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;
}
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[])
{
boolean canbeplotted;
boolean wasplotted = false;
#ifdef MAC
OSErr retcode;
FInfo fndrinfo;
#ifdef OSX_CARBON
FSRef fileRef;
FSSpec fileSpec;
#endif
#ifdef __MWERKS__
SIOUXSetTitle("\pPHYLIP: Drawtree");
#endif
argv[0] = "Drawgram";
#endif
grbg = NULL;
progname = argv[0];
#ifndef X_DISPLAY_MISSING
nargc=1;
nargv=argv;
#endif
init(argc, argv);
emboss_getoptions("fdrawgram",argc,argv);
setup_environment(argv, &canbeplotted);
user_loop(&canbeplotted);
if (!((previewer == winpreview || previewer == xpreview || previewer == mac)
&& (winaction == quitnow))) {
previewing = false;
initplotter(spp,fontname);
numlines = dotmatrix ? ((long)floor(yunitspercm * ysize + 0.5)/strpdeep) : 1;
if (plotter != ibm)
printf("\nWriting plot file ...\n");
drawit(fontname,&xoffset,&yoffset,numlines,root);
finishplotter();
FClose(plotfile);
wasplotted = true;
printf("\nPlot written to file \"%s\"\n\n", pltfilename);
}
FClose(intree);
#ifdef MAC
if (plotter == pict && wasplotted){
#ifdef OSX_CARBON
FSPathMakeRef((unsigned char *)pltfilename, &fileRef, NULL);
FSGetCatalogInfo(&fileRef, kFSCatInfoNone, NULL, NULL, &fileSpec, NULL);
FSpGetFInfo(&fileSpec, &fndrinfo);
fndrinfo.fdType='PICT';
fndrinfo.fdCreator='MDRW';
FSpSetFInfo(&fileSpec, &fndrinfo);
#else
retcode=GetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
fndrinfo.fdType='PICT';
fndrinfo.fdCreator='MDRW';
retcode=SetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
#endif
}
if (plotter == lw && wasplotted){
#ifdef OSX_CARBON
FSPathMakeRef((unsigned char *)pltfilename, &fileRef, NULL);
FSGetCatalogInfo(&fileRef, kFSCatInfoNone, NULL, NULL, &fileSpec, NULL);
FSpGetFInfo(&fileSpec, &fndrinfo);
fndrinfo.fdType='TEXT';
FSpSetFInfo(&fileSpec, &fndrinfo);
#else
retcode=GetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
fndrinfo.fdType='TEXT';
retcode=SetFInfo(CtoPstr(PLOTFILE),0,&fndrinfo);
#endif
}
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
embExit();
return 0;
}
