openOutputFile(weightedFile, out);
sumFile = globaldata->getTreeFile() + ".wsummary";
openOutputFile(sumFile, outSum);
- distFile = globaldata->getTreeFile() + ".wdistrib";
- openOutputFile(distFile, outDist);
-
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- }else {
- //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) {
- numGroups = tmap->getNumGroups();
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- }else if (globaldata->Groups.size() == 1) {
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- }else { numGroups = globaldata->Groups.size(); }
- }
-
- //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- numComp = 0;
- int n = 1;
- for (int i=1; i<numGroups; i++) {
- numComp += i;
- for (int l = n; l < numGroups; l++) {
- //set group comparison labels
- if (globaldata->Groups.size() != 0) {
- groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
- }else {
- groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
- }
- }
- n++;
- }
-
+
+ setGroups(); //sets the groups the user wants to analyze
convert(globaldata->getIters(), iters); //how many random trees to generate
weighted = new Weighted(tmap);
totalrscoreFreq.resize(numComp);
uCumul.resize(numComp);
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "Tree#" << '\t' << "Iter" << '\t' << "Groups"<< '\t' << "WScore" << endl;
-
-
//create new tree with same num nodes and leaves as users
randT = new Tree();
//add random score to valid scores
validScores[p][randomData[p]] = randomData[p];
-
- //output info to uwdistrib file
- outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << groupComb[p] << '\t'<< randomData[p] << endl;
}
}
printWeightedFile();
printWSummaryFile();
- //reset randomTree parameter to 0
- globaldata->setRandomTree("0");
-
//clear out users groups
globaldata->Groups.clear();
try {
//column headers
outSum << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" << endl;
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
for (int i = 0; i < T.size(); i++) {
for (int j = 0; j < numComp; j++) {
outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl;
count++;
}
}
}
/***********************************************************/
+void UnifracWeightedCommand::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() == 0) {
+ numGroups = tmap->getNumGroups();
+ }else {
+ if (globaldata->getGroups() != "all") {
+ //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) {
+ numGroups = tmap->getNumGroups();
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ }else if (globaldata->Groups.size() == 1) {
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ numGroups = tmap->getNumGroups();
+ globaldata->Groups.clear();
+ }else { numGroups = globaldata->Groups.size(); }
+ }else { //users wants all groups
+ numGroups = tmap->getNumGroups();
+ globaldata->Groups.clear();
+ globaldata->setGroups("");
+ }
+ }
+
+ //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+ numComp = 0;
+ int n = 1;
+ for (int i=1; i<numGroups; i++) {
+ numComp += i;
+ for (int l = n; l < numGroups; l++) {
+ //set group comparison labels
+ if (globaldata->Groups.size() != 0) {
+ groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
+ }else {
+ groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+ }
+ }
+ n++;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
projects / mothur.git / blobdiff