added ordergroup parameter to read.otu

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index b305e9a7d9f3256eef03cac34387caea99f4b4ae..0f3e7ef2289b39f9ab4807ccda5cbe179ff51d04 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,25 +26,27 @@ class GlobalData;
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
        ~SharedCommand();
        int execute();  
        void help() {}
        
 private:
        void printSharedData(vector<SharedRAbundVector*>);
-       void createMisMatchFile();
+       int createMisMatchFile();
+       int readOrderFile();
        bool isValidGroup(string, vector<string>);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
        GroupMap* groupMap;
-       vector<string> groups;
+       vector<string> groups, outputNames, order;
        ofstream out;
-       string filename, fileroot;
-       bool firsttime;
+       string filename, fileroot, outputDir;
+       bool firsttime, pickedGroups;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;