changing command name classify.shared to classifyrf.shared

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index f1e7c48cd71ee7ff1984e43cb7bb5676a3ee42a5..39ef9a7a1ebc17f830103cf33d84520aca975f97 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -30,25 +30,31 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getHelpString(); 
        
+       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"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSharedData(vector<SharedRAbundVector*>);
-       int createMisMatchFile();
+       void printSharedData(vector<SharedRAbundVector*>, ofstream&);
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+    int createSharedFromListGroup(string);
+    int createSharedFromBiom(string);
+    string getTag(string&);
+    vector<string> readRows(string, int&); 
+    int getDims(string, int&, int&);
+    vector<SharedRAbundVector*> readData(string, string, string, 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, countfile;
        bool firsttime, pickedGroups, abort, allLines;
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;