removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index de1e3d9d6aff8595a098cf8bf2fd6c1d5c79ec9f..d99151ec022dfdafcfa2327998466549cbcb3eda 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -19,19 +19,21 @@ class RemoveSeqsCommand : public Command {
                RemoveSeqsCommand(string);      
                RemoveSeqsCommand();
                ~RemoveSeqsCommand(){}
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "remove.seqs";                         }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
                string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();