added dups parameter to chimera.uchime. working on make.contigs command.

[mothur.git] / splitgroupscommand.h

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index 6705ba98e3ab9ebd165429260828632eca43ede4..62e063d8a0fe93c3942959527cde646996e3430d 100644 (file)
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -30,23 +30,24 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "split.group";                         }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+       string getDescription()         { return "split a name or fasta file by group"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       int readNames(); 
-       int splitFasta(); 
-       
        vector<string> outputNames;
-       map<string, vector<string> > nameMap;
-       map<string, vector<string> >::iterator itNames;
-       GroupMap* groupMap;
-       
-       string outputDir, namefile, groupfile, groups, fastafile;
+               
+       string outputDir, namefile, groupfile, countfile, groups, fastafile;
        vector<string> Groups;
        bool abort;
+    
+    int runNameGroup();
+    int runCount();
 };
 
 /***************************************************************************************/