X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=createdatabasecommand.h;h=79b5646b864ddf13f59f69c3adb205d5df74fc16;hp=9fc84d7740ebfa4098dce2ee33dc6fb902c1c003;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=a33a385cc5b7481488f92f794425f01fbf40a543

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
index 9fc84d7..79b5646 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:
@@ -21,25 +22,28 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "create.database";		}
 	string getCommandCategory()		{ return "OTU-Based Approaches"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
 	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 sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir, countfile;
 	
 	vector<string> outputNames;
 		
-	int readFasta();
-	int readNames();
-    int readTax();
-	int processList(ListVector*&);
+	vector<int> readFasta(vector<Sequence>&);
+    vector<int> readTax(vector<string>&, vector<string>&);
+	ListVector* getList();
+    vector<SharedRAbundVector*> getShared();
+    int findIndex(vector<string>&, string);
 	
 };