true chimera testing using reference sequences

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index d18fc23076d83a8a3d4083ce2423af47cfd08e2f..60712c95e8455e020e9fc77a0a851d41c36f06c4 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -17,13 +17,19 @@ class RemoveLineageCommand : public Command {
        public:
        
                RemoveLineageCommand(string);
+               RemoveLineageCommand();
                ~RemoveLineageCommand(){};
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
                set<string> names;
                vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
@@ -34,6 +40,7 @@ class RemoveLineageCommand : public Command {
                int readList();
                int readTax();  
                string removeConfidences(string);
+               vector< map<string, int> > getTaxons(string);
 };
 
 #endif