+/***********************************************************/
+
+void UnifracWeightedCommand::calculateFreqsCumuls() {
+ try {
+ //clear out old tree values
+ rScoreFreq.clear();
+ rScoreFreq.resize(numComp);
+ rCumul.clear();
+ rCumul.resize(numComp);
+ validScores.clear();
+
+ //calculate frequency
+ for (int f = 0; f < numComp; f++) {
+ for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
+ validScores[rScores[f][i]] = rScores[f][i];
+ it = rScoreFreq[f].find(rScores[f][i]);
+ if (it != rScoreFreq[f].end()) {
+ rScoreFreq[f][rScores[f][i]]++;
+ }else{
+ rScoreFreq[f][rScores[f][i]] = 1;
+ }
+ }
+ }
+
+ //calculate rcumul
+ for(int a = 0; a < numComp; a++) {
+ float rcumul = 1.0000;
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (it = validScores.begin(); it != validScores.end(); it++) {
+ //make rscoreFreq map and rCumul
+ it2 = rScoreFreq[a].find(it->first);
+ rCumul[a][it->first] = rcumul;
+ //get percentage of random trees with that info
+ if (it2 != rScoreFreq[a].end()) { rScoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rScoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/*****************************************************************/
+
+void UnifracWeightedCommand::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(weightedFileout, out);
+ openInputFile(weightedFile, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ out << inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else{
+ openOutputFile(weightedFileout, out);
+ out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }
+
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void UnifracWeightedCommand::output(vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ out << inputBuffer << setprecision(globaldata->getIters().length()) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ else{
+ out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void UnifracWeightedCommand::resetFile(){
+ try {
+ if(counter != 0){
+ out.close();
+ inFile.close();
+ }
+ else{
+ out.close();
+ }
+ counter = 1;
+
+ remove(weightedFile.c_str());
+ rename(weightedFileout.c_str(), weightedFile.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+