fixes while testing 1.33.0

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 1100c3d30afc344119538e89e7c40a8dfa839578..a916c854280c74d035968bfc84ec4ab88a4f70e6 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,8 +30,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
        string getDescription()         { return "make a shared file from a list and group file"; }
 
@@ -40,21 +41,20 @@ public:
        
 private:
        void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-       int createMisMatchFile(SharedListVector*, GroupMap*);
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        int ListGroupSameSeqs(vector<string>&, SharedListVector*);
-    int createSharedFromListGroup(string);
-    int createSharedFromBiom(string);
+    int createSharedFromListGroup();
+    int createSharedFromBiom();
     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;