globaldata = GlobalData::getInstance();
//randomtree will tell us if user had their own treefile or if they just want the random distribution
- convert(globaldata->getRandomTree(), randomtree);
+ randomtree = globaldata->getRandomTree();
//user has entered their own tree
- if (randomtree == 0) {
+ if (randomtree == "") {
T = globaldata->gTree;
tmap = globaldata->gTreemap;
parsFile = globaldata->getTreeFile() + ".parsimony";
openOutputFile(parsFile, out);
sumFile = globaldata->getTreeFile() + ".psummary";
openOutputFile(sumFile, outSum);
- distFile = globaldata->getTreeFile() + ".pdistrib";
- openOutputFile(distFile, outDist);
-
+ //set users groups to analyze
+ setGroups();
}else { //user wants random distribution
+ savetmap = globaldata->gTreemap;
getUserInput();
- parsFile = "rd_parsimony";
+ parsFile = randomtree + ".rd_parsimony";
openOutputFile(parsFile, out);
}
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 == 0) {
+ 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]);
if (it == uscoreFreq.end()) {//new score
//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 {
//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++) {
- if (randomtree == 0) {
+ if (randomtree == "") {
it2 = uscoreFreq.find(it->first);
//user data has that score
if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second; }
printParsimonyFile();
printUSummaryFile();
- //reset randomTree parameter to 0
- globaldata->setRandomTree("0");
+ //reset globaldata's treemap if you just did random distrib
+ if (randomtree != "") { globaldata->gTreemap = savetmap; }
+
+ //reset randomTree parameter to ""
+ globaldata->setRandomTree("");
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
return 0;
void ParsimonyCommand::printParsimonyFile() {
try {
//column headers
- if (randomtree == 0) {
+ if (randomtree == "") {
out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
}else {
out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
//print each line
for (it = validScores.begin(); it != validScores.end(); it++) {
- if (randomtree == 0) {
+ if (randomtree == "") {
out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
}else{
out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
}
/***********************************************************/
+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);
+ }
+
+}
+/*****************************************************************/
+
+
projects / mothur.git / blobdiff