added nseqs and sharednseqs calculators, removed excess tabs in output files.

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 4b3435e7e465535d8b93ffe370645cd6e936c2fb..e7d64e5201a5f1e29c3fce9c85d0622793138837 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -226,8 +226,8 @@ void ParsimonyCommand::printParsimonyFile() {
 void ParsimonyCommand::printUSummaryFile() {
        try {
                //column headers
-               outSum << "Tree#" << '\t' << "Comb" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
-               cout << "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);
@@ -237,11 +237,11 @@ void ParsimonyCommand::printUSummaryFile() {
                for (int i = 0; i< T.size(); i++) {
                        for(int a = 0; a < numComp; a++) {
                                if (UScoreSig[a][i] > (1/(float)iters)) {
-                                       outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+                                       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(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-                                       cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+                                       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;
                                }
                        }
                }
@@ -397,7 +397,7 @@ void ParsimonyCommand::initFile(string label){
                        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;
+                               out <<  inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
                        }
                }else{
                        openOutputFile(parsFileout, out);
@@ -405,7 +405,7 @@ void ParsimonyCommand::initFile(string label){
                        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 << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
                        }
                }
 
@@ -431,16 +431,16 @@ void ParsimonyCommand::output(vector<double> data){
                        getline(inFile, inputBuffer);
                
                        if (randomtree == "") {
-                               out << inputBuffer << '\t' << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+                               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(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+                               out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
                        }
                }
                else{
                        if (randomtree == "") {
-                               out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
+                               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(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+                               out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
                        }
                }