T = globaldata->gTree;
tmap = globaldata->gTreemap;
parsFile = globaldata->getTreeFile() + ".parsimony";
- openOutputFile(parsFile, out);
+ parsFileout = globaldata->getTreeFile() + "temp" + ".parsimony";
sumFile = globaldata->getTreeFile() + ".psummary";
openOutputFile(sumFile, outSum);
- //set users groups to analyze
- setGroups();
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
getUserInput();
- parsFile = randomtree + ".rd_parsimony";
- openOutputFile(parsFile, out);
+ parsFile = randomtree;
+ parsFileout = globaldata->getTreeFile() + "temp";
}
+ //set users groups to analyze
+ setGroups();
convert(globaldata->getIters(), iters); //how many random trees to generate
pars = new Parsimony(tmap);
+ counter = 0;
}
catch(exception& e) {
/***********************************************************/
int ParsimonyCommand::execute() {
try {
-
+
+ //get pscore for users tree
+ userData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ rscoreFreq.resize(numComp);
+ uscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ uCumul.resize(numComp);
+ userTreeScores.resize(numComp);
+ UScoreSig.resize(numComp);
if (randomtree == "") {
- //get pscore for users tree
- userData.resize(numComp,0); //data = AB, AC, BC, ABC.
- randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
- rscoreFreq.resize(numComp);
- uscoreFreq.resize(numComp);
- rCumul.resize(numComp);
- uCumul.resize(numComp);
- validScores.resize(numComp);
- userTreeScores.resize(numComp);
- UScoreSig.resize(numComp);
-
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- cout << "Processing tree " << i+1 << endl;
userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
//output scores for each combination
for(int k = 0; k < numComp; k++) {
- cout << "Tree " << i+1 << " Combination " << groupComb[k] << " parsimony score = " << userData[k] << endl;
//update uscoreFreq
it = uscoreFreq[k].find(userData[k]);
if (it == uscoreFreq[k].end()) {//new score
}else{ uscoreFreq[k][userData[k]]++; }
//add users score to valid scores
- validScores[k][userData[k]] = userData[k];
+ validScores[userData[k]] = userData[k];
//save score for summary file
userTreeScores[k].push_back(userData[k]);
}
//add randoms score to validscores
- validScores[r][randomData[r]] = randomData[r];
+ validScores[randomData[r]] = randomData[r];
}
delete randT;
}
//add randoms score to validscores
- validScores[r][randomData[r]] = randomData[r];
+ validScores[randomData[r]] = randomData[r];
}
delete randT;
}
}
- float rcumul = 0.0000;
- float ucumul = 0.0000;
-
for(int a = 0; a < numComp; a++) {
- //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
- for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
+ float rcumul = 0.0000;
+ float ucumul = 0.0000;
+ //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++) {
if (randomtree == "") {
it2 = uscoreFreq[a].find(it->first);
//user data has that score
if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; }
else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
//make uCumul map
- uCumul[a][it->first] = ucumul-a;
+ uCumul[a][it->first] = ucumul;
}
//make rscoreFreq map and rCumul
//get percentage of random trees with that info
if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul+= it2->second; }
else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
- rCumul[a][it->first] = rcumul-a;
+ rCumul[a][it->first] = rcumul;
}
//find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
}
printParsimonyFile();
- printUSummaryFile();
+ if (randomtree == "") { printUSummaryFile(); }
//reset globaldata's treemap if you just did random distrib
- if (randomtree != "") { globaldata->gTreemap = savetmap; }
+ if (randomtree != "") {
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
+ globaldata->gTreemap = savetmap;
+ }
//reset randomTree parameter to ""
globaldata->setRandomTree("");
/***********************************************************/
void ParsimonyCommand::printParsimonyFile() {
try {
- //column headers
- if (randomtree == "") {
- out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }else {
- out << "Comb" << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }
+ vector<double> data;
//format output
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
+
for(int a = 0; a < numComp; a++) {
+ initFile(groupComb[a]);
//print each line
- for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
+ for (it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t'<< uscoreFreq[a][it->first] << '\t' << uCumul[a][it->first] << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
}else{
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
}
+ output(data);
+ data.clear();
}
+ resetFile();
}
- out.close();
+ out.close();
+ inFile.close();
+ remove(parsFileout.c_str());
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
void ParsimonyCommand::printUSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "Comb" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl;
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
//print each line
for (int i = 0; i< T.size(); i++) {
for(int a = 0; a < numComp; a++) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+ if (UScoreSig[a][i] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+ }else {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
+ }
}
}
//set tmaps seqsPerGroup
tmap->seqsPerGroup[toString(i)] = num;
+ tmap->namesOfGroups.push_back(toString(i));
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
getline(cin, s);
//save tmap for later
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
globaldata->gTreemap = tmap;
}
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
globaldata->Groups.push_back(tmap->namesOfGroups[i]);
numGroups++;
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
+ allGroups += globaldata->Groups[i] + "-";
numGroups++;
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
}
}else{//user has enter "all" and wants the default groups
+ globaldata->Groups.clear();
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
globaldata->Groups.push_back(tmap->namesOfGroups[i]);
numGroups++;
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
globaldata->setGroups("");
}
}else {
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i];
+ allGroups += tmap->namesOfGroups[i] + "-";
}
+ allGroups = allGroups.substr(0, allGroups.length()-1);
numGroups = 1;
}
numComp = 0;
for (int r=0; r<numGroups; r++) {
for (int l = r+1; l < numGroups; l++) {
- groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
+ groupComb.push_back(globaldata->Groups[r]+ "-" +globaldata->Groups[l]);
numComp++;
}
}
//ABC
- groupComb.push_back(allGroups);
- numComp++;
+ if (numComp != 1) {
+ groupComb.push_back(allGroups);
+ numComp++;
+ }
}
catch(exception& e) {
}
/*****************************************************************/
+void ParsimonyCommand::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(parsFileout, out);
+ openInputFile(parsFile, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ if (randomtree == "") {
+ out << inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else {
+ out << inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }
+ }else{
+ openOutputFile(parsFileout, out);
+ //column headers
+ if (randomtree == "") {
+ out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else {
+ out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ }
+ }
+
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ParsimonyCommand::output(vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ if (randomtree == "") {
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+ }else{
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ }
+ else{
+ if (randomtree == "") {
+ out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+ }else{
+ out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void ParsimonyCommand::resetFile(){
+ try {
+ if(counter != 0){
+ out.close();
+ inFile.close();
+ }
+ else{
+ out.close();
+ }
+ counter = 1;
+
+ remove(parsFile.c_str());
+ rename(parsFileout.c_str(), parsFile.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
projects / mothur.git / blobdiff