added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get...

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index ca0ddd833636e6550cb48832517cdc96f912977e..b305e9a7d9f3256eef03cac34387caea99f4b4ae 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -33,15 +33,20 @@ public:
        
 private:
        void printSharedData(vector<SharedRAbundVector*>);
+       void createMisMatchFile();
+       bool isValidGroup(string, vector<string>);
+       
        GlobalData* globaldata;
        ReadOTUFile* read;
        SharedListVector* SharedList;
        InputData* input;
-       //map<string, SharedRAbundVector*>::iterator it;
-       //vector<SharedRAbundVector*> lookup;
+       GroupMap* groupMap;
+       vector<string> groups;
        ofstream out;
-       string filename;
+       string filename, fileroot;
        bool firsttime;
+       map<string, ofstream*> filehandles;
+       map<string, ofstream*>::iterator it3;
 
 };