added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 3467c7b1d9e6beb1bcd2b5af9a63f9d9bbaf8045..3d39b8b7a54ba348966f80d41cf1cea3b9bc9283 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,21 +26,26 @@ class GlobalData;
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
        ~SharedCommand();
        int execute();  
        void help() {}
        
 private:
        void printSharedData(vector<SharedRAbundVector*>);
+       void createMisMatchFile();
+       bool isValidGroup(string, vector<string>);
+       void eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
        GroupMap* groupMap;
+       vector<string> groups;
        ofstream out;
-       string filename, fileroot;
-       bool firsttime;
+       string filename, fileroot, outputDir;
+       bool firsttime, pickedGroups;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;