working on pam

[mothur.git] / createdatabasecommand.h

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
index 9fc84d7740ebfa4098dce2ee33dc6fb902c1c003..79b5646b864ddf13f59f69c3adb205d5df74fc16 100644 (file)
--- 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);
        
 };