X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=createdatabasecommand.h;h=79b5646b864ddf13f59f69c3adb205d5df74fc16;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=643ff6ec9fc3691c4a9de5f146cbfb1fdcaff354;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
index 643ff6e..79b5646 100644
--- a/createdatabasecommand.h
+++ b/createdatabasecommand.h
@@ -22,7 +22,9 @@ 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"; }
     
@@ -33,14 +35,15 @@ public:
 private:
 	
 	bool abort;
-	string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
+	string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir, countfile;
 	
 	vector<string> outputNames;
 		
 	vector<int> readFasta(vector<Sequence>&);
-    vector<int> readTax(vector<string>&);
-    int readNames(map<string, string>&); 
+    vector<int> readTax(vector<string>&, vector<string>&);
 	ListVector* getList();
+    vector<SharedRAbundVector*> getShared();
+    int findIndex(vector<string>&, string);
 	
 };