added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 179a1b3becb27091fbe5fc6e78d1b1f91a70e10d..d19a396410f2e2c9850f9b20a93d65c03000bac2 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -19,7 +19,6 @@
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -43,8 +42,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.oturep";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
+       string getDescription()         { return "gets a representative sequence for each OTU"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -79,6 +81,7 @@ private:
        SeqMap getMap(int);
        string findRep(vector<string>);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
        int processNames(string, string);
+       int processFastaNames(string, string);
 };
 
 #endif