void getoptions()
{
/* interactively set options */
long reps0;
long inseed, inseed0, loopcount, loopcount2;
Char ch;
boolean done1;
data = seqs;
seq = dna;
blocksize = 1;
fracsample = 1.0;
interleaved = true;
loopcount = 0;
initseed(&inseed, &inseed0, seed);
/* These warnings only appear when user has changed an option that
* subsequently became inapplicable */
} /* getoptions */
void maketree()
{ /* construct the tree */
long i;
if (usertree) {
/* Open in binary: ftell() is broken for UNIX line-endings under WIN32 */
openfile(&intree,INTREE,"input tree file", "rb",progname,intreename);
numtrees = countsemic(&intree);
if(numtrees > MAXSHIMOTREES)
shimotrees = MAXSHIMOTREES;
else
shimotrees = numtrees;
if (numtrees > 2)
initseed(&inseed, &inseed0, seed);
if (treeprint) {
fprintf(outfile, "User-defined tree");
if (numtrees > 1)
putc('s', outfile);
putc('\n', outfile);
}
setuptree(&curtree, nonodes2);
for (which = 1; which <= spp; which++)
inittip(which, &curtree);
which = 1;
while (which <= numtrees) {
for (i = 0 ; i < nonodes2 ; i++) {
if ( i > spp) {
/* must do this since not all nodes may be used if an
unrooted tree is read in after a rooted one */
curtree.nodep[i]->back = NULL;
curtree.nodep[i]->next->back = NULL;
curtree.nodep[i]->next->next->back = NULL;
}
else curtree.nodep[i]->back = NULL;
}
treeread2 (intree, &curtree.start, curtree.nodep,
lengths, &trweight, &goteof, &haslengths, &spp,false,nonodes2);
curtree.start = curtree.nodep[outgrno - 1]->back;
treevaluate();
printree();
summarize();
which++;
}
FClose(intree);
if (numtrees > 1 && loci > 1 ) {
weight = (long *)Malloc(loci*sizeof(long));
for (i = 0; i < loci; i++)
weight[i] = 1;
standev2(numtrees, maxwhich, 0, loci-1, maxlogl, l0gl, l0gf, seed);
free(weight);
fprintf(outfile, "\n\n");
}
} else { /* if ( !usertree ) */
if (jumb == 1) {
setuptree(&curtree, nonodes2);
setuptree(&priortree, nonodes2);
setuptree(&bestree, nonodes2);
if (njumble > 1)
setuptree(&bestree2, nonodes2);
}
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
nextsp = 3;
buildsimpletree(&curtree);
curtree.start = curtree.nodep[enterorder[0] - 1]->back;
if (jumb == 1) numtrees = 1;
nextsp = 4;
if (progress) {
printf("Adding species:\n");
writename(0, 3, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
while (nextsp <= spp) {
buildnewtip(enterorder[nextsp - 1], &curtree, nextsp);
copy_(&curtree, &priortree);
bestree.likelihood = -DBL_MAX;
addtraverse(curtree.nodep[enterorder[nextsp - 1] - 1]->back,
curtree.start, true );
copy_(&bestree, &curtree);
if (progress) {
writename(nextsp - 1, 1, enterorder);
#ifdef WIN32
phyFillScreenColor();
#endif
}
if (global && nextsp == spp) {
if (progress) {
printf("\nDoing global rearrangements\n");
printf(" !");
for (i = 1; i <= spp - 2; i++)
if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 )
putchar('-');
printf("!\n");
printf(" ");
}
}
succeeded = true;
while (succeeded) {
succeeded = false;
if ( global && nextsp == spp )
globrearrange();
else
rearrange(curtree.start);
if (global && nextsp == spp)
putc('\n', outfile);
}
if (global && nextsp == spp && progress)
putchar('\n');
if (njumble > 1) {
if (jumb == 1 && nextsp == spp)
copy_(&bestree, &bestree2);
else if (nextsp == spp) {
if (bestree2.likelihood < bestree.likelihood)
copy_(&bestree, &bestree2);
}
}
if (nextsp == spp && jumb == njumble) {
if (njumble > 1) copy_(&bestree2, &curtree);
curtree.start = curtree.nodep[outgrno - 1]->back;
printree();
summarize();
}
nextsp++;
}
}
if ( jumb < njumble)
return;
if (progress) {
printf("\nOutput written to file \"%s\"\n", outfilename);
if (trout)
printf("\nTree also written onto file \"%s\"\n", outtreename);
}
freeview(&curtree, nonodes2);
if (!usertree) {
freeview(&bestree, nonodes2);
freeview(&priortree, nonodes2);
}
for (i = 0; i < spp; i++)
free(x[i]);
if (!contchars) {
free(locus);
free(pbar);
}
} /* maketree */
void getoptions()
{
/* interactively set options */
long reps0;
long inseed, inseed0, loopcount, loopcount2;
Char ch;
boolean done1;
data = seqs;
seq = dna;
bootstrap = true;
jackknife = false;
permute = false;
ild = false;
lockhart = false;
blocksize = 1;
regular = true;
fracsample = 1.0;
all = false;
reps = 100;
weights = false;
mixture = false;
ancvar = false;
categories = false;
justwts = false;
printdata = false;
dotdiff = true;
progress = true;
interleaved = true;
xml = false;
nexus = false;
factors = false;
loopcount = 0;
for (;;) {
cleerhome();
printf("\nBootstrapping algorithm, version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" D Sequence, Morph, Rest., Gene Freqs? %s\n",
(data == seqs ) ? "Molecular sequences" :
(data == morphology ) ? "Discrete Morphology" :
(data == restsites) ? "Restriction Sites" :
(data == genefreqs) ? "Gene Frequencies" : "");
if (data == restsites)
printf(" E Number of enzymes? %s\n",
enzymes ? "Present in input file" :
"Not present in input file");
if (data == genefreqs)
printf(" A All alleles present at each locus? %s\n",
all ? "Yes" : "No, one absent at each locus");
if ((!lockhart) && (data == morphology))
printf(" F Use factors information? %s\n",
factors ? "Yes" : "No");
printf(" J Bootstrap, Jackknife, Permute, Rewrite? %s\n",
regular && jackknife ? "Delete-half jackknife" :
(!regular) && jackknife ? "Delete-fraction jackknife" :
permute ? "Permute species for each character" :
ild ? "Permute character order" :
lockhart ? "Permute within species" :
regular && bootstrap ? "Bootstrap" :
(!regular) && bootstrap ? "Partial bootstrap" :
rewrite ? "Rewrite data" : "(unknown)" );
if (bootstrap || jackknife) {
printf(" %% Regular or altered sampling fraction? ");
if (regular)
printf("regular\n");
else {
if (fabs(fracsample*100 - (int)(fracsample*100)) > 0.01) {
printf("%.1f%% sampled\n", 100.0*fracsample);
} else {
printf("%.0f%% sampled\n", 100.0*fracsample);
}
}
}
if ((data == seqs) && rewrite) {
printf(" P PHYLIP, NEXUS, or XML output format? %s\n",
nexus ? "NEXUS" : xml ? "XML" : "PHYLIP");
if (xml || ((data == seqs) && nexus)) {
printf(" S Type of molecular sequences? " );
switch (seq) {
case (dna) : printf("DNA\n"); break;
case (rna) : printf("RNA\n"); break;
case (protein) : printf("Protein\n"); break;
}
}
}
if ((data == morphology) && rewrite)
printf(" P PHYLIP or NEXUS output format? %s\n",
nexus ? "NEXUS" : "PHYLIP");
if (bootstrap) {
if (blocksize > 1)
printf(" B Block size for block-bootstrapping? %ld\n", blocksize);
else
printf(" B Block size for block-bootstrapping? %ld (regular bootstrap)\n", blocksize);
}
if (!rewrite)
printf(" R How many replicates? %ld\n", reps);
if (jackknife || bootstrap || permute || ild) {
printf(" W Read weights of characters? %s\n",
(weights ? "Yes" : "No"));
if (data == morphology) {
printf(" X Read mixture file? %s\n",
(mixture ? "Yes" : "No"));
printf(" N Read ancestors file? %s\n",
(ancvar ? "Yes" : "No"));
}
if (data == seqs)
printf(" C Read categories of sites? %s\n",
(categories ? "Yes" : "No"));
if ((!permute)) {
printf(" S Write out data sets or just weights? %s\n",
(justwts ? "Just weights" : "Data sets"));
}
}
if (data == seqs || data == restsites)
printf(" I Input sequences interleaved? %s\n",
interleaved ? "Yes" : "No, sequential");
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)");
printf(" 1 Print out the data at start of run %s\n",
printdata ? "Yes" : "No");
if (printdata)
printf(" . Use dot-differencing to display them %s\n",
dotdiff ? "Yes" : "No");
printf(" 2 Print indications of progress of run %s\n",
progress ? "Yes" : "No");
printf("\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
if (ch == 'Y')
break;
if (
(bootstrap && (strchr("ABCDEFSJPRWXNI%1.20",ch) != NULL)) ||
(jackknife && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
(permute && (strchr("ACDEFSJPRWXNI%1.20",ch) != NULL)) ||
((ild || lockhart) && (strchr("ACDESJPRXNI%1.20",ch) != NULL)) ||
((!(bootstrap || jackknife || permute || ild || lockhart)) &&
((!xml) && (strchr("ADEFJPI1.20",ch) != NULL))) ||
(((data == morphology) || (data == seqs))
&& (nexus || xml) && (strchr("ADEFJPSI1.20",ch) != NULL))
) {
switch (ch) {
case 'D':
if (data == genefreqs)
data = seqs;
else
data = (datatype)((long)data + 1);
break;
case 'A':
all = !all;
break;
case 'E':
enzymes = !enzymes;
break;
case 'J':
if (bootstrap) {
bootstrap = false;
jackknife = true;
} else if (jackknife) {
jackknife = false;
permute = true;
} else if (permute) {
permute = false;
ild = true;
} else if (ild) {
ild = false;
lockhart = true;
} else if (lockhart) {
lockhart = false;
rewrite = true;
} else if (rewrite) {
rewrite = false;
bootstrap = true;
} else {
assert(0); /* Shouldn't happen */
bootstrap
= true;
jackknife = permute = ild = lockhart = rewrite
= false;
}
break;
case '%':
regular = !regular;
if (!regular) {
loopcount2 = 0;
do {
printf("Samples as percentage of");
if ((data == seqs) || (data == restsites))
printf(" sites?\n");
if (data == morphology)
printf(" characters?\n");
if (data == genefreqs)
printf(" loci?\n");
fflush(stdout);
scanf("%lf%*[^\n]", &fracsample);
getchar();
done1 = (fracsample > 0.0);
if (!done1) {
printf("BAD NUMBER: must be positive\n");
}
fracsample = fracsample/100.0;
countup(&loopcount2, 10);
} while (done1 != true);
}
break;
case 'P':
if (data == seqs) {
if (!xml && !nexus)
nexus = true;
else {
if (nexus) {
nexus = false;
xml = true;
}
else xml = false;
}
}
if (data == morphology) {
nexus = !nexus;
xml = false;
}
break;
case 'S':
if(!rewrite){
justwts = !justwts;
} else {
switch (seq) {
case (dna): seq = rna; break;
case (rna): seq = protein; break;
case (protein): seq = dna; break;
}
}
break;
case 'B':
loopcount2 = 0;
do {
printf("Block size?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
scanf("%ld%*[^\n]", &blocksize);
getchar();
done1 = (blocksize > 0);
if (!done1) {
printf("BAD NUMBER: must be positive\n");
}
countup(&loopcount2, 10);
} while (done1 != true);
break;
case 'R':
reps0 = reps;
loopcount2 = 0;
do {
printf("Number of replicates?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
scanf("%ld%*[^\n]", &reps);
getchar();
done1 = (reps > 0);
if (!done1) {
printf("BAD NUMBER: must be positive\n");
reps = reps0;
}
countup(&loopcount2, 10);
} while (done1 != true);
break;
case 'W':
weights = !weights;
break;
case 'X':
mixture = !mixture;
break;
case 'N':
ancvar = !ancvar;
break;
case 'C':
categories = !categories;
break;
case 'F':
factors = !factors;
break;
case 'I':
interleaved = !interleaved;
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '.':
dotdiff = !dotdiff;
break;
case '2':
progress = !progress;
break;
}
} else
printf("Not a possible option!\n");
countup(&loopcount, 100);
}
if (bootstrap || jackknife) {
if (jackknife && regular)
fracsample = 0.5;
if (bootstrap && regular)
fracsample = 1.0;
}
if (!rewrite)
initseed(&inseed, &inseed0, seed);
/* These warnings only appear when user has changed an option that
* subsequently became inapplicable */
if (factors && lockhart) {
printf("Warning: Cannot use factors when permuting within species.\n");
factors = false;
}
if (data != seqs) {
if (xml) {
printf("warning: XML output not available for this type of data\n");
xml = false;
}
if (categories) {
printf("warning: cannot use categories file with this type of data\n");
categories = false;
}
}
if (data != morphology) {
if (mixture) {
printf("warning: cannot use mixture file with this type of data\n");
mixture = false;
}
if (ancvar) {
printf("warning: cannot use ancestors file with this type of data\n");
ancvar = false;
}
}
} /* getoptions */
void getoptions()
{
/* interactively set options */
long inseed0=0, loopcount;
Char ch;
boolean done=false;
putchar('\n');
minev = false;
global = false;
jumble = false;
njumble = 1;
lengths = false;
lower = false;
negallowed = false;
outgrno = 1;
outgropt = false;
power = 2.0;
replicates = false;
trout = true;
upper = false;
usertree = false;
printdata = false;
progress = true;
treeprint = true;
loopcount = 0;
do {
cleerhome();
printf("\nFitch-Margoliash method version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" D Method (F-M, Minimum Evolution)? %s\n",
(minev ? "Minimum Evolution" : "Fitch-Margoliash"));
printf(" U Search for best tree? %s\n",
(usertree ? "No, use user trees in input file" : "Yes"));
if (usertree) {
printf(" N Use lengths from user trees? %s\n",
(lengths ? "Yes" : "No"));
}
printf(" P Power?%9.5f\n",power);
printf(" - Negative branch lengths allowed? %s\n",
negallowed ? "Yes" : "No");
printf(" O Outgroup root?");
if (outgropt)
printf(" Yes, at species number%3ld\n", outgrno);
else
printf(" No, use as outgroup species%3ld\n", outgrno);
printf(" L Lower-triangular data matrix?");
if (lower)
printf(" Yes\n");
else
printf(" No\n");
printf(" R Upper-triangular data matrix?");
if (upper)
printf(" Yes\n");
else
printf(" No\n");
printf(" S Subreplicates?");
if (replicates)
printf(" Yes\n");
else
printf(" No\n");
if (!usertree) {
printf(" G Global rearrangements?");
if (global)
printf(" Yes\n");
else
printf(" No\n");
printf(" J Randomize input order of species?");
if (jumble)
printf(" Yes (seed =%8ld,%3ld times)\n", inseed0, njumble);
else
printf(" No. Use input order\n");
}
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)?");
if (ibmpc)
printf(" IBM PC\n");
if (ansi)
printf(" ANSI\n");
if (!(ibmpc || ansi))
printf(" (none)\n");
printf(" 1 Print out the data at start of run");
if (printdata)
printf(" Yes\n");
else
printf(" No\n");
printf(" 2 Print indications of progress of run");
if (progress)
printf(" Yes\n");
else
printf(" No\n");
printf(" 3 Print out tree");
if (treeprint)
printf(" Yes\n");
else
printf(" No\n");
printf(" 4 Write out trees onto tree file?");
if (trout)
printf(" Yes\n");
else
printf(" No\n");
printf(
"\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
done = (ch == 'Y');
if (!done) {
if (strchr("DJOUNPG-LRSM01234",ch) != NULL) {
switch (ch) {
case 'D':
minev = !minev;
if (minev && (!negallowed))
negallowed = true;
break;
case '-':
negallowed = !negallowed;
break;
case 'G':
global = !global;
break;
case 'J':
jumble = !jumble;
if (jumble)
initjumble(&inseed, &inseed0, seed, &njumble);
else njumble = 1;
break;
case 'L':
lower = !lower;
break;
case 'N':
lengths = !lengths;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
break;
case 'P':
initpower(&power);
break;
case 'R':
upper = !upper;
break;
case 'S':
replicates = !replicates;
break;
case 'U':
usertree = !usertree;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
jumble = true;
if (jumble)
initseed(&inseed, &inseed0, seed);
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
}
countup(&loopcount, 100);
} while (!done);
if (lower && upper) {
printf("ERROR: Data matrix cannot be both uppeR and Lower triangular\n");
exxit(-1);
}
} /* getoptions */
void getoptions()
{
/* interactively set options */
long inseed0 = 0, loopcount;
Char ch;
fprintf(outfile, "\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
putchar('\n');
jumble = false;
lower = false;
outgrno = 1;
outgropt = false;
replicates = false;
trout = true;
upper = false;
printdata = false;
progress = true;
treeprint = true;
njoin = true;
loopcount = 0;
for(;;) {
cleerhome();
printf("\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" N Neighbor-joining or UPGMA tree? %s\n",
(njoin ? "Neighbor-joining" : "UPGMA"));
if (njoin) {
printf(" O Outgroup root?");
if (outgropt)
printf(" Yes, at species number%3ld\n", outgrno);
else
printf(" No, use as outgroup species%3ld\n", outgrno);
}
printf(" L Lower-triangular data matrix? %s\n",
(lower ? "Yes" : "No"));
printf(" R Upper-triangular data matrix? %s\n",
(upper ? "Yes" : "No"));
printf(" S Subreplicates? %s\n",
(replicates ? "Yes" : "No"));
printf(" J Randomize input order of species?");
if (jumble)
printf(" Yes (random number seed =%8ld)\n", inseed0);
else
printf(" No. Use input order\n");
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
(ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)"));
printf(" 1 Print out the data at start of run %s\n",
(printdata ? "Yes" : "No"));
printf(" 2 Print indications of progress of run %s\n",
(progress ? "Yes" : "No"));
printf(" 3 Print out tree %s\n",
(treeprint ? "Yes" : "No"));
printf(" 4 Write out trees onto tree file? %s\n",
(trout ? "Yes" : "No"));
printf("\n\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
if (ch == '\n')
ch = ' ';
uppercase(&ch);
if (ch == 'Y')
break;
if (strchr("NJOULRSM01234",ch) != NULL){
switch (ch) {
case 'J':
jumble = !jumble;
if (jumble)
initseed(&inseed, &inseed0, seed);
break;
case 'L':
lower = !lower;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
else
outgrno = 1;
break;
case 'R':
upper = !upper;
break;
case 'S':
replicates = !replicates;
break;
case 'N':
njoin = !njoin;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
jumble = true;
if (jumble)
initseed(&inseed, &inseed0, seed);
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
countup(&loopcount, 100);
}
} /* getoptions */
