some changes while testing 1.9

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index ca0ddd833636e6550cb48832517cdc96f912977e..399f3d3966bf828ec32cd790dd0d7d14c7e08c25 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,22 +26,28 @@ class GlobalData;
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
        ~SharedCommand();
        int execute();  
        void help() {}
        
 private:
        void printSharedData(vector<SharedRAbundVector*>);
+       int createMisMatchFile();
+       bool isValidGroup(string, vector<string>);
+       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
-       //map<string, SharedRAbundVector*>::iterator it;
-       //vector<SharedRAbundVector*> lookup;
+       GroupMap* groupMap;
+       vector<string> groups, outputNames;
        ofstream out;
-       string filename;
-       bool firsttime;
+       string filename, fileroot, outputDir;
+       bool firsttime, pickedGroups;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };