merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index bbcd6af5595d186610dae2818836d4d74b15f0f3..63980c254545ea07e7a4ffe71b1d9c496407ecf1 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -20,53 +20,48 @@
 class GlobalData;
 
 class ParsimonyCommand : public Command {
+
+public:
+       ParsimonyCommand(string);       
+       ~ParsimonyCommand() { delete pars; delete util; delete output; }
+       int execute();  
+       void help();
+
+private:
+       GlobalData* globaldata;
+       SharedUtil* util;
+       FileOutput* output;
+       vector<Tree*> T;           //user trees
+       Tree* randT;  //random tree
+       Tree* copyUserTree; 
+       TreeMap* tmap; 
+       TreeMap* savetmap;
+       Parsimony* pars;
+       vector<string> groupComb; // AB. AC, BC...
+       string sumFile, randomtree, allGroups;
+       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
+       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.
        
-       public:
-               ParsimonyCommand(string);       
-               ~ParsimonyCommand() { delete pars; delete util; delete output; }
-               int execute();  
-               void help();
+       ofstream outSum;
        
-       private:
-               GlobalData* globaldata;
-               SharedUtil* util;
-               FileOutput* output;
-               vector<Tree*> T;           //user trees
-               Tree* randT;  //random tree
-               Tree* copyUserTree; 
-               TreeMap* tmap; 
-               TreeMap* savetmap;
-               Parsimony* pars;
-               vector<string> groupComb; // AB. AC, BC...
-               string sumFile, randomtree, allGroups;
-               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
-               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;
-               ifstream inFile;
-               
-               OptionParser* parser;
-               map<string, string> parameters;
-               map<string, string>::iterator it4;
-               bool abort;
-               string groups, itersString;
-               vector<string> Groups; //holds groups to be used
 
-               void printParsimonyFile();  
-               void printUSummaryFile();
-               void getUserInput();
-               
+       bool abort;
+       string groups, itersString;
+       vector<string> Groups; //holds groups to be used
+
+       void printParsimonyFile();  
+       void printUSummaryFile();
+       void getUserInput();
+       
 };