ListVector::ListVector(ifstream& f) : DataVector(), maxRank(0), numBins(0), numSeqs(0) {
try {
int hold;
- f >> label >> hold;
+
+ //are we at the beginning of the file??
+ if (m->saveNextLabel == "") {
+ f >> label;
+
+ //is this a shared file that has headers
+ if (label == "label") {
+
+ //gets "numOtus"
+ f >> label; m->gobble(f);
+
+ //eat rest of line
+ label = m->getline(f); m->gobble(f);
+
+ //parse labels to save
+ istringstream iStringStream(label);
+ m->listBinLabelsInFile.clear();
+ while(!iStringStream.eof()){
+ if (m->control_pressed) { break; }
+ string temp;
+ iStringStream >> temp; m->gobble(iStringStream);
+
+ m->listBinLabelsInFile.push_back(temp);
+ }
+
+ f >> label >> hold;
+ }else {
+ //read in first row
+ f >> hold;
+
+ //make binlabels because we don't have any
+ string snumBins = toString(hold);
+ m->listBinLabelsInFile.clear();
+ for (int i = 0; i < hold; i++) {
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ m->listBinLabelsInFile.push_back(binLabel);
+ }
+ }
+ m->saveNextLabel = label;
+ }else {
+ f >> label >> hold;
+ m->saveNextLabel = label;
+ }
+ binLabels.assign(m->listBinLabelsInFile.begin(), m->listBinLabelsInFile.begin()+hold);
+
data.assign(hold, "");
string inputData = "";
set(i, inputData);
}
m->gobble(f);
+
+ if (f.eof()) { m->saveNextLabel = ""; }
}
catch(exception& e) {
m->errorOut(e, "ListVector", "ListVector");
string ListVector::get(int index){
return data[index];
}
+/***********************************************************************/
+
+void ListVector::setLabels(vector<string> labels){
+ try {
+ binLabels = labels;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListVector", "setLabels");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+//could potentially end up with duplicate binlabel names with code below.
+//we don't currently use them in a way that would do that.
+//if you had a listfile that had been subsampled and then added to it, dup names would be possible.
+vector<string> ListVector::getLabels(){
+ try {
+
+ string tagHeader = "Otu";
+ if (m->sharedHeaderMode == "tax") { tagHeader = "PhyloType"; }
+
+ if (binLabels.size() < data.size()) {
+ string snumBins = toString(numBins);
+
+ for (int i = 0; i < numBins; i++) {
+ string binLabel = tagHeader;
+
+ if (i < binLabels.size()) { //label exists, check leading zeros length
+ string sbinNumber = m->getSimpleLabel(binLabels[i]);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ binLabels[i] = binLabel;
+ }else{
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ binLabels.push_back(binLabel);
+ }
+ }
+ }
+ return binLabels;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListVector", "getLabels");
+ exit(1);
+ }
+}
/***********************************************************************/
}
+/***********************************************************************/
+void ListVector::printHeaders(ostream& output){
+ try {
+ string snumBins = toString(numBins);
+ output << "label\tnumOtus\t";
+ if (m->sharedHeaderMode == "tax") {
+ for (int i = 0; i < numBins; i++) {
+
+ //if there is a bin label use it otherwise make one
+ string binLabel = "PhyloType";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < binLabels.size()) { binLabel = binLabels[i]; }
+
+ output << binLabel << '\t';
+ }
+ output << endl;
+ }else {
+ for (int i = 0; i < numBins; i++) {
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < binLabels.size()) { binLabel = binLabels[i]; }
+
+ output << binLabel << '\t';
+ }
+
+ output << endl;
+ }
+ m->printedListHeaders = true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListVector", "printHeaders");
+ exit(1);
+ }
+}
+
/***********************************************************************/
void ListVector::print(ostream& output){