openOutputFile(sumFile, outSum);
distFile = globaldata->getTreeFile() + ".uwdistrib";
openOutputFile(distFile, outDist);
-
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
-
+ setGroups(); //sets users groups to analyze
convert(globaldata->getIters(), iters); //how many random trees to generate
unweighted = new Unweighted(tmap);
//format output
outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+
+ outDist << "Groups Used ";
+ for (int m = 0; m < globaldata->Groups.size(); m++) {
+ outDist << globaldata->Groups[m] << " ";
+ }
+ outDist << endl;
+
outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
//create new tree with same num nodes and leaves as users
randT = new Tree();
-
+
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
cout << "Processing tree " << i+1 << endl;
try {
//column headers
+ out << "Groups Used ";
+ for (int m = 0; m < globaldata->Groups.size(); m++) {
+ out << globaldata->Groups[m] << " ";
+ }
+ out << endl;
+
out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
//format output
void UnifracUnweightedCommand::printUWSummaryFile() {
try {
//column headers
+
+ outSum << "Groups Used ";
+ for (int m = 0; m < globaldata->Groups.size(); m++) {
+ outSum << globaldata->Groups[m] << " ";
+ }
+ outSum << endl;
+
outSum << "Tree#" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
//format output
}
}
-/***********************************************************/
\ No newline at end of file
+/***********************************************************/
+
+void UnifracUnweightedCommand::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+
+ }else {
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/*****************************************************************/
+