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);
}else { //user wants random distribution
setGroups();
convert(globaldata->getIters(), iters); //how many random trees to generate
pars = new Parsimony(tmap);
+ counter = 0;
}
catch(exception& e) {
uscoreFreq.resize(numComp);
rCumul.resize(numComp);
uCumul.resize(numComp);
- validScores.resize(numComp);
userTreeScores.resize(numComp);
UScoreSig.resize(numComp);
}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
/***********************************************************/
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::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' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "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 << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "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] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+ }else{
+ out << inputBuffer << '\t' << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ }
+ else{
+ if (randomtree == "") {
+ out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+ }else{
+ out << setprecision(6) << data[0] << '\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);
+ }
+}
+
TreeMap* savetmap;
Parsimony* pars;
vector<string> groupComb; // AB. AC, BC...
- string parsFile, sumFile, randomtree;
- int iters, numGroups, numComp;
+ string parsFile, parsFileout, sumFile, randomtree;
+ int iters, numGroups, numComp, counter;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector< vector<float> > userTreeScores; //scores for users trees for each comb.
vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
EstOutput userData; //pscore info for user tree
EstOutput randomData; //pscore info for random trees
- vector< map<int, double> > validScores; //map contains scores from both user and random
+ map<int, double> validScores; //map contains scores from both user and random
vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
map<int, double>::iterator it2;
ofstream out, outSum;
+ ifstream inFile;
void printParsimonyFile();
void printUSummaryFile();
void getUserInput();
void setGroups();
+ void initFile(string);
+ void output(vector<double>);
+ void resetFile();
+
};
projects / mothur.git / commitdiff