added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / createdatabasecommand.h

diff --git a/createdatabasecommand.h b/createdatabasecommand.h
index 85e23675b2b770d476dfff45b901da03f6581546..741feba082958ae8e4f2ec73f7a188255208b069 100644 (file)
--- a/createdatabasecommand.h
+++ b/createdatabasecommand.h
@@ -34,13 +34,15 @@ public:
 private:
        
        bool abort;
-       string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
+       string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
        
        vector<string> outputNames;
                
        vector<int> readFasta(vector<Sequence>&);
-    vector<int> readTax(vector<string>&);
+    vector<int> readTax(vector<string>&, vector<string>&);
        ListVector* getList();
+    vector<SharedRAbundVector*> getShared();
+    int findIndex(vector<string>&, string);
        
 };