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;
- }
- }
-
+ 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;
saveRandomScores(); //save all random scores for unweighted file
//find the signifigance of the score
- float rcumul = 0.0000;
+ float rcumul = 1.0000;
for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
+ rCumul[it->first] = rcumul;
//get percentage of random trees with that info
rscoreFreq[it->first] /= iters;
- rcumul+= it->second;
- rCumul[it->first] = rcumul;
+ rcumul-= it->second;
+
}
//save the signifigance of the users score for printing later
rCumul.clear();
}
- float ucumul = 0.0000;
- float rcumul = 0.0000;
+ float ucumul = 1.0000;
+ 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++) {
it2 = uscoreFreq.find(it->first);
- //user data has that score
- if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
- else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
//make uCumul map
uCumul[it->first] = ucumul;
-
+ //user data has that score
+ if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second; }
+ else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
+
//make rscoreFreq map and rCumul
it2 = totalrscoreFreq.find(it->first);
+ rCumul[it->first] = rcumul;
//get percentage of random trees with that info
- if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul+= it2->second; }
+ if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second; }
else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
- rCumul[it->first] = rcumul;
+
}
printUnweightedFile();
printUWSummaryFile();
- //reset randomTree parameter to 0
- globaldata->setRandomTree("0");
+ //reset groups parameter
+ globaldata->Groups.clear();
delete randT;
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);
+ }
+
+}
+/*****************************************************************/
+
projects / mothur.git / blobdiff