added countable class to read and store count file. added count parameter to make...

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 1100c3d30afc344119538e89e7c40a8dfa839578..9d9c194dbbaab4ff7a079058c1c43421937659fe 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -40,7 +40,6 @@ public:
        
 private:
        void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-       int createMisMatchFile(SharedListVector*, GroupMap*);
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
@@ -48,13 +47,13 @@ private:
     int createSharedFromListGroup(string);
     int createSharedFromBiom(string);
     string getTag(string&);
-    vector<string> readRows(string, ifstream&, int&); 
+    vector<string> readRows(string, int&); 
     int getDims(string, int&, int&);
-    vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
+    vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
        
        vector<string> Groups, outputNames, order;
        set<string> labels;
-       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
+       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
        bool firsttime, pickedGroups, abort, allLines;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;