int main(int argc, Char *argv[])
{
int i;
#ifdef MAC
argc = 1; /* macsetup("Fitch",""); */
argv[0]="Fitch";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
strcpy(progname,argv[0]);
openfile(&infile,INFILE,"input file","r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
firstset = true;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file","w",argv[0],outtreename);
for (i=0;i<spp;++i){
enterorder[i]=0;}
for (ith = 1; ith <= datasets; ith++) {
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n",ith);
if (progress)
printf("\nData set # %ld:\n\n",ith);
}
fitch_getinput();
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
firstset = false;
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
}
if (trout)
FClose(outtree);
FClose(outfile);
FClose(infile);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
#ifdef MAC
argc = 1; /* macsetup("Neighbor",""); */
argv[0] = "Neighbor";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
ith = 1;
while (ith <= datasets) {
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n",ith);
if (progress)
printf("Data set # %ld:\n",ith);
}
getinput();
maketree();
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
ith++;
}
FClose(infile);
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
int main(int argc, Char *argv[])
{ /* distances from restriction sites or fragments */
#ifdef MAC
argc = 1; /* macsetup("Restdist",""); */
argv[0] = "Restdist";
#endif
#ifdef WIN32
phySetConsoleAttributes();
phyClearScreen();
#endif
strcpy(progname,argv[0]);
openfile(&infile,INFILE,"input data file","r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file","w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
firstset = true;
doinit();
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1 && progress)
printf("\nData set # %ld:\n\n",ith);
makedists();
writedists();
}
FClose(infile);
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
} /* distances from restriction sites or fragments */
void dolmove_printree()
{
/* prints out diagram of the tree */
long tipy;
long i, dow;
if (!subtree)
nuroot = root;
if (changed || newtree)
evaluate(root);
if (display)
dolmove_hypstates();
#ifdef WIN32
if(ibmpc || ansi){
phyClearScreen();
} else {
printf("\n");
}
#else
if (ansi || ibmpc)
printf("\033[2J\033[H");
else
putchar('\n');
#endif
tipy = 1;
dow = down;
if (spp * dow > screenlines && !subtree)
dow--;
printf("(unrooted)");
if (display) {
printf(" ");
makechar(onne);
printf(":1 ");
makechar(question);
printf(":? ");
makechar(zerro);
printf(":0 ");
makechar(polym);
printf(":0/1");
} else
printf(" ");
if (!earlytree) {
printf("%10.1f Steps", -like);
}
if (display)
printf(" SITE%4ld", dispchar);
else
printf(" ");
if (!earlytree) {
printf(" %3ld chars compatible\n", compatible);
}
printf("%-20s",dollo ? "Dollo" : "Polymorphism");
if (changed && !earlytree) {
if (-like < bestyet) {
printf(" BEST YET!");
bestyet = -like;
} else if (fabs(-like - bestyet) < 0.000001)
printf(" (as good as best)");
else {
if (-like < gotlike)
printf(" better");
else if (-like > gotlike)
printf(" worse!");
}
}
printf("\n");
farthest = 0;
coordinates(nuroot, &tipy, 1.5, &farthest);
vmargin = 5;
treelines = tipy - dow;
if (topedge != 1){
printf("** %ld lines above screen **\n", topedge - 1);
vmargin++;}
if ((treelines - topedge + 1) > (screenlines - vmargin))
vmargin++;
for (i = 1; i <= treelines; i++) {
if (i >= topedge && i < topedge + screenlines - vmargin)
dolmove_drawline(i);
}
if ((treelines - topedge + 1) > (screenlines - vmargin))
printf("** %ld lines below screen **\n",
treelines - (topedge - 1 + screenlines - vmargin));
if (treelines - topedge + vmargin + 1 < screenlines)
putchar('\n');
gotlike = -like;
changed = false;
} /* dolmove_printree */
