fixed an mpi bug in shhh.seqs

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 8238c649489e3dff52371fa06ab8e2f49b93258f..de1e3d9d6aff8595a098cf8bf2fd6c1d5c79ec9f 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,15 +17,21 @@ 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, taxfile, outputDir;
+               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();
@@ -34,6 +40,7 @@ class RemoveSeqsCommand : public Command {
                void readAccnos();
                int readList();
                int readTax();
+               int readQual();
                
 };