changed cluster.classic so that it does not adjust the cutoff

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 1ad1eee835e4ba0bf48e1be44b7c89631367f22e..8321212fff48bb240c54f1a1df4516b393f7216f 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,21 +17,29 @@ class RemoveSeqsCommand : public Command {
        public:
        
                RemoveSeqsCommand(string);      
-               ~RemoveSeqsCommand(){};
+               RemoveSeqsCommand();
+               ~RemoveSeqsCommand(){}
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile;
-               bool abort;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+               bool abort, dups;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
                void readAccnos();
-               void readList();
+               int readList();
+               int readTax();
                
 };