void doinit()
{
/* initializes variables */
inputnumbers2(&spp, &nonodes2, 1);
if (inputnumbers2error)
return;
nonodes2--;
alloctree(&curtree.nodep, nonodes2);
allocd(nonodes2, curtree.nodep);
allocw(nonodes2, curtree.nodep);
alloctree(&bestree.nodep, nonodes2);
allocd(nonodes2, bestree.nodep);
allocw(nonodes2, bestree.nodep);
alloctree(&priortree.nodep, nonodes2);
allocd(nonodes2, priortree.nodep);
allocw(nonodes2, priortree.nodep);
if (njumble > 1) {
alloctree(&bestree2.nodep, nonodes2);
allocd(nonodes2, bestree2.nodep);
allocw(nonodes2, bestree2.nodep);
}
allocrest();
} /* doinit */
void doinit()
{
/* initializes variables */
inputnumbers2(&spp, &nonodes2, 1);
getoptions();
if ( !usertree )
nonodes2--;
alloctree(&curtree.nodep, nonodes2);
allocd(nonodes2, curtree.nodep);
allocw(nonodes2, curtree.nodep);
if (!usertree) {
alloctree(&bestree.nodep, nonodes2);
allocd(nonodes2, bestree.nodep);
allocw(nonodes2, bestree.nodep);
alloctree(&priortree.nodep, nonodes2);
allocd(nonodes2, priortree.nodep);
allocw(nonodes2, priortree.nodep);
if (njumble > 1) {
alloctree(&bestree2.nodep, nonodes2);
allocd(nonodes2, bestree2.nodep);
allocw(nonodes2, bestree2.nodep);
}
}
allocrest();
} /* doinit */
void doinput(int argc, Char *argv[])
{ /* reads the input data */
getoptions();
seqboot_inputnumbers();
allocrest();
inputoptions();
seqboot_inputdata();
} /* doinput */
void doinput(int argc, Char *argv[])
{ /* reads the input data */
seqboot_inputnumbersfreq(phylofreqs);
allocrest();
inputoptions();
seqboot_inputdatafreq(phylofreqs);
} /* doinput */
void doinit()
{
/* initializes variables */
restdist_inputnumbers();
getoptions();
if (printdata)
fprintf(outfile, "\n %4ld Species, %4ld Sites\n", spp, sites);
allocrest();
} /* doinit */
void doinit(U2::MemoryLocker& memLocker)
{
/* initializes variables */
//inputnumbers(&spp, &sites, &nonodes, 1);
getoptions();
if (printdata) {
fprintf(outfile, "%2ld species, %3ld sites\n", spp, sites);
}
allocrest(memLocker);
} /* doinit */
void doinit(void)
{
/* initializes variables */
inputnumbersstate(phylostates[0], &spp, &chars, &nonodes, 1);
words = chars / bits + 1;
// if (printdata)
// fprintf(outfile, "%2ld species, %3ld characters\n\n", spp, chars);
alloctree(&treenode);
setuptree(treenode);
allocrest();
} /* doinit */
void doinit()
{
/* initializes variables */
inputnumbers(&spp, &chars, &nonodes, 1);
words = chars / bits + 1;
getoptions();
if (printdata)
fprintf(outfile, "%2ld species, %3ld characters\n", spp, chars);
alloctree2(&treenode);
setuptree2(treenode);
allocrest();
} /* doinit */
void doinit()
{
/* initializes variables */
node *p;
inputnumbers2(&spp, &nonodes2, 2);
nonodes2 += (njoin ? 0 : 1);
getoptions();
alloctree(&curtree.nodep, nonodes2+1);
p = curtree.nodep[nonodes2]->next->next;
curtree.nodep[nonodes2]->next = curtree.nodep[nonodes2];
free(p);
allocrest();
} /* doinit */
void doinit()
{ /* initializes variables */
inputnumbersfreq(phylofreq, &spp, &loci, &nonodes2, 2);
if (printdata)
fprintf(outfile, "\n%4ld Populations, %4ld Loci\n", spp, loci);
alloctree(&curtree.nodep, nonodes2);
if (!usertree) {
alloctree(&bestree.nodep, nonodes2);
alloctree(&priortree.nodep, nonodes2);
if (njumble > 1) {
alloctree(&bestree2.nodep, nonodes2);
}
}
allocrest();
} /* doinit */
void doinput(int argc, Char *argv[])
{ /* reads the input data */
getoptions();
seqboot_inputnumbers();
allocrest();
if (weights)
openfile(&weightfile,WEIGHTFILE,"input weight file",
"r",argv[0],weightfilename);
if (mixture){
openfile(&mixfile,MIXFILE,"mixture file", "r",argv[0],mixfilename);
openfile(&outmixfile,"outmixture","output mixtures file","w",argv[0],
outmixfilename);
seqboot_inputaux(mixdata, mixfile);
}
if (ancvar){
openfile(&ancfile,ANCFILE,"ancestor file", "r",argv[0],ancfilename);
openfile(&outancfile,"outancestors","output ancestors file","w",argv[0],
outancfilename);
seqboot_inputaux(ancdata, ancfile);
}
if (categories) {
openfile(&catfile,CATFILE,"input category file","r",argv[0],catfilename);
openfile(&outcatfile,"outcategories","output category file","w",argv[0],
outcatfilename);
inputcategs(0, sites, category, 9, "SeqBoot");
}
if (factors){
openfile(&factfile,FACTFILE,"factors file","r",argv[0],factfilename);
openfile(&outfactfile,"outfactors","output factors file","w",argv[0],
outfactfilename);
}
if (justwts && !permute)
openfile(&outweightfile,"outweights","output weight file",
"w",argv[0],outweightfilename);
else {
openfile(&outfile,OUTFILE,"output data file","w",argv[0],outfilename);
}
inputoptions();
seqboot_inputdata();
} /* doinput */
void doinput()
{
/* reads the input data */
inputnumbers(&spp, &chars, &nonodes, 1);
words = chars / bits + 1;
printf("%2ld species, %3ld characters\n", spp, chars);
printf("\nReading input file ...\n\n");
getoptions();
if (weights)
openfile(&weightfile,WEIGHTFILE,"weights file","r",progname,weightfilename);
if(ancvar)
openfile(&ancfile,ANCFILE,"ancestors file", "r",progname,ancfilename);
if(factors)
openfile(&factfile,FACTFILE,"factors file", "r",progname,factfilename);
alloctree(&treenode);
setuptree(treenode);
allocrest();
inputoptions();
inputdata(treenode, dollo, false, stdout);
} /* doinput */
