parsimony with groups

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index e741b5e914770e34b49ac5c244e31b041f8520d2..c40dde0c86c323560c850348940530293a1f6659 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -25,8 +25,6 @@ ParsimonyCommand::ParsimonyCommand() {
                        openOutputFile(parsFile, out);
                        sumFile = globaldata->getTreeFile() + ".psummary";
                        openOutputFile(sumFile, outSum);
-                       //set users groups to analyze
-                       setGroups();
                }else { //user wants random distribution
                        savetmap = globaldata->gTreemap;
                        getUserInput();
@@ -34,6 +32,8 @@ ParsimonyCommand::ParsimonyCommand() {
                        openOutputFile(parsFile, out);
                }
                
+               //set users groups to analyze
+               setGroups();
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                pars = new Parsimony(tmap);
 
@@ -50,20 +50,19 @@ ParsimonyCommand::ParsimonyCommand() {
 /***********************************************************/
 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);  
+               validScores.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;
@@ -167,10 +166,10 @@ int ParsimonyCommand::execute() {
                }
                
                printParsimonyFile();
-               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("");
@@ -274,6 +273,7 @@ void ParsimonyCommand::getUserInput() {
                                
                        //set tmaps seqsPerGroup
                        tmap->seqsPerGroup[toString(i)] = num;
+                       tmap->namesOfGroups.push_back(toString(i));
                        
                        //set tmaps namesOfSeqs
                        for (int j = 0; j < num; j++) {