X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=createdatabasecommand.h;fp=createdatabasecommand.h;h=643ff6ec9fc3691c4a9de5f146cbfb1fdcaff354;hb=8da8321bc4d705f6c156248d6229c60a0204f750;hp=9fc84d7740ebfa4098dce2ee33dc6fb902c1c003;hpb=b86361f726a0d1dfc9f2e91b795e402d97c46f9d;p=mothur.git

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
index 9fc84d7..643ff6e 100644
--- a/createdatabasecommand.h
+++ b/createdatabasecommand.h
@@ -11,6 +11,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "sequence.hpp"
 
 class CreateDatabaseCommand : public Command {
 public:
@@ -26,20 +27,20 @@ public:
 	string getDescription()		{ return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
     
 	
-	int execute() {}; 
+	int execute(); 
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	
 	bool abort;
-	string listfile, groupfile, repfastafile, repnamesfile, constaxonomyfile, label, outputDir;
+	string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
 	
 	vector<string> outputNames;
 		
-	int readFasta();
-	int readNames();
-    int readTax();
-	int processList(ListVector*&);
+	vector<int> readFasta(vector<Sequence>&);
+    vector<int> readTax(vector<string>&);
+    int readNames(map<string, string>&); 
+	ListVector* getList();
 	
 };