remove.rare command

[mothur.git] / metastatscommand.h

diff --git a/metastatscommand.h b/metastatscommand.h
index 9c9f455b4e8b4f45d309e5453da5c41fbba813d7..8c633b5417cbe07dc96827cf80c8e0b5522c0fad 100644 (file)
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -21,26 +21,40 @@ class MetaStatsCommand : public Command {
 
 public:
        MetaStatsCommand(string);
+       MetaStatsCommand();
        ~MetaStatsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
+       struct linePair {
+               int start;
+               int num;
+               linePair(int i, int j) : start(i), num(j) {}
+       };
+       vector<linePair> lines;
+       
        GlobalData* globaldata;
        GroupMap* designMap;
        ReadOTUFile* read;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
+       map<string, vector<string> > outputTypes;
        
        bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
-       string groups, label, outputDir, inputDir, designfile;
-       vector<string> Groups, outputNames;
-       int iters, g;
+       string groups, label, outputDir, inputDir, designfile, sets;
+       vector<string> Groups, outputNames, Sets;
+       vector< vector<string> > namesOfGroupCombos;
+       int iters, processors;
        float threshold;
        
        int process(vector<SharedRAbundVector*>&);
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int driver(int, int, vector<SharedRAbundVector*>&);
 };
 
 #endif