fixed parsimony with groups and worked on unifrac.unweighted with groups

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index c40dde0c86c323560c850348940530293a1f6659..a527a18d28e8ef8613f39c3ce2d2da6b177f3af5 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -70,7 +70,6 @@ int ParsimonyCommand::execute() {
                                
                                //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
@@ -166,10 +165,10 @@ int ParsimonyCommand::execute() {
                }
                
                printParsimonyFile();
-               if (randomtree != "") { printUSummaryFile(); }
+               if (randomtree == "") { printUSummaryFile(); }
                
                //reset globaldata's treemap if you just did random distrib
-               if (randomtree == "") { globaldata->gTreemap = savetmap; }
+               if (randomtree != "") { globaldata->gTreemap = savetmap; }
                
                //reset randomTree parameter to ""
                globaldata->setRandomTree("");
@@ -238,6 +237,7 @@ void ParsimonyCommand::printUSummaryFile() {
                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;
+                               cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
                        }
                }
                
@@ -357,8 +357,10 @@ void ParsimonyCommand::setGroups() {
                }
                
                //ABC
-               groupComb.push_back(allGroups);
-               numComp++;
+               if (numComp != 1) {
+                       groupComb.push_back(allGroups);
+                       numComp++;
+               }
                
        }
        catch(exception& e) {