added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 861632ce7d6a8026c14b463387b9d8dbb320522d..5d0daa2fdc484f55b78613541e1e82ef547a7d09 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -38,20 +38,22 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSharedData(vector<SharedRAbundVector*>);
-       int createMisMatchFile();
+       void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+       int createMisMatchFile(SharedListVector*, GroupMap*);
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
-       int ListGroupSameSeqs();
+       int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup(string);
+    int createSharedFromBiom(string);
+    string getTag(string&);
+    vector<string> readRows(string, ifstream&, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
        
-       SharedListVector* SharedList;
-       InputData* input;
-       GroupMap* groupMap;
        vector<string> Groups, outputNames, order;
        set<string> labels;
-       ofstream out;
-       string filename, fileroot, outputDir, listfile, groupfile, ordergroupfile;
+       string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
        bool firsttime, pickedGroups, abort, allLines;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;