int main(int argc, char ** argv) {
int iline=0, i, iarg=1, nfields=1, jmax=0, writetxt=0, writemat=0, grpsize=1;
int membuf=1048576;
char * here, *linebuf, *readbuf;
string ifname = "", ofname = "", mfname = "", ffname = "", matfname = "", fdelim="\t", suffix="";
if (argc < 2) {
printf("%s", usage);
return 1;
}
while (iarg < argc) {
if (strncmp(argv[iarg], "-d", 2) == 0) {
fdelim = argv[++iarg];
} else if (strncmp(argv[iarg], "-c", 2) == 0) {
suffix=".gz";
} else if (strncmp(argv[iarg], "-f", 2) == 0) {
ffname = argv[++iarg];
} else if (strncmp(argv[iarg], "-i", 2) == 0) {
ifname = argv[++iarg];
} else if (strncmp(argv[iarg], "-m", 2) == 0) {
mfname = argv[++iarg];
} else if (strncmp(argv[iarg], "-o", 2) == 0) {
ofname = argv[++iarg];
} else if (strncmp(argv[iarg], "-s", 2) == 0) {
membuf = strtol(argv[++iarg],NULL,10);
} else if (strncmp(argv[iarg], "-?", 2) == 0) {
printf("%s", usage);
return 1;
} else if (strncmp(argv[iarg], "-h", 2) == 0) {
printf("%s", usage);
return 1;
} else {
cout << "Unknown option " << argv[iarg] << endl;
exit(1);
}
iarg++;
}
if (mfname.size() == 0) mfname = ofname;
ivector tvec(0);
svector delims(0);
svector dnames(0);
nfields = parseFormat(ffname, tvec, dnames, delims, &grpsize);
srivector srv(nfields);
ftvector ftv(nfields);
istream * ifstr;
linebuf = new char[membuf];
readbuf = new char[membuf];
ifstr = open_in_buf(ifname, readbuf, membuf);
while (!ifstr->bad() && !ifstr->eof()) {
ifstr->getline(linebuf, membuf-1);
linebuf[membuf-1] = 0;
if (ifstr->fail()) {
ifstr->clear();
ifstr->ignore(LONG_MAX,'\n');
}
if (strlen(linebuf) > 0) {
jmax++;
try {
parseLine(linebuf, membuf, ++iline, fdelim.c_str(), tvec, delims, srv, ftv, grpsize);
} catch (int e) {
cerr << "Continuing" << endl;
}
}
if ((jmax % 100000) == 0) {
cout<<"\r"<<jmax<<" lines processed";
cout.flush();
}
}
if (ifstr) delete ifstr;
cout<<"\r"<<jmax<<" lines processed";
cout.flush();
for (i = 0; i < nfields; i++) {
switch (tvec[i]) {
case ftype_int: case ftype_dt: case ftype_mdt: case ftype_date: case ftype_mdate: case ftype_cmdate:
ftv[i].writeInts(ofname + dnames[i] + ".imat" + suffix);
break;
case ftype_dint:
ftv[i].writeDInts(ofname + dnames[i] + ".dimat" + suffix);
break;
case ftype_qhex:
ftv[i].writeQInts(ofname + dnames[i] + ".imat" + suffix);
break;
case ftype_float:
ftv[i].writeFloats(ofname + dnames[i] + ".fmat" + suffix);
break;
case ftype_double:
ftv[i].writeDoubles(ofname + dnames[i] + ".dmat" + suffix);
break;
case ftype_word:
ftv[i].writeInts(ofname + dnames[i] + ".imat" + suffix);
srv[i].writeMap(mfname + dnames[i], suffix);
break;
case ftype_string: case ftype_group:
ftv[i].writeIVecs(ofname + dnames[i] + ".imat" + suffix);
srv[i].writeMap(mfname + dnames[i], suffix);
break;
case ftype_igroup:
ftv[i].writeIVecs(ofname + dnames[i] + ".imat" + suffix);
break;
case ftype_digroup:
ftv[i].writeDIVecs(ofname + dnames[i]);
break;
default:
break;
}
}
printf("\n");
if (linebuf) delete [] linebuf;
return 0;
}
//[[Rcpp::export]]
Rcpp::NumericMatrix SUPERMATRIX(Rcpp::List a,bool keep_names) {
size_t i,j,k;
Rcpp::NumericMatrix mat;
int tot=0;
Rcpp::CharacterVector rnam;
Rcpp::CharacterVector cnam;
Rcpp::CharacterVector this_nam;
Rcpp::List dnames(2);
bool any_rnames=false;
bool any_cnames=false;
for(i=0; i < a.size(); i++) {
mat = Rcpp::as<Rcpp::NumericMatrix>(a[i]);
if(mat.nrow() ==0) continue;
if(mat.nrow() != mat.ncol()) Rcpp::stop("Not all matrices are square");
tot = tot + mat.nrow();
if(!keep_names) continue;
dnames = mat.attr("dimnames");
if(dnames.size()==0) {
for(j=0; j < mat.nrow(); j++) {
rnam.push_back(".");
cnam.push_back(".");
}
continue;
}
if(!Rf_isNull(dnames[0])) {
any_rnames=true;
this_nam = dnames[0];
for(j=0; j< this_nam.size(); j++) rnam.push_back(this_nam[j]);
} else {
for(j=0; j < mat.nrow(); j++) rnam.push_back(".");
}
if(!Rf_isNull(dnames[1])) {
any_cnames=true;
this_nam = dnames[1];
for(j=0; j< this_nam.size(); j++) cnam.push_back(this_nam[j]);
} else {
for(j=0; j < mat.ncol(); j++) cnam.push_back(".");
}
}
int totrow = 0;
int totcol = 0;
Rcpp::NumericMatrix ret(tot,tot);
for(i=0; i < a.size(); i++) {
mat = Rcpp::as<Rcpp::NumericMatrix>(a[i]);
for(j=0; j < mat.nrow(); j++) {
for(k=0; k < mat.ncol(); k++) {
ret(totrow+j,totcol+k) = mat(j,k);
}
}
totrow = totrow + mat.nrow();
totcol = totcol + mat.ncol();
}
if(keep_names) {
Rcpp::List dn = Rcpp::List::create(rnam,cnam);
ret.attr("dimnames") = dn;
}
return(ret);
}
