Merge remote-tracking branch 'origin/master'

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 5d0daa2fdc484f55b78613541e1e82ef547a7d09..9d9c194dbbaab4ff7a079058c1c43421937659fe 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,6 +30,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
        string getDescription()         { return "make a shared file from a list and group file"; }
@@ -39,7 +40,6 @@ public:
        
 private:
        void printSharedData(vector<SharedRAbundVector*>, ofstream&);
-       int createMisMatchFile(SharedListVector*, GroupMap*);
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
@@ -47,13 +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;