parsimony output changed

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index db062c6d84a67b72dd1b0b7163f0eae9ca8f0aa5..8907e2165c82ac291a902fe04ca3dd00638bd3db 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -33,14 +33,14 @@ class ParsimonyCommand : public Command {
                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.
@@ -49,11 +49,16 @@ class ParsimonyCommand : public Command {
                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();
+
                
 };