command()
{
double tval;
int i,echeck;
int pmin,pmax,pstep;
while (echeck = getstring(": ")) {
if (echeck == EOF) {
fileinput(EOF);
}
else if (in[0] == '\0') {
errprint("");
}
else if (startsame(in,"cycle")) {
cycle();
}
else if (startsame(in,"clear")) {
clear();
}
else if (startsame(in,"coarticulation")) {
getint(&coartflag);
}
else if (startsame(in,"rc")) {
zarrays();
cycle();
}
else if (startsame(in,"wordacts")) {
scr_words(printmin,printmax,3,0,"MAX");
}
else if (startsame(in,"wtacts")) {
scr_words(printmin,printmax,3,0,"ALL");
}
else if (startsame(in,"owtacts")) {
getstring("word: ");
scr_words(printmin,printmax,3,0,in);
}
else if (startsame(in,"phonacts")) {
scr_phonemes(printmin,printmax,3,0);
}
else if (startsame(in,"featacts")) {
scr_features();
}
else if (startsame(in,"sfeatacts")) {
getstring("fname: ");
sfeatacts(in);
}
else if (startsame(in,"memo")) {
getstring("string: ");
strcpy(memo,in);
}
else if (startsame(in,"expr")) {
setex();
}
else if (startsame(in,"fcopt")) {
getint(&fcflag);
}
else if (startsame(in,"fpcyc")) {
getint(&fpcyc);
}
else if (startsame(in,"finput")) {
fileinput(NONSTD);
}
else if (startsame(in,"inoise")) {
getval(&inoise);
}
else if (startsame(in,"inspecs")) {
getstring("File name (- = stdin): ");
inspecs(in);
}
else if (startsame(in,"infeatures")) {
getstring("File name: ");
infeats(in);
}
/* NOT PRESENTLY OPERATIVE -- JLM 10-5-82
else if (startsame(in,"wsubset")) {
wordsubset();
}
*/
else if (startsame(in,"test")) {
getstring("test string: ");
strcpy(memo,in);
test(in);
}
else if (startsame(in,"topdown")) {
topdown();
}
else if (startsame(in,"output")) {
setout();
}
else if (startsame(in,"ofile")) {
getstring("give filename (or - for none): ");
setoutfile(in);
}
else if (in[0] == '?') {
help();
}
else if (startsame(in,"help")) {
help();
}
else if (startsame(in,"lexicon")) {
getlex();
}
else if (startsame(in,"params")) {
getpars();
}
else if (startsame(in,"quit")) {
quit();
}
else if (startsame(in,"decay")) {
getdouble(decay,NLEVS,levlabs);
}
else if (startsame(in,"alpha")) {
getdouble(alpha,NPARAMS,conlabs);
}
else if (startsame(in,"gamma")) {
getdouble(ga,NLEVS,levlabs);
}
else if (startsame(in,"grace")) {
getint(&grace);
}
else if (startsame(in,"rest")) {
tval = rest[W];
getdouble(rest,NLEVS,levlabs);
if (tval != rest[W]) {
initialize();
}
}
else if (startsame(in,"fweight")) {
getdouble(fweight,NCONTINS,contname);
}
else if (startsame(in,"pthresh")) {
getdouble(pthresh,NLEVS,levlabs);
}
else if (startsame(in,"ngraph")) {
newgraph(pmin,ng_max,pstep);
}
else if (startsame(in,"ngmax")) {
getint(&ng_max);
}
else if (startsame(in,"ngwscale")) {
getval(&ng_wscale);
}
else if (startsame(in,"ngsscale")) {
getval(&ng_sscale);
}
else if (startsame(in,"ngpscale")) {
getval(&ng_pscale);
}
else if (startsame(in,"nreps")) {
getint(&nreps);
}
else if (startsame(in,"pfreq")) {
getint(&printfreq);
}
else if (startsame(in,"rarate")) {
getval(&rarate);
}
else if (startsame(in,"sumpr")) {
scr_sum(pmin,pmax,pstep);
}
else if (startsame(in,"sinspec")) {
sinspec();
}
else if (startsame(in,"sfeatures")) {
getstring("Filename: ");
sfeatures(in);
}
else if (startsame(in,"dinspec")) {
dinspec();
}
else if (startsame(in,"sumopt")) {
getint(&sumflag);
}
else if (startsame(in,"pmin")) {
getint(&pmin);
}
else if (startsame(in,"pmax")) {
getint(&pmax);
}
else if (startsame(in,"pstep")) {
getint(&pstep);
}
else if (startsame(in,"min")) {
getval(&min);
}
else if (startsame(in,"max")) {
getval(&max);
}
else if (startsame(in,"windowcent")) {
getval(&windowcent);
}
else if (startsame(in,"wbase")) {
getval(&wbase);
}
else if (startsame(in,"wgraph")) {
wgraph(pmin,ng_max,pstep);
}
else if (startsame(in,"wchange")) {
getval(&wchange);
}
else if (startsame(in,"wgain")) {
getval(&wgain);
}
else if (startsame(in,"wramp")) {
getval(&wramp);
}
else if (startsame(in,"imax")) {
getval(&imax);
}
else if (startsame(in,"sscale")) {
getval(&sscale);
}
else if (startsame(in,"nsscale")) {
getval(&nsscale);
}
else if (startsame(in,"freqscale")) {
tval = fscale;
getval(&fscale);
if (tval != fscale) {
initialize();
}
}
else if (startsame(in,"abort")) {
abort(); /* to get a core dump for sdb */
}
else {
errprint("Unrecognized request: For help type ?.");
if (infp != stdin) fileinput(STD);
}
wait(0);
}
}
void default1D(struct data *d)
{
struct file fref;
struct data ref;
struct datablockhead *dbh;
int /*dim1,dim2,*/dim3,nr;
int i,j;
int wref=FALSE;
#ifdef DEBUG
char function[20];
strcpy(function,"default1D"); /* Set function name */
#endif
/* Open data and phasefile file pointers for writing */
openfpw(d,DATA_FILE);
openfpw(d,PHAS_FILE);
/* Write data and phasefile file headers */
wdfh(d,DATA_FILE);
wdfh(d,PHAS_FILE);
/* Set data dimensions */
//dim1=d->np/2;
//dim2=1;
dim3=d->fh.ntraces;
nr=d->nr;
/* Set nuber of "volumes" */
d->nvols=d->fh.nblocks/nr;
/* Check if there is a water reference */
if (spar(d,"ws","y") && spar(d,"wref","y") && spar(d,"wrefstatus","ws")) wref=TRUE;
/* Prepare water reference */
if (wref) {
setreffile(&fref,d,"waterref"); /* Set reference file */
getpars(fref.procpar[0],&ref); /* Get pars from reference procpar */
opendata(fref.fid[0],&ref); /* Open reference data file fid */
getvol1D(&ref,0,NDCC); /* Get volume without applying dbh.lvl and dbh.tlt */
weightdata1D(&ref,STD,D1); /* Weight data using standard VnmrJ parameters */
}
/* Allocate memory for blocks headers from all receivers */
if ((dbh = malloc(nr*sizeof(d->bh))) == NULL) nomem();
/* For spectra we anticipate there is easily sufficient memory for data
from all receiver blocks */
for (d->vol=0;d->vol<d->nvols;d->vol++) { /* loop over "volumes" */
for (i=0;i<nr;i++) { /* loop over receivers */
getdbh(d,nr*d->vol+i); /* Get block header */
copydbh(&d->bh,&dbh[i]); /* Store the block headers for writing */
}
getvol1D(d,d->vol,NDCC); /* Get data block without applying dbh.lvl and dbh.tlt */
weightdata1D(d,STD,D1); /* Weight data using standard VnmrJ parameters */
if (wref) refcorr1D(d,&ref); /* Phase correct using the reference */
else combine1D(d); /* Combine data from multiple receivers */
zerofill1D(d,STD,D1); /* Zero fill data using standard VnmrJ parameters */
fft1D(d,D1); /* 1D fft */
shiftdata1D(d,STD,D1); /* Shift data to get spectra */
for (i=0;i<nr;i++) { /* loop over receivers */
copydbh(&dbh[i],&d->bh); /* Copy block header for writing */
for (j=0;j<dim3;j++) {
d->bh.index=d->vol*nr*dim3+i*dim3+j; /* Set block index */
wdbh(d,DATA_FILE); /* Write block header */
wdbh(d,PHAS_FILE); /* Write block header */
w1Dtrace(d,i,j,DATA_FILE); /* Write block */
w1Dtrace(d,i,j,PHAS_FILE); /* Write block */
}
}
clear1Ddata(d); /* Clear data "volume" from memory */
}
clear1Dall(d); /* Clear everything from memory */
closefp(d,DATA_FILE);
closefp(d,PHAS_FILE);
}
void main()
{
int i, j, k,
trialnr;
/* input pars */
getpars();
/* input training set and test set */
getsets();
if (maxtrials>20)
maxtrials=20;
if (bias1==1)
in_mod++;
if (bias2==1)
hid_mod++;
hi_in_mod = in_mod+hid_mod;
cell_mod=hi_in_mod;
for (i=0;i<num_blocks;i++)
cell_mod+=(2+block_size[i]);
ges_mod = cell_mod+out_mod;
if (ges_mod>max_units)
{
printf("Program terminated!\n");
printf("You have to set the constant max_units at begin\n");
printf("of the program file greater or equal %d and then\n",ges_mod);
printf("compile the program again.\n");
exit(0);
}
srand(ran_sta);
for (trialnr=0;trialnr<maxtrials;trialnr++)
{
outfile = outf[trialnr];
weightfile = weig[trialnr];
fp1 = fopen(outfile, "w");
fprintf(fp1,"Trial Nr.:%.1d\n",trialnr);
fclose(fp1);
fp2 = fopen(weightfile, "w");
fprintf(fp2,"Trial Nr.:%.1d\n",trialnr);
fclose(fp2);
initia();
examples=0;
epoch=0;
maxepoch=maxepoch_init;
stop_learn=0;
learn = 1;
while (learn == 1)
{
/* executing the environment
and setting the input
*/
execute_act();
/* forward pass */
forward_pass();
if (targ==1) /* only if target for this input */
{
/* compute error */
for (k=cell_mod,j=0;k<ges_mod;k++,j++)
{
error[j]= target_a[j] - Yk_mod_new[k];
};
/* Training error */
comp_err();
}
/* backward pass */
if (targ==1) /* only if target for this input */
{
backward_pass();
}
else
{
derivatives();
}
/* set old activations */
for (i=0;i<ges_mod;i++)
{
Yk_mod_old[i] = Yk_mod_new[i];
}
/* update weights */
if (weight_up==1)
{
weight_up=0;
weight_update();
}
/* stop if maxepoch reached */
if (epoch>maxepoch)
learn=0;
}
weight_out();
test();
}
exit(0);
}
void defaultEPI(struct data *d)
{
int DISCARD=-1;
int refEPI=FALSE,refSGE=FALSE;
int getscaleref=FALSE;
double oversample,lro,lpe;
struct data ref1,ref2,ref3,ref4,ref5,ref6;
struct segscale scale1,scale2;
enum {
OFF = 0,
POINTWISE = 1,
TRIPLE = 2,
SCALED_TRIPLE = 3
} epi_pc;
#ifdef DEBUG
char function[20];
strcpy(function,"defaultEPI"); /* Set function name */
#endif
/* Set EPI correction scheme */
if (spar(d,"epi_pc","POINTWISE")) epi_pc=POINTWISE;
else if (spar(d,"epi_pc","TRIPLE")) epi_pc=TRIPLE;
else if (spar(d,"epi_pc","SCALED_TRIPLE")) epi_pc=SCALED_TRIPLE;
else epi_pc=OFF;
/* Check whether to output or discard reference scans */
if (spar(d,"imRF","y")) refEPI=TRUE;
if (spar(d,"imSGE","y")) refSGE=TRUE;
/* Set reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
getpars(d->procpar,&ref1);
initdata(&ref1);
getpars(d->procpar,&ref3); /* ref3 used in pointwise phase correction of inverted */
initdata(&ref3); /* reference scans if reference output is selected */
}
if (epi_pc > POINTWISE) { /* Triple reference phase corrections */
getpars(d->procpar,&ref2);
initdata(&ref2);
getpars(d->procpar,&ref4);
initdata(&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
getpars(d->procpar,&ref5);
initdata(&ref5);
getpars(d->procpar,&ref6);
initdata(&ref6);
}
d->nv=(int)*val("nphase",&d->p); /* Set d->nv for dimorder2D */
d->pssorder=sliceorder(d,d->ns,"pss"); /* Fill pssorder with the slice order */
d->dim2order=phaseorder(d,d->nv,"par_does_not_exist"); /* Set dim2order=-1 for sequential phase encode order */
d->dim3order=phaseorder(d,d->nv,"sgepelist"); /* Fill dim3order with the standard gradient echo phase encode order */
d->nv2=d->nv; /* Set d->nv2 for dim3order */
d->dimorder=IM2D; /* Set dimorder flag */
d->nv=(int)*val("nseg",&d->p); /* Use d->nv for the number of shots */
setnvolsEPI(d); /* Set the number of data volumes */
/* Allow for scaled FOV in ASL test setup expt */
lro=*val("lro",&d->p)**val("aslfov",&d->p);
lpe=*val("lpe",&d->p)**val("aslfov",&d->p);
/* Set default of no compressed segment scaling just in case it's never set */
scale1.data=FALSE;
scale2.data=FALSE;
/* Loop over data blocks */
for (d->block=0;d->block<d->nblocks;d->block++) {
d->outvol=0; /* Initialise output data volume (that will not include reference scans) */
for (d->vol=0;d->vol<d->nvols;d->vol++) { /* Loop over "volumes" */
setoutvolEPI(d); /* Set output data volume */
if (d->outvol>d->endvol) break; /* Break if last requested volume has been processed */
getblockEPI(d,d->vol,NDCC); /* Get block without applying dbh.lvl and dbh.tlt */
zeromax(d); /* Zero max structure & coordinates of maximum */
zeronoise(d); /* Zero values in noise structure */
#ifdef DEBUG
fprintf(stdout,"\n%s: %s()\n",SOURCEFILE,function);
switch (epi_pc) {
case OFF: fprintf(stdout," Correction: OFF \n"); break;
case POINTWISE: fprintf(stdout," Correction: POINTWISE \n"); break;
case TRIPLE: fprintf(stdout," Correction: TRIPLE \n"); break;
case SCALED_TRIPLE: fprintf(stdout," Correction: SCALED_TRIPLE \n"); break;
}
fflush(stdout);
#endif
/* Process data as directed by image parameter */
switch ((int)getelem(d,"image",d->vol)) {
case 0: /* Reference, no phase-encode */
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
if (epi_pc > OFF) { /* If there is phase correction */
ftnpEPI(d); /* FT along readout dimension */
clear2Ddata(&ref1); /* Clear ref1 */
copy2Ddata(d,&ref1); /* Copy to ref1 */
ref1.datamode=EPIREF; /* Flag as EPIREF data */
} else { /* else there is no phase correction */
ref1.datamode=NONE; /* Flag as no data */
if (refEPI) ftnpEPI(d); /* FT along readout dimension */
}
setsegscale(d,&scale1); /* Set scaling for compressed segments */
segscale(d,&scale1); /* Scale compressed segments */
if (refEPI) /* If reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -1: /* Inverted Readout Reference, with phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if triple or scaled triple reference phase correction */
clear2Ddata(&ref2); /* Clear ref2 */
copy2Ddata(d,&ref2); /* Copy to ref2 */
ref2.datamode=EPIREF; /* Flag ref2 as EPIREF data */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPI(d,&ref3); /* Phase correct with the reference */
}
navcorrEPI(d); /* Phase correct with the navigator */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -2: /* Inverted Readout Reference, no phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -2 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol);
ftnpEPI(d); /* FT along readout dimension */
setsegscale(d,&scale2); /* Set scaling for compressed segments */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if old triple or triple reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
if (ref2.datamode == EPIREF) { /* if there is ref2 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (epi_pc == POINTWISE) { /* if pointwise reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
}
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case 1: /* Regular image */
#ifdef DEBUG
fprintf(stdout," Processing image 1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (d->outvol>=d->startvol)
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
switch (epi_pc) {
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
clear2Ddata(&ref5); /* Clear ref5 */
copy2Ddata(d,&ref5); /* Copy to ref5 */
ref5.datamode=EPIREF; /* Flag ref5 as EPIREF data */
prepEPIref(&ref5,&ref1); /* Prepare ref5 data so it can be used to scale ref4 data */
}
break;
default:
break;
}
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale1); /* Scale compressed segments */
phaseEPI(d,&ref1); /* Phase correct with the reference */
navcorrEPI(d); /* Phase correct with the navigator */
/* analyseEPInav(d); // Analyse the navigators */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
switch (epi_pc) {
case TRIPLE: /* Triple reference phase correction */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
break;
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
getscaleref=FALSE; /* Flag that scale reference has been acquired */
} else {
addscaledEPIref(d,&ref4,&ref5); /* Scale ref4 data according to d/ref5, then add to d */
}
break;
default:
break;
}
if (d->outvol>=d->startvol) {
phasedata2D(d,VJ); /* Phase data if required */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Write 2D fdf data from volume */
wnifti(d,VJ,FLT32,d->vol);
}
break;
default: /* Reference Standard Gradient Echo */
setblockSGE(d);
setval(&d->p,"lro",lro); /* Set suitable lro in case it has been scaled */
setval(&d->p,"lpe",lpe); /* Set suitable lpe in case it has been scaled */
if (refSGE) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
getmax(d); /* Get coordinates of maximum */
shiftdata2D(d,OPT); /* Shift FID data for fft */
equalizenoise2D(d,STD); /* Scale for equal noise in all receivers */
phaseramp2D(d,READ); /* Phase ramp the data to correct for readout offset pro */
phaseramp2D(d,PHASE); /* Phase ramp the data to correct for phase encode offset ppe */
weightdata2D(d,STD); /* Weight data using standard VnmrJ parameters */
oversample=*val("oversample",&d->p); /* Check to see if there is oversampling */
d->fn *=oversample; /* Correct d->fn for oversample */
zerofill2D(d,STD); /* Zero fill data using standard VnmrJ parameters */
fft2D(d); /* 2D fft */
phasedata2D(d,VJ); /* Phase data if required */
shiftdata2D(d,STD); /* Shift data to get images */
if (oversample>1) zoomEPI(d); /* If oversampled, zoom to get the requested FOV */
if (refSGE) /* If standard gradient echo reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
} /* end image parameter switch */
clear2Ddata(d); /* Clear data volume from memory */
setdatapars(d); /* Sets d->nv=1 */
d->nv=*val("nseg",&d->p); /* Use d->nv for the number of shots */
d->nv2=(int)*val("nphase",&d->p); /* Use d->nv2 for number of standard gradient echo phase encodes */
d->zerofill=FALSE; /* Make sure setdatapars will not overwrite d->nv */
} /* end volume loop */
} /* end data block loop */
/* Clear all reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
clear2Dall(&ref1);
clear2Dall(&ref3);
}
if (epi_pc > POINTWISE) { /* Triple and scaled triple reference phase correction */
clear2Dall(&ref2);
clear2Dall(&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
clear2Dall(&ref5);
clear2Dall(&ref6);
}
clear2Dall(d); /* Clear everything from memory */
}
/*********************************************************
* *
* Main Function *
* ------------- *
* *
*********************************************************
| Takes arguments and launches the gof simulations. |
*-------------------------------------------------------*/
int main(int argc, char *argv[]) // Array of char=arguments line
{
//--- Declarations & Call Function ---//
int i=0, j=0, k=0, count=0, howmany=0, segsites=0, okim=0, oksim=0, numsim=0, totsim=0, nokl=0, nokl0=0;
int **statseg=NULL, **nbvariant=NULL, oks[3], okstot[3];
FILE *pf=NULL, *fopen(const char*, const char*); // Pointer on File for outputs (pf) and IM input file
double tajd();
char **list=NULL; // Haplotype list
void updatemainparams(struct params*);
int gensam(struct params*, char**, int**, int*);
int **imatrix(int, int);
//// From rand1.c ////
/* Celine changed 03/18/2010 */
void seedit(char*, FILE*, struct params *);/*/////*/
char **cmatrix(int, int);
//// From params.c ////
void changeparams(struct params*);
void changeparamslocus(struct params*, int);
struct params getpars(int, char*[], int*);
//--- Structure declaration---//
struct params param;
//--- Get arguments ---//
param=getpars(argc, argv, &howmany); // Get input by user for parameters
pf=stdout; // Output
/* Celine changed 03/18/2010 */
if( !param.commandlineseedflag ) seedit("s", pf, ¶m);// WRITE seeds in summary output file
/*/////*/
/* Uncommented for Celine's use */
/* for(i=0;i<argc;i++) // Information on simulation
fprintf(pf, "%s ", argv[i]);
*/////\
//---------- Initialisation & Memory allocation ------------------//
nbvariant=imatrix(param.cp.npop+1, maxsites); // array of nb of frequency spectrum
typeseg=(int*)malloc((unsigned)(maxsites*sizeof(int))); // type of sites
statseg=imatrix(param.cp.npop+3, howmany); // Records locus specific S1, S2, Ss, Sf,
changeparams(¶m); // Change estimates parameters from priors
updatemainparams(¶m); // Update parameters for the coalescent
oksim=totsim=okstot[0]=okstot[1]=okstot[1]=okstot[2]=0; // simulation check, total #of sim, check on statistics for all simulations
for(numsim=0; numsim<param.cp.nsim;numsim++) // Loop along number of simulations for this set of parameters
{
//--- Initialization and reset of quality checks ---//
count=nokl=nokl0=okim=oks[0]=oks[1]=oks[1]=oks[2]=0; // number of loci, # loci with ok genealogies, no set sites, #statistics ok
for(i=0;i<11;i++) // Sim specific Stats
param.cp.sSiFst[i]=0;
//--- Loop along the loci in the simulation ---//
while((howmany-count++))
{
if(okim==0) // Case All loci ok in the sample
{
for(i=0;i<11;i++)
{
param.cp.lSiFst[i]=0.0;
if(i<9)
param.lp[count-1].tpH[i]=0;
}
changeparamslocus(¶m, count-1); // Get locus specific parameters
list=cmatrix(param.cp.nsam, maxsites+1); // Allocate list of haplotypes
segsites=gensam(¶m, list, nbvariant, param.lp[count-1].S);// Generate a new gene ARG
statseg[0][count-1]=segsites; // Total number of seg sites in sample
for(i=1;i<3+param.cp.npop;i++)
statseg[i][count-1]=0;
if((segsites>0)) // Case segsite>0: get stats
{
/* fprintf(pf, "segsites:%d\npositions:\n",segsites); */
/* for(i=0;i<param.cp.nsam;i++) fprintf(pf, "%s\n", list[i]); */
/* fprintf(pf, "\n"); */
if(segsites<=param.cp.nsites) // Case segsite < lenght of locus
{
for(k=0;k<param.cp.nsam;k++)
{
for(i=k+1;i<param.cp.nsam;i++)
{
if((k<param.lp[count-1].ni[1])&&(i<param.lp[count-1].ni[1])) // pop1
{
param.lp[count-1].tpH[0]++; // # chromosomes
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[1]++; // # seg sites
}
}
else if((k>=param.lp[count-1].ni[1])&&(i>=param.lp[count-1].ni[1])) // pop2
{
param.lp[count-1].tpH[2]++; // # chromosomes
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[3]++; // # seg sites
}
}
else // total sample
{
param.lp[count-1].tpH[4]++;; // Totsal sample size
for(j=0;j<segsites;j++)
{
if(list[k][j]!=list[i][j])
param.lp[count-1].tpH[5]++; // total S
}
}
}// Loop on chromosome
}// Loop along all sampled sequence for the locus
for(i=0;i<segsites;i++) // Calulate S statistics for the locus
{
if(typeseg[i]<0) statseg[3][count-1]++; // shared
else if(typeseg[i]<param.cp.npop+1) statseg[typeseg[i]][count-1]++; // population specific
else statseg[4][count-1]++; // fixed
}
for(i=1;i<5;i++) //--- Record S1 S2 Ss Sf forthe locus ---//
param.cp.lSiFst[i-1]+=statseg[i][count-1];
for(i=0;i<param.cp.nsam;i++) // Free memory for this locus
free(list[i]);
free(list);
}// End case segsite<lenght of locus
else // Case segsites>lenght of locus
{
okim=1; // Sample have a wrong locus
oksim=1; // stop this simulation
break;
}
}// End locus polymorphic
else // Locus without seg sites
{
okim=1; // Sample have a wrong locus (S=0)
oksim=2; // 0 for all stats
}
}// End Sample good until now
if(okim==0) // All loci good until now
{
nokl++; // +1 good locus
nokl0++; // +1 polymorphic locus
for(i=0;i<7;i++)
{
if(i<4)
param.cp.sSiFst[i]+=param.cp.lSiFst[i]; // sum of Sk
param.lp[count-1].H[i]=param.lp[count-1].tpH[i]; // locus specific stats
}
param.cp.lSiFst[5]=param.lp[count-1].H[1]/=param.lp[count-1].H[0]; // Hw1
param.cp.lSiFst[6]=param.lp[count-1].H[3]/=param.lp[count-1].H[2]; // Hw2
param.lp[count-1].H[5]/=param.lp[count-1].H[4]; // Hb
param.cp.lSiFst[4]=param.lp[count-1].H[6]=1-((param.lp[count-1].H[1]+param.lp[count-1].H[3])/2)/ param.lp[count-1].H[5];// locis specific Fst
if((param.lp[count-1].S[0]>0)&&(param.lp[count-1].ni[1]>2)) // Locus popymorphic in pop1
{
param.cp.lSiFst[7]=tajd(param.lp[count-1].ni[1], param.lp[count-1].S[0], param.lp[count-1].H[1]);
param.cp.sSiFst[7]+=param.cp.lSiFst[7];
oks[0]++; // +1 good stat for pop1
}
if((param.lp[count-1].S[1]>0)&&(param.lp[count-1].ni[2]>2)) // Locus popymorphic in pop2
{
param.cp.lSiFst[8]=tajd(param.lp[count-1].ni[2], param.lp[count-1].S[1], param.lp[count-1].H[3]);
param.cp.sSiFst[8]+=param.cp.lSiFst[8];
oks[1]++; // +1 good stat for pop2
}
if(statseg[1][count-1]>0) // Locus popymorphic private in pop1
param.lp[count-1].H[7]=param.cp.lSiFst[9]+=(double) param.lp[count-1].S[2]/(statseg[1][count-1]*param.lp[count-1].ni[1]*2); // p(1)
if(statseg[2][count-1]>0) // Locus popymorphic private in pop2
param.lp[count-1].H[7]=param.cp.lSiFst[9]+=(double) param.lp[count-1].S[3]/(statseg[2][count-1]*param.lp[count-1].ni[2]*2); // p(1)
param.cp.sSiFst[9]+=param.cp.lSiFst[9]; // sum p1
if(statseg[3][count-1]>0) // Locus popymorphic private in pop2
{
param.lp[count-1].H[8]=param.cp.lSiFst[10]=(double) param.lp[count-1].S[4]/(statseg[3][count-1]*(param.lp[count-1].ni[2]+param.lp[count-1].ni[1])); // p(2)
param.cp.sSiFst[10]+=param.cp.lSiFst[10]; // sum p2
oks[2]++;
}
param.cp.sSiFst[4]+=param.lp[count-1].H[6]; // sum Fst
param.cp.sSiFst[5]+=param.lp[count-1].H[1]; // sum Hw1
param.cp.sSiFst[6]+=param.lp[count-1].H[3]; // sum Hw2
}
else if(oksim==2) // Case no seg site for that locus
{
oksim=0; // reset checks
okim=0;
nokl++; // 1+ locus to count in mean (all 0 values)
for(i=0;i<9;i++)
param.lp[count-1].H[i]=param.lp[count-1].tpH[i]; // locus specific stats
}
}// End loop on loci
if(nokl==howmany) // All sample good
{
totsim++; // 1+ good simulation
for(i=0;i<4;i++)
param.cp.SiFst[i]+=param.cp.sSiFst[i]; // sum of S stats along simulations
for(i=4;i<11;i++)
{
if(((i<7)||(i>=9))&&(nokl0>0))
param.cp.SiFst[i]+=(double)param.cp.sSiFst[i]/nokl0; // mean of other stats along simulations
if((i>=7)&&(i<9)&&(oks[i-7]>0))
{
param.cp.SiFst[i]+=(double)param.cp.sSiFst[i]/oks[i-7];
okstot[i-7]++;
}
}
}
}// End loop on simulations
if(oksim==0) // All simulations worked
{
/* Uncommented for Celine's use */
/* for(i=0;i<11;i++) */////
for(i=0;i<9;i++)
{
if((i<7)||(i>=9))
fprintf(pf, "%lg\t", (double) param.cp.SiFst[i]/(totsim)); // write mean of sum of S stats, Fst and Hws over simulations
if((i>=7)&&(i<9))
{
if(oks[i-7]>0)
fprintf(pf, "%lg\t", (double) param.cp.SiFst[i]/(okstot[i-7])); // write mean Tds if S>0 in pops
else fprintf(pf, "NA\t" );
}
}
fprintf(pf, "\n");
}
else // Case one locus with too much seg sites
{
for(i=0;i<9;i++)
fprintf(pf, "NA\t" );
fprintf(pf, "\n");
}
/* Celine changed 03/18/2010 */
seedit("end", pf, ¶m); // in randx.c, flag[0]!="s" so create/rewrite seed in seedmimar
/*/////*/
fclose(pf);
free(typeseg);
for(i=0;i<param.cp.npop+3;i++)
{
if(i<param.cp.npop+1)
free(nbvariant[i]);
free(statseg[i]);
}
free(nbvariant);
free(statseg);
///////// FREE PARAM ///////
for(i=0;i<param.cp.npop;i++)
free(param.cp.mig_mat[i]);
free(param.cp.mig_mat);
free(param.cp.config);
/* Celine changed 11/27/2009 */
for(i=9;i>=0;i--)
if(param.cp.listevent[i]!=NULL && param.cp.listevent[i]->nextde!=NULL)
free(param.cp.listevent[i]->nextde);
if(param.cp.listevent!=NULL)
free(param.cp.listevent);
/*/////*/
free(param.cp.deventlist);
free(param.cp.size);
free(param.cp.alphag);
for(i=0;i<3;i++)
free(param.cp.uniform[i]);
free(param.cp.uniform);
free(param.cp.oldest);
free(param.cp.newest);
free(param.cp.newparam);
/* Celine changed 11/27/2009 */
for(i=0;i<howmany;i++)
free(param.lp[i].name);
/*/////*/
free(param.lp);
/* Celine changed 03/18/2010 */
free( param.tableseeds); /*/////*/
exit(0);
}// End main function
int
main(int argc, char *argv[])
{
int i, k, howmany, segsites ;
char **list, **cmatrix(), **tbsparamstrs ;
FILE *pf, *fopen() ;
double probss, tmrca, ttot ;
void seedit( const char * ) ;
void getpars( int argc, char *argv[], int *howmany ) ;
int gensam( char **list, double *probss, double *ptmrca, double *pttot ) ;
ntbs = 0 ; /* these next few lines are for reading in parameters from a file (for each sample) */
tbsparamstrs = (char **)malloc( argc*sizeof(char *) ) ;
for( i=0; i<argc; i++) printf("%s ",argv[i]);
for( i =0; i<argc; i++) tbsparamstrs[i] = (char *)malloc(30*sizeof(char) ) ;
for( i = 1; i<argc ; i++)
if( strcmp( argv[i],"tbs") == 0 ) argv[i] = tbsparamstrs[ ntbs++] ;
count=0;
if( ntbs > 0 ) for( k=0; k<ntbs; k++) scanf(" %s", tbsparamstrs[k] );
getpars( argc, argv, &howmany) ; /* results are stored in global variable, pars */
if( !pars.commandlineseedflag ) seedit( "s");
pf = stdout ;
if( pars.mp.segsitesin == 0 ) {
list = cmatrix(pars.cp.nsam,maxsites+1);
posit = (double *)malloc( (unsigned)( maxsites*sizeof( double)) ) ;
}
else {
list = cmatrix(pars.cp.nsam, pars.mp.segsitesin+1 ) ;
posit = (double *)malloc( (unsigned)( pars.mp.segsitesin*sizeof( double)) ) ;
if( pars.mp.theta > 0.0 ) {
segfac = 1.0 ;
for( i= pars.mp.segsitesin; i > 1; i--) segfac *= i ;
}
}
while( howmany-count++ ) {
if( (ntbs > 0) && (count >1 ) ) {
for( k=0; k<ntbs; k++) {
if( scanf(" %s", tbsparamstrs[k]) == EOF ) {
if( !pars.commandlineseedflag ) seedit( "end" );
exit(0);
}
}
getpars( argc, argv, &howmany) ;
}
fprintf(pf,"\n//");
if( ntbs >0 ) {
for(k=0; k< ntbs; k++) printf("\t%s", tbsparamstrs[k] ) ;
}
printf("\n");
segsites = gensam( list, &probss, &tmrca, &ttot ) ;
if( pars.mp.timeflag ) fprintf(pf,"time:\t%lf\t%lf\n",tmrca, ttot ) ;
if( (segsites > 0 ) || ( pars.mp.theta > 0.0 ) ) {
if( (pars.mp.segsitesin > 0 ) && ( pars.mp.theta > 0.0 ))
fprintf(pf,"prob: %g\n", probss ) ;
fprintf(pf,"segsites: %d\n",segsites);
if( segsites > 0 ) fprintf(pf,"positions: ");
for( i=0; i<segsites; i++)
fprintf(pf,"%6.*lf ", pars.output_precision,posit[i] );
fprintf(pf,"\n");
if( segsites > 0 )
for(i=0; i<pars.cp.nsam; i++) {
fprintf(pf,"%s\n", list[i] );
}
}
}
if( !pars.commandlineseedflag ) seedit( "end" );
}
int main(int argc, char *argv[]) {
int i,j/*,k,test*/;
int ndomain,total,add;
int gottrans;
int T_FLAG;
/* char c; */
char *env;
char *deffile,*keyword,*value;
FILE *PARMS,*TRANS,*PDB;
struct parameters *parms;
struct domain_loc *domain;
if(argc<2) exit_error();
/* get environment variable */
if((env=getenv("STAMPDIR"))==NULL) {
fprintf(stderr,"error: environment variable STAMPDIR must be set\n");
exit(-1);
}
parms=(struct parameters*)malloc(sizeof(struct parameters));
strcpy(parms[0].stampdir,env);
/* read in default parameters from $STAMPDIR/stamp.defaults */
deffile=(char*)malloc(1000*sizeof(char));
#if defined(_MSC_VER)
sprintf(deffile,"%s\\stamp.defaults",env);
#else
sprintf(deffile,"%s/stamp.defaults",env);
#endif
if((PARMS=fopen(deffile,"r"))==NULL) {
fprintf(stderr,"error: default parameter file %s does not exist\n",deffile);
exit(-1);
}
if(getpars(PARMS,parms)==-1) exit(-1);
fclose(PARMS);
/* define DSSP directory file name */
sprintf(&parms[0].dsspfile[0],"%s/dssp.directories",env);
/* now search the command line for commands */
keyword=(char*)malloc(1000*sizeof(char));
value=(char*)malloc(1000*sizeof(char));
for(i=1; i<argc; ++i) {
if(argv[i][0]!='-') exit_error();
strcpy(keyword,&argv[i][1]);
if(i+1<argc) strcpy(value,argv[i+1]);
else strcpy(value,"none");
for(j=0; j<strlen(keyword); ++j)
keyword[j]=ltou(keyword[j]); /* change to upper case */
T_FLAG=(value[0]=='Y' || value[0]=='y' || value[0]=='1' ||
value[0]=='T' || value[0]=='t' || value[0]=='o' ||
value[0]=='O');
/* enables one to write '1', 'YES', 'Yes', 'yes', 'T_FLAG', 'True' or 'true' to
* set any boolean parmsiable to one */
if((strcmp(&argv[i][1],"l")==0) || (strcmp(&argv[i][1],"f")==0) || (strcmp(&argv[i][1],"p")==0)) {
if(i+1>=argc) exit_error();
/* listfile name */
strcpy(parms[0].listfile,argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"P")==0) {
/* want to read in parameter file */
if(i+1>=argc) exit_error();
if((PARMS=fopen(argv[i+1],"r"))==NULL) {
fprintf(stderr,"error opening file %s\n",argv[i+1]);
exit(-1);
}
if(getpars(PARMS,parms)==-1) exit(-1);
fclose(PARMS);
i++;
} else if(strcmp(&argv[i][1],"o")==0) {
/* output file */
if(i+1>=argc) exit_error();
strcpy(parms[0].logfile,argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"help")==0) {
help_exit_error();
} else if((strcmp(&argv[i][1],"V")==0) || (strcmp(&argv[i][1],"v")==0)) {
parms[0].verbose=1;
strcpy(parms[0].logfile,"stdout");
} else if(strcmp(&argv[i][1],"s")==0) {
parms[0].SCAN=1;
parms[0].TREEWISE=parms[0].PAIRWISE=0;
} else if(strcmp(&argv[i][1],"n")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%d",&parms[0].NPASS);
i++;
if(parms[0].NPASS!=1 && parms[0].NPASS!=2) exit_error();
} else if(strcmp(keyword,"PAIRPEN") == 0 || strcmp(keyword,"PEN")==0 || strcmp(keyword,"SECOND_PAIRPEN")==0) {
sscanf(value,"%f",&parms[0].second_PAIRPEN);
i++;
} else if(strcmp(keyword,"FIRST_PAIRPEN")==0) {
sscanf(value,"%f",&parms[0].first_PAIRPEN);
i++;
} else if(strcmp(keyword,"MAXPITER") == 0 || strcmp(keyword,"MAXSITER") == 0) {
sscanf(value,"%d",&parms[0].MAXPITER);
i++;
} else if(strcmp(keyword,"MAXTITER") == 0) {
sscanf(value,"%d",&parms[0].MAXTITER);
i++;
} else if(strcmp(keyword,"TREEPEN") == 0 || strcmp(keyword,"SECOND_TREEPEN")==0) {
sscanf(value,"%f",&parms[0].second_TREEPEN);
i++;
} else if(strcmp(keyword,"FIRST_TREEPEN")==0) {
sscanf(value,"%f",&parms[0].first_TREEPEN);
i++;
} else if(strcmp(keyword,"SCORETOL") == 0) {
sscanf(value,"%f",&parms[0].SCORETOL);
i++;
} else if(strcmp(keyword,"CLUSTMETHOD") == 0) {
sscanf(value,"%d",&parms[0].CLUSTMETHOD);
i++;
} else if(strcmp(keyword,"E1") == 0 || strcmp(keyword,"SECOND_E1")==0) {
sscanf(value,"%f",&parms[0].second_E1);
i++;
} else if(strcmp(keyword,"E2") == 0 || strcmp(keyword,"SECOND_E2")==0) {
sscanf(value,"%f",&parms[0].second_E2);
i++;
} else if(strcmp(keyword,"FIRST_E1")==0) {
sscanf(value,"%f",&parms[0].first_E1);
i++;
} else if(strcmp(keyword,"FIRST_E2")==0) {
sscanf(value,"%f",&parms[0].first_E2);
i++;
} else if(strcmp(keyword,"NPASS")==0) {
sscanf(value,"%d",&parms[0].NPASS);
i++;
if(parms[0].NPASS!=1 && parms[0].NPASS!=2) {
fprintf(stderr,"error: NPASS must be either 1 or 2\n");
return -1;
}
} else if(strcmp(keyword,"CUTOFF") == 0 || strcmp(keyword,"SECOND_CUTOFF")==0) {
sscanf(value,"%f",&parms[0].second_CUTOFF);
i++;
} else if(strcmp(keyword,"FIRST_CUTOFF")==0) {
sscanf(value,"%f",&parms[0].first_CUTOFF);
i++;
} else if(strcmp(keyword,"TREEPLOT") == 0) {
parms[0].TREEPLOT=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRPLOT") == 0) {
parms[0].PAIRPLOT=T_FLAG;
i++;
} else if(strcmp(keyword,"NALIGN") == 0) {
sscanf(value,"%d",&parms[0].NALIGN);
i++;
} else if(strcmp(keyword,"DISPALL") == 0) {
parms[0].DISPALL=T_FLAG;
i++;
} else if(strcmp(keyword,"HORIZ") ==0) {
parms[0].HORIZ=T_FLAG;
i++;
} else if(strcmp(keyword,"ADD") ==0) {
sscanf(value,"%f",&parms[0].ADD);
i++;
} else if(strcmp(keyword,"NMEAN") ==0) {
sscanf(value,"%f",&parms[0].NMEAN);
i++;
} else if(strcmp(keyword,"NSD") ==0) {
sscanf(value,"%f",&parms[0].NSD);
i++;
} else if(strcmp(keyword,"STATS") ==0) {
parms[0].STATS=T_FLAG;
i++;
} else if(strcmp(keyword,"NA") == 0) {
sscanf(value,"%f",&parms[0].NA);
i++;
} else if(strcmp(keyword,"NB") == 0) {
sscanf(value,"%f",&parms[0].NB);
i++;
} else if(strcmp(keyword,"NASD") == 0) {
sscanf(value,"%f",&parms[0].NASD);
i++;
} else if(strcmp(keyword,"NBSD") == 0) {
sscanf(value,"%f",&parms[0].NBSD);
i++;
} else if(strcmp(keyword,"PAIRWISE") == 0) {
parms[0].PAIRWISE=T_FLAG;
i++;
} else if(strcmp(keyword,"TREEWISE") == 0) {
parms[0].TREEWISE=T_FLAG;
i++;
} else if(strcmp(keyword,"ORDFILE") == 0) {
strcpy(parms[0].ordfile,value);
i++;
} else if(strcmp(keyword,"TREEFILE") == 0) {
strcpy(parms[0].treefile,value);
i++;
} else if(strcmp(keyword,"PLOTFILE") == 0) {
strcpy(parms[0].plotfile,value);
i++;
} else if(strcmp(keyword,"PREFIX") == 0 || strcmp(keyword,"TRANSPREFIX")==0 || strcmp(keyword,"STAMPPREFIX")==0) {
strcpy(parms[0].transprefix,value);
i++;
} else if(strcmp(keyword,"MATFILE") == 0) {
strcpy(parms[0].matfile,value);
i++;
} else if(strcmp(keyword,"THRESH") ==0) {
sscanf(value,"%f",&parms[0].THRESH);
i++;
} else if(strcmp(keyword,"TREEALIGN")==0) {
parms[0].TREEALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"TREEALLALIGN")==0) {
parms[0].TREEALLALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRALIGN")==0 || strcmp(keyword,"SCANALIGN")==0) {
parms[0].PAIRALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PAIRALLALIGN")==0 || strcmp(keyword,"SCANALLALIGN")==0) {
parms[0].PAIRALLALIGN=T_FLAG;
i++;
} else if(strcmp(keyword,"PRECISION")==0) {
sscanf(value,"%d",&parms[0].PRECISION);
i++;
} else if(strcmp(keyword,"MAX_SEQ_LEN")==0) {
sscanf(value,"%d",&parms[0].MAX_SEQ_LEN);
i++;
} else if(strcmp(keyword,"ROUGHFIT")==0) {
parms[0].ROUGHFIT=T_FLAG;
i++;
} else if(strcmp(keyword,"ROUGH")==0) {
parms[0].ROUGHFIT=1;
} else if(strcmp(keyword,"ROUGHOUT")==0) {
parms[0].roughout=1;
} else if(strcmp(keyword,"ROUGHOUTFILE")==0) {
if(i+1>=argc) exit_error();
strcpy(&parms[0].roughoutfile[0],argv[i+1]);
i++;
parms[0].roughout=1;
} else if(strcmp(keyword,"BOOLCUT")==0 || strcmp(keyword,"SECOND_BOOLCUT")==0) {
sscanf(value,"%f",&parms[0].second_BOOLCUT);
i++;
} else if(strcmp(keyword,"FIRST_BOOLCUT")==0) {
sscanf(value,"%f",&parms[0].first_BOOLCUT);
i++;
} else if(strcmp(keyword,"SCANSLIDE")==0) {
sscanf(value,"%d",&parms[0].SCANSLIDE);
i++;
} else if(strcmp(keyword,"SCAN")==0) {
parms[0].SCAN=T_FLAG;
i++;
if(T_FLAG)
parms[0].PAIRWISE=parms[0].TREEWISE=0;
} else if(strcmp(keyword,"SCANMODE")==0) {
sscanf(value,"%d",&parms[0].SCANMODE);
i++;
if(parms[0].SCANMODE==1) parms[0].PAIRALIGN=1;
} else if(strcmp(keyword,"SCANCUT")==0) {
sscanf(value,"%f",&parms[0].SCANCUT);
i++;
} else if(strcmp(keyword,"SECSCREEN")==0) {
parms[0].SECSCREEN=T_FLAG;
i++;
} else if(strcmp(keyword,"SECSCREENMAX")==0) {
sscanf(value,"%f",&parms[0].SECSCREENMAX);
i++;
} else if(strcmp(keyword,"SCANTRUNC")==0) {
parms[0].SCANTRUNC=T_FLAG;
i++;
} else if(strcmp(keyword,"SCANTRUNCFACTOR")==0) {
sscanf(value,"%f",&parms[0].SCANTRUNCFACTOR);
i++;
} else if(strcmp(keyword,"DATABASE")==0) {
strcpy(&parms[0].database[0],value);
i++;
} else if(strcmp(keyword,"SCANFILE")==0) {
strcpy(&parms[0].scanfile[0],value);
i++;
} else if(strcmp(keyword,"LOGFILE")==0) {
strcpy(&parms[0].logfile[0],value);
i++;
} else if(strcmp(keyword,"SECTYPE")==0) {
sscanf(value,"%d",&parms[0].SECTYPE);
i++;
} else if(strcmp(keyword,"SCANSEC")==0) {
sscanf(value,"%d",&parms[0].SCANSEC);
i++;
} else if(strcmp(keyword,"SECFILE")==0) {
strcpy(&parms[0].secfile[0],value);
i++;
parms[0].SECTYPE=2;
} else if(strcmp(keyword,"BOOLEAN")==0) {
parms[0].BOOLEAN=T_FLAG;
i++;
} else if(strcmp(keyword,"BOOLMETHOD")==0) {
sscanf(value,"%d",&parms[0].BOOLMETHOD);
i++;
} else if(strcmp(keyword,"LISTFILE")==0) {
strcpy(&parms[0].listfile[0],value);
i++;
} else if(strcmp(keyword,"STAMPDIR")==0) {
strcpy(&parms[0].stampdir[0],value);
i++;
} else if(strcmp(keyword,"CLUST")==0) {
parms[0].CLUST=T_FLAG;
i++;
} else if(strcmp(keyword,"COLUMNS")==0) {
sscanf(value,"%d",&parms[0].COLUMNS);
i++;
} else if(strcmp(keyword,"SW")==0) {
sscanf(value,"%d",&parms[0].SW);
i++;
} else if(strcmp(keyword,"CCFACTOR")==0) {
sscanf(value,"%f",&parms[0].CCFACTOR);
i++;
} else if(strcmp(keyword,"CCADD")==0) {
parms[0].CCADD=T_FLAG;
i++;
} else if(strcmp(keyword,"MINFIT")==0) {
sscanf(value,"%d",&parms[0].MINFIT);
i++;
} else if(strcmp(keyword,"ROUGHALIGN")==0) {
strcpy(parms[0].roughalign,value);
i++;
} else if(strcmp(keyword,"FIRST_THRESH")==0) {
sscanf(value,"%f",&parms[0].first_THRESH);
i++;
} else if(strcmp(keyword,"MIN_FRAC")==0) {
sscanf(value,"%f",&parms[0].MIN_FRAC);
i++;
} else if(strcmp(keyword,"SCORERISE")==0) {
parms[0].SCORERISE=T_FLAG;
i++;
} else if(strcmp(keyword,"SKIPAHEAD")==0) {
parms[0].SKIPAHEAD=T_FLAG;
i++;
} else if(strcmp(keyword,"SCANSCORE")==0) {
sscanf(value,"%d",&parms[0].SCANSCORE);
i++;
} else if(strcmp(keyword,"PAIROUTPUT")==0) {
parms[0].PAIROUTPUT=T_FLAG;
i++;
} else if(strcmp(keyword,"ALLPAIRS")==0) {
parms[0].ALLPAIRS=T_FLAG;
i++;
} else if (strcmp(keyword,"ATOMTYPE")==0) {
parms[0].ATOMTYPE=T_FLAG;
i++;
} else if(strcmp(keyword,"DSSP")==0) {
parms[0].DSSP=T_FLAG;
i++;
} else if(strcmp(keyword,"SLOWSCAN")==0) {
parms[0].SLOWSCAN=T_FLAG;
i++;
} else if(strcmp(keyword,"SLOW")==0) {
parms[0].SLOWSCAN=1;
} else if(strcmp(keyword,"CUT")==0) {
parms[0].CO=1;
} else if(strcmp(&argv[i][1],"slide")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%d",&parms[0].SCANSLIDE);
i++;
} else if(strcmp(&argv[i][1],"d")==0) {
/* database file */
if(i+1>=argc) exit_error();
strcpy(&parms[0].database[0],argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"pen1")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].first_PAIRPEN);
i++;
} else if(strcmp(&argv[i][1],"pen2")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].second_PAIRPEN);
i++;
} else if(strcmp(&argv[i][1],"prefix")==0) {
if(i+1>=argc) exit_error();
strcpy(&parms[0].transprefix[0],argv[i+1]);
i++;
} else if(strcmp(&argv[i][1],"scancut")==0) {
if(i+1>=argc) exit_error();
sscanf(argv[i+1],"%f",&parms[0].SCANCUT);
i++;
} else if(strcmp(&argv[i][1],"opd")==0) {
parms[0].opd=1;
} else {
exit_error();
}
}
free(keyword);
free(value);
/* make the names of all the output files using the prefix */
sprintf(&parms[0].ordfile[0],"%s.ord",parms[0].transprefix);
sprintf(&parms[0].treefile[0],"%s.tree",parms[0].transprefix);
sprintf(&parms[0].plotfile[0],"%s.plot",parms[0].transprefix);
sprintf(&parms[0].matfile[0],"%s.mat",parms[0].transprefix);
sprintf(&parms[0].roughalign[0],"%s_align.rough",parms[0].transprefix);
sprintf(&parms[0].scanfile[0],"%s.scan",parms[0].transprefix);
if(strcmp(parms[0].logfile,"stdout")==0 ||
strcmp(parms[0].logfile,"STDOUT")==0) {
parms[0].LOG=stdout;
} else if(strcmp(parms[0].logfile,"silent")==0 ||
strcmp(parms[0].logfile,"SILENT")==0) {
#if defined(_MSC_VER)
parms[0].LOG=stdout;
#else
parms[0].LOG=fopen("/dev/null","w");
#endif
} else {
if((parms[0].LOG=fopen(parms[0].logfile,"w"))==NULL) {
fprintf(stderr,"error opening file %s\n",parms[0].logfile);
exit(-1);
}
}
if(strcmp(parms[0].logfile,"silent")==0) {
printf("\nSTAMP Structural Alignment of Multiple Proteins\n");
printf(" by Robert B. Russell & Geoffrey J. Barton \n");
printf(" Please cite PROTEINS, v14, 309-323, 1992\n\n");
}
fprintf(parms[0].LOG,"-------------------------------------------------------------------------------\n");
fprintf(parms[0].LOG," S t A M P\n");
fprintf(parms[0].LOG," Structural Alignment of\n");
fprintf(parms[0].LOG," Multiple Proteins\n");
fprintf(parms[0].LOG," By Robert B. Russell & Geoffrey J. Barton \n");
fprintf(parms[0].LOG," Last Modified: %s\n",lastmod);
fprintf(parms[0].LOG," Please cite Ref: Russell and GJ Barton, PROTEINS, v14, 309-323, 1992\n");
fprintf(parms[0].LOG,"-------------------------------------------------------------------------------\n\n");
fprintf(parms[0].LOG,"STAMPDIR has been set to %s\n\n\n",parms[0].stampdir);
/* read in coordinate locations and initial transformations */
if((TRANS = fopen(parms[0].listfile,"r")) == NULL) {
fprintf(stderr,"error: file %s does not exist\n",parms[0].listfile);
exit(-1);
}
/* determine the number of domains specified */
ndomain=count_domain(TRANS);
domain=(struct domain_loc*)malloc(ndomain*sizeof(struct domain_loc));
rewind(TRANS);
if(getdomain(TRANS,domain,&ndomain,ndomain,&gottrans,parms[0].stampdir,parms[0].DSSP,parms[0].LOG)==-1) exit(-1);
fclose(TRANS);
fprintf(parms[0].LOG,"Details of this run:\n");
if(parms[0].PAIRWISE) fprintf(parms[0].LOG,"PAIRWISE mode specified\n");
if(parms[0].TREEWISE) fprintf(parms[0].LOG,"TREEWISE mode specified\n");
if(parms[0].SCAN) fprintf(parms[0].LOG,"SCAN mode specified\n");
if(!parms[0].SCAN) {
/* if no MINFIT has been given, then take the smallest length and divide it by two */
if(parms[0].MINFIT==-1) {
parms[0].MINFIT=parms[0].MAXLEN;
for(i=0; i<ndomain; ++i) if(domain[i].ncoords<parms[0].MINFIT) parms[0].MINFIT=domain[i].ncoords;
parms[0].MINFIT/=2;
}
fprintf(parms[0].LOG," pairwise score file: %s\n",parms[0].matfile);
if(parms[0].TREEWISE) {
fprintf(parms[0].LOG," tree order file: %s\n",parms[0].ordfile);
fprintf(parms[0].LOG," tree file: %s\n",parms[0].treefile);
fprintf(parms[0].LOG," tree plot file: %s\n",parms[0].plotfile);
}
} else {
fprintf(parms[0].LOG," SCANMODE set to %d\n",parms[0].SCANMODE);
fprintf(parms[0].LOG," SCANSCORE set to %d\n",parms[0].SCANSCORE);
fprintf(parms[0].LOG," (see documentation for an explanation)\n");
if(parms[0].opd==1) fprintf(parms[0].LOG," Domains will be skipped after the first match is found\n");
if(parms[0].SCANMODE==1) {
fprintf(parms[0].LOG," Transformations for Sc values greater than %f are to be output\n",parms[0].SCANCUT);
fprintf(parms[0].LOG," to the file %s\n",parms[0].transprefix);
} else {
fprintf(parms[0].LOG," Only the scores are to be output to the file %s\n",parms[0].scanfile);
}
fprintf(parms[0].LOG," secondary structures are ");
switch(parms[0].SCANSEC) {
case 0:
fprintf(parms[0].LOG," not to be considered\n");
break;
case 1:
fprintf(parms[0].LOG," to be from DSSP\n");
break;
case 2:
fprintf(parms[0].LOG," to be read in from %s\n",parms[0].secfile);
break;
default:
fprintf(parms[0].LOG," not to be considered\n");
}
if(parms[0].SECSCREEN) {
fprintf(parms[0].LOG," An initial screen on secondary structure content is to performed when possible\n");
fprintf(parms[0].LOG," Secondary structure summaries farther than %6.2f %% apart result in\n",parms[0].SECSCREENMAX);
fprintf(parms[0].LOG," a comparison being ignored\n");
}
fprintf(parms[0].LOG," Initial fits are to be performed by aligning the N-terminus of the query\n with every %d residue of the database sequence\n",parms[0].SCANSLIDE);
fprintf(parms[0].LOG," of the query along the database structure.\n");
if(parms[0].SCANTRUNC) {
fprintf(parms[0].LOG," If sequences in the database are > %5.3f x the query sequence length\n",parms[0].SCANTRUNCFACTOR);
fprintf(parms[0].LOG," then a fraction of the the database structure, corresponding to this\n");
fprintf(parms[0].LOG," of length %5.3f x the query, will be considered\n",parms[0].SCANTRUNCFACTOR);
fprintf(parms[0].LOG," comparisons are to be ignored if the database structure is less than\n %6.4f x the length of the query structure\n",parms[0].MIN_FRAC);
}
fprintf(parms[0].LOG," Domain database file to be scanned %s\n",parms[0].database);
}
if(parms[0].TREEWISE)
fprintf(parms[0].LOG," output files prefix: %s\n",parms[0].transprefix);
fprintf(parms[0].LOG,"\n\nParameters:\n");
fprintf(parms[0].LOG,"Rossmann and Argos parameters:\n");
if(parms[0].NPASS==2) {
fprintf(parms[0].LOG," Two fits are to be performed, the first fit with:\n");
fprintf(parms[0].LOG," E1=%7.3f,",parms[0].first_E1);
fprintf(parms[0].LOG," E2=%7.3f,",parms[0].first_E2);
fprintf(parms[0].LOG," CUT=%7.3f,",parms[0].first_CUTOFF);
fprintf(parms[0].LOG," PAIRPEN=%7.3f,",parms[0].first_PAIRPEN);
fprintf(parms[0].LOG," TREEPEN=%7.3f\n",parms[0].first_TREEPEN);
/* fprintf(parms[0].LOG," E1=%7.3f, E2=%7.3f, CUT=%7.3f, PAIRPEN=%7.3f, TREEPEN=%7.3f\n",
parms[0].first_E1,parms[0].first_E2,parms[0].first_CUTOFF,parms[0].first_PAIRPEN,parms[0].first_TREEPEN); */
fprintf(parms[0].LOG," The second fit with:\n");
} else
fprintf(parms[0].LOG," One fit is to performed with:\n");
fprintf(parms[0].LOG," E1=%7.3f, E2=%7.3f, CUT=%7.3f, PAIRPEN=%7.3f, TREEPEN=%7.3f\n",
parms[0].second_E1,parms[0].second_E2,parms[0].second_CUTOFF,parms[0].second_PAIRPEN,parms[0].second_TREEPEN);
if(parms[0].BOOLEAN) {
fprintf(parms[0].LOG," BOOLEAN mode specified\n");
fprintf(parms[0].LOG," A boolean matrix will be calculated corresponding to whether\n");
fprintf(parms[0].LOG," positions have Pij values greater than:\n");
if(parms[0].NPASS==2)
fprintf(parms[0].LOG," %7.3f, for the first fit and\n",parms[0].first_BOOLCUT);
fprintf(parms[0].LOG," %7.3f",parms[0].second_BOOLCUT);
if(parms[0].NPASS==2)
fprintf(parms[0].LOG," for the second fit.\n");
else
fprintf(parms[0].LOG,".\n");
fprintf(parms[0].LOG," In the multiple case, this criteria must be satisfied for *all*\n");
fprintf(parms[0].LOG," possible pairwise comparisons\n");
}
if(parms[0].SW==1) {
fprintf(parms[0].LOG," Corner cutting is to be performed\n");
fprintf(parms[0].LOG," Corner cutting length: %6.2f\n",parms[0].CCFACTOR);
if(parms[0].CCADD)
fprintf(parms[0].LOG," The length difference is to be added to this value\n");
} else {
fprintf(parms[0].LOG," The entire SW matrix is to be calculated and used\n");
}
fprintf(parms[0].LOG," The minimum length of alignment to be evaluated further is %3d residues\n",parms[0].MINFIT);
fprintf(parms[0].LOG,"\n");
fprintf(parms[0].LOG," Convergence tolerance SCORETOL= %f %%\n", parms[0].SCORETOL);
fprintf(parms[0].LOG," Other parameters:\n");
fprintf(parms[0].LOG," MAX_SEQ_LEN=%d, MAXPITER=%d, MAXTITER=%d\n",
parms[0].MAX_SEQ_LEN,parms[0].MAXPITER,parms[0].MAXTITER);
fprintf(parms[0].LOG," PAIRPLOT (SCANPLOT) = %d, TREEPLOT = %d, PAIRALIGN (SCANALIGN) = %d, TREEALIGN = %d\n",
parms[0].PAIRPLOT,parms[0].TREEPLOT,parms[0].PAIRALIGN,parms[0].TREEALIGN);
fprintf(parms[0].LOG," PAIRALLALIGN (SCANALLALIGN) = %d, TREEALLALIGN = %d\n",parms[0].PAIRALLALIGN,parms[0].TREEALLALIGN);
if(!parms[0].BOOLEAN) {
fprintf(parms[0].LOG,"\n\nDetails of Confidence value calculations:\n");
if(parms[0].STATS) fprintf(parms[0].LOG," actual mean and standard deviations are to be\n used for determination of Pij' values.\n");
else {
fprintf(parms[0].LOG," pre-set mean and standard deviations are to be used\n and multiple comparisons are to be corrected.\n");
fprintf(parms[0].LOG," mean Xt = %f, standard deviation SDt = %f\n", parms[0].NMEAN,parms[0].NSD);
fprintf(parms[0].LOG," for the multiple case:\n");
fprintf(parms[0].LOG," pairwise means are to be calculated from:\n Xp = exp(%6.4f * log(length) + %6.4f)\n",parms[0].NA,parms[0].NB);
fprintf(parms[0].LOG," and pairwise standard deviations from:\n SDp = exp(%6.4f * log(length) + %6.4f)\n",parms[0].NASD,parms[0].NBSD);
fprintf(parms[0].LOG," the mean to be used is calculated from: \n Xc = (Xm/Xp) * Xt).\n");
fprintf(parms[0].LOG," and the standard deviation from: \n SDc = (SDm/SDp)*SDt).\n");
} /* End of if(parms[0].STATS) */
} else {
fprintf(parms[0].LOG," Positional values will consist of one's or zeros depending on whether\n");
fprintf(parms[0].LOG," a position satisfies the BOOLEAN criterion above\n");
fprintf(parms[0].LOG," The score (Sp) for each alignment will be a sum of these positions.\n");
} /* end of if(parms[0].BOOLEAN */
if(!parms[0].SCAN && parms[0].TREEWISE) {
fprintf(parms[0].LOG,"\n\nTree is to be generated by ");
if(parms[0].CLUSTMETHOD==0) fprintf(parms[0].LOG,"1/rms values.\n");
if(parms[0].CLUSTMETHOD==1) {
fprintf(parms[0].LOG,"scores from path tracings modified as follows:\n");
fprintf(parms[0].LOG," Sc = (Sp/Lp) * ((Lp-ia)/La) * ((Lp-ib)/Lb),\n");
fprintf(parms[0].LOG," where Sp is the actual score, Lp is the path length.\n");
fprintf(parms[0].LOG," and La & Lb are the lengths of the structures considered.\n");
} /* End of if(parms[0].METHOD==2) */
}
fprintf(parms[0].LOG,"\n\n");
fprintf(parms[0].LOG,"Reading coordinates...\n");
for(i=0; i<ndomain; ++i) {
fprintf(parms[0].LOG,"Domain %3d %s %s\n ",i+1,domain[i].filename,domain[i].id);
if((PDB=openfile(domain[i].filename,"r"))==NULL) {
fprintf(stderr,"error opening file %s\n",domain[i].filename);
exit(-1);
}
domain[i].ncoords=0;
domain[i].coords=(int**)malloc(parms[0].MAX_SEQ_LEN*sizeof(int*));
domain[i].aa=(char*)malloc((parms[0].MAX_SEQ_LEN+1)*sizeof(char));
domain[i].numb=(struct brookn*)malloc((parms[0].MAX_SEQ_LEN)*sizeof(struct brookn));
total=0;
fprintf(parms[0].LOG," ");
for(j=0; j<domain[i].nobj; ++j) {
if(!parms[0].DSSP) {
if(igetca(PDB,&domain[i].coords[total],&domain[i].aa[total],&domain[i].numb[total],
&add,domain[i].start[j],domain[i].end[j],domain[i].type[j],(parms[0].MAX_SEQ_LEN-total),
domain[i].reverse[j],parms[0].PRECISION,parms[0].ATOMTYPE,parms[0].LOG)==-1) {
fprintf(stderr,"Error in domain %s object %d \n",domain[i].id,j+1);
exit(-1);
}
} else {
if(igetcadssp(PDB,&domain[i].coords[total],&domain[i].aa[total],&domain[i].numb[total],
&add,domain[i].start[j],domain[i].end[j],domain[i].type[j],(parms[0].MAX_SEQ_LEN-total),
domain[i].reverse[j],parms[0].PRECISION,parms[0].LOG)==-1) exit(-1);
}
switch(domain[i].type[j]) {
case 1:
fprintf(parms[0].LOG," all residues");
break;
case 2:
fprintf(parms[0].LOG," chain %c",domain[i].start[j].cid);
break;
case 3:
fprintf(parms[0].LOG," from %c %4d %c to %c %4d %c",
domain[i].start[j].cid,domain[i].start[j].n,domain[i].start[j].in,
domain[i].end[j].cid,domain[i].end[j].n,domain[i].end[j].in);
break;
}
fprintf(parms[0].LOG,"%4d CAs ",add);
total+=add;
closefile(PDB,domain[i].filename);
PDB=openfile(domain[i].filename,"r");
}
domain[i].ncoords=total;
fprintf(parms[0].LOG,"=> %4d CAs in total\n",domain[i].ncoords);
fprintf(parms[0].LOG,"Applying the transformation... \n");
printmat(domain[i].R,domain[i].V,3,parms[0].LOG);
fprintf(parms[0].LOG," ...to these coordinates.\n");
matmult(domain[i].R,domain[i].V,domain[i].coords,domain[i].ncoords,parms[0].PRECISION);
closefile(PDB,domain[i].filename);
}
fprintf(parms[0].LOG,"\n\n");
fprintf(parms[0].LOG,"Secondary structure...\n");
for(i=0; i<ndomain; ++i)
domain[i].sec=(char*)malloc(parms[0].MAX_SEQ_LEN*sizeof(char));
switch(parms[0].SECTYPE) {
case 0: {
fprintf(parms[0].LOG,"No secondary structure assignment will be considered\n");
for(i=0; i<ndomain; ++i) {
for(j=0; j<domain[i].ncoords; ++j) domain[i].sec[j]='?';
domain[i].sec[j]='\0';
}
parms[0].SECSCREEN=0;
}
break;
case 1: {
fprintf(parms[0].LOG,"Will try to find Kabsch and Sander DSSP assignments\n");
if(getks(domain,ndomain,parms)!=0) parms[0].SECSCREEN=0;
}
break;
case 2: {
fprintf(parms[0].LOG,"Reading in secondary structure assignments from file: %s\n",parms[0].secfile);
if(getsec(domain,ndomain,parms)!=0) parms[0].SECSCREEN=0;
}
break;
default: {
fprintf(stderr,"error: unrecognised secondary structure assignment option\n");
exit(-1);
}
}
fprintf(parms[0].LOG,"\n\n");
if(parms[0].SCAN) {
i=0;
fprintf(parms[0].LOG,"Scanning with domain %s\n",&(domain[i].id[0]));
if(strcmp(parms[0].logfile,"silent")==0) {
printf("Results of scan will be written to file %s\n",parms[0].scanfile);
printf("Fits = no. of fits performed, Sc = STAMP score, RMS = RMS deviation\n");
printf("Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues\n");
printf("Secs = no. equiv. secondary structures, %%I = seq. identity, %%S = sec. str. identity\n");
printf("P(m) = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694\n");
printf("\n");
printf(" Domain1 Domain2 Fits Sc RMS Len1 Len2 Align Fit Eq. Secs %%I %%S P(m)\n");
}
if(parms[0].SLOWSCAN==1) {
if(slow_scan(domain[i],parms)==-1) exit(-1);
} else {
if(scan(domain[i],parms)==-1) exit(-1);
}
if(strcmp(parms[0].logfile,"silent")==0)
printf("See the file %s.scan\n",parms[0].transprefix);
fprintf(parms[0].LOG,"\n");
} else {
if(parms[0].ROUGHFIT) if(roughfit(domain,ndomain,parms)==-1) exit(-1);
if(parms[0].PAIRWISE) if(pairwise(domain,ndomain,parms)==-1) exit(-1);
if(parms[0].TREEWISE) if(treewise(domain,ndomain,parms)==-1) exit(-1);
} /* end of if(parms[0].SCAN... */
/* freeing memory to keep purify happy */
/*
for(i=0; i<ndomain; ++i) {
free(domain[i].aa);
free(domain[i].sec);
free(domain[i].v); free(domain[i].V);
for(j=0; j<3; ++j) {
free(domain[i].R[j]);
free(domain[i].r[j]);
}
free(domain[i].R);
free(domain[i].r);
for(j=0; j<domain[i].ncoords; ++j)
free(domain[i].coords[j]);
free(domain[i].coords);
free(domain[i].type);
free(domain[i].start);
free(domain[i].end);
free(domain[i].reverse);
free(domain[i].numb);
}
*/
free(domain);
exit(0);
}
command()
{
float tval;
int i,echeck;
int pmin,pmax,pstep;
char tbuf[20];
while (echeck = getstring(": ")) {
if (echeck == EOF) {
fileinput(STD);
}
else if (startsame(in,"cycle")) {
cycle();
}
else if (startsame(in,"coarticulation")) {
ttyprint("coarticulation %s: change? ",(coartflag ? "ON":"OFF"));
fscanf(infp,"%s",in);
if(in[0] == 'n') continue;
coartflag = 1 - coartflag;
}
else if (startsame(in,"rc")) {
printf("reset and cycle\n");
zarrays();
cycle();
}
else if (startsame(in,"wordacts")) {
printwords(printmin,printmax,3,stdout);
if (outfile) printwords(printmin,printmax,3,outfile);
}
else if (startsame(in,"wtacts")) {
printwt(printmin,printmax,3,stdout);
if (outfile) printwt(printmin,printmax,3,outfile);
}
else if (startsame(in,"owtacts")) {
getstring("word: ");
strcpy(tbuf,in);
printonewt(tbuf,printmin,printmax,3,stdout);
if (outfile) printonewt(tbuf,printmin,printmax,3,outfile);
}
else if (startsame(in,"phonacts")) {
printphonemes(printmin,printmax,3,stdout);
if (outfile)
printphonemes(printmin,printmax,3,outfile);
}
else if (startsame(in,"featacts")) {
printf("feature activations - give min,max,step: ");
scanf("%d %d %d",&pmin,&pmax,&pstep);
printfeatures(pmin,pmax,pstep,stdout);
if (outfile) printfeatures(pmin,pmax,pstep,outfile);
}
else if (startsame(in,"expression")) {
setex();
}
else if (startsame(in,"fileinput")) {
fileinput(NONSTD);
}
else if (startsame(in,"inspecs")) {
ttyprint("File name (- = stdin): ");
fscanf(infp,"%s",in);
inspecs(in);
}
else if (startsame(in,"infeatures")) {
ttyprint("File name: ");
fscanf(infp,"%s",in);
infeats(in);
}
/* NOT PRESENTLY OPERATIVE -- JLM 10-5-82
else if (startsame(in,"wsubset")) {
wordsubset();
}
*/
else if (startsame(in,"test")) {
getstring("test string: ");
test(in);
}
else if (startsame(in,"topdown")) {
topdown();
}
else if (startsame(in,"output")) {
setout();
}
else if (startsame(in,"ofile")) {
getstring("give filename (or - for none): ");
setoutfile(in);
}
else if (in[0] == '!') {
system(&in[1]);
}
else if (in[0] == '?') {
help();
}
else if (startsame(in,"help")) {
help();
}
else if (startsame(in,"lexicon")) {
getlex();
}
else if (startsame(in,"parameters")) {
getpars();
}
else if (startsame(in,"quit")) {
quit();
}
else if (startsame(in,"decay")) {
ttyprint ("decay values:\n");
getfloat(decay,NLEVS,"F","P","W");
}
else if (startsame(in,"alpha")) {
ttyprint ("alpha values:\n");
getfloat(alpha,NPARAMS,
"IF","FF","FP","PP","PW","WW","WP","PF","PFC");
}
else if (startsame(in,"gamma")) {
ttyprint ("gamma values:\n");
getfloat(ga,NLEVS,"F","P","W");
}
else if (startsame(in,"grace")) {
ttyprint ("grace %s: change? ",(grace ? "ON" : "OFF"));
fscanf(infp,"%s",in);
if (in[0] == 'n') continue;
grace = 1 - grace;
}
else if (startsame(in,"rest")) {
tval = rest[W];
ttyprint ("rest values:\n");
getfloat(rest,NLEVS,"F","P","W");
if (tval != rest[W]) {
initialize();
}
}
else if (startsame(in,"fweight")) {
ttyprint ("fweight values:\n");
getfloat(fweight,NCONTINS,
"POW","PIT","VOI","ABT","DIF","ACU","CON","LWS",
"MDS", "HIS","FT1","FT2","FT3","FT4","FT5","FT6");
}
else if (startsame(in,"pthresh")) {
ttyprint ("pthresh values:\n");
getfloat(pthresh,NLEVS,"F","P","W");
}
else if (startsame(in,"nreps")) {
ttyprint ("%d nreps: change? ",nreps);
fscanf(infp,"%s",in);
if (in[0] == 'n') continue;
sscanf(in,"%d",&nreps);
}
else if (startsame(in,"pfreq")) {
ttyprint ("%d pfreq: change? ",printfreq);
fscanf(infp,"%s",in);
if (in[0] == 'n') continue;
sscanf(in,"%d",&printfreq);
}
else if (startsame(in,"summarypr")) {
ttyprint("give min, max, and step: ");
fscanf(infp,"%d %d %d",&pmin,&pmax,&pstep);
summarypr(pmin,pmax,pstep,stdout);
if (outfile) summarypr(pmin,pmax,pstep,outfile);
}
else if (startsame(in,"spointers")) {
qsort(wordptr,nwptrs,sizeof(struct word *),ecomp);
}
else if (startsame(in,"sinspec")) {
sinspec();
}
else if (startsame(in,"sfeatures")) {
ttyprint("file name: ");
fscanf(infp,"%s",in);
sfeatures(in);
}
else if (startsame(in,"dinspec")) {
dinspec();
}
else if (startsame(in,"acoustinput")) {
ttyprint("give min, max, and step: ");
fscanf(infp,"%d %d %d",&pmin,&pmax,&pstep);
acoustinput(pmin,pmax,pstep,stdout);
if (outfile) acoustinput(pmin,pmax,pstep,outfile);
}
else if (startsame(in,"sumopt")) {
ttyprint ("summaryprint %s: change? ",(sumflag ? "ON" : "OFF"));
fscanf(infp,"%s",in);
if (in[0] == 'n') continue;
sumflag = 1 - sumflag;
}
else if (startsame(in,"echooutput")) {
ttyprint ("echooutput %s: change? ",(echoflag ? "ON" : "OFF"));
fscanf(infp,"%s",in);
if (in[0] == 'n') continue;
echoflag = 1 - echoflag;
}
else if (startsame(in,"min")) {
ttyprint ("min = ");
getval(&min);
}
else if (startsame(in,"max")) {
ttyprint ("max = ");
getval(&max);
}
else if (startsame(in,"windowcent")) {
ttyprint ("windowcent = ");
getval(&windowcent);
}
else if (startsame(in,"wbase")) {
ttyprint ("wbase = ");
getval(&wbase);
}
else if (startsame(in,"wchange")) {
ttyprint ("wchange = ");
getval(&wchange);
}
else if (startsame(in,"wgain")) {
ttyprint ("wgain = ");
getval(&wgain);
}
else if (startsame(in,"wramp")) {
ttyprint ("wramp = ");
getval(&wramp);
}
else if (startsame(in,"imax")) {
ttyprint ("imax = ");
getval(&imax);
}
else if (startsame(in,"freqscale")) {
ttyprint ("freqscale = ");
tval = fscale;
getval(&fscale);
if (tval != fscale) {
initialize();
}
}
else if (startsame(in,"abort")) {
abort(); /* to get a core dump for sdb */
}
else {
printf("Unrecognized request: For help type ?.\n");
if (infp != stdin) fileinput(STD);
}
wait(0);
}
}
