/
char *tempname = NULL;
char seqid[MAXLINE], *seqidptr = seqid;
char stempstore[256], *stemp = stempstore;
FILE *ftmp=NULL, *fin=NULL, *fout=NULL;
long outindexmax= 0, noutindex= 0, *outindex = NULL;
#define exit_main(err) { \
if (closeout) fclose(fout); \
if (closein) fclose(fin); \
if (tempname != NULL) remove(tempname); \
Exit(err); }
#define indexout() 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);\
}
resetGlobals();
foo = stdout;
progname = argv[0];
*oname = 0;
/* initialize gPretty ?? -- done in header */
for (i=1; i < argc; i++) {
err= readopt( argv[i]);
if (err <= 0) exit_main(err);
}
/* pipe input from stdin !? */
if (dopipe && !gotinputfile) {
int c;
int fd;
/*
tmpnam(tempname);
inputfile = tempname;
ftmp = fopen( inputfile, "w");
*/
tempname = strdup("readseqXXXXXX");
fd = mkstemp(tempname);
if (fd == -1) { erralert(eFileCreate); exit_main(eFileCreate); }
strcpy(inputfile, tempname);
while ((c = getc(stdin)) != EOF) write(fd, &c, 1);
close(fd);
gotinputfile= true;
}
quietly = (dopipe || (gotinputfile && (listonly || whichSeq != 0)));
if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, "%s", title);
ifile = 1;
/* UI: Choose output */
if (askout && !closeout && !quietly) {
askout = false;
fprintf(stderr,"\nName of output file (?=help, defaults to display): \n");
fgets(oname= onamestore, 128, stdin);
skipwhitespace(oname);
if (*oname == '?') { usage(); exit_main(0); }
else if (*oname != 0) {
closeout = true;
foo = fopen( oname, "w");
if (!foo) { erralert(eFileCreate); exit_main(eFileCreate); }
}
}
fout = foo;
if (outform == kNoformat) outform = chooseFormat(quietly);
/* set up formats ... */
switch ((int) outform) {
case kPhylip2:
interleaved= false;
phylvers = 2;
outform = kPhylip;
break;
case kPhylip4:
interleaved= true;
phylvers = 4;
outform = kPhylip;
break;
case kMSF:
case kPAUP:
interleaved= true;
break;
case kPretty:
gPretty.isactive= true;
interleaved= true;
break;
}
if (gPretty.isactive && gPretty.noleaves) interleaved= false;
if (interleaved) {
fout = ftmp = tmpfile();
outindexmax= 30; noutindex= 0;
outindex = (long*) malloc(outindexmax*sizeof(long));
if (outindex==NULL) { err= eMemFull; erralert(err); exit_main(err); }
}
/* big loop over all input files */
do {
/* select next input file */
/*gotinputfile = (*tempname != 0);*/
gotinputfile = (tempname != NULL);
while ((ifile < argc) && (!gotinputfile)) {
if (*argv[ifile] != '-') {
strcpy( inputfile, argv[ifile]);
gotinputfile = (*inputfile != 0);
--nfile;
}
ifile++;
}
while (!gotinputfile) {
fprintf(stderr,"\nName an input sequence or -option: \n");
inputfile= inputfilestore;
fgets(stemp= stempstore, 256, stdin);
if (*stemp==0) goto fini; /* !! need this to finish work during interactive use */
stemp= strtok(stempstore, " \n\r\t");
while (stemp) {
err= readopt( stemp); /* will read inputfile if it exists */
if (err<0) exit_main(err);
stemp= strtok( NULL, " \n\r\t");
}
}
/* thanks to [email protected] for this PHYLIP3 fix: */
/* head for end (interleave if needed) */
if (*inputfile == 0) break;
format = seqFileFormat( inputfile, &skiplines, &err);
if (err == 0) {
#ifdef NCBI
if (format == kASNseqentry || format == kASNseqset)
seqlist = listASNSeqs( inputfile, skiplines, format, &nseq, &err);
else
#endif
seqlist = listSeqs( inputfile, skiplines, format, &nseq, &err);
}
if (err != 0)
erralert(err);
else if (listonly) {
dumpSeqList(seqlist,format);
free( seqlist);
}
else {
/* choose whichSeq if needed */
if (nseq == 1 || chooseall || (quietly && whichSeq == 0)) {
chooseall= true;
whichSeq = 1;
quietly = true; /* no loop */
}
else if (whichSeq > nseq && quietly) {
erralert(eItemNotFound);
err= eItemNotFound;
}
else if (whichSeq > nseq || !quietly) {
dumpSeqList(seqlist, format);
fprintf(stderr,"\nChoose a sequence (# or All): \n");
fgets(stemp= stempstore, 256, stdin);
skipwhitespace(stemp);
if (to_lower(*stemp) == 'a') {
chooseall= true;
whichSeq = 1;
quietly = true; /* !? this means we don't ask for another file
as well as no more whichSeqs... */
}
else if (isdigit((int) *stemp)) whichSeq= atol(stemp);
else whichSeq= 1; /* default */
}
free( seqlist);
if (false /*chooseall*/) { /* this isn't debugged yet...*/
fin = fopen(inputfile, "r");
closein= true;
}
while (whichSeq > 0 && whichSeq <= nseq) {
/* need to open multiple output files ? */
manyout = ((chooseall || nwhichlist>1) && nseq > 1
&& (outform == kPlain || outform == kGCG));
if (manyout) {
if ( whichSeq == 1 ) erralert(eOneFormat);
else if (closeout) {
sprintf( stemp,"%s_%ld", oname, whichSeq);
freopen( stemp, "w", fout);
fprintf( stderr,"Writing sequence %ld to file %s\n",
whichSeq, stemp);
}
}
if (closein) {
/* !! this fails... skips most seqs... */
/* !! in sequential read, must count seqs already read from whichSeq ... */
/* need major revision of ureadseq before we can do this */
atseq= whichSeq-1;
seqidptr= seqid;
seq = readSeqFp( whichSeq, fin, skiplines, format,
&seqlen, &atseq, &err, seqidptr);
skiplines= 0;
}
else {
atseq= 0;
seqidptr= seqid;
#ifdef NCBI
if (format == kASNseqentry || format == kASNseqset) {
seqidptr= NULL;
seq = readASNSeq( whichSeq, inputfile, skiplines, format,
&seqlen, &atseq, &err, &seqidptr);
}
else
#endif
seq = readSeq( whichSeq, inputfile, skiplines, format,
&seqlen, &atseq, &err, seqidptr);
}
if (gPretty.degap) {
char *newseq;
long newlen;
newseq= compressSeq( gPretty.gapchar, seq, seqlen, &newlen);
if (newseq) {
free(seq); seq= newseq; seqlen= newlen;
}
}
if (outform == kMSF) checksum= GCGchecksum(seq, seqlen, &checkall);
else if (verbose) checksum= seqchecksum(seq, seqlen, &checkall);
if (verbose)
fprintf( stderr,
"Sequence %ld, length= %ld, checksum= %X, format= %s, id= %s\n",
whichSeq, seqlen, (int)checksum, formatstr(format), seqidptr);
if (err != 0) erralert(err);
else {
/* format fixes that writeseq doesn't do */
switch ((int) outform) {
case kPIR:
if (seqout == 0) fprintf( foo,"\\\\\\\n");
break;
case kASN1:
if (seqout == 0) fprintf( foo, "%s", kASN1headline);
break;
case kPhylip:
if (seqout == 0) {
if (!interleaved) { /* bug, nseq is for 1st infile only */
if (chooseall) i= nseq; else i=1;
if (phylvers >= 4) fprintf(foo," %ld %ld\n", i, seqlen);
else fprintf(foo," %ld %ld YF\n", i, seqlen);
}
seqlen0 = seqlen;
}
else if (seqlen != seqlen0) {
erralert(eUnequalSize);
if (seqlen < seqlen0) seq = (char *)realloc(seq, seqlen0);
for (i=seqlen; i<seqlen0; i++) seq[i]= gPretty.gapchar;
seqlen = seqlen0;
seq[seqlen] = 0;
}
break;
case kPAUP:
if (seqout == 0) {
seqtype= getseqtype(seq, seqlen);
seqlen0 = seqlen;
}
else if (seqlen != seqlen0) {
erralert(eUnequalSize);
if (seqlen < seqlen0) seq = (char *)realloc(seq, seqlen0);
for (i=seqlen; i<seqlen0; i++) seq[i]= gPretty.gapchar;
seqlen = seqlen0;
seq[seqlen] = 0;
}
break;
}
if (doupper)
for (i = 0; i<seqlen; i++) seq[i] = to_upper(seq[i]);
else if (dolower)
for (i = 0; i<seqlen; i++) seq[i] = to_lower(seq[i]);
if (doreverse) {
long j, k;
char ctemp;
for (j=0, k=seqlen-1; j <= k; j++, k--) {
ctemp = compl[seq[j] - ' '];
seq[j] = compl[seq[k] - ' '];
seq[k] = ctemp;
}
}
if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq != NULL) {
for (i=0; i<seqlen; i++)
if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
}
if (gPretty.isactive && gPretty.numtop && seqout == 0) {
gPretty.numline = 1;
indexout();
(void) writeSeq( fout, seq, seqlen, outform, seqidptr);
gPretty.numline = 2;
indexout();
(void) writeSeq( fout, seq, seqlen, outform, seqidptr);
gPretty.numline = 0;
}
indexout();
nlines = writeSeq( fout, seq, seqlen, outform, seqidptr);
seqout++;
}
if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq == NULL) {
firstseq= seq;
seq = NULL;
}
else if (seq!=NULL) { free(seq); seq = NULL; }
#ifdef NCBI
if ( (format == kASNseqentry || format == kASNseqset)
&& seqidptr && seqidptr!= seqid)
free(seqidptr);
#endif
if (chooseall) whichSeq++;
else if (iwhichlist<nwhichlist) whichSeq= whichlist[iwhichlist++];
else whichSeq= 0;
}
if (closein) { fclose(fin); closein= false; }
}
whichSeq = 0;
} while (nfile > 0 || !quietly);
fini:
if (firstseq) { free(firstseq); firstseq= NULL; }
if (err || listonly) exit_main(err);
if (gPretty.isactive && gPretty.numbot) {
gPretty.numline = 2;
indexout();
(void) writeSeq( fout, seq, seqlen, outform, seqidptr);
gPretty.numline = 1;
indexout();
(void) writeSeq( fout, seq, seqlen, outform, seqidptr);
gPretty.numline = 0;
}
if (outform == kMSF) {
if (*oname) cp= oname; else cp= inputfile;
fprintf(foo,
"\n %s MSF: %ld Type: N January 01, 1776 12:00 Check: %ld ..\n\n",
cp, seqlen, checkall);
}
if (outform == kPAUP) {
fprintf(foo,"#NEXUS\n");
if (*oname) cp= oname; else cp= inputfile;
fprintf(foo,"[%s -- data title]\n\n", cp);
/* ! now have header lines for each sequence... put them before "begin data;... */
}
if (outform==kPhylip && interleaved) {
if (phylvers >= 4) fprintf(foo," %d %ld\n", seqout, seqlen);
else fprintf(foo," %d %ld YF\n", seqout, seqlen);
}
if (interleaved) {
/* interleave species lines in true output */
/* nlines is # lines / sequence */
short iline, j, leaf, iseq;
char *s = stempstore;
indexout(); noutindex--; /* mark eof */
for (leaf=0; leaf<nlines; leaf++) {
if (outform == kMSF && leaf == 1) {
fputs("//\n\n", foo);
}
if (outform == kPAUP && leaf==1) {
switch (seqtype) {
case kDNA : cp= "dna"; break;
case kRNA : cp= "rna"; break;
case kNucleic : cp= "dna"; break;
case kAmino : cp= "protein"; break;
case kOtherSeq: cp= "dna"; break;
}
fprintf(foo,"\nbegin data;\n");
fprintf(foo," dimensions ntax=%d nchar=%ld;\n", seqout, seqlen);
fprintf(foo," format datatype=%s interleave missing=%c", cp, gPretty.gapchar);
if (gPretty.domatch) fprintf(foo," matchchar=%c", gPretty.matchchar);
fprintf(foo,";\n matrix\n");
}
for (iseq=0; iseq<noutindex; iseq++) {
fseek(ftmp, outindex[iseq], 0);
for (iline=0; iline<=leaf; iline++)
if (!fgets(s, 256, ftmp)) *s= 0;
if (ftell(ftmp) <= outindex[iseq+1])
fputs( s, foo);
}
for (j=0; j<gPretty.interline; j++)
fputs( "\n", foo); /* some want spacer line */
}
fclose(ftmp); /* tmp disappears */
fout= foo;
}
if (outform == kASN1) fprintf( foo, "} }\n");
if (outform == kPAUP) fprintf( foo,";\n end;\n");
if (outindex != NULL) free(outindex);
exit_main(0);
}