added distance search method to classify.seqs

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index b305e9a7d9f3256eef03cac34387caea99f4b4ae..3d39b8b7a54ba348966f80d41cf1cea3b9bc9283 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -26,7 +26,7 @@ class GlobalData;
 class SharedCommand : public Command {
        
 public:
-       SharedCommand();        
+       SharedCommand(string);  
        ~SharedCommand();
        int execute();  
        void help() {}
@@ -35,6 +35,7 @@ private:
        void printSharedData(vector<SharedRAbundVector*>);
        void createMisMatchFile();
        bool isValidGroup(string, vector<string>);
+       void eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        
        GlobalData* globaldata;
        ReadOTUFile* read;
@@ -43,8 +44,8 @@ private:
        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;