void gfmUserDefd_InitializeChain(void)
{
long temp1, temp2;
if(gUseSameSeeds == 1) {
setall((long)gC->Seed1, (long)gC->Seed2);
}
else {
getsd(&temp1, &temp2);
gC->Seed1 = temp1;
gC->Seed2 = temp2;
}
InitializeChain(gC);
}
int main(int argc, char *argv[])
{
char File[100];
int temp,priorchoice;
double temp_d;
enum prior_type PiP = JEFFREYS, ThP = JEFFREYS;
char gnog;
int DoAsBurnIn = 0, DoAsReps = 0,i,g;
time_t StartTime, CurrTime, LastTime, RealRepStartTime;
cli_opts *CL_Opts=NULL;
int tempSeed1,tempSeed2;
hyb_data *D;
hyb_prior *P;
hyb_chain *C;
gPiFixed = 0; /* default is not fixed */
if(argc>1) {
CL_Opts = Get_NewHybs_CLI_Opts(argc,argv);
fprintCL_Probs(stdout, CL_Opts);
}
else {
#ifdef COMPILE_NEW_HYB_WITH_NO_GUI
fprintf(stderr,"\n\nThis version of NewHybrids was compiled with COMPILE_NEW_HYB_WITH_NO_GUI defined. Therefore\n");
fprintf(stderr,"you must use the command-line interface to run it. Issue the --help option for more information.\n\n");
exit(1);
#endif
/* if no command line options, then do it interactively */
/* the very first thing that we want to do is get the current working directory
and store it in a global variable, because when it enters the GLUT
interface it is going to forget about that altogether... */
sprintf(gPWD,"%s/",getenv("PWD"));
printf("Welcome to the program currently named \"NewHybrids\" Version 1.1 beta");
printf("\nPre-Released 2 OCTOBER 2002.");
printf("\nwritten by Eric C. Anderson ([email protected])");
printf("\nCopyright (c) by The Regents of the University of California\n");
printf("Please see user documentation for full software agreement.");
printf("\n-----------------------\nEnter a \n\t0 to load \"TestDat.txt\"");
printf("\n\t1 to load \"TestDatWithOptions.dat\"");
printf("\n\t2 to load \"TestAFLP.dat\"");
printf("\n\t3 to load \"TestAFLPWithOptions.dat\"");
printf("\nas the Data File\n");
printf("\nOr enter the name of the file you wish to use.");
printf("\n\nRemember that file must be in the directory in which\nthe program resides.\n\n->");
/* read the DATA FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TestDat.dat");
}
if(temp == 1 && temp_d == 1.0) {
sprintf(File,"TestDatWithOptions.dat");
}
if(temp == 1 && temp_d == 2.0) {
sprintf(File,"TestAFLP.dat");
}
if(temp == 1 && temp_d == 3.0) {
sprintf(File,"TestAFLPWithOptions.dat");
}
/* get the DATA: */
D = GetData(File);
/* Now Process Cline Info */
ProcessClineOptions(D, gClines);
/* now read in the gtyp freq categories */
printf("\n\n-----------------\n");
printf("\nNow enter a 0 to read the genotype frequency classes in the file");
printf("\"TwoGensGtypFreq.txt\". Or enter the name of the file holding your");
printf("\nown definitions of genotype frequency classes.\n\n->");
/* read the GTYP FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TwoGensGtypFreq.txt");
}
GetGtypFreqCats(D,File);
/* now we can process the individual options a little bit */
ProcessIndivOptions(D);
/* put alleles from indivs known to be in Purebred categories into the
"PriorizedAllelesPile" */
PriorizeAllelesFromFixedZ(D);
AddPriorizeAllelesFromFile(D, NULL);
printf("\n\nGive me two small integers (>0) for random number seeds\n\n");
scanf("%d%d",&tempSeed1,&tempSeed2);
setall((long)tempSeed1,(long)tempSeed2);
printf("\n\nEnter the choices for prior type for pi (mixing proportion):\n\t0 for Jeffreys\n\t1 for Uniform\n\t2 to specify it with fixed values\n->");
scanf("%d",&priorchoice);
switch(priorchoice) {
case(0):
PiP = JEFFREYS;
break;
case(1):
PiP = UNIFORM;
break;
case(2):
PiP=FIXED_PRIOR; /* I have to make a new enum for this that reports it properly */
gPiFixed = 1;
gPiFixedValues = (double *)ECA_CALLOC(D->Gn->v,sizeof(double));
temp_d = 0.0;
printf("\nEnter values for fixed components of Pi.\nThese will be rescaled so as to sum to 1.0 if necessary.\n");
CYCLE_g(D)
printf("%s? --> ",D->CategoryNames[g]);
scanf("%lf",&(gPiFixedValues[g]));
temp_d += gPiFixedValues[g];
END1CYCLE
printf("\nThank You! Using values:\n");
CYCLE_g(D)
gPiFixedValues[g] /= temp_d;
printf("%s: %f\n",D->CategoryNames[g],gPiFixedValues[g]);
END1CYCLE
break;
default:
PiP = JEFFREYS;
printf("\n\nInvalid choice. Pi Prior set to Jeffreys by default.\n\n");
}
P = CreatePriors(D,PiP,ThP);
C = CreateLatentChain(D,P);
InitializeChain(C);
C->Seed1 = tempSeed1;
C->Seed2 = tempSeed2;
printf("\n\nData all read and ready!!!\n\n");
printf("\n\nEntering GLUT interface...\n\n");
}
if(CL_Opts != NULL) { /* if we didn't do it all interactively, then we have to copy some variables, etc., over */
/* get the DATA: */
printf("DATA_INITIALIZATION: Preparing to read data from %s\n",CL_Opts->DataFilePath);
D = GetData(CL_Opts->DataFilePath);
/* Now Process Cline Info */
printf("DATA_INITIALIZATION: Processing cline options (if any)\n");
ProcessClineOptions(D, gClines);
/* then initialize the gtyp frequency category probabilities */
printf("DATA_INITIALIZATION: Initializing genotype frequency category probabilities\n");
if(strlen(CL_Opts->GtypCatFilePath)>0) {
GetGtypFreqCats(D,CL_Opts->GtypCatFilePath);
}
else {
CopyGtypFreqCatsFromCL(D,CL_Opts);
}
/* now we can process the individual options a little bit */
ProcessIndivOptions(D);
/* put alleles from indivs known to be in Purebred categories into the
"PriorizedAllelesPile" */
PriorizeAllelesFromFixedZ(D);
/* then add them in from a file, if there is one */
if(strcmp(CL_Opts->AlleFreqPriorPath,"UNSET") != 0) {
AddPriorizeAllelesFromFile(D, CL_Opts->AlleFreqPriorPath);
}
/* and copy across information about the pi priors */
PiP = CL_Opts->PiPriType;
ThP = CL_Opts->ThetaPriType;
if(PiP==FIXED_PRIOR) { int i;
gPiFixed = 1;
gPiFixedValues = (double *)ECA_CALLOC(D->Gn->v,sizeof(double));
for(i=0;i<D->Gn->v;i++) {
gPiFixedValues[i] = CL_Opts->PiFixedValues[i];
}
}
/* copy across the Trace Report request to the D structure */
D->PiTraceReport = CL_Opts->PiTraceReport;
P = CreatePriors(D,PiP,ThP);
C = CreateLatentChain(D,P);
if(CL_Opts->Seed1==0 && CL_Opts->Seed2==0) {
SeedFromFile("newhyb_seeds");
}
else {
printf("SEEDS_FROM_COMMAND_LINE : %ld %ld\n",CL_Opts->Seed1,CL_Opts->Seed2);
setall(CL_Opts->Seed1,CL_Opts->Seed1);
C->Seed1 = (int)CL_Opts->Seed1;
C->Seed2 = (int)CL_Opts->Seed2;
}
InitializeChain(C);
}
/* Here this is set up so that if you use the interactive version, you end up having to use the
GUI, for now. You have the choice if you use the command line */
if(CL_Opts==NULL || CL_Opts->NoGui==0) {
#ifndef COMPILE_NEW_HYB_WITH_NO_GUI
/* make the global pointer point to where it ought to */
gC = C;
/* then allocate space for a sliding trace struct that holds up to 1,000 entries */
gCompleteDataLogLike = gfduAllocSlidingTrace(1000,1);
/* here must call glutInit from within main, with the command line option */
/* pointer, and then call gfmInitGFM, and that does it. */
glutInit(&argc, argv);
gfmInitGFM();
#else
fprintf(stderr,"\n\nThis version of NewHybrids was compiled with COMPILE_NEW_HYB_WITH_NO_GUI defined. Therefore\n");
fprintf(stderr,"it MUST be invoked with the --no-gui option. Try adding --no-gui to your last command line. Cheers.\n\n");
exit(1);
#endif
}
else {int dummy;
dummy = RunWithoutGraphics(C, CL_Opts->NumBurnIn, CL_Opts->NumPostBurnIn);
}
return(1);
}
int main(void)
{
char File[100], DatFile[100], GtypFile[100];
int temp;
double temp_d;
enum prior_type PiP = JEFFREYS, ThP = JEFFREYS;
int DoAsBurnIn = 0, DoAsReps = 0,i,g;
time_t StartTime, CurrTime, LastTime, RealRepStartTime, DummyTime;
double SecondsPerSweep, SecondsRemain;
int priorchoice;
long Seed1, Seed2;
int boing;
hyb_data *D;
hyb_prior *P;
hyb_chain *C;
printf("Welcome to the program currently named \"NewHybrids\" Version 1.1 beta");
printf("\nPre-Released 2 OCTOBER 2002.");
printf("\nwritten by Eric C. Anderson ([email protected])");
printf("\nCopyright (c) by The Regents of the University of California\n");
printf("Please see user documentation for full software agreement.");
printf("\n-----------------------\nEnter a \n\t0 to load \"TestDat.txt\"");
printf("\n\t1 to load \"TestDatWithOptions.dat\"");
printf("\n\t2 to load \"TestAFLP.dat\"");
printf("\n\t3 to load \"TestAFLPWithOptions.dat\"");
printf("\nas the Data File\n");
printf("\nOr enter the name of the file you wish to use.");
printf("\n\nRemember that file must be in the directory in which\nthe program resides.\n\n->");
/* read the DATA FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TestDat.dat");
}
if(temp == 1 && temp_d == 1.0) {
sprintf(File,"TestDatWithOptions.dat");
}
if(temp == 1 && temp_d == 2.0) {
sprintf(File,"TestAFLP.dat");
}
if(temp == 1 && temp_d == 3.0) {
sprintf(File,"TestAFLPWithOptions.dat");
}
/* get the DATA: */
D = GetData(File);
sprintf(DatFile,"%s",File);
/* now read in the gtyp freq categories */
printf("\n\n-----------------\n");
printf("\nNow enter a 0 to read the genotype frequency classes in the file");
printf("\"TwoGensGtypFreq.txt\". Or enter the name of the file holding your");
printf("\nown definitions of genotype frequency classes.\n\n->");
/* read the GTYP FILE name or a 0 */
temp = erdGetNext(File,&temp_d,stdin);
if(temp == 1 && temp_d == 0.0) { /* if input was an int equal to zero set File to "TestDat.txt" */
sprintf(File,"TwoGensGtypFreq.txt");
}
GetGtypFreqCats(D,File);
sprintf(GtypFile,"%s",File);
/* now we can process the individual options a little bit */
ProcessIndivOptions(D);
/* put alleles from indivs known to be in Purebred categories into the
"PriorizedAllelesPile" */
PriorizeAllelesFromFixedZ(D);
AddPriorizeAllelesFromFile(D);
printf("\n\nGive me two small integers (>0) for random number seeds\n\n");
scanf("%d%d",&Seed1,&Seed2);
setall((long)Seed1,(long)Seed2);
printf("\n\nEnter the choices for prior type for pi (mixing proportion):\n\t0 for Jeffreys\n\t1 for Uniform\n->");
scanf("%d",&priorchoice);
switch(priorchoice) {
case(0):
PiP = JEFFREYS;
break;
case(1):
PiP = UNIFORM;
break;
default:
PiP = JEFFREYS;
printf("\n\nInvalid choice. Pi Prior set to Jeffreys by default.\n\n");
}
printf("\n\nEnter the choices for theta type for pi (mixing proportion):\n\t0 for Jeffreys\n\t1 for Uniform\n->");
scanf("%d",&priorchoice);
switch(priorchoice) {
case(0):
ThP = JEFFREYS;
break;
case(1):
ThP = UNIFORM;
break;
default:
ThP = JEFFREYS;
printf("\n\nInvalid choice. Theta Prior set to Jeffreys by default.\n\n");
}
P = CreatePriors(D,PiP,ThP);
C = CreateLatentChain(D,P);
C->Seed1 = Seed1;
C->Seed2 = Seed2;
InitializeChain(C);
printf("\n\nData all read and ready!!!\n\n");
printf("\n\nEntering Graphics-Free version...\n\n");
printf("\nPlease enter the number of sweeps for BurnIn (must be an integer) \n->");
scanf("%d",&DoAsBurnIn);
printf("\nPlease enter the number of sweeps to be done after BurnIn (must be an integer) \n->");
scanf("%d",&DoAsReps);
StartTime = time(NULL);
LastTime = time(NULL);
printf("\nStarting execution at %s\n\n",ctime(&StartTime));
/* then start doing the burn-in reps */
for(i=0;i<DoAsBurnIn;i++) {
SingleSweep(C);
IncrementValues(C,1);
if(i%300==0 && i > 0) {
OutputHistograms(C);
fprint_PofZ(C);
}
CurrTime = time(NULL);
if(difftime(CurrTime,LastTime) > 5.0) { /* if it has been 5 seconds since a report */
LastTime = time(NULL);
printf("\n\n\n\n\n\nNewHybrids started: %s", ctime(&StartTime));
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\nCurrently on BurnIn Sweep %d of %d",i,DoAsBurnIn);
SecondsPerSweep = difftime(LastTime,StartTime)/(double)i;
printf("\nSweeps per second = %f Seconds per sweep = %f ",1.0/SecondsPerSweep,SecondsPerSweep);
SecondsRemain = (SecondsPerSweep * (double)(DoAsBurnIn-i));
printf("\nShould finish BurnIn in %.0f seconds. %.2f minutes. %.4f hours. %.4f days.",
SecondsRemain,SecondsRemain/60,SecondsRemain/3600,SecondsRemain/(3600*24));
/* print out the current pi and the average pi */
printf("\n\nCurrent Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->v);
END1CYCLE
printf("\nAverage Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->Ave);
END1CYCLE
printf("\n\n\n\n\n\n");
fflush(stdout);
}
}
printf("\n\n\n************************\n\nDone with %d Burn-In Sweeps\n\n\n*********************\n\n",DoAsBurnIn);
/* then reset the averages */
ResetAllAveragesEtc(C);
printf("\n\n\n\nAverages reset...\n\nStarting data accumulation reps...\n\n");
/* then do the actual data collection reps */
for(i=0;i<DoAsReps;i++) {
SingleSweep(C);
IncrementValues(C,1);
printf("%d ",i);
if(i%300==0 && i > 0) {
OutputHistograms(C);
fprint_PofZ(C);
printf("\n\n\n\n\n\n\n\n\nNewHybrids Proceeding:");
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\nCurrently on Sweep %d of %d",i,DoAsReps);
/* print out the current pi and the average pi */
printf("\n\nCurrent Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->v);
END1CYCLE
printf("\nAverage Pi:\n");
CYCLE_g(C->Dat)
printf(" %.4f",C->Lat->Pi[g]->Ave);
END1CYCLE
printf("\n\n\n\n\n\n");
fflush(stdout);
}
}
/* output the final bits of information */
OutputHistograms(C);
fprint_PofZ(C);
/* then let the user know it has finished */
printf("\n\nProgram New Hybrids completed. ");
printf("\nData = %s, GtypFile = %s, PiPrior = %s, ThetaPrior = %s, Seeds = %d %d",DatFile,GtypFile, PriorType2str(PiP), PriorType2str(ThP), Seed1, Seed2);
printf("\n\nOutput is in the following files:");
printf("\n\taa-LociAndAlleles.txt --- A listing of loci and alleles read");
printf("\n\taa-Pi.hist --- text file of a histogram representation for");
printf("\n\t\tthe posterior distribution of Pi");
printf("\n\taa-PofZ.txt --- for each individual in the sample, the posterior probability");
printf("\n\t\tthat it falls into each of the genotype frequency categories");
printf("\n\taa-Theta.hist ---- a histogram representation of the posterior distributions");
printf("\n\t\tof the allele frequencies in the different populations");
printf("\n\n");
printf("\n\n\nEnter any integer to exit\n->");
scanf("%d",&boing);
return(0);
}
