removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 9e756b884fb087f95ca0d43c23027c8caaa33b3f..274cac4e94f46b51aca95695f9fc4d7a4ba9c981 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -15,25 +15,26 @@
 #include "progress.hpp"
 #include "sharedutilities.h"
 #include "fileoutput.h"
+#include "readtree.h"
 
 
-class GlobalData;
-
 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();
-
+       ~ParsimonyCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "parsimony";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
 private:
-       GlobalData* globaldata;
+       ReadTree* read;
        SharedUtil* util;
        FileOutput* output;
        vector<Tree*> T;           //user trees
@@ -43,8 +44,8 @@ private:
        TreeMap* savetmap;
        Parsimony* pars;
        vector<string> groupComb; // AB. AC, BC...
-       string sumFile, randomtree, allGroups, outputDir;
-       int iters, numGroups, numComp, counter, processors;
+       string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+       int iters, numGroups, numComp, counter, processors, numUniquesInName;
        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.
@@ -57,16 +58,15 @@ private:
        vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
        
        ofstream outSum;
-       
-
        bool abort;
        string groups, itersString;
        vector<string> Groups, outputNames; //holds groups to be used
-       map<string, vector<string> > outputTypes;
-
+       map<string, string> nameMap;
+       
        void printParsimonyFile();  
        int printUSummaryFile();
        void getUserInput();
+       int readNamesFile();
        
 };