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[])
{ /* Read in sequences or frequencies and bootstrap or jackknife them */
init(argc,argv);
openfile(&infile, argv[1], "input file", "r", argv[0], infilename);
reps = atol(argv[2]);
doinput(argc, argv);
bootwrite();
freenewer();
freenew();
freerest();
if (nodep)
matrix_char_delete(nodep, spp);
FClose(infile);
return 0;
}
int main(int argc, Char *argv[])
{ /* main program */
#ifdef MAC
argc = 1; /* macsetup("Neighbor",""); */
argv[0] = "Neighbor";
#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;
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);
}
inputoptions();
maketree();
if (eoln(infile) && (ith < datasets))
scan_eoln(infile);
ith++;
}
FClose(infile);
FClose(outfile);
FClose(outtree);
freerest();
#ifdef MAC
fixmacfile(outfilename);
fixmacfile(outtreename);
#endif
printf("Done.\n\n");
#ifdef WIN32
phyRestoreConsoleAttributes();
#endif
return 0;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{ /* main program */
double *outputval, *inputval;
int mrows, ncols;
if (nrhs != 1) {
mexPrintf("Format for calling 'NEIGHBOR' executable:\n");
mexPrintf("\tNEIGHBOR( <outgrno> )\n");
mexErrMsgTxt("Wrong number of input args.");
}
/* Read in the argument: either a double or NULL '[]' */
if (((mxIsDouble(prhs[0]) != 1) & (!mxIsEmpty(prhs[0]))) == 1) {
mexErrMsgTxt("The argument should be a double.\n");
}
else if (((mxIsDouble(prhs[0]) == 1) & (!mxIsEmpty(prhs[0])) == 1)) {
mrows = mxGetM(prhs[0]);
ncols = mxGetN(prhs[0]);
if ((mrows * ncols) > 1)
mexErrMsgTxt("The argument should be a single value.\n");
else {
inputval = mxGetPr(prhs[0]);
outgrno = (long)*inputval;
}
}
else if (mxIsEmpty(prhs[0])) {
mexErrMsgTxt("numDouble = NULL\n");
}
else
mexErrMsgTxt("ERROR in <input_double> processing code.\n");
openfile(&infile,INFILE,"input file", "r","Neighbor",infilename);
openfile(&outfile,OUTFILE,"output file", "w","Neighbor",outfilename);
ibmpc = IBMCRT;
ansi = ANSICRT;
mulsets = false;
datasets = 1;
doinit();
if (trout){
openfile(&outtree,OUTTREE,"output tree file", "w","Neighbor",outtreename);
/* The next line is added to make a 'real' rooted tree -- James J. Cai 6/6/2006 */
putc('(', outtree);
}
ith = 1;
while (ith <= datasets) {
if (datasets > 1) {
fprintf(outfile, "Data set # %ld:\n",ith);
if (progress)
mexPrintf("Data set # %ld:\n",ith);
}
inputoptions();
maketree();
if (eoln(infile) && (ith < datasets))
scan_eoln(infile);
ith++;
}
FClose(infile);
FClose(outfile);
FClose(outtree);
freerest();
/* mexPrintf("Done.\n\n"); */
plhs[0] = mxCreateDoubleMatrix(1, 1, mxREAL);
outputval = mxGetPr(plhs[0]);
/* memcpy(output, 1.0, sizeof(double)); */
outputval[0] = 0;
return;
}