working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 0f12d421ab291e176df2415c70b2ee27365a92ad..9e756b884fb087f95ca0d43c23027c8caaa33b3f 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -23,7 +23,12 @@ class ParsimonyCommand : public Command {
 
 public:
        ParsimonyCommand(string);       
+       ParsimonyCommand();
        ~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; }  }
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
 
@@ -38,8 +43,8 @@ private:
        TreeMap* savetmap;
        Parsimony* pars;
        vector<string> groupComb; // AB. AC, BC...
-       string sumFile, randomtree, allGroups;
-       int iters, numGroups, numComp, counter;
+       string sumFile, randomtree, allGroups, outputDir;
+       int iters, numGroups, numComp, counter, processors;
        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.
@@ -56,10 +61,11 @@ private:
 
        bool abort;
        string groups, itersString;
-       vector<string> Groups; //holds groups to be used
+       vector<string> Groups, outputNames; //holds groups to be used
+       map<string, vector<string> > outputTypes;
 
        void printParsimonyFile();  
-       void printUSummaryFile();
+       int printUSummaryFile();
        void getUserInput();
        
 };