openOutputFile(parsFile, out);
sumFile = globaldata->getTreeFile() + ".psummary";
openOutputFile(sumFile, outSum);
- distFile = globaldata->getTreeFile() + ".pdistrib";
- 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]);
- }
- }
-
+ //set users groups to analyze
+ setGroups();
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
getUserInput();
userData.resize(1,0); //data[0] = pscore.
randomData.resize(1,0); //data[0] = pscore.
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
-
if (randomtree == "") {
+ copyUserTree = new Tree();
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
+ //copy users tree so that you can redo pgroups
+ copyUserTree->getCopy(T[i]);
cout << "Processing tree " << i+1 << endl;
- userData = pars->getValues(T[i]); //userData[0] = pscore
+ userData = pars->getValues(copyUserTree); //userData[0] = pscore
cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
//update uscoreFreq
it = uscoreFreq.find(userData[0]);
//add randoms score to validscores
validScores[randomData[0]] = randomData[0];
- //output info to pdistrib file
- outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
-
delete randT;
}
}else {
//reset randomTree parameter to ""
globaldata->setRandomTree("");
//reset groups parameter
- globaldata->Groups.clear();
+ globaldata->Groups.clear(); globaldata->setGroups("");
return 0;
}
/***********************************************************/
+void ParsimonyCommand::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ if (globaldata->Groups[0] != "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) {
+ 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{//user has enter "all" and wants the default groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ globaldata->setGroups("");
+ }
+ }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 ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/*****************************************************************/
+
+