//********************************************************************************************************************
//sorts lowest to highest
inline bool compareBin(repStruct left, repStruct right){
- return (left.bin < right.bin);
+ return (left.simpleBin < right.simpleBin);
}
//********************************************************************************************************************
//sorts lowest to highest
}
//for each bin in the list vector
+ vector<string> binLabels = processList->getLabels();
for (int i = 0; i < processList->size(); i++) {
if (m->control_pressed) {
out.close();
if (Groups.size() == 0) {
nameRep = findRep(namesInBin, "");
- newNamesOutput << i << '\t' << nameRep << '\t';
+ newNamesOutput << binLabels[i] << '\t' << nameRep << '\t';
//put rep at first position in names line
string outputString = nameRep + ",";
nameRep = findRep(NamesInGroup[Groups[j]], Groups[j]);
//output group rep and other members of this group
- (*(filehandles[Groups[j]])) << i << '\t' << nameRep << '\t';
+ (*(filehandles[Groups[j]])) << binLabels[i] << '\t' << nameRep << '\t';
//put rep at first position in names line
string outputString = nameRep + ",";
ifstream in;
m->openInputFile(filename, in);
- int i = 0;
string tempGroup = "";
in >> tempGroup; m->gobble(in);
int thistotal = 0;
while (!in.eof()) {
- string rep, binnames;
- in >> i >> rep >> binnames; m->gobble(in);
+ string rep, binnames, binLabel;
+ in >> binLabel >> rep >> binnames; m->gobble(in);
vector<string> names;
m->splitAtComma(binnames, names);
if (sequence != "not found") {
if (sorted == "") { //print them out
- rep = rep + "\t" + toString(i+1);
+ rep = rep + "\t" + binLabel;
rep = rep + "|" + toString(binsize);
if (group != "") {
rep = rep + "|" + group;
out << ">" << rep << endl;
out << sequence << endl;
}else { //save them
- repStruct newRep(rep, i+1, binsize, group);
+ int simpleLabel;
+ m->mothurConvert(m->getSimpleLabel(binLabel), simpleLabel);
+ repStruct newRep(rep, binLabel, simpleLabel, binsize, group);
reps.push_back(newRep);
}
}else {
//print them
for (int i = 0; i < reps.size(); i++) {
string sequence = fasta->getSequence(reps[i].name);
- string outputName = reps[i].name + "\t" + toString(reps[i].bin);
+ string outputName = reps[i].name + "\t" + reps[i].bin;
outputName = outputName + "|" + toString(reps[i].size);
if (reps[i].group != "") {
outputName = outputName + "|" + reps[i].group;
ifstream in;
m->openInputFile(filename, in);
- int i = 0;
string rep, binnames;
string tempGroup = "";
while (!in.eof()) {
if (m->control_pressed) { break; }
- in >> i >> rep >> binnames; m->gobble(in);
+ string binLabel;
+ in >> binLabel >> rep >> binnames; m->gobble(in);
if (countfile == "") { out2 << rep << '\t' << binnames << endl; }
else {