int main(int argc, Char *argv[])
{ /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
argc = 1; /* macsetup("SeqBoot",""); */
argv[0] = "SeqBoot";
#endif
init(argc,argv);
openfile(&infile, INFILE, "input file", "r", argv[0], infilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
doinput(argc, argv);
bootwrite();
freenewer();
freenew();
freerest();
if (nodep)
matrix_char_delete(nodep, spp);
if (nodef)
matrix_double_delete(nodef, spp);
FClose(infile);
if (factors) {
FClose(factfile);
FClose(outfactfile);
}
if (weights)
FClose(weightfile);
if (categories) {
FClose(catfile);
FClose(outcatfile);
}
if(mixture)
FClose(outmixfile);
if(ancvar)
FClose(outancfile);
if (justwts && !permute) {
FClose(outweightfile);
}
else
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
if (justwts && !permute)
fixmacfile(outweightfilename);
if (categories)
fixmacfile(outcatfilename);
if (mixture)
fixmacfile(outmixfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
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 */
long i;
#ifdef MAC
argc = 1; /* macsetup("Contml",""); */
argv[0] = "Contml";
#endif
init(argc, argv);
emboss_getoptions("fcontml", argc, argv);
progname = argv[0];
ibmpc = IBMCRT;
ansi = ANSICRT;
firstset = true;
doinit();
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n", ith);
if (progress)
printf("\nData set # %ld:\n", ith);
}
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
free(l0gf[i]);
}
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("\nDone.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
ajPhyloFreqDel(&phylofreq);
ajPhyloTreeDelarray(&phylotrees);
ajFileClose(&embossoutfile);
ajFileClose(&embossouttree);
embExit();
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
long i;
#ifdef MAC
argc = 1; /* macsetup("Contml",""); */
argv[0] = "Contml";
#endif
init(argc, argv);
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;
firstset = true;
datasets = 1;
doinit();
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
for (ith = 1; ith <= datasets; ith++) {
getinput();
if (ith == 1)
firstset = false;
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n\n", ith);
if (progress)
printf("\nData set # %ld:\n", ith);
}
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
free(l0gf[i]);
}
FClose(outfile);
FClose(outtree);
FClose(infile);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("\nDone.\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[])
{ /* Read in sequences or frequencies and bootstrap or jackknife them */
#ifdef MAC
argc = 1; /* macsetup("SeqBoot",""); */
argv[0] = "SeqBoot";
#endif
init(argc,argv);
emboss_getoptions("ffreqboot", argc, argv);
ibmpc = IBMCRT;
ansi = ANSICRT;
doinput(argc, argv);
bootwrite();
FClose(infile);
if (weights)
FClose(weightfile);
if (categories) {
FClose(catfile);
FClose(outcatfile);
}
if(mixture)
FClose(outmixfile);
if(ancvar)
FClose(outancfile);
if (justwts && !permute) {
FClose(outweightfile);
}
else
FClose(outfile);
#ifdef MAC
fixmacfile(outfilename);
if (justwts && !permute)
fixmacfile(outweightfilename);
if (categories)
fixmacfile(outcatfilename);
if (mixture)
fixmacfile(outmixfilename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
embExit();
return 0;
}
void treeoptions(boolean waswritten, Char *ch, FILE **outtree,
Char *outtreename, Char *progname)
{ /* interactively get options for writing a tree */
char input[100];
if (waswritten) {
printf("\nTree file already was open.\n");
printf(" A Add to this tree to tree file\n");
printf(" R Replace tree file contents by this tree\n");
printf(" F Write out tree to a different tree file\n");
printf(" N Do Not write out this tree\n");
do {
printf("Which should we do? ");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(input);
*ch = input[0];
uppercase(ch);
} while (*ch != 'A' && *ch != 'R' && *ch != 'N' && *ch != 'F');
}
if (*ch == 'F') {
outtreename[0] = '\0';
while (outtreename[0] =='\0') {
printf("Please enter a tree file name>");
#ifdef MAC
fixmacfile(outtreename);
#endif
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
getstryng(outtreename);
}
FClose(*outtree);
}
if (*ch == 'R' || *ch == 'A' || *ch == 'F' || !waswritten) {
openfile(outtree,outtreename,"output tree file",
(*ch == 'A' && waswritten) ? "a" : "w",
progname,outtreename);
}
} /* treeoptions */
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 */
int main(int argc, Char *argv[])
{ /* Dollo or polymorphism parsimony by uphill search */
#ifdef MAC
argc = 1; /* macsetup("Dollop",""); */
argv[0] = "Dollop";
#endif
init(argc, argv);
emboss_getoptions("fdollop", argc, argv);
/* reads in spp, chars, and the data. Then calls maketree to
construct the tree */
progname = argv[0];
ibmpc = IBMCRT;
ansi = ANSICRT;
garbage = NULL;
firstset = true;
bits = 8*sizeof(long) - 1;
doinit();
if (dollo)
fprintf(outfile, "Dollo");
else
fprintf(outfile, "Polymorphism");
fprintf(outfile, " parsimony method\n\n");
if (printdata && justwts)
fprintf(outfile, "%2ld species, %3ld characters\n\n", spp, chars);
for (ith = 1; ith <= (msets); ith++) {
if (msets > 1 && !justwts) {
fprintf(outfile, "Data set # %ld:\n\n",ith);
if (progress)
printf("\nData set # %ld:\n",ith);
}
if (justwts){
fprintf(outfile, "Weights set # %ld:\n\n", ith);
if (progress)
printf("\nWeights set # %ld:\n\n", ith);
}
if (printdata && !justwts)
fprintf(outfile, "%2ld species, %3ld characters\n\n", spp, chars);
doinput();
if (ith == 1)
firstset = false;
for (jumb = 1; jumb <= njumble; jumb++)
maketree();
}
/* this would be an appropriate place to deallocate memory, including these items:
*/
free(steps);
FClose(infile);
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
embExit();
return 0;
} /* Dollo or polymorphism parsimony by uphill search */
int main(int argc, Char *argv[])
{ /* Penny's branch-and-bound method */
/* Reads in the number of species, number of characters,
options and data. Then finds all most parsimonious trees */
#ifdef MAC
argc = 1; /* macsetup("Penny",""); */
argv[0] = "Penny";
#endif
init(argc,argv);
openfile(&infile,INFILE,"input file", "r",argv[0],infilename);
openfile(&outfile,OUTFILE,"output file", "w",argv[0],outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
msets = 1;
firstset = true;
garbage = NULL;
bits = 8*sizeof(long) - 1;
doinit();
if (weights || justwts)
openfile(&weightfile,WEIGHTFILE,"weights file","r",argv[0],weightfilename);
if (trout)
openfile(&outtree,OUTTREE,"output tree file", "w",argv[0],outtreename);
if(ancvar)
openfile(&ancfile,ANCFILE,"ancestors file", "r",argv[0],ancfilename);
if(mixture)
openfile(&mixfile,MIXFILE,"mixture file", "r",argv[0],mixfilename);
for (ith = 1; ith <= msets; ith++) {
if(firstset) {
if (allsokal && !mixture)
fprintf(outfile, "Camin-Sokal parsimony method\n\n");
if (allwagner && !mixture)
fprintf(outfile, "Wagner parsimony method\n\n");
}
doinput();
if (msets > 1 && !justwts) {
fprintf(outfile, "Data set # %ld:\n\n",ith);
if (progress)
printf("\nData set # %ld:\n",ith);
}
if (justwts) {
if(firstset && mixture && printdata)
printmixture(outfile, wagner);
fprintf(outfile, "Weights set # %ld:\n\n", ith);
if (progress)
printf("\nWeights set # %ld:\n\n", ith);
}
else if (mixture && printdata)
printmixture(outfile, wagner);
if (printdata) {
if (weights || justwts)
printweights(outfile, 0, chars, weight, "Characters");
if (ancvar)
printancestors(outfile, anczero, ancone);
}
if (ith == 1)
firstset = false;
maketree();
}
FClose(infile);
FClose(outfile);
FClose(outtree);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
} /* Penny's branch-and-bound method */
int main(int argc, Char *argv[])
{
pattern_elm ***pattern_array;
long tip_count = 0;
double ln_maxgrp;
double ln_maxgrp1;
double ln_maxgrp2;
node * p;
#ifdef MAC
argc = 1; /* macsetup("Treedist", ""); */
argv[0] = "Treedist";
#endif
init(argc, argv);
emboss_getoptions("ftreedist",argc,argv);
/* Initialize option-based variables, then ask for changes regarding
their values. */
ntrees = 0.0;
lasti = -1;
/* read files to determine size of structures we'll be working with */
countcomma(ajStrGetuniquePtr(&phylotrees[0]->Tree),&tip_count);
tip_count++; /* countcomma does a raw comma count, tips is one greater */
/*
* EWFIX.BUG.756 -- this section may be killed if a good solution
* to bug 756 is found
*
* inside cons.c there are several arrays which are allocated
* to size "maxgrp", the maximum number of groups (sets of
* tips more closely connected than the rest of the tree) we
* can see as the code executes.
*
* We have two measures we use to determine how much space to
* allot:
* (1) based on the tip count of the trees in the infile
* (2) based on total number of trees in infile, and
*
* (1) -- Tip Count Method
* Since each group is a subset of the set of tips we must
* represent at most pow(2,tips) different groups. (Technically
* two fewer since we don't store the empty or complete subsets,
* but let's keep this simple.
*
* (2) -- Total Tree Size Method
* Each tree we read results in
* singleton groups for each tip, plus
* a group for each interior node except the root
* Since the singleton tips are identical for each tree, this gives
* a bound of #tips + ( #trees * (# tips - 2 ) )
*
*
* Ignoring small terms where expedient, either of the following should
* result in an adequate allocation:
* pow(2,#tips)
* (#trees + 1) * #tips
*
* Since "maxgrp" is a limit on the number of items we'll need to put
* in a hash, we double it to make space for quick hashing
*
* BUT -- all of this has the possibility for overflow, so -- let's
* make the initial calculations with doubles and then convert
*
*/
/* limit chosen to make hash arithmetic work */
maxgrp = LONG_MAX / 2;
ln_maxgrp = log((double)maxgrp);
/* 2 * (#trees + 1) * #tips */
ln_maxgrp1 = log(2.0 * (double)tip_count *
((double)trees_in_1 + (double)trees_in_2));
/* ln only for 2 * pow(2,#tips) */
ln_maxgrp2 = (double)(1 + tip_count) * log(2.0);
/* now -- find the smallest of the three */
if(ln_maxgrp1 < ln_maxgrp)
{
maxgrp = 2 * (trees_in_1 + trees_in_2 + 1) * tip_count;
ln_maxgrp = ln_maxgrp1;
}
if(ln_maxgrp2 < ln_maxgrp)
{
maxgrp = pow(2,tip_count+1);
}
/* Read the (first) tree file and put together grouping, order, and
timesseen */
read_groups (&pattern_array, trees_in_1 + trees_in_2, tip_count, phylotrees);
if ((tree_pairing == ADJACENT_PAIRS) ||
(tree_pairing == ALL_IN_FIRST)) {
/* Here deal with the adjacent or all-in-first pairing
difference computation */
compute_distances (pattern_array, trees_in_1, 0);
} else if (tree_pairing == NO_PAIRING) {
/* Compute the consensus tree. */
putc('\n', outfile);
/* consensus(); Reserved for future development */
}
if (progress)
printf("\nOutput written to file \"%s\"\n\n", outfilename);
FClose(outtree);
FClose(intree);
FClose(outfile);
if ((tree_pairing == ALL_IN_1_AND_2) ||
(tree_pairing == CORR_IN_1_AND_2))
FClose(intree2);
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
free_patterns (pattern_array, trees_in_1 + trees_in_2);
clean_up_final();
/* clean up grbg */
p = grbg;
while (p != NULL) {
node * r = p;
p = p->next;
free(r->nodeset);
free(r->view);
free(r);
}
printf("Done.\n\n");
embExit();
return 0;
} /* main */