parsimony with groups

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index ba30d4016886123c1d8b33967899d699619b30b4..db062c6d84a67b72dd1b0b7163f0eae9ca8f0aa5 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -32,20 +32,21 @@ class ParsimonyCommand : public Command {
                TreeMap* tmap; 
                TreeMap* savetmap;
                Parsimony* pars;
+               vector<string> groupComb; // AB. AC, BC...
                string parsFile, sumFile, randomtree;
-               int iters, numGroups;
+               int iters, numGroups, numComp;
                vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
-               vector<float> userTreeScores; //scores for users trees
-               vector<float> UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+               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
-               map<int, float> validScores;  //contains scores from both user and random
-               map<int, float> rscoreFreq;  //pscore, number of random trees with that score.
-               map<int, float> uscoreFreq;  //pscore, number of user trees with that score.
-               map<int, float> rCumul;  //pscore, cumulative percentage of number of random trees with that score or lower.
-               map<int, float> uCumul;  //pscore, cumulative percentage of number of user trees with that score or lower .
-               map<int, float>::iterator it;
-               map<int, float>::iterator it2;
+               vector< 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.
+               vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+               map<int, double>::iterator it;
+               map<int, double>::iterator it2;
                
                ofstream out, outSum;